Publications: Journal articles, conference papers and theses from department members

2019
1. Ahmad M, Helms V, Kalinina OV, Lengauer T: Relative Principal Components Analysis: Application to Analyzing Biomolecular Conformational Changes. Journal of Chemical Theory and Computation 2019, 15.
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@article{Ahmad2019, TITLE = {Relative Principal Components Analysis: {A}pplication to Analyzing Biomolecular Conformational Changes}, AUTHOR = {Ahmad, Mazen and Helms, Volkhard and Kalinina, Olga V. and Lengauer, Thomas}, LANGUAGE = {eng}, ISSN = {1549-9618}, DOI = {10.1021/acs.jctc.8b01074}, PUBLISHER = {ACM}, ADDRESS = {Washington, D.C.}, YEAR = {2019}, MARGINALMARK = {$\bullet$}, DATE = {2019}, JOURNAL = {Journal of Chemical Theory and Computation}, VOLUME = {15}, NUMBER = {4}, PAGES = {2166--2178}, }
Endnote
%0 Journal Article %A Ahmad, Mazen %A Helms, Volkhard %A Kalinina, Olga V. %A Lengauer, Thomas %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T Relative Principal Components Analysis: Application to Analyzing Biomolecular Conformational Changes : %G eng %U http://hdl.handle.net/21.11116/0000-0003-8671-6 %R 10.1021/acs.jctc.8b01074 %2 PMC6728065 %7 2019 %D 2019 %J Journal of Chemical Theory and Computation %O J. Chem. Theory Comput. %V 15 %N 4 %& 2166 %P 2166 - 2178 %I ACM %C Washington, D.C. %@ false
2. Blum A, Khalifa S, Nordstroem K, Simon M, Schulz MH, Schmitt MJ: Transcriptomics of a KDELR1 Knockout Cell Line Reveals Modulated Cell Adhesion Properties. Scientific Reports 2019, 9.
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@article{Blum2019, TITLE = {Transcriptomics of a {KDELR1} Knockout Cell Line Reveals Modulated Cell Adhesion Properties}, AUTHOR = {Blum, Andrea and Khalifa, Saleem and Nordstroem, Karl and Simon, Martin and Schulz, Marcel Holger and Schmitt, Manfred J.}, LANGUAGE = {eng}, ISSN = {2045-2322}, DOI = {10.1038/s41598-019-47027-5}, PUBLISHER = {Nature Publishing Group}, ADDRESS = {London, UK}, YEAR = {2019}, MARGINALMARK = {$\bullet$}, JOURNAL = {Scientific Reports}, VOLUME = {9}, EID = {10611}, }
Endnote
%0 Journal Article %A Blum, Andrea %A Khalifa, Saleem %A Nordstroem, Karl %A Simon, Martin %A Schulz, Marcel Holger %A Schmitt, Manfred J. %+ External Organizations External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations %T Transcriptomics of a KDELR1 Knockout Cell Line Reveals Modulated Cell Adhesion Properties : %G eng %U http://hdl.handle.net/21.11116/0000-0004-8320-3 %R 10.1038/s41598-019-47027-5 %7 2019 %D 2019 %J Scientific Reports %O Sci. Rep. %V 9 %Z sequence number: 10611 %I Nature Publishing Group %C London, UK %@ false
3. Chaisson MJP, Sanders AD, Zhao X, Malhotra A, Porubsky D, Rausch T, Gardner EJ, Rodriguez OL, Guo L, Collins RL, Fan X, Wen J, Handsaker RE, Fairley S, Kronenberg ZN, Kong X, Hormozdiari F, Lee D, Wenger AM, Hastie AR, Antaki D, Anantharaman T, Audano PA, Brand H, Cantsilieris S, Cao H, Cerveira E, Chen C, Chen X, Chin C-S, et al.: Multi-platform Discovery of Haplotype-resolved Structural Variation in Human Genomes. Nature Communications 2019, 10.
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@article{Chaisson2019, TITLE = {Multi-platform Discovery of Haplotype-resolved Structural Variation in Human Genomes}, AUTHOR = {Chaisson, Mark J. P. and Sanders, Ashley D. and Zhao, Xuefang and Malhotra, Ankit and Porubsky, David and Rausch, Tobias and Gardner, Eugene J. and Rodriguez, Oscar L. and Guo, Li and Collins, Ryan L. and Fan, Xian and Wen, Jia and Handsaker, Robert E. and Fairley, Susan and Kronenberg, Zev N. and Kong, Xiangmeng and Hormozdiari, Fereydoun and Lee, Dillon and Wenger, Aaron M. and Hastie, Alex R. and Antaki, Danny and Anantharaman, Thomas and Audano, Peter A. and Brand, Harrison and Cantsilieris, Stuart and Cao, Han and Cerveira, Eliza and Chen, Chong and Chen, Xintong and Chin, Chen-Shan and Chong, Zechen and Chuang, Nelson T. and Lambert, Christine C. and Church, Deanna M. and Clarke, Laura and Farrell, Andrew and Flores, Joey and Galeev, Timur and Gorkin, David U. and Gujral, Madhusudan and Guryev, Victor and Heaton, William Haynes and Korlach, Jonas and Kumar, Sushant and Kwon, Jee Young and Lam, Ernest T. and Lee, Jong Eun and Lee, Joyce and Lee, Wan-Ping and Lee, Sau Peng and Li, Shantao and Marks, Patrick and Viaud-Martinez, Karine and Meiers, Sascha and Munson, Katherine M. and Navarro, Fabio C. P. and Nelson, Bradley J. and Nodzak, Conor and Noor, Amina and Kyriazopoulou-Panagiotopoulou, Sofia and Pang, Andy W. C. and Qiu, Yunjiang and Rosanio, Gabriel and Ryan, Mallory and Stuetz, Adrian and Spierings, Diana C. J. and Ward, Alistair and Welch, AnneMarie E. and Xiao, Ming and Xu, Wei and Zhang, Chengsheng and Zhu, Qihui and Zheng-Bradley, Xiangqun and Lowy, Ernesto and Yakneen, Sergei and McCarroll, Steven and Jun, Goo and Ding, Li and Koh, Chong Lek and Ren, Bing and Flicek, Paul and Chen, Ken and Gerstein, Mark B. and Kwok, Pui-Yan and Lansdorp, Peter M. and Marth, Gabor T. and Sebat, Jonathan and Shi, Xinghua and Bashir, Ali and Ye, Kai and Devine, Scott E. and Talkowski, Michael E. and Mills, Ryan E. and Marschall, Tobias and Korbel, Jan O. and Eichler, Evan E. and Lee, Charles}, LANGUAGE = {eng}, ISSN = {2041-1723}, DOI = {10.1038/s41467-018-08148-z}, PUBLISHER = {Nature Publishing Group}, ADDRESS = {London}, YEAR = {2019}, MARGINALMARK = {$\bullet$}, JOURNAL = {Nature Communications}, VOLUME = {10}, EID = {1784}, }
Endnote
%0 Journal Article %A Chaisson, Mark J. P. %A Sanders, Ashley D. %A Zhao, Xuefang %A Malhotra, Ankit %A Porubsky, David %A Rausch, Tobias %A Gardner, Eugene J. %A Rodriguez, Oscar L. %A Guo, Li %A Collins, Ryan L. %A Fan, Xian %A Wen, Jia %A Handsaker, Robert E. %A Fairley, Susan %A Kronenberg, Zev N. %A Kong, Xiangmeng %A Hormozdiari, Fereydoun %A Lee, Dillon %A Wenger, Aaron M. %A Hastie, Alex R. %A Antaki, Danny %A Anantharaman, Thomas %A Audano, Peter A. %A Brand, Harrison %A Cantsilieris, Stuart %A Cao, Han %A Cerveira, Eliza %A Chen, Chong %A Chen, Xintong %A Chin, Chen-Shan %A Chong, Zechen %A Chuang, Nelson T. %A Lambert, Christine C. %A Church, Deanna M. %A Clarke, Laura %A Farrell, Andrew %A Flores, Joey %A Galeev, Timur %A Gorkin, David U. %A Gujral, Madhusudan %A Guryev, Victor %A Heaton, William Haynes %A Korlach, Jonas %A Kumar, Sushant %A Kwon, Jee Young %A Lam, Ernest T. %A Lee, Jong Eun %A Lee, Joyce %A Lee, Wan-Ping %A Lee, Sau Peng %A Li, Shantao %A Marks, Patrick %A Viaud-Martinez, Karine %A Meiers, Sascha %A Munson, Katherine M. %A Navarro, Fabio C. P. %A Nelson, Bradley J. %A Nodzak, Conor %A Noor, Amina %A Kyriazopoulou-Panagiotopoulou, Sofia %A Pang, Andy W. C. %A Qiu, Yunjiang %A Rosanio, Gabriel %A Ryan, Mallory %A Stuetz, Adrian %A Spierings, Diana C. J. %A Ward, Alistair %A Welch, AnneMarie E. %A Xiao, Ming %A Xu, Wei %A Zhang, Chengsheng %A Zhu, Qihui %A Zheng-Bradley, Xiangqun %A Lowy, Ernesto %A Yakneen, Sergei %A McCarroll, Steven %A Jun, Goo %A Ding, Li %A Koh, Chong Lek %A Ren, Bing %A Flicek, Paul %A Chen, Ken %A Gerstein, Mark B. %A Kwok, Pui-Yan %A Lansdorp, Peter M. %A Marth, Gabor T. %A Sebat, Jonathan %A Shi, Xinghua %A Bashir, Ali %A Ye, Kai %A Devine, Scott E. %A Talkowski, Michael E. %A Mills, Ryan E. %A Marschall, Tobias %A Korbel, Jan O. %A Eichler, Evan E. %A Lee, Charles %+ External Organizations External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations %T Multi-platform Discovery of Haplotype-resolved Structural Variation in Human Genomes : %G eng %U http://hdl.handle.net/21.11116/0000-0003-865E-D %R 10.1038/s41467-018-08148-z %7 2019 %D 2019 %J Nature Communications %O Nat. Commun. %V 10 %Z sequence number: 1784 %I Nature Publishing Group %C London %@ false
4. De Luca A, Pezzotti P, Boucher C, Döring M, Incardona F, Kaiser R, Lengauer T, Pfeifer N, Schülter E, Vandamme A-M, Zazzi M, Geretti AM: Clinical Use, Efficacy, and Durability of Maraviroc for Antiretroviral Therapy in Routine Care: A European Survey. PLoS One 2019, 11.
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@article{DeLuca_2019, TITLE = {Clinical Use, Efficacy, and Durability of Maraviroc for Antiretroviral Therapy in Routine Care: {A} European Survey}, AUTHOR = {De Luca, Andrea and Pezzotti, Patrizio and Boucher, Charles and D{\"o}ring, Matthias and Incardona, Francesca and Kaiser, Rolf and Lengauer, Thomas and Pfeifer, Nico and Sch{\"u}lter, Eugen and Vandamme, Anne-Mieke and Zazzi, Maurizio and Geretti, Anna Maria and {EucoHIV Study Group}}, LANGUAGE = {eng}, ISSN = {1932-6203}, DOI = {10.1371/journal.pone.0225381}, PUBLISHER = {Public Library of Science}, ADDRESS = {San Francisco, CA}, YEAR = {2019}, MARGINALMARK = {$\bullet$}, JOURNAL = {PLoS One}, VOLUME = {11}, NUMBER = {14}, EID = {e0225381}, }
Endnote
%0 Journal Article %A De Luca, Andrea %A Pezzotti, Patrizio %A Boucher, Charles %A Döring, Matthias %A Incardona, Francesca %A Kaiser, Rolf %A Lengauer, Thomas %A Pfeifer, Nico %A Schülter, Eugen %A Vandamme, Anne-Mieke %A Zazzi, Maurizio %A Geretti, Anna Maria %A EucoHIV Study Group, %+ External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations External Organizations %T Clinical Use, Efficacy, and Durability of Maraviroc for Antiretroviral Therapy in Routine Care: A European Survey : %G eng %U http://hdl.handle.net/21.11116/0000-0005-4921-4 %R 10.1371/journal.pone.0225381 %7 2019 %D 2019 %J PLoS One %V 11 %N 14 %Z sequence number: e0225381 %I Public Library of Science %C San Francisco, CA %@ false
5. Dheghani Amirabad A: From genes to transcripts : integrative modeling and analysis of regulatory networks. Universität des Saarlandes; 2019.
Abstract
Although all the cells in an organism posses the same genome, the regulatory mechanisms lead to highly specific cell types. Elucidating these regulatory mechanisms is a great challenge in systems biology research. Nonetheless, it is known that a large fraction of our genome is comprised of regulatory elements, the precise mechanisms by which different combinations of regulatory elements are involved in controlling gene expression and cell identity are poorly understood. This thesis describes algorithms and approaches for modeling and analysis of different modes of gene regulation. We present POSTIT a novel algorithm for modeling and inferring transcript isoform regulation from transcriptomics and epigenomics data. POSTIT uses multi-task learning with structured-sparsity inducing regularizer to share the regulatory information between isoforms of a gene, which is shown to lead to accurate isoform expression prediction and inference of regulators. Furthermore, it can use isoform expression level and annotation as informative priors for gene expression prediction. Hence, it constitute a novel accurate approach applicable to gene or transcript isoform centric analysis using expression data. In an application to microRNA (miRNA) target prioritization, we demonstrate that it out-competes classical gene centric methods. Moreover, pinpoints important transcription factors and miRNAs that regulate differentially expressed isoforms in any biological system. Competing endogenous RNA (ceRNA) interactions mediated by miRNAs were postulated as an important cellular regulatory network, in which cross-talk between different transcripts involves competition for joint regulators. We developed a novel statistical method, called SPONGE, for large-scale inference of ceRNA networks. In this framework, we designed an efficient empirical p-value computation approach, by sampling from derived null models, which addresses important confounding factors such as sample size, number of involved regulators and strength of correlation. In an application to a large pan-cancer dataset with 31 cancers we discovered protein-coding and non-coding RNAs that are generic ceRNAs in cancer. Finally, we present an integrative analysis of miRNA and protein-based posttranscriptional regulation. We postulate a competitive regulation of the RNAbinding protein IMP2 with miRNAs binding the same RNAs using expression and RNA binding data. This function of IMP2 is relevant in the contribution to disease in the context of adult cellular metabolism. As a summary, in this thesis we have presented a number of different novel approaches for inference and the integrative analysis of regulatory networks that we believe will find wide applicability in the biological sciences.
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@phdthesis{Dehghaniphd2019, TITLE = {From genes to transcripts : integrative modeling and analysis of regulatory networks}, AUTHOR = {Dheghani Amirabad, Azim}, LANGUAGE = {eng}, DOI = {10.22028/D291-28659}, SCHOOL = {Universit{\"a}t des Saarlandes}, ADDRESS = {Saarbr{\"u}cken}, YEAR = {2019}, MARGINALMARK = {$\bullet$}, DATE = {2019}, ABSTRACT = {Although all the cells in an organism posses the same genome, the regulatory mechanisms lead to highly specific cell types. Elucidating these regulatory mechanisms is a great challenge in systems biology research. Nonetheless, it is known that a large fraction of our genome is comprised of regulatory elements, the precise mechanisms by which different combinations of regulatory elements are involved in controlling gene expression and cell identity are poorly understood. This thesis describes algorithms and approaches for modeling and analysis of different modes of gene regulation. We present POSTIT a novel algorithm for modeling and inferring transcript isoform regulation from transcriptomics and epigenomics data. POSTIT uses multi-task learning with structured-sparsity inducing regularizer to share the regulatory information between isoforms of a gene, which is shown to lead to accurate isoform expression prediction and inference of regulators. Furthermore, it can use isoform expression level and annotation as informative priors for gene expression prediction. Hence, it constitute a novel accurate approach applicable to gene or transcript isoform centric analysis using expression data. In an application to microRNA (miRNA) target prioritization, we demonstrate that it out-competes classical gene centric methods. Moreover, pinpoints important transcription factors and miRNAs that regulate differentially expressed isoforms in any biological system. Competing endogenous RNA (ceRNA) interactions mediated by miRNAs were postulated as an important cellular regulatory network, in which cross-talk between different transcripts involves competition for joint regulators. We developed a novel statistical method, called SPONGE, for large-scale inference of ceRNA networks. In this framework, we designed an efficient empirical p-value computation approach, by sampling from derived null models, which addresses important confounding factors such as sample size, number of involved regulators and strength of correlation. In an application to a large pan-cancer dataset with 31 cancers we discovered protein-coding and non-coding RNAs that are generic ceRNAs in cancer. Finally, we present an integrative analysis of miRNA and protein-based posttranscriptional regulation. We postulate a competitive regulation of the RNAbinding protein IMP2 with miRNAs binding the same RNAs using expression and RNA binding data. This function of IMP2 is relevant in the contribution to disease in the context of adult cellular metabolism. As a summary, in this thesis we have presented a number of different novel approaches for inference and the integrative analysis of regulatory networks that we believe will find wide applicability in the biological sciences.}, }
Endnote
%0 Thesis %A Dheghani Amirabad, Azim %Y Schulz, Marcel %A referee: Keller, Andreas %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society International Max Planck Research School, MPI for Informatics, Max Planck Society External Organizations External Organizations %T From genes to transcripts : integrative modeling and analysis of regulatory networks : %G eng %U http://hdl.handle.net/21.11116/0000-0005-438D-1 %R 10.22028/D291-28659 %I Universität des Saarlandes %C Saarbrücken %D 2019 %P 139 p. %V phd %9 phd %X Although all the cells in an organism posses the same genome, the regulatory mechanisms lead to highly specific cell types. Elucidating these regulatory mechanisms is a great challenge in systems biology research. Nonetheless, it is known that a large fraction of our genome is comprised of regulatory elements, the precise mechanisms by which different combinations of regulatory elements are involved in controlling gene expression and cell identity are poorly understood. This thesis describes algorithms and approaches for modeling and analysis of different modes of gene regulation. We present POSTIT a novel algorithm for modeling and inferring transcript isoform regulation from transcriptomics and epigenomics data. POSTIT uses multi-task learning with structured-sparsity inducing regularizer to share the regulatory information between isoforms of a gene, which is shown to lead to accurate isoform expression prediction and inference of regulators. Furthermore, it can use isoform expression level and annotation as informative priors for gene expression prediction. Hence, it constitute a novel accurate approach applicable to gene or transcript isoform centric analysis using expression data. In an application to microRNA (miRNA) target prioritization, we demonstrate that it out-competes classical gene centric methods. Moreover, pinpoints important transcription factors and miRNAs that regulate differentially expressed isoforms in any biological system. Competing endogenous RNA (ceRNA) interactions mediated by miRNAs were postulated as an important cellular regulatory network, in which cross-talk between different transcripts involves competition for joint regulators. We developed a novel statistical method, called SPONGE, for large-scale inference of ceRNA networks. In this framework, we designed an efficient empirical p-value computation approach, by sampling from derived null models, which addresses important confounding factors such as sample size, number of involved regulators and strength of correlation. In an application to a large pan-cancer dataset with 31 cancers we discovered protein-coding and non-coding RNAs that are generic ceRNAs in cancer. Finally, we present an integrative analysis of miRNA and protein-based posttranscriptional regulation. We postulate a competitive regulation of the RNAbinding protein IMP2 with miRNAs binding the same RNAs using expression and RNA binding data. This function of IMP2 is relevant in the contribution to disease in the context of adult cellular metabolism. As a summary, in this thesis we have presented a number of different novel approaches for inference and the integrative analysis of regulatory networks that we believe will find wide applicability in the biological sciences. %U https://publikationen.sulb.uni-saarland.de/handle/20.500.11880/27669
6. Doncheva NT, Domingues FS, McGivern DR, Shimakami T, Zeuzem S, Lengauer T, Lange CM, Albrecht M, Welsch C: Near-Neighbor Interactions in the NS3-4A Protease of HCV Impact Replicative Fitness of Drug-Resistant Viral Variants. Journal of Molecular Biology 2019, 431.
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@article{Doncheva2019, TITLE = {Near-Neighbor Interactions in the {NS3}-{4A} Protease of {HCV} Impact Replicative Fitness of Drug-Resistant Viral Variants}, AUTHOR = {Doncheva, Nadezhda Tsankova and Domingues, Francisco S. and McGivern, David R. and Shimakami, Tetsuro and Zeuzem, Stefan and Lengauer, Thomas and Lange, Christian M. and Albrecht, Mario and Welsch, Christoph}, LANGUAGE = {eng}, ISSN = {0022-2836}, DOI = {10.1016/j.jmb.2019.04.034}, PUBLISHER = {Elsevier}, ADDRESS = {Amsterdam}, YEAR = {2019}, MARGINALMARK = {$\bullet$}, DATE = {2019}, JOURNAL = {Journal of Molecular Biology}, VOLUME = {431}, NUMBER = {12}, PAGES = {2354--2368}, }
Endnote
%0 Journal Article %A Doncheva, Nadezhda Tsankova %A Domingues, Francisco S. %A McGivern, David R. %A Shimakami, Tetsuro %A Zeuzem, Stefan %A Lengauer, Thomas %A Lange, Christian M. %A Albrecht, Mario %A Welsch, Christoph %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T Near-Neighbor Interactions in the NS3-4A Protease of HCV Impact Replicative Fitness of Drug-Resistant Viral Variants : %G eng %U http://hdl.handle.net/21.11116/0000-0004-3FC9-4 %R 10.1016/j.jmb.2019.04.034 %7 2019 %D 2019 %J Journal of Molecular Biology %O J Mol Biol %V 431 %N 12 %& 2354 %P 2354 - 2368 %I Elsevier %C Amsterdam %@ false
7. Döring M: Computational Approaches for Improving Treatment and Prevention of Viral Infections. Universität des Saarlandes; 2019.
Abstract
The treatment of infections with HIV or HCV is challenging. Thus, novel drugs and new computational approaches that support the selection of therapies are required. This work presents methods that support therapy selection as well as methods that advance novel antiviral treatments. geno2pheno[ngs-freq] identifies drug resistance from HIV-1 or HCV samples that were subjected to next-generation sequencing by interpreting their sequences either via support vector machines or a rules-based approach. geno2pheno[coreceptor-hiv2] determines the coreceptor that is used for viral cell entry by analyzing a segment of the HIV-2 surface protein with a support vector machine. openPrimeR is capable of finding optimal combinations of primers for multiplex polymerase chain reaction by solving a set cover problem and accessing a new logistic regression model for determining amplification events arising from polymerase chain reaction. geno2pheno[ngs-freq] and geno2pheno[coreceptorhiv2] enable the personalization of antiviral treatments and support clinical decision making. The application of openPrimeR on human immunoglobulin sequences has resulted in novel primer sets that improve the isolation of broadly neutralizing antibodies against HIV-1. The methods that were developed in this work thus constitute important contributions towards improving the prevention and treatment of viral infectious diseases.
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@phdthesis{Doringphd2013, TITLE = {Computational Approaches for Improving Treatment and Prevention of Viral Infections}, AUTHOR = {D{\"o}ring, Matthias}, LANGUAGE = {eng}, DOI = {10.22028/D291-27946}, SCHOOL = {Universit{\"a}t des Saarlandes}, ADDRESS = {Saarbr{\"u}cken}, YEAR = {2019}, MARGINALMARK = {$\bullet$}, DATE = {2019}, ABSTRACT = {The treatment of infections with HIV or HCV is challenging. Thus, novel drugs and new computational approaches that support the selection of therapies are required. This work presents methods that support therapy selection as well as methods that advance novel antiviral treatments. geno2pheno[ngs-freq] identifies drug resistance from HIV-1 or HCV samples that were subjected to next-generation sequencing by interpreting their sequences either via support vector machines or a rules-based approach. geno2pheno[coreceptor-hiv2] determines the coreceptor that is used for viral cell entry by analyzing a segment of the HIV-2 surface protein with a support vector machine. openPrimeR is capable of finding optimal combinations of primers for multiplex polymerase chain reaction by solving a set cover problem and accessing a new logistic regression model for determining amplification events arising from polymerase chain reaction. geno2pheno[ngs-freq] and geno2pheno[coreceptorhiv2] enable the personalization of antiviral treatments and support clinical decision making. The application of openPrimeR on human immunoglobulin sequences has resulted in novel primer sets that improve the isolation of broadly neutralizing antibodies against HIV-1. The methods that were developed in this work thus constitute important contributions towards improving the prevention and treatment of viral infectious diseases.}, }
Endnote
%0 Thesis %A Döring, Matthias %Y Pfeifer, Nico %A referee: Lengauer, Thomas %A referee: Kalinina, Olga V. %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society International Max Planck Research School, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T Computational Approaches for Improving Treatment and Prevention of Viral Infections : %G eng %U http://hdl.handle.net/21.11116/0000-0003-AEBA-8 %R 10.22028/D291-27946 %I Universität des Saarlandes %C Saarbrücken %D 2019 %P 337 p. %V phd %9 phd %X The treatment of infections with HIV or HCV is challenging. Thus, novel drugs and new computational approaches that support the selection of therapies are required. This work presents methods that support therapy selection as well as methods that advance novel antiviral treatments. geno2pheno[ngs-freq] identifies drug resistance from HIV-1 or HCV samples that were subjected to next-generation sequencing by interpreting their sequences either via support vector machines or a rules-based approach. geno2pheno[coreceptor-hiv2] determines the coreceptor that is used for viral cell entry by analyzing a segment of the HIV-2 surface protein with a support vector machine. openPrimeR is capable of finding optimal combinations of primers for multiplex polymerase chain reaction by solving a set cover problem and accessing a new logistic regression model for determining amplification events arising from polymerase chain reaction. geno2pheno[ngs-freq] and geno2pheno[coreceptorhiv2] enable the personalization of antiviral treatments and support clinical decision making. The application of openPrimeR on human immunoglobulin sequences has resulted in novel primer sets that improve the isolation of broadly neutralizing antibodies against HIV-1. The methods that were developed in this work thus constitute important contributions towards improving the prevention and treatment of viral infectious diseases. %U https://publikationen.sulb.uni-saarland.de/handle/20.500.11880/27443
8. Döring M, Kreer C, Lehnen N, Klein F, Pfeifer N: Modeling the Amplification of Immunoglobulins through Machine Learning on Sequence-Specific Features. Scientific Reports 2019, 9.
Abstract
Successful primer design for polymerase chain reaction (PCR) hinges on the ability to identify primers that efciently amplify template sequences. Here, we generated a novel Taq PCR data set that reports the amplifcation status for pairs of primers and templates from a reference set of 47 immunoglobulin heavy chain variable sequences and 20 primers. Using logistic regression, we developed TMM, a model for predicting whether a primer amplifes a template given their nucleotide sequences. The model suggests that the free energy of annealing, ΔG, is the key driver of amplifcation (p=7.35e-12) and that 3′ mismatches should be considered in dependence on ΔG and the mismatch closest to the 3′ terminus (p=1.67e-05). We validated TMM by comparing its estimates with those from the thermodynamic model of DECIPHER (DE) and a model based solely on the free energy of annealing (FE). TMM outperformed the other approaches in terms of the area under the receiver operating characteristic curve (TMM: 0.953, FE: 0.941, DE: 0.896). TMM can improve primer design and is freely available via openPrimeR (http://openPrimeR.mpi-inf.mpg.de).
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@article{DoringPfeiferModel, TITLE = {Modeling the Amplification of Immunoglobulins through Machine Learning on Sequence-Specific Features}, AUTHOR = {D{\"o}ring, Matthias and Kreer, Christoph and Lehnen, Nathalie and Klein, Florian and Pfeifer, Nico}, LANGUAGE = {eng}, ISSN = {2045-2322}, DOI = {10.1038/s41598-019-47173-w}, PUBLISHER = {Nature Publishing Group}, ADDRESS = {London, UK}, YEAR = {2019}, MARGINALMARK = {$\bullet$}, ABSTRACT = {Successful primer design for polymerase chain reaction (PCR) hinges on the ability to identify primers that efciently amplify template sequences. Here, we generated a novel Taq PCR data set that reports the amplifcation status for pairs of primers and templates from a reference set of 47 immunoglobulin heavy chain variable sequences and 20 primers. Using logistic regression, we developed TMM, a model for predicting whether a primer amplifes a template given their nucleotide sequences. The model suggests that the free energy of annealing, $\Delta$G, is the key driver of amplifcation (p=7.35e-12) and that 3′ mismatches should be considered in dependence on $\Delta$G and the mismatch closest to the 3′ terminus (p=1.67e-05). We validated TMM by comparing its estimates with those from the thermodynamic model of DECIPHER (DE) and a model based solely on the free energy of annealing (FE). TMM outperformed the other approaches in terms of the area under the receiver operating characteristic curve (TMM: 0.953, FE: 0.941, DE: 0.896). TMM can improve primer design and is freely available via openPrimeR (http://openPrimeR.mpi-inf.mpg.de).}, JOURNAL = {Scientific Reports}, VOLUME = {9}, EID = {10748}, }
Endnote
%0 Journal Article %A Döring, Matthias %A Kreer, Christoph %A Lehnen, Nathalie %A Klein, Florian %A Pfeifer, Nico %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T Modeling the Amplification of Immunoglobulins through Machine Learning on Sequence-Specific Features : %G eng %U http://hdl.handle.net/21.11116/0000-0004-5F56-2 %R 10.1038/s41598-019-47173-w %7 2019-07-24 %D 2019 %8 24.07.2019 %X Successful primer design for polymerase chain reaction (PCR) hinges on the ability to identify primers that efciently amplify template sequences. Here, we generated a novel Taq PCR data set that reports the amplifcation status for pairs of primers and templates from a reference set of 47 immunoglobulin heavy chain variable sequences and 20 primers. Using logistic regression, we developed TMM, a model for predicting whether a primer amplifes a template given their nucleotide sequences. The model suggests that the free energy of annealing, ΔG, is the key driver of amplifcation (p=7.35e-12) and that 3′ mismatches should be considered in dependence on ΔG and the mismatch closest to the 3′ terminus (p=1.67e-05). We validated TMM by comparing its estimates with those from the thermodynamic model of DECIPHER (DE) and a model based solely on the free energy of annealing (FE). TMM outperformed the other approaches in terms of the area under the receiver operating characteristic curve (TMM: 0.953, FE: 0.941, DE: 0.896). TMM can improve primer design and is freely available via openPrimeR (http://openPrimeR.mpi-inf.mpg.de). %J Scientific Reports %O Sci. Rep. %V 9 %Z sequence number: 10748 %I Nature Publishing Group %C London, UK %@ false
9. Durai DA, Schulz MH: Improving in-silico Normalization using Read Weights. Scientific Reports 2019, 9.
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@article{Durai2019, TITLE = {Improving in-silico Normalization using Read Weights}, AUTHOR = {Durai, Dilip Ariyur and Schulz, Marcel Holger}, LANGUAGE = {eng}, ISSN = {2045-2322}, DOI = {10.1038/s41598-019-41502-9}, PUBLISHER = {Nature Publishing Group}, ADDRESS = {London, UK}, YEAR = {2019}, MARGINALMARK = {$\bullet$}, JOURNAL = {Scientific Reports}, VOLUME = {9}, EID = {5133}, }
Endnote
%0 Journal Article %A Durai, Dilip Ariyur %A Schulz, Marcel Holger %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T Improving in-silico Normalization using Read Weights : %G eng %U http://hdl.handle.net/21.11116/0000-0003-5F5F-A %R 10.1038/s41598-019-41502-9 %7 2019 %D 2019 %J Scientific Reports %O Sci. Rep. %V 9 %Z sequence number: 5133 %I Nature Publishing Group %C London, UK %@ false %U https://doi.org/10.1038/s41598-019-41502-9
10. Ebert P: What we leave behind : reproducibility in chromatin analysis within and across species. Universität des Saarlandes; 2019.
Abstract
Epigenetics is the field of biology that investigates heritable factors regulating gene expression without being directly encoded in the genome of an organism. The human genome is densely packed inside a cell's nucleus in the form of chromatin. Certain constituents of chromatin play a vital role as epigenetic factors in the dynamic regulation of gene expression. Epigenetic changes on the chromatin level are thus an integral part of the mechanisms governing the development of the functionally diverse cell types in multicellular species such as human. Studying these mechanisms is not only important to understand the biology of healthy cells, but also necessary to comprehend the epigenetic component in the formation of many complex diseases. Modern wet lab technology enables scientists to probe the epigenome with high throughput and in extensive detail. The fast generation of epigenetic datasets burdens computational researchers with the challenge of rapidly performing elaborate analyses without compromising on the scientific reproducibility of the reported findings. To facilitate reproducible computational research in epigenomics, this thesis proposes a task-oriented metadata model, relying on web technology and supported by database engineering, that aims at consistent and human-readable documentation of standardized computational workflows. The suggested approach features, e.g., computational validation of metadata records, automatic error detection, and progress monitoring of multi-step analyses, and was successfully field-tested as part of a large epigenome research consortium. This work leaves aside theoretical considerations, and intentionally emphasizes the realistic need of providing scientists with tools that assist them in performing reproducible research. Irrespective of the technological progress, the dynamic and cell-type specific nature of the epigenome commonly requires restricting the number of analyzed samples due to resource limitations. The second project of this thesis introduces the software tool SCIDDO, which has been developed for the differential chromatin analysis of cellular samples with potentially limited availability. By combining statistics, algorithmics, and best practices for robust software development, SCIDDO can quickly identify biologically meaningful regions of differential chromatin marking between cell types. We demonstrate SCIDDO's usefulness in an exemplary study in which we identify regions that establish a link between chromatin and gene expression changes. SCIDDO's quantitative approach to differential chromatin analysis is user-customizable, providing the necessary flexibility to adapt SCIDDO to specific research tasks. Given the functional diversity of cell types and the dynamics of the epigenome in response to environmental changes, it is hardly realistic to map the complete epigenome even for a single organism like human or mouse. For non-model organisms, e.g., cow, pig, or dog, epigenome data is particularly scarce. The third project of this thesis investigates to what extent bioinformatics methods can compensate for the comparatively little effort that is invested in charting the epigenome of non-model species. This study implements a large integrative analysis pipeline, including state-of-the-art machine learning, to transfer chromatin data for predictive modeling between 13 species. The evidence presented here indicates that a partial regulatory epigenetic signal is stably retained even over millions of years of evolutionary distance between the considered species. This finding suggests complementary and cost-effective ways for bioinformatics to contribute to comparative epigenome analysis across species boundaries.
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@phdthesis{Ebertphd2019, TITLE = {What we leave behind : reproducibility in chromatin analysis within and across species}, AUTHOR = {Ebert, Peter}, LANGUAGE = {eng}, URL = {urn:nbn:de:bsz:291--ds-278311}, DOI = {doi.org/10.22028/D291-27831}, SCHOOL = {Universit{\"a}t des Saarlandes}, ADDRESS = {Saarbr{\"u}cken}, YEAR = {2019}, MARGINALMARK = {$\bullet$}, DATE = {2019}, ABSTRACT = {Epigenetics is the field of biology that investigates heritable factors regulating gene expression without being directly encoded in the genome of an organism. The human genome is densely packed inside a cell's nucleus in the form of chromatin. Certain constituents of chromatin play a vital role as epigenetic factors in the dynamic regulation of gene expression. Epigenetic changes on the chromatin level are thus an integral part of the mechanisms governing the development of the functionally diverse cell types in multicellular species such as human. Studying these mechanisms is not only important to understand the biology of healthy cells, but also necessary to comprehend the epigenetic component in the formation of many complex diseases. Modern wet lab technology enables scientists to probe the epigenome with high throughput and in extensive detail. The fast generation of epigenetic datasets burdens computational researchers with the challenge of rapidly performing elaborate analyses without compromising on the scientific reproducibility of the reported findings. To facilitate reproducible computational research in epigenomics, this thesis proposes a task-oriented metadata model, relying on web technology and supported by database engineering, that aims at consistent and human-readable documentation of standardized computational workflows. The suggested approach features, e.g., computational validation of metadata records, automatic error detection, and progress monitoring of multi-step analyses, and was successfully field-tested as part of a large epigenome research consortium. This work leaves aside theoretical considerations, and intentionally emphasizes the realistic need of providing scientists with tools that assist them in performing reproducible research. Irrespective of the technological progress, the dynamic and cell-type specific nature of the epigenome commonly requires restricting the number of analyzed samples due to resource limitations. The second project of this thesis introduces the software tool SCIDDO, which has been developed for the differential chromatin analysis of cellular samples with potentially limited availability. By combining statistics, algorithmics, and best practices for robust software development, SCIDDO can quickly identify biologically meaningful regions of differential chromatin marking between cell types. We demonstrate SCIDDO's usefulness in an exemplary study in which we identify regions that establish a link between chromatin and gene expression changes. SCIDDO's quantitative approach to differential chromatin analysis is user-customizable, providing the necessary flexibility to adapt SCIDDO to specific research tasks. Given the functional diversity of cell types and the dynamics of the epigenome in response to environmental changes, it is hardly realistic to map the complete epigenome even for a single organism like human or mouse. For non-model organisms, e.g., cow, pig, or dog, epigenome data is particularly scarce. The third project of this thesis investigates to what extent bioinformatics methods can compensate for the comparatively little effort that is invested in charting the epigenome of non-model species. This study implements a large integrative analysis pipeline, including state-of-the-art machine learning, to transfer chromatin data for predictive modeling between 13 species. The evidence presented here indicates that a partial regulatory epigenetic signal is stably retained even over millions of years of evolutionary distance between the considered species. This finding suggests complementary and cost-effective ways for bioinformatics to contribute to comparative epigenome analysis across species boundaries.}, }
Endnote
%0 Thesis %A Ebert, Peter %Y Lengauer, Thomas %A referee: Lenhof, Hans-Peter %A referee: Weikum, Gerhard %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society International Max Planck Research School, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Algorithms and Complexity, MPI for Informatics, Max Planck Society Databases and Information Systems, MPI for Informatics, Max Planck Society %T What we leave behind : reproducibility in chromatin analysis within and across species : %G eng %U http://hdl.handle.net/21.11116/0000-0003-9ADF-5 %R doi.org/10.22028/D291-27831 %U urn:nbn:de:bsz:291--ds-278311 %I Universität des Saarlandes %C Saarbrücken %D 2019 %P 152 p. %V phd %9 phd %X Epigenetics is the field of biology that investigates heritable factors regulating gene expression without being directly encoded in the genome of an organism. The human genome is densely packed inside a cell's nucleus in the form of chromatin. Certain constituents of chromatin play a vital role as epigenetic factors in the dynamic regulation of gene expression. Epigenetic changes on the chromatin level are thus an integral part of the mechanisms governing the development of the functionally diverse cell types in multicellular species such as human. Studying these mechanisms is not only important to understand the biology of healthy cells, but also necessary to comprehend the epigenetic component in the formation of many complex diseases. Modern wet lab technology enables scientists to probe the epigenome with high throughput and in extensive detail. The fast generation of epigenetic datasets burdens computational researchers with the challenge of rapidly performing elaborate analyses without compromising on the scientific reproducibility of the reported findings. To facilitate reproducible computational research in epigenomics, this thesis proposes a task-oriented metadata model, relying on web technology and supported by database engineering, that aims at consistent and human-readable documentation of standardized computational workflows. The suggested approach features, e.g., computational validation of metadata records, automatic error detection, and progress monitoring of multi-step analyses, and was successfully field-tested as part of a large epigenome research consortium. This work leaves aside theoretical considerations, and intentionally emphasizes the realistic need of providing scientists with tools that assist them in performing reproducible research. Irrespective of the technological progress, the dynamic and cell-type specific nature of the epigenome commonly requires restricting the number of analyzed samples due to resource limitations. The second project of this thesis introduces the software tool SCIDDO, which has been developed for the differential chromatin analysis of cellular samples with potentially limited availability. By combining statistics, algorithmics, and best practices for robust software development, SCIDDO can quickly identify biologically meaningful regions of differential chromatin marking between cell types. We demonstrate SCIDDO's usefulness in an exemplary study in which we identify regions that establish a link between chromatin and gene expression changes. SCIDDO's quantitative approach to differential chromatin analysis is user-customizable, providing the necessary flexibility to adapt SCIDDO to specific research tasks. Given the functional diversity of cell types and the dynamics of the epigenome in response to environmental changes, it is hardly realistic to map the complete epigenome even for a single organism like human or mouse. For non-model organisms, e.g., cow, pig, or dog, epigenome data is particularly scarce. The third project of this thesis investigates to what extent bioinformatics methods can compensate for the comparatively little effort that is invested in charting the epigenome of non-model species. This study implements a large integrative analysis pipeline, including state-of-the-art machine learning, to transfer chromatin data for predictive modeling between 13 species. The evidence presented here indicates that a partial regulatory epigenetic signal is stably retained even over millions of years of evolutionary distance between the considered species. This finding suggests complementary and cost-effective ways for bioinformatics to contribute to comparative epigenome analysis across species boundaries. %U https://publikationen.sulb.uni-saarland.de/handle/20.500.11880/27387
11. Ebler J, Haukness M, Pesout T, Marschall T, Paten B: Haplotype-aware Diplotyping from Noisy Long Reads. Genome Biology 2019, 20.
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@article{Ebler2019, TITLE = {Haplotype-aware Diplotyping from Noisy Long Reads}, AUTHOR = {Ebler, Jana and Haukness, Marina and Pesout, Trevor and Marschall, Tobias and Paten, Benedict}, LANGUAGE = {eng}, ISSN = {1465-6906}, DOI = {10.1186/s13059-019-1709-0}, PUBLISHER = {BioMed Central Ltd.}, ADDRESS = {London}, YEAR = {2019}, MARGINALMARK = {$\bullet$}, JOURNAL = {Genome Biology}, VOLUME = {20}, EID = {116}, }
Endnote
%0 Journal Article %A Ebler, Jana %A Haukness, Marina %A Pesout, Trevor %A Marschall, Tobias %A Paten, Benedict %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations %T Haplotype-aware Diplotyping from Noisy Long Reads : %G eng %U http://hdl.handle.net/21.11116/0000-0003-D417-4 %R 10.1186/s13059-019-1709-0 %2 PMC6547545 %7 2019 %D 2019 %J Genome Biology %V 20 %Z sequence number: 116 %I BioMed Central Ltd. %C London %@ false
12. Gérard D, Schmidt F, Ginolhac A, Schmitz M, Halder R, Ebert P, Schulz MH, Sauter T, Sinkkonen L: Temporal Enhancer Profiling of Parallel Lineages Identifies AHR and GLIS1 as Regulators of Mesenchymal Multipotency. Nucleic Acids Research 2019, 47.
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@article{Gerard2019, TITLE = {Temporal enhancer profiling of parallel lineages identifies {AHR} and {GLIS1} as regulators of mesenchymal multipotency}, AUTHOR = {G{\'e}rard, Deborah and Schmidt, Florian and Ginolhac, Aur{\'e}lien and Schmitz, Martine and Halder, Rashi and Ebert, Peter and Schulz, Marcel Holger and Sauter, Thomas and Sinkkonen, Lasse}, LANGUAGE = {eng}, ISSN = {0305-1048}, DOI = {10.1093/nar/gky1240}, PUBLISHER = {Oxford University Press}, ADDRESS = {Oxford}, YEAR = {2019}, MARGINALMARK = {$\bullet$}, DATE = {2019}, JOURNAL = {Nucleic Acids Research}, VOLUME = {47}, NUMBER = {3}, PAGES = {1141--1163}, }
Endnote
%0 Journal Article %A Gérard, Deborah %A Schmidt, Florian %A Ginolhac, Aurélien %A Schmitz, Martine %A Halder, Rashi %A Ebert, Peter %A Schulz, Marcel Holger %A Sauter, Thomas %A Sinkkonen, Lasse %+ External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations %T Temporal Enhancer Profiling of Parallel Lineages Identifies AHR and GLIS1 as Regulators of Mesenchymal Multipotency : %G eng %U http://hdl.handle.net/21.11116/0000-0003-1AFD-4 %R 10.1093/nar/gky1240 %7 2018 %D 2019 %J Nucleic Acids Research %O Nucleic Acids Res %V 47 %N 3 %& 1141 %P 1141 - 1163 %I Oxford University Press %C Oxford %@ false
13. Ghaffaari A, Marschall T: Fully-sensitive Seed Finding in Sequence Graphs Using a Hybrid Index. Bioinformatics (Proc ISMB/ECCB 2019) 2019, 35.
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@article{Ghaffaari2019, TITLE = {Fully-sensitive Seed Finding in Sequence Graphs Using a Hybrid Index}, AUTHOR = {Ghaffaari, Ali and Marschall, Tobias}, LANGUAGE = {eng}, ISSN = {1367-4803}, DOI = {10.1093/bioinformatics/btz341}, PUBLISHER = {Oxford University Press}, ADDRESS = {Oxford}, YEAR = {2019}, MARGINALMARK = {$\bullet$}, DATE = {2019}, JOURNAL = {Bioinformatics (Proc. ISMB/ECCB)}, VOLUME = {35}, NUMBER = {14}, PAGES = {i81--i89}, BOOKTITLE = {ISMB/ECCB 2019 Proceedings}, }
Endnote
%0 Journal Article %A Ghaffaari, Ali %A Marschall, Tobias %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T Fully-sensitive Seed Finding in Sequence Graphs Using a Hybrid Index : %G eng %U http://hdl.handle.net/21.11116/0000-0004-7BC8-1 %R 10.1093/bioinformatics/btz341 %7 2019 %D 2019 %J Bioinformatics %V 35 %N 14 %& i81 %P i81 - i89 %I Oxford University Press %C Oxford %@ false %B ISMB/ECCB 2019 Proceedings %O ISMB/ECCB 2019 The biennial joint meeting of ISMB (27th Annual Conference on Intelligent Systems for Molecular Biology) and ECCB (18th European Conference on Computational Biology) ; Basel, Switzerland, July 21–25, 2019
14. Gier S, Simon M, Nordstroem K, Khalifa S, Schulz MH, Schmitt MJ, Breinig F: Transcriptome Kinetics of Saccharomyces cerevisiae in Response to Viral Killer Toxin K1. Frontiers in Microbiology 2019, 10.
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@article{Gier2019, TITLE = {Transcriptome Kinetics of Saccharomyces cerevisiae in Response to Viral Killer Toxin {K1}}, AUTHOR = {Gier, Stefanie and Simon, Martin and Nordstroem, Karl and Khalifa, Salem and Schulz, Marcel Holger and Schmitt, Manfred J. and Breinig, Frank}, LANGUAGE = {eng}, ISSN = {1664-302X}, DOI = {10.3389/fmicb.2019.01102}, PUBLISHER = {Frontiers Media}, ADDRESS = {Lausanne}, YEAR = {2019}, MARGINALMARK = {$\bullet$}, JOURNAL = {Frontiers in Microbiology}, VOLUME = {10}, EID = {1102}, }
Endnote
%0 Journal Article %A Gier, Stefanie %A Simon, Martin %A Nordstroem, Karl %A Khalifa, Salem %A Schulz, Marcel Holger %A Schmitt, Manfred J. %A Breinig, Frank %+ External Organizations External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations %T Transcriptome Kinetics of Saccharomyces cerevisiae in Response to Viral Killer Toxin K1 : %G eng %U http://hdl.handle.net/21.11116/0000-0003-B2F8-C %R 10.3389/fmicb.2019.01102 %7 2019 %D 2019 %J Frontiers in Microbiology %V 10 %Z sequence number: 1102 %I Frontiers Media %C Lausanne %@ false
15. Halbritter F, Farlik M, Schwentner R, Jug G, Fortelny N, Schnoeller T, Pisa H, Schuster LC, Reinprecht A, Czech T, Gojo J, Holter W, Minkov M, Bauer WM, Simonitsch-Klupp I, Bock C, Hutter C: Epigenomics and Singe-Cell Sequencing Define a Developmental Hierarchy in Langerhans Cell Histiocytosis. Cancer Discovery 2019, 9.
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@article{Halbritter_2019, TITLE = {Epigenomics and Singe-Cell Sequencing Define a Developmental Hierarchy in Langerhans Cell Histiocytosis}, AUTHOR = {Halbritter, Florian and Farlik, Matthias and Schwentner, Raphaela and Jug, Gunhild and Fortelny, Nikolaus and Schnoeller, Thomas and Pisa, Hanja and Schuster, Linda C. and Reinprecht, Andrea and Czech, Thomas and Gojo, Johannes and Holter, Wolfgang and Minkov, Milen and Bauer, Wolfgang M. and Simonitsch-Klupp, Ingrid and Bock, Christoph and Hutter, Caroline}, LANGUAGE = {eng}, DOI = {10.1158/2159-8290.CD-19-0138}, PUBLISHER = {AACR}, YEAR = {2019}, MARGINALMARK = {$\bullet$}, JOURNAL = {Cancer Discovery}, VOLUME = {9}, NUMBER = {10}, }
Endnote
%0 Journal Article %A Halbritter, Florian %A Farlik, Matthias %A Schwentner, Raphaela %A Jug, Gunhild %A Fortelny, Nikolaus %A Schnoeller, Thomas %A Pisa, Hanja %A Schuster, Linda C. %A Reinprecht, Andrea %A Czech, Thomas %A Gojo, Johannes %A Holter, Wolfgang %A Minkov, Milen %A Bauer, Wolfgang M. %A Simonitsch-Klupp, Ingrid %A Bock, Christoph %A Hutter, Caroline %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T Epigenomics and Singe-Cell Sequencing Define a Developmental Hierarchy in Langerhans Cell Histiocytosis : %G eng %U http://hdl.handle.net/21.11116/0000-0004-EA55-5 %R 10.1158/2159-8290.CD-19-0138 %7 2019 %D 2019 %J Cancer Discovery %V 9 %N 10 %I AACR
16. Hamdane N, Juhling F, Crouchet E, El Saghire H, Thumann C, Oudot MA, Bandiera S, Saviano A, Ponsolles C, Suarez AAR, Li S, Fujiwara N, Ono A, Davidson I, Bardeesy N, Schmidl C, Bock C, Schuster C, Lupberger J, Habersetzer F, Doffoel M, Piardi T, Sommacale D, Imamura M, Uchida T, Ohdan H, Aikata H, Chayama K, Boldanova T, Pessaux P, et al.: HCV-Induced Epigenetic Changes Associated With Liver Cancer Risk Persist After Sustained Virologic Response. Gastroenterology 2019, 156.
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@article{Hamdane2019, TITLE = {{HCV}-Induced Epigenetic Changes Associated With Liver Cancer Risk Persist After Sustained Virologic Response}, AUTHOR = {Hamdane, Nourdine and Juhling, Frank and Crouchet, Emilie and El Saghire, Houssein and Thumann, Christine and Oudot, Marine A. and Bandiera, Simonetta and Saviano, Antonio and Ponsolles, Clara and Suarez, Armando Andres Roca and Li, Shen and Fujiwara, Naoto and Ono, Atsushi and Davidson, Irwin and Bardeesy, Nabeel and Schmidl, Christian and Bock, Christoph and Schuster, Catherine and Lupberger, Joachim and Habersetzer, Francois and Doffoel, Michel and Piardi, Tullio and Sommacale, Daniele and Imamura, Michio and Uchida, Takuro and Ohdan, Hideki and Aikata, Hiroshi and Chayama, Kazuaki and Boldanova, Tujana and Pessaux, Patrick and Fuchs, Bryan C. and Hoshida, Yujin and Zeisel, Mirjam B. and Duong, Francois H. T. and Baumert, Thomas F.}, LANGUAGE = {eng}, ISSN = {0016-5085}, DOI = {10.1053/j.gastro.2019.02.038}, PUBLISHER = {W.B. Saunders}, ADDRESS = {Philadelphia, Pa}, YEAR = {2019}, MARGINALMARK = {$\bullet$}, DATE = {2019}, JOURNAL = {Gastroenterology}, VOLUME = {156}, NUMBER = {8}, PAGES = {2313--2329}, EID = {e7}, }
Endnote
%0 Journal Article %A Hamdane, Nourdine %A Juhling, Frank %A Crouchet, Emilie %A El Saghire, Houssein %A Thumann, Christine %A Oudot, Marine A. %A Bandiera, Simonetta %A Saviano, Antonio %A Ponsolles, Clara %A Suarez, Armando Andres Roca %A Li, Shen %A Fujiwara, Naoto %A Ono, Atsushi %A Davidson, Irwin %A Bardeesy, Nabeel %A Schmidl, Christian %A Bock, Christoph %A Schuster, Catherine %A Lupberger, Joachim %A Habersetzer, Francois %A Doffoel, Michel %A Piardi, Tullio %A Sommacale, Daniele %A Imamura, Michio %A Uchida, Takuro %A Ohdan, Hideki %A Aikata, Hiroshi %A Chayama, Kazuaki %A Boldanova, Tujana %A Pessaux, Patrick %A Fuchs, Bryan C. %A Hoshida, Yujin %A Zeisel, Mirjam B. %A Duong, Francois H. T. %A Baumert, Thomas F. %+ External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations %T HCV-Induced Epigenetic Changes Associated With Liver Cancer Risk Persist After Sustained Virologic Response : %G eng %U http://hdl.handle.net/21.11116/0000-0003-C353-3 %R 10.1053/j.gastro.2019.02.038 %7 2019 %D 2019 %J Gastroenterology %O Gastroenterology %V 156 %N 8 %& 2313 %P 2313 - 2329 %Z sequence number: e7 %I W.B. Saunders %C Philadelphia, Pa %@ false
17. Handl L, Jalali A, Scherer M, Eggeling R, Pfeifer N: Weighted Elastic Net for Unsupervised Domain Adaptation with Application to Age Prediction from DNA Methylation Data. Bioinformatics (Proc ISMB/ECCB 2019) 2019, 35.
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@article{Handl2019, TITLE = {Weighted Elastic Net for Unsupervised Domain Adaptation with Application to Age Prediction from {DNA} Methylation Data}, AUTHOR = {Handl, Lisa and Jalali, Adrin and Scherer, Michael and Eggeling, Ralf and Pfeifer, Nico}, LANGUAGE = {eng}, ISSN = {1367-4803}, DOI = {10.1093/bioinformatics/btz338}, PUBLISHER = {Oxford University Press}, ADDRESS = {Oxford}, YEAR = {2019}, MARGINALMARK = {$\bullet$}, DATE = {2019}, JOURNAL = {Bioinformatics (Proc. ISMB/ECCB)}, VOLUME = {35}, NUMBER = {14}, PAGES = {i154--i163}, BOOKTITLE = {ISMB/ECCB 2019 Proceedings}, }
Endnote
%0 Journal Article %A Handl, Lisa %A Jalali, Adrin %A Scherer, Michael %A Eggeling, Ralf %A Pfeifer, Nico %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T Weighted Elastic Net for Unsupervised Domain Adaptation with Application to Age Prediction from DNA Methylation Data : %G eng %U http://hdl.handle.net/21.11116/0000-0004-7BC6-3 %R 10.1093/bioinformatics/btz338 %7 2019 %D 2019 %J Bioinformatics %V 35 %N 14 %& i154 %P i154 - i163 %I Oxford University Press %C Oxford %@ false %B ISMB/ECCB 2019 Proceedings %O ISMB/ECCB 2019 The biennial joint meeting of ISMB (27th Annual Conference on Intelligent Systems for Molecular Biology) and ECCB (18th European Conference on Computational Biology) ; Basel, Switzerland, July 21–25, 2019.
18. Kanduri C, Bock C, Gundersen S, Hovig E, Sandve GK: Colocalization Analyses of Genomic Elements: Approaches, Recommendations and Challenges. Bioinformatics 2019, 35.
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@article{Kanduri2019, TITLE = {Colocalization Analyses of Genomic Elements: Approaches, Recommendations and Challenges}, AUTHOR = {Kanduri, Chakravarthi and Bock, Christoph and Gundersen, Sveinung and Hovig, Eivind and Sandve, Geir Kjetil}, LANGUAGE = {eng}, ISSN = {1367-4803}, DOI = {10.1093/bioinformatics/bty835}, PUBLISHER = {Oxford University Press}, ADDRESS = {Oxford, UK}, YEAR = {2019}, MARGINALMARK = {$\bullet$}, JOURNAL = {Bioinformatics}, VOLUME = {35}, NUMBER = {9}, PAGES = {1615--1624}, }
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%0 Journal Article %A Kanduri, Chakravarthi %A Bock, Christoph %A Gundersen, Sveinung %A Hovig, Eivind %A Sandve, Geir Kjetil %+ External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations %T Colocalization Analyses of Genomic Elements: Approaches, Recommendations and Challenges : %G eng %U http://hdl.handle.net/21.11116/0000-0003-C2A6-6 %R 10.1093/bioinformatics/bty835 %2 PMC6499241 %7 2019 %D 2019 %J Bioinformatics %V 35 %N 9 %& 1615 %P 1615 - 1624 %I Oxford University Press %C Oxford, UK %@ false
19. Karunanithi S, Simon M, Schulz MH: Automated Analysis of Small RNA Datasets with RAPID. PeerJ 2019, 7.
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@article{Karunanithi2019, TITLE = {Automated analysis of small {RNA} datasets with {RAPID}}, AUTHOR = {Karunanithi, Sivarajan and Simon, Martin and Schulz, Marcel Holger}, LANGUAGE = {eng}, ISSN = {2167-8359}, DOI = {10.7717/peerj.6710}, PUBLISHER = {PeerJ Inc.}, ADDRESS = {San Francisco, USA}, YEAR = {2019}, MARGINALMARK = {$\bullet$}, JOURNAL = {PeerJ}, VOLUME = {7}, EID = {e6710}, }
Endnote
%0 Journal Article %A Karunanithi, Sivarajan %A Simon, Martin %A Schulz, Marcel Holger %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T Automated Analysis of Small RNA Datasets with RAPID : %G eng %U http://hdl.handle.net/21.11116/0000-0003-7D5F-8 %R 10.7717/peerj.6710 %7 2019 %D 2019 %J PeerJ %O PeerJ %V 7 %Z sequence number: e6710 %I PeerJ Inc. %C San Francisco, USA %@ false
20. Karunanithi S, Oruganti V, Marker S, Rodriguez-Viana AM, Drews F, Pirritano M, Nordström K, Simon M, Schulz MH: Exogenous RNAi Mechanisms Contribute to Transcriptome Adaptation by Phased siRNA Clusters in Paramecium. Nucleic Acids Research (London) 2019.
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@article{Karunanithi2019, TITLE = {Exogenous {RNAi} mechanisms contribute to transcriptome adaptation by phased {siRNA} clusters in {Paramecium}}, AUTHOR = {Karunanithi, Sivarajan and Oruganti, Vidya and Marker, Simone and Rodriguez-Viana, Angela M. and Drews, Franziska and Pirritano, Marcello and Nordstr{\"o}m, Karl and Simon, Martin and Schulz, Marcel Holger}, LANGUAGE = {eng}, ISSN = {0305-1048}, DOI = {10.1093/nar/gkz553}, PUBLISHER = {Oxford University Press}, ADDRESS = {Oxford}, YEAR = {2019}, MARGINALMARK = {$\bullet$}, JOURNAL = {Nucleic Acids Research (London)}, EID = {gkz553}, }
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%0 Journal Article %A Karunanithi, Sivarajan %A Oruganti, Vidya %A Marker, Simone %A Rodriguez-Viana, Angela M. %A Drews, Franziska %A Pirritano, Marcello %A Nordström, Karl %A Simon, Martin %A Schulz, Marcel Holger %+ External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T Exogenous RNAi Mechanisms Contribute to Transcriptome Adaptation by Phased siRNA Clusters in Paramecium : %G eng %U http://hdl.handle.net/21.11116/0000-0003-E818-D %R 10.1093/nar/gkz553 %2 PMC6735861 %7 2019 %D 2019 %J Nucleic Acids Research (London) %O Nucleic Acids Res %Z sequence number: gkz553 %I Oxford University Press %C Oxford %@ false
21. Kosack L, Wingelhofer B, Popa A, Orlova A, Agerer B, Vilagos B, Majek P, Parapatics K, Lercher A, Ringler A, Klughammer J, Smyth M, Khamina K, Baazim H, de Araujo ED, Rosa DA, Park J, Tin G, Ahmar S, Gunning PT, Bock C, Siddle HV, Woods GM, Kubicek S, Murchison EP, Bennett KL, Moriggl R, Bergthaler A: The ERBB-STAT3 Axis Drives Tasmanian Devil Facial Tumor Disease. Cancer Cell 2019, 35.
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@article{Kosack2019, TITLE = {The {ERBB}-{STAT3} Axis Drives {T}asmanian Devil Facial Tumor Disease}, AUTHOR = {Kosack, Lindsay and Wingelhofer, Bettina and Popa, Alexandra and Orlova, Anna and Agerer, Benedikt and Vilagos, Bojan and Majek, Peter and Parapatics, Katja and Lercher, Alexander and Ringler, Anna and Klughammer, Johanna and Smyth, Mark and Khamina, Kseniya and Baazim, Hatoon and de Araujo, Elvin D. and Rosa, David A. and Park, Jisung and Tin, Gary and Ahmar, Siawash and Gunning, Patrick T. and Bock, Christoph and Siddle, Hannah V. and Woods, Gregory M. and Kubicek, Stefan and Murchison, Elizabeth P. and Bennett, Keiryn L. and Moriggl, Richard and Bergthaler, Andreas}, LANGUAGE = {eng}, ISSN = {1535-6108}, DOI = {10.1016/j.ccell.2018.11.018}, PUBLISHER = {Cell Press}, ADDRESS = {Cambridge, Mass.}, YEAR = {2019}, MARGINALMARK = {$\bullet$}, JOURNAL = {Cancer Cell}, VOLUME = {35}, NUMBER = {1}, PAGES = {125--139}, EID = {e9}, }
Endnote
%0 Journal Article %A Kosack, Lindsay %A Wingelhofer, Bettina %A Popa, Alexandra %A Orlova, Anna %A Agerer, Benedikt %A Vilagos, Bojan %A Majek, Peter %A Parapatics, Katja %A Lercher, Alexander %A Ringler, Anna %A Klughammer, Johanna %A Smyth, Mark %A Khamina, Kseniya %A Baazim, Hatoon %A de Araujo, Elvin D. %A Rosa, David A. %A Park, Jisung %A Tin, Gary %A Ahmar, Siawash %A Gunning, Patrick T. %A Bock, Christoph %A Siddle, Hannah V. %A Woods, Gregory M. %A Kubicek, Stefan %A Murchison, Elizabeth P. %A Bennett, Keiryn L. %A Moriggl, Richard %A Bergthaler, Andreas %+ External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations %T The ERBB-STAT3 Axis Drives Tasmanian Devil Facial Tumor Disease : %G eng %U http://hdl.handle.net/21.11116/0000-0002-F715-0 %R 10.1016/j.ccell.2018.11.018 %7 2019 %D 2019 %J Cancer Cell %O Cancer Cell %V 35 %N 1 %& 125 %P 125 - 139 %Z sequence number: e9 %I Cell Press %C Cambridge, Mass. %@ false
22. List M, Dheghani Amirabad A, Kostka D, Schulz MH: Large-scale Inference of Competing Endogenous RNA Networks with Sparse Partial Correlation. Bioinformatics (Proc ISMB/ECCB 2019) 2019, 35.
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@article{List2019, TITLE = {Large-scale Inference of Competing Endogenous {RNA} Networks with Sparse Partial Correlation}, AUTHOR = {List, Markus and Dheghani Amirabad, Azim and Kostka, Dennis and Schulz, Marcel Holger}, LANGUAGE = {eng}, ISSN = {1367-4803}, DOI = {10.1093/bioinformatics/btz314}, PUBLISHER = {Oxford University Press}, ADDRESS = {Oxford}, YEAR = {2019}, MARGINALMARK = {$\bullet$}, DATE = {2019}, JOURNAL = {Bioinformatics (Proc. ISMB/ECCB)}, VOLUME = {35}, NUMBER = {14}, PAGES = {i596--i604}, BOOKTITLE = {ISMB/ECCB 2019 Proceedings}, }
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%0 Journal Article %A List, Markus %A Dheghani Amirabad, Azim %A Kostka, Dennis %A Schulz, Marcel Holger %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T Large-scale Inference of Competing Endogenous RNA Networks with Sparse Partial Correlation : %G eng %U http://hdl.handle.net/21.11116/0000-0004-7CC2-6 %R 10.1093/bioinformatics/btz314 %7 2019 %D 2019 %J Bioinformatics %V 35 %N 14 %& i596 %P i596 - i604 %I Oxford University Press %C Oxford %@ false %B ISMB/ECCB 2019 Proceedings %O ISMB/ECCB 2019 The biennial joint meeting of ISMB (27th Annual Conference on Intelligent Systems for Molecular Biology) and ECCB (18th European Conference on Computational Biology) ; Basel, Switzerland, July 21–25, 2019
23. Li Z, Schulz MH, Look T, Begemann M, Zenke M, Costa IG: Identification of Transcription Factor Binding Sites using ATAC-seq. Genome Research 2019, 20.
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@article{Li2019, TITLE = {Identification of transcription factor binding sites using {ATAC}-seq}, AUTHOR = {Li, Zhijian and Schulz, Marcel Holger and Look, Thomas and Begemann, Matthias and Zenke, Martin and Costa, Ivan G.}, LANGUAGE = {eng}, ISSN = {1088-9051}, DOI = {10.1186/s13059-019-1642-2}, PUBLISHER = {Cold Spring Harbor Laboratory Press}, ADDRESS = {Cold Spring Harbor, N.Y.}, YEAR = {2019}, MARGINALMARK = {$\bullet$}, JOURNAL = {Genome Research}, VOLUME = {20}, EID = {45}, }
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%0 Journal Article %A Li, Zhijian %A Schulz, Marcel Holger %A Look, Thomas %A Begemann, Matthias %A Zenke, Martin %A Costa, Ivan G. %+ External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations External Organizations %T Identification of Transcription Factor Binding Sites using ATAC-seq : %G eng %U http://hdl.handle.net/21.11116/0000-0003-2AF1-E %R 10.1186/s13059-019-1642-2 %7 2019 %D 2019 %J Genome Research %V 20 %Z sequence number: 45 %I Cold Spring Harbor Laboratory Press %C Cold Spring Harbor, N.Y. %@ false
24. Luebke N, Jensen B, Huettig F, Feldt T, Walker A, Thielen A, Daeumer M, Obermeier M, Kaiser R, Knops E, Heger E, Sierra S, Oette M, Lengauer T, Timm J, Haeussinger D: Failure of Dolutegravir First-Line ART with Selection of Virus Carrying R263K and G118R. The New England Journal of Medicine : NEJM / Publ by the Massachusetts Medical Society 2019, 381.
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@article{Luebke2019, TITLE = {Failure of Dolutegravir First-Line {ART} with Selection of Virus Carrying {R263K} and {G118R}}, AUTHOR = {Luebke, Nadine and Jensen, Bjoern and Huettig, Falk and Feldt, Torsten and Walker, Andreas and Thielen, Alexander and Daeumer, Martin and Obermeier, Martin and Kaiser, Rolf and Knops, Elena and Heger, Eva and Sierra, Saleta and Oette, Mark and Lengauer, Thomas and Timm, Joerg and Haeussinger, Dieter}, LANGUAGE = {eng}, ISSN = {0028-4793}, DOI = {10.1056/NEJMc1806554}, PUBLISHER = {New England Journal of Medicine}, ADDRESS = {Boston}, YEAR = {2019}, MARGINALMARK = {$\bullet$}, DATE = {2019}, JOURNAL = {The New England Journal of Medicine : NEJM / Publ. by the Massachusetts Medical Society}, VOLUME = {381}, NUMBER = {9}, PAGES = {887--889}, }
Endnote
%0 Journal Article %A Luebke, Nadine %A Jensen, Bjoern %A Huettig, Falk %A Feldt, Torsten %A Walker, Andreas %A Thielen, Alexander %A Daeumer, Martin %A Obermeier, Martin %A Kaiser, Rolf %A Knops, Elena %A Heger, Eva %A Sierra, Saleta %A Oette, Mark %A Lengauer, Thomas %A Timm, Joerg %A Haeussinger, Dieter %+ External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations %T Failure of Dolutegravir First-Line ART with Selection of Virus Carrying R263K and G118R : %G eng %U http://hdl.handle.net/21.11116/0000-0004-B780-C %R 10.1056/NEJMc1806554 %7 2019 %D 2019 %J The New England Journal of Medicine : NEJM / Publ. by the Massachusetts Medical Society %O N. Engl. J. Med. %V 381 %N 9 %& 887 %P 887 - 889 %I New England Journal of Medicine %C Boston %@ false
25. Müller F, Scherer M, Assenov Y, Lutsik P, Walter J, Lengauer T, Bock C: RnBeads 2.0: Comprehensive Analysis of DNA Methylation Data. Genome Biology 2019, 20.
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@article{Mueller_GenomeBiology2019, TITLE = {{RnBeads} 2.0: {C}omprehensive analysis of {DNA} methylation data}, AUTHOR = {M{\"u}ller, Fabian and Scherer, Michael and Assenov, Yassen and Lutsik, Pavlo and Walter, J{\"o}rn and Lengauer, Thomas and Bock, Christoph}, LANGUAGE = {eng}, ISSN = {1465-6906}, DOI = {10.1186/s13059-019-1664-9}, PUBLISHER = {BioMed Central Ltd.}, ADDRESS = {London}, YEAR = {2019}, MARGINALMARK = {$\bullet$}, JOURNAL = {Genome Biology}, VOLUME = {20}, EID = {55}, }
Endnote
%0 Journal Article %A Müller, Fabian %A Scherer, Michael %A Assenov, Yassen %A Lutsik, Pavlo %A Walter, Jörn %A Lengauer, Thomas %A Bock, Christoph %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T RnBeads 2.0: Comprehensive Analysis of DNA Methylation Data : %G eng %U http://hdl.handle.net/21.11116/0000-0003-2DF3-9 %R 10.1186/s13059-019-1664-9 %7 2019 %D 2019 %J Genome Biology %V 20 %Z sequence number: 55 %I BioMed Central Ltd. %C London %@ false
26. Neininger K, Marschall T, Helms V: SNP and Indel Frequencies at Transcription Start Sites and at Canonical and Alternative Translation Initiation Sites in the Human Genome. PLoS One 2019, 14.
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@article{Neininger2019, TITLE = {{SNP} and indel frequencies at transcription start sites and at canonical and alternative translation initiation sites in the human genome}, AUTHOR = {Neininger, Kerstin and Marschall, Tobias and Helms, Volkhard}, LANGUAGE = {eng}, ISSN = {1932-6203}, DOI = {10.1371/journal.pone.0214816}, PUBLISHER = {Public Library of Science}, ADDRESS = {San Francisco, CA}, YEAR = {2019}, MARGINALMARK = {$\bullet$}, JOURNAL = {PLoS One}, VOLUME = {14}, NUMBER = {4}, EID = {e0214816}, }
Endnote
%0 Journal Article %A Neininger, Kerstin %A Marschall, Tobias %A Helms, Volkhard %+ External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations %T SNP and Indel Frequencies at Transcription Start Sites and at Canonical and Alternative Translation Initiation Sites in the Human Genome : %G eng %U http://hdl.handle.net/21.11116/0000-0003-866B-E %R 10.1371/journal.pone.0214816 %7 2019-04-12 %D 2019 %8 12.04.2019 %J PLoS One %V 14 %N 4 %Z sequence number: e0214816 %I Public Library of Science %C San Francisco, CA %@ false
27. Nikumbh S: Interpretable Machine Learning Methods for Prediction and Analysis of Genome Regulation in 3D. Universität des Saarlandes; 2019.
Abstract
With the development of chromosome conformation capture-based techniques, we now know that chromatin is packed in three-dimensional (3D) space inside the cell nucleus. Changes in the 3D chromatin architecture have already been implicated in diseases such as cancer. Thus, a better understanding of this 3D conformation is of interest to help enhance our comprehension of the complex, multipronged regulatory mechanisms of the genome. The work described in this dissertation largely focuses on development and application of interpretable machine learning methods for prediction and analysis of long-range genomic interactions output from chromatin interaction experiments. In the first part, we demonstrate that the genetic sequence information at the ge- nomic loci is predictive of the long-range interactions of a particular locus of interest (LoI). For example, the genetic sequence information at and around enhancers can help predict whether it interacts with a promoter region of interest. This is achieved by building string kernel-based support vector classifiers together with two novel, in- tuitive visualization methods. These models suggest a potential general role of short tandem repeat motifs in the 3D genome organization. But, the insights gained out of these models are still coarse-grained. To this end, we devised a machine learning method, called CoMIK for Conformal Multi-Instance Kernels, capable of providing more fine-grained insights. When comparing sequences of variable length in the su- pervised learning setting, CoMIK can not only identify the features important for classification but also locate them within the sequence. Such precise identification of important segments of the whole sequence can help in gaining de novo insights into any role played by the intervening chromatin towards long-range interactions. Although CoMIK primarily uses only genetic sequence information, it can also si- multaneously utilize other information modalities such as the numerous functional genomics data if available. The second part describes our pipeline, pHDee, for easy manipulation of large amounts of 3D genomics data. We used the pipeline for analyzing HiChIP experimen- tal data for studying the 3D architectural changes in Ewing sarcoma (EWS) which is a rare cancer affecting adolescents. In particular, HiChIP data for two experimen- tal conditions, doxycycline-treated and untreated, and for primary tumor samples is analyzed. We demonstrate that pHDee facilitates processing and easy integration of large amounts of 3D genomics data analysis together with other data-intensive bioinformatics analyses.
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@phdthesis{Nikumbhphd2019, TITLE = {Interpretable Machine Learning Methods for Prediction and Analysis of Genome Regulation in {3D}}, AUTHOR = {Nikumbh, Sarvesh}, LANGUAGE = {eng}, DOI = {10.22028/D291-28153}, SCHOOL = {Universit{\"a}t des Saarlandes}, ADDRESS = {Saarbr{\"u}cken}, YEAR = {2019}, MARGINALMARK = {$\bullet$}, DATE = {2019}, ABSTRACT = {With the development of chromosome conformation capture-based techniques, we now know that chromatin is packed in three-dimensional (3D) space inside the cell nucleus. Changes in the 3D chromatin architecture have already been implicated in diseases such as cancer. Thus, a better understanding of this 3D conformation is of interest to help enhance our comprehension of the complex, multipronged regulatory mechanisms of the genome. The work described in this dissertation largely focuses on development and application of interpretable machine learning methods for prediction and analysis of long-range genomic interactions output from chromatin interaction experiments. In the first part, we demonstrate that the genetic sequence information at the ge- nomic loci is predictive of the long-range interactions of a particular locus of interest (LoI). For example, the genetic sequence information at and around enhancers can help predict whether it interacts with a promoter region of interest. This is achieved by building string kernel-based support vector classifiers together with two novel, in- tuitive visualization methods. These models suggest a potential general role of short tandem repeat motifs in the 3D genome organization. But, the insights gained out of these models are still coarse-grained. To this end, we devised a machine learning method, called CoMIK for Conformal Multi-Instance Kernels, capable of providing more fine-grained insights. When comparing sequences of variable length in the su- pervised learning setting, CoMIK can not only identify the features important for classification but also locate them within the sequence. Such precise identification of important segments of the whole sequence can help in gaining de novo insights into any role played by the intervening chromatin towards long-range interactions. Although CoMIK primarily uses only genetic sequence information, it can also si- multaneously utilize other information modalities such as the numerous functional genomics data if available. The second part describes our pipeline, pHDee, for easy manipulation of large amounts of 3D genomics data. We used the pipeline for analyzing HiChIP experimen- tal data for studying the 3D architectural changes in Ewing sarcoma (EWS) which is a rare cancer affecting adolescents. In particular, HiChIP data for two experimen- tal conditions, doxycycline-treated and untreated, and for primary tumor samples is analyzed. We demonstrate that pHDee facilitates processing and easy integration of large amounts of 3D genomics data analysis together with other data-intensive bioinformatics analyses.}, }
Endnote
%0 Thesis %A Nikumbh, Sarvesh %Y Pfeifer, Nico %A referee: Marschall, Tobias %A referee: Ebert, Peter %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society International Max Planck Research School, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T Interpretable Machine Learning Methods for Prediction and Analysis of Genome Regulation in 3D : %G eng %U http://hdl.handle.net/21.11116/0000-0004-A5CE-A %R 10.22028/D291-28153 %I Universität des Saarlandes %C Saarbrücken %D 2019 %P 150 p. %V phd %9 phd %X With the development of chromosome conformation capture-based techniques, we now know that chromatin is packed in three-dimensional (3D) space inside the cell nucleus. Changes in the 3D chromatin architecture have already been implicated in diseases such as cancer. Thus, a better understanding of this 3D conformation is of interest to help enhance our comprehension of the complex, multipronged regulatory mechanisms of the genome. The work described in this dissertation largely focuses on development and application of interpretable machine learning methods for prediction and analysis of long-range genomic interactions output from chromatin interaction experiments. In the first part, we demonstrate that the genetic sequence information at the ge- nomic loci is predictive of the long-range interactions of a particular locus of interest (LoI). For example, the genetic sequence information at and around enhancers can help predict whether it interacts with a promoter region of interest. This is achieved by building string kernel-based support vector classifiers together with two novel, in- tuitive visualization methods. These models suggest a potential general role of short tandem repeat motifs in the 3D genome organization. But, the insights gained out of these models are still coarse-grained. To this end, we devised a machine learning method, called CoMIK for Conformal Multi-Instance Kernels, capable of providing more fine-grained insights. When comparing sequences of variable length in the su- pervised learning setting, CoMIK can not only identify the features important for classification but also locate them within the sequence. Such precise identification of important segments of the whole sequence can help in gaining de novo insights into any role played by the intervening chromatin towards long-range interactions. Although CoMIK primarily uses only genetic sequence information, it can also si- multaneously utilize other information modalities such as the numerous functional genomics data if available. The second part describes our pipeline, pHDee, for easy manipulation of large amounts of 3D genomics data. We used the pipeline for analyzing HiChIP experimen- tal data for studying the 3D architectural changes in Ewing sarcoma (EWS) which is a rare cancer affecting adolescents. In particular, HiChIP data for two experimen- tal conditions, doxycycline-treated and untreated, and for primary tumor samples is analyzed. We demonstrate that pHDee facilitates processing and easy integration of large amounts of 3D genomics data analysis together with other data-intensive bioinformatics analyses. %U https://publikationen.sulb.uni-saarland.de/handle/20.500.11880/27471
28. Pfitzer L, Moser C, Gegenfurtner F, Arner A, Foerster F, Atzberger C, Zisis T, Kubisch-Dohmen R, Busse J, Smith R, Timinszky G, Kalinina OV, Müller R, Wagner E, Vollmar AM, Zahler S: Targeting Actin Inhibits Repair of Doxorubicin-induced DNA Damage: A Novel Therapeutic Approach for Combination Therapy. Cell Death and Disease 2019, 10.
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@article{Pfitzer2019, TITLE = {Targeting actin inhibits repair of doxorubicin-induced {DNA} damage: {A} novel therapeutic approach for combination therapy}, AUTHOR = {Pfitzer, Lisa and Moser, Christina and Gegenfurtner, Florian and Arner, Anja and Foerster, Florian and Atzberger, Carina and Zisis, Themistoklis and Kubisch-Dohmen, Rebekka and Busse, Johanna and Smith, Rebecca and Timinszky, Gyula and Kalinina, Olga V. and M{\"u}ller, Rolf and Wagner, Ernst and Vollmar, Angelika M. and Zahler, Stefan}, LANGUAGE = {eng}, DOI = {10.1038/s41419-019-1546-9}, PUBLISHER = {Nature Publishing Group}, ADDRESS = {London}, YEAR = {2019}, MARGINALMARK = {$\bullet$}, JOURNAL = {Cell Death and Disease}, VOLUME = {10}, EID = {302}, }
Endnote
%0 Journal Article %A Pfitzer, Lisa %A Moser, Christina %A Gegenfurtner, Florian %A Arner, Anja %A Foerster, Florian %A Atzberger, Carina %A Zisis, Themistoklis %A Kubisch-Dohmen, Rebekka %A Busse, Johanna %A Smith, Rebecca %A Timinszky, Gyula %A Kalinina, Olga V. %A Müller, Rolf %A Wagner, Ernst %A Vollmar, Angelika M. %A Zahler, Stefan %+ External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations External Organizations %T Targeting Actin Inhibits Repair of Doxorubicin-induced DNA Damage: A Novel Therapeutic Approach for Combination Therapy : %G eng %U http://hdl.handle.net/21.11116/0000-0003-8A7E-5 %R 10.1038/s41419-019-1546-9 %7 2019 %D 2019 %J Cell Death and Disease %O Cell Death Dis %V 10 %Z sequence number: 302 %I Nature Publishing Group %C London
29. Piper CJM, Rosser EC, Oleinika K, Nistala K, Krausgruber T, Rendeiro AF, Banos A, Drozdov I, Villa M, Thomson S, Xanthou G, Bock C, Stockinger B, Mauri C: Aryl Hydrocarbon Receptor Contributes to the Transcriptional Program of IL-10-Producing Regulatory B Cells. Cell Reports 2019, 29.
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@article{Piper2019, TITLE = {Aryl Hydrocarbon Receptor Contributes to the Transcriptional Program of {IL}-10-Producing Regulatory {B} Cells}, AUTHOR = {Piper, Christopher J.M. and Rosser, Elizabeth C. and Oleinika, Kristine and Nistala, Kiran and Krausgruber, Thomas and Rendeiro, Andr{\'e} F. and Banos, Aggelos and Drozdov, Ignat and Villa, Matteo and Thomson, Scott and Xanthou, Georgina and Bock, Christoph and Stockinger, Brigitta and Mauri, Claudia}, LANGUAGE = {eng}, ISSN = {2211-1247}, DOI = {10.1016/j.celrep.2019.10.018}, PUBLISHER = {Cell Press}, ADDRESS = {Maryland Heights, MO}, YEAR = {2019}, MARGINALMARK = {$\bullet$}, JOURNAL = {Cell Reports}, VOLUME = {29}, NUMBER = {7}, PAGES = {1878--1892}, EID = {e7}, }
Endnote
%0 Journal Article %A Piper, Christopher J.M. %A Rosser, Elizabeth C. %A Oleinika, Kristine %A Nistala, Kiran %A Krausgruber, Thomas %A Rendeiro, André F. %A Banos, Aggelos %A Drozdov, Ignat %A Villa, Matteo %A Thomson, Scott %A Xanthou, Georgina %A Bock, Christoph %A Stockinger, Brigitta %A Mauri, Claudia %+ External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations %T Aryl Hydrocarbon Receptor Contributes to the Transcriptional Program of IL-10-Producing Regulatory B Cells : %G eng %U http://hdl.handle.net/21.11116/0000-0005-5CAA-5 %R 10.1016/j.celrep.2019.10.018 %7 2019 %D 2019 %J Cell Reports %V 29 %N 7 %& 1878 %P 1878 - 1892 %Z sequence number: e7 %I Cell Press %C Maryland Heights, MO %@ false
30. Rautiainen M, Mäkinen V, Marschall T: Bit-parallel Sequence-to-Graph Alignment. Bioinformatics 2019, 35.
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@article{Rautiainen_2019, TITLE = {Bit-parallel Sequence-to-Graph Alignment}, AUTHOR = {Rautiainen, Mikko and M{\"a}kinen, Veli and Marschall, Tobias}, LANGUAGE = {eng}, ISSN = {1367-4803}, DOI = {10.1093/bioinformatics/btz162}, PUBLISHER = {Oxford University Press}, ADDRESS = {Oxford}, YEAR = {2019}, MARGINALMARK = {$\bullet$}, DATE = {2019}, JOURNAL = {Bioinformatics}, VOLUME = {35}, NUMBER = {19}, PAGES = {3599--3607}, }
Endnote
%0 Journal Article %A Rautiainen, Mikko %A Mäkinen, Veli %A Marschall, Tobias %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T Bit-parallel Sequence-to-Graph Alignment : %G eng %U http://hdl.handle.net/21.11116/0000-0004-E4CA-7 %R 10.1093/bioinformatics/btz162 %2 PMC6761980 %7 2019 %D 2019 %J Bioinformatics %V 35 %N 19 %& 3599 %P 3599 - 3607 %I Oxford University Press %C Oxford %@ false
31. Roeder B, Kersten N, Herr M, Speicher NK, Pfeifer N: web-rMKL: A Web Server for Dimensionality Reduction and Sample Clustering of Multi-view Data Based on Unsupervised Multiple Kernel Learning. Nucleic Acids Research (London) 2019, 47.
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@article{Roeder2019, TITLE = {{web-rMKL}: {A} Web Server for Dimensionality Reduction and Sample Clustering of Multi-view Data Based on Unsupervised Multiple Kernel Learning}, AUTHOR = {Roeder, Benedict and Kersten, Nicolas and Herr, Marius and Speicher, Nora K. and Pfeifer, Nico}, LANGUAGE = {eng}, ISSN = {0305-1048}, DOI = {10.1093/nar/gkz422}, PUBLISHER = {Oxford University Press}, ADDRESS = {Oxford}, YEAR = {2019}, MARGINALMARK = {$\bullet$}, DATE = {2019}, JOURNAL = {Nucleic Acids Research (London)}, VOLUME = {47}, NUMBER = {W1}, PAGES = {W605--W609}, }
Endnote
%0 Journal Article %A Roeder, Benedict %A Kersten, Nicolas %A Herr, Marius %A Speicher, Nora K. %A Pfeifer, Nico %+ External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T web-rMKL: A Web Server for Dimensionality Reduction and Sample Clustering of Multi-view Data Based on Unsupervised Multiple Kernel Learning : %G eng %U http://hdl.handle.net/21.11116/0000-0004-7AE0-6 %R 10.1093/nar/gkz422 %7 2019 %D 2019 %J Nucleic Acids Research (London) %O Nucleic Acids Res %V 47 %N W1 %& W605 %P W605 - W609 %I Oxford University Press %C Oxford %@ false
32. Schick S, Rendeiro AF, Runggatscher K, Ringler A, Boidol B, Hinkel M, Majek P, Vulliard L, Penz T, Parapatics K, Schmidl C, Menche J, Boehmelt G, Petronczki M, Mueller AC, Bock C, Kubicek S: Systematic Characterization of BAF Mutations Provides Insights into Intracomplex Synthetic Lethalities in Human Cancers. Nature Genetics 2019, 51.
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@article{Schick2019, TITLE = {Systematic characterization of {BAF} mutations provides insights into intracomplex synthetic lethalities in human cancers}, AUTHOR = {Schick, Sandra and Rendeiro, Andre F. and Runggatscher, Kathrin and Ringler, Anna and Boidol, Bernd and Hinkel, Melanie and Majek, Peter and Vulliard, Loan and Penz, Thomas and Parapatics, Katja and Schmidl, Christian and Menche, Joerg and Boehmelt, Guido and Petronczki, Mark and Mueller, Andre C. and Bock, Christoph and Kubicek, Stefan}, LANGUAGE = {eng}, ISSN = {1061-4036}, DOI = {10.1038/s41588-019-0477-9}, PUBLISHER = {Nature America, Inc.}, ADDRESS = {New York, NY}, YEAR = {2019}, MARGINALMARK = {$\bullet$}, DATE = {2019}, JOURNAL = {Nature Genetics}, VOLUME = {51}, NUMBER = {9}, PAGES = {1399--1410}, }
Endnote
%0 Journal Article %A Schick, Sandra %A Rendeiro, Andre F. %A Runggatscher, Kathrin %A Ringler, Anna %A Boidol, Bernd %A Hinkel, Melanie %A Majek, Peter %A Vulliard, Loan %A Penz, Thomas %A Parapatics, Katja %A Schmidl, Christian %A Menche, Joerg %A Boehmelt, Guido %A Petronczki, Mark %A Mueller, Andre C. %A Bock, Christoph %A Kubicek, Stefan %+ External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations %T Systematic Characterization of BAF Mutations Provides Insights into Intracomplex Synthetic Lethalities in Human Cancers : %G eng %U http://hdl.handle.net/21.11116/0000-0004-B774-B %R 10.1038/s41588-019-0477-9 %7 2019 %D 2019 %J Nature Genetics %O Nature Genet. %V 51 %N 9 %& 1399 %P 1399 - 1410 %I Nature America, Inc. %C New York, NY %@ false
33. Schmidl C, Vladimer GI, Rendeiro AF, Schnabl S, Krausgruber T, Taubert C, Krall N, Pemovska T, Araghi M, Snijder B, Hubmann R, Ringler A, Runggatscher K, Demirtas D, Lopez de la Fuente O, Hilgarth M, Skrabs C, Porpaczy E, Gruber M, Hoermann G, Kubicek S, Staber PB, Shehata M, Superti-Furga G, Jaeger U, Bock C: Combined Chemosensitivity and Chromatin Profiling Prioritizes Drug Combinations in CLL. Nature Chemical Biology 2019, 15.
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@article{Schmidl2019, TITLE = {Combined Chemosensitivity and Chromatin Profiling Prioritizes Drug Combinations in {CLL}}, AUTHOR = {Schmidl, Christian and Vladimer, Gregory I. and Rendeiro, Andre F. and Schnabl, Susanne and Krausgruber, Thomas and Taubert, Christina and Krall, Nikolaus and Pemovska, Tea and Araghi, Mohammad and Snijder, Berend and Hubmann, Rainer and Ringler, Anna and Runggatscher, Kathrin and Demirtas, Dita and Lopez de la Fuente, Oscar and Hilgarth, Martin and Skrabs, Cathrin and Porpaczy, Edit and Gruber, Michaela and Hoermann, Gregor and Kubicek, Stefan and Staber, Philipp B. and Shehata, Medhat and Superti-Furga, Giulio and Jaeger, Ulrich and Bock, Christoph}, LANGUAGE = {eng}, ISSN = {1552-4450}, DOI = {10.1038/s41589-018-0205-2}, PUBLISHER = {Nature Pub. Group}, ADDRESS = {New York, NY}, YEAR = {2019}, MARGINALMARK = {$\bullet$}, DATE = {2019}, JOURNAL = {Nature Chemical Biology}, VOLUME = {15}, NUMBER = {3}, PAGES = {232--240}, }
Endnote
%0 Journal Article %A Schmidl, Christian %A Vladimer, Gregory I. %A Rendeiro, Andre F. %A Schnabl, Susanne %A Krausgruber, Thomas %A Taubert, Christina %A Krall, Nikolaus %A Pemovska, Tea %A Araghi, Mohammad %A Snijder, Berend %A Hubmann, Rainer %A Ringler, Anna %A Runggatscher, Kathrin %A Demirtas, Dita %A Lopez de la Fuente, Oscar %A Hilgarth, Martin %A Skrabs, Cathrin %A Porpaczy, Edit %A Gruber, Michaela %A Hoermann, Gregor %A Kubicek, Stefan %A Staber, Philipp B. %A Shehata, Medhat %A Superti-Furga, Giulio %A Jaeger, Ulrich %A Bock, Christoph %+ External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T Combined Chemosensitivity and Chromatin Profiling Prioritizes Drug Combinations in CLL : %G eng %U http://hdl.handle.net/21.11116/0000-0003-1434-C %R 10.1038/s41589-018-0205-2 %2 PMC6746620 %7 2019 %D 2019 %J Nature Chemical Biology %O Nat. Chem. Biol. %V 15 %N 3 %& 232 %P 232 - 240 %I Nature Pub. Group %C New York, NY %@ false
34. Schmidt F, Schulz MH: On the Problem of Confounders in Modeling Gene Expression. Bioinformatics 2019, 35.
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@article{Schmidt2019, TITLE = {On the Problem of Confounders in Modeling Gene Expression}, AUTHOR = {Schmidt, Florian and Schulz, Marcel Holger}, LANGUAGE = {eng}, ISSN = {1367-4803}, DOI = {10.1093/bioinformatics/bty674}, PUBLISHER = {Oxford University Press}, ADDRESS = {Oxford}, YEAR = {2019}, MARGINALMARK = {$\bullet$}, DATE = {2019}, JOURNAL = {Bioinformatics}, VOLUME = {35}, NUMBER = {4}, PAGES = {711--719}, }
Endnote
%0 Journal Article %A Schmidt, Florian %A Schulz, Marcel Holger %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T On the Problem of Confounders in Modeling Gene Expression : %G eng %U http://hdl.handle.net/21.11116/0000-0003-2094-1 %R 10.1093/bioinformatics/bty674 %2 PMC6530814 %7 2018 %D 2019 %J Bioinformatics %V 35 %N 4 %& 711 %P 711 - 719 %I Oxford University Press %C Oxford %@ false
35. Schmidt F, Kern F, Ebert P, Baumgarten N, Schulz MH: TEPIC 2 - an Extended Framework for Transcription Factor Binding Prediction and Integrative Epigenomic Analysis. Bioinformatics 2019, 35.
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@article{Schmidt2019, TITLE = {{TEPIC} 2 -- an Extended Framework for Transcription Factor Binding Prediction and Integrative Epigenomic Analysis}, AUTHOR = {Schmidt, Florian and Kern, Fabian and Ebert, Peter and Baumgarten, Nina and Schulz, Marcel Holger}, LANGUAGE = {eng}, ISSN = {1367-4803}, DOI = {10.1093/bioinformatics/bty856}, PUBLISHER = {Oxford University Press}, ADDRESS = {Oxford, UK}, YEAR = {2019}, MARGINALMARK = {$\bullet$}, JOURNAL = {Bioinformatics}, VOLUME = {35}, NUMBER = {9}, PAGES = {1608--1609}, }
Endnote
%0 Journal Article %A Schmidt, Florian %A Kern, Fabian %A Ebert, Peter %A Baumgarten, Nina %A Schulz, Marcel Holger %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T TEPIC 2 - an Extended Framework for Transcription Factor Binding Prediction and Integrative Epigenomic Analysis : %G eng %U http://hdl.handle.net/21.11116/0000-0003-C333-7 %R 10.1093/bioinformatics/bty856 %2 PMC6499243 %7 2019 %D 2019 %J Bioinformatics %V 35 %N 9 %& 1608 %P 1608 - 1609 %I Oxford University Press %C Oxford, UK %@ false
36. Sdelci S, Rendeiro AF, Rathert P, You W, Lin J-MG, Ringler A, Hofstaetter G, Moll HP, Guertl B, Farlik M, Schick S, Klepsch F, Oldach M, Buphamalai P, Schischlik F, Majek P, Parapatics K, Schmidl C, Schuster M, Penz T, Buckley DL, Hudecz O, Imre R, Wang S-Y, Maric HM, Kralovics R, Bennett KL, Mueller AC, Mechtler K, Menche J, et al.: MTHFD1 Interaction with BRD4 Links Folate Metabolism to Transcriptional Regulation. Nature Genetics 2019, 51.
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@article{Sdelci2019, TITLE = {{MTHFD1} interaction with {BRD4} links folate metabolism to transcriptional regulation}, AUTHOR = {Sdelci, Sara and Rendeiro, Andre F. and Rathert, Philipp and You, Wanhui and Lin, Jung-Ming G. and Ringler, Anna and Hofstaetter, Gerald and Moll, Herwig P. and Guertl, Bettina and Farlik, Matthias and Schick, Sandra and Klepsch, Freya and Oldach, Matthew and Buphamalai, Pisanu and Schischlik, Fiorella and Majek, Peter and Parapatics, Katja and Schmidl, Christian and Schuster, Michael and Penz, Thomas and Buckley, Dennis L. and Hudecz, Otto and Imre, Richard and Wang, Shuang-Yan and Maric, Hans Michael and Kralovics, Robert and Bennett, Keiryn L. and Mueller, Andre C. and Mechtler, Karl and Menche, Joerg and Bradner, James E. and Winter, Georg E. and Klavins, Kristaps and Casanova, Emilio and Bock, Christoph and Zuber, Johannes and Kubicek, Stefan}, LANGUAGE = {eng}, ISSN = {1061-4036}, DOI = {10.1038/s41588-019-0413-z}, PUBLISHER = {Nature America, Inc.}, ADDRESS = {New York, NY}, YEAR = {2019}, MARGINALMARK = {$\bullet$}, DATE = {2019}, JOURNAL = {Nature Genetics}, VOLUME = {51}, NUMBER = {6}, PAGES = {990--998}, }
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%0 Journal Article %A Sdelci, Sara %A Rendeiro, Andre F. %A Rathert, Philipp %A You, Wanhui %A Lin, Jung-Ming G. %A Ringler, Anna %A Hofstaetter, Gerald %A Moll, Herwig P. %A Guertl, Bettina %A Farlik, Matthias %A Schick, Sandra %A Klepsch, Freya %A Oldach, Matthew %A Buphamalai, Pisanu %A Schischlik, Fiorella %A Majek, Peter %A Parapatics, Katja %A Schmidl, Christian %A Schuster, Michael %A Penz, Thomas %A Buckley, Dennis L. %A Hudecz, Otto %A Imre, Richard %A Wang, Shuang-Yan %A Maric, Hans Michael %A Kralovics, Robert %A Bennett, Keiryn L. %A Mueller, Andre C. %A Mechtler, Karl %A Menche, Joerg %A Bradner, James E. %A Winter, Georg E. %A Klavins, Kristaps %A Casanova, Emilio %A Bock, Christoph %A Zuber, Johannes %A Kubicek, Stefan %+ External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations %T MTHFD1 Interaction with BRD4 Links Folate Metabolism to Transcriptional Regulation : %G eng %U http://hdl.handle.net/21.11116/0000-0003-D413-8 %R 10.1038/s41588-019-0413-z %7 2019 %D 2019 %J Nature Genetics %O Nature Genet. %V 51 %N 6 %& 990 %P 990 - 998 %I Nature America, Inc. %C New York, NY %@ false
37. Soldatov R, Kaucka M, Kastriti ME, Petersen J, Chontorotzea T, Englmaier L, Akkuratova N, Yang Y, Haring M, Dyachuk V, Bock C, Farlik M, Piacentino ML, Boismoreau F, Hilscher MM, Yokota C, Qian X, Nilsson M, Bronner ME, Croci L, Hsiao W-Y, Guertin DA, Brunet J-F, Consalez GG, Ernfors P, Fried K, Kharchenko PV, Adameyko I: Spatiotemporal Structure of Cell Fate Decisions in Murine Neural Crest. Science 2019, 364.
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@article{Soldatov2019, TITLE = {Spatiotemporal Structure of Cell Fate Decisions in Murine Neural Crest}, AUTHOR = {Soldatov, Ruslan and Kaucka, Marketa and Kastriti, Maria Eleni and Petersen, Julian and Chontorotzea, Tatiana and Englmaier, Lukas and Akkuratova, Natalia and Yang, Yunshi and Haring, Martin and Dyachuk, Viacheslav and Bock, Christoph and Farlik, Matthias and Piacentino, Michael L. and Boismoreau, Franck and Hilscher, Markus M. and Yokota, Chika and Qian, Xiaoyan and Nilsson, Mats and Bronner, Marianne E. and Croci, Laura and Hsiao, Wen-Yu and Guertin, David A. and Brunet, Jean-Francois and Consalez, Gian Giacomo and Ernfors, Patrik and Fried, Kaj and Kharchenko, Peter V. and Adameyko, Igor}, LANGUAGE = {eng}, ISSN = {0036-8075}, DOI = {10.1126/science.aas9536}, PUBLISHER = {AAAS}, ADDRESS = {Washington, D.C.}, YEAR = {2019}, MARGINALMARK = {$\bullet$}, DATE = {2019}, JOURNAL = {Science}, VOLUME = {364}, NUMBER = {64444}, EID = {eaas9536}, }
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%0 Journal Article %A Soldatov, Ruslan %A Kaucka, Marketa %A Kastriti, Maria Eleni %A Petersen, Julian %A Chontorotzea, Tatiana %A Englmaier, Lukas %A Akkuratova, Natalia %A Yang, Yunshi %A Haring, Martin %A Dyachuk, Viacheslav %A Bock, Christoph %A Farlik, Matthias %A Piacentino, Michael L. %A Boismoreau, Franck %A Hilscher, Markus M. %A Yokota, Chika %A Qian, Xiaoyan %A Nilsson, Mats %A Bronner, Marianne E. %A Croci, Laura %A Hsiao, Wen-Yu %A Guertin, David A. %A Brunet, Jean-Francois %A Consalez, Gian Giacomo %A Ernfors, Patrik %A Fried, Kaj %A Kharchenko, Peter V. %A Adameyko, Igor %+ External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations %T Spatiotemporal Structure of Cell Fate Decisions in Murine Neural Crest : %G eng %U http://hdl.handle.net/21.11116/0000-0003-E117-5 %R 10.1126/science.aas9536 %7 2019 %D 2019 %J Science %O Science %V 364 %N 64444 %Z sequence number: eaas9536 %I AAAS %C Washington, D.C. %@ false
38. Ulz P, Perakis S, Zhou Q, Moser T, Belic J, Lazzeri I, Woelfler A, Zebisch A, Gerger A, Pristauz G, Petru E, White B, Roberts CES, St Johns J, Schimek MG, Geigl JB, Bauernhofer T, Sill H, Bock C, Heitzer E, Speicher MR: Inference of Transcription Factor Binding from Cell-free DNA Enables Tumor Subtype Prediction and Early Detection. Nature Communications 2019, 10.
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@article{Ulz_2019, TITLE = {Inference of Transcription Factor Binding from Cell-free {DNA} Enables Tumor Subtype Prediction and Early Detection}, AUTHOR = {Ulz, Peter and Perakis, Samantha and Zhou, Qing and Moser, Tina and Belic, Jelena and Lazzeri, Isaac and Woelfler, Albert and Zebisch, Armin and Gerger, Armin and Pristauz, Gunda and Petru, Edgar and White, Brandon and Roberts, Charles E. S. and St Johns, John and Schimek, Michael G. and Geigl, Jochen B. and Bauernhofer, Thomas and Sill, Heinz and Bock, Christoph and Heitzer, Ellen and Speicher, Michael R.}, LANGUAGE = {eng}, ISSN = {2041-1723}, DOI = {10.1038/s41467-019-12714-4}, PUBLISHER = {Nature Publishing Group}, ADDRESS = {London}, YEAR = {2019}, MARGINALMARK = {$\bullet$}, DATE = {2019}, JOURNAL = {Nature Communications}, VOLUME = {10}, EID = {4666}, }
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%0 Journal Article %A Ulz, Peter %A Perakis, Samantha %A Zhou, Qing %A Moser, Tina %A Belic, Jelena %A Lazzeri, Isaac %A Woelfler, Albert %A Zebisch, Armin %A Gerger, Armin %A Pristauz, Gunda %A Petru, Edgar %A White, Brandon %A Roberts, Charles E. S. %A St Johns, John %A Schimek, Michael G. %A Geigl, Jochen B. %A Bauernhofer, Thomas %A Sill, Heinz %A Bock, Christoph %A Heitzer, Ellen %A Speicher, Michael R. %+ External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations %T Inference of Transcription Factor Binding from Cell-free DNA Enables Tumor Subtype Prediction and Early Detection : %G eng %U http://hdl.handle.net/21.11116/0000-0004-E6B9-8 %R 10.1038/s41467-019-12714-4 %7 2019 %D 2019 %J Nature Communications %O Nat. Commun. %V 10 %Z sequence number: 4666 %I Nature Publishing Group %C London %@ false
39. Wiegand SB, Beggel B, Wranke A, Aliabadi E, Jaroszewicz J, Xu C-J, Li Y, Manns MP, Lengauer T, Wedemeyer H, Kraft ARM, Falk CS, Cornberg M: Soluble Immune Markers in the Different Phases of Chronic Hepatitis B Virus Infection. Scientific Reports 2019, 9.
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@article{Wiegand_2019, TITLE = {Soluble immune markers in the different phases of chronic hepatitis {B} virus infection}, AUTHOR = {Wiegand, Steffen B. and Beggel, Bastian and Wranke, Anika and Aliabadi, Elmira and Jaroszewicz, Jerzy and Xu, Cheng-Jian and Li, Yang and Manns, Michael P. and Lengauer, Thomas and Wedemeyer, Heiner and Kraft, Anke R. M. and Falk, Christine S. and Cornberg, Markus}, LANGUAGE = {eng}, ISSN = {2045-2322}, DOI = {10.1038/s41598-019-50729-5}, PUBLISHER = {Nature Publishing Group}, ADDRESS = {London, UK}, YEAR = {2019}, MARGINALMARK = {$\bullet$}, JOURNAL = {Scientific Reports}, VOLUME = {9}, EID = {14118}, }
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%0 Journal Article %A Wiegand, Steffen B. %A Beggel, Bastian %A Wranke, Anika %A Aliabadi, Elmira %A Jaroszewicz, Jerzy %A Xu, Cheng-Jian %A Li, Yang %A Manns, Michael P. %A Lengauer, Thomas %A Wedemeyer, Heiner %A Kraft, Anke R. M. %A Falk, Christine S. %A Cornberg, Markus %+ External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations External Organizations %T Soluble Immune Markers in the Different Phases of Chronic Hepatitis B Virus Infection : %G eng %U http://hdl.handle.net/21.11116/0000-0004-E49F-8 %R 10.1038/s41598-019-50729-5 %2 PMC6773856 %7 2019 %D 2019 %J Scientific Reports %O Sci. Rep. %V 9 %Z sequence number: 14118 %I Nature Publishing Group %C London, UK %@ false
40. Yi G, Wierenga ATJ, Petraglia F, Narang P, Janssen-Megens EM, Mandoli A, Merkel A, Berentsen K, Kim B, Matarese F, Singh AA, Habibi E, Prange KHM, Mulder AB, Jansen JH, Clarke L, Heath S, van der Reijden BA, Flicek P, Yaspo M-L, Gut I, Bock C, Schuringa JJ, Altucci L, Vellenga E, Stunnenberg HG, Martens J, H. A: Chromatin-Based Classification of Genetically Heterogeneous AMLs into Two Distinct Subtypes with Diverse Stemness Phenotypes. Cell Reports 2019, 26.
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@article{Yi2019, TITLE = {Chromatin-Based Classification of Genetically Heterogeneous {AMLs} into Two Distinct Subtypes with Diverse Stemness Phenotypes}, AUTHOR = {Yi, Guoqiang and Wierenga, Albertus T. J. and Petraglia, Francesca and Narang, Pankaj and Janssen-Megens, Eva M. and Mandoli, Amit and Merkel, Angelika and Berentsen, Kim and Kim, Bowon and Matarese, Filomena and Singh, Abhishek A. and Habibi, Ehsan and Prange, Koen H. M. and Mulder, Andre B. and Jansen, Joop H. and Clarke, Laura and Heath, Simon and van der Reijden, Bert A. and Flicek, Paul and Yaspo, Marie-Laure and Gut, Ivo and Bock, Christoph and Schuringa, Jan Jacob and Altucci, Lucia and Vellenga, Edo and Stunnenberg, Hendrik G. and Martens, Joost and H., A.}, LANGUAGE = {eng}, ISSN = {2211-1247}, DOI = {10.1016/j.celrep.2018.12.098}, PUBLISHER = {Cell Press}, ADDRESS = {Maryland Heights, MO}, YEAR = {2019}, MARGINALMARK = {$\bullet$}, JOURNAL = {Cell Reports}, VOLUME = {26}, NUMBER = {4}, PAGES = {1059--1069}, EID = {e6}, }
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%0 Journal Article %A Yi, Guoqiang %A Wierenga, Albertus T. J. %A Petraglia, Francesca %A Narang, Pankaj %A Janssen-Megens, Eva M. %A Mandoli, Amit %A Merkel, Angelika %A Berentsen, Kim %A Kim, Bowon %A Matarese, Filomena %A Singh, Abhishek A. %A Habibi, Ehsan %A Prange, Koen H. M. %A Mulder, Andre B. %A Jansen, Joop H. %A Clarke, Laura %A Heath, Simon %A van der Reijden, Bert A. %A Flicek, Paul %A Yaspo, Marie-Laure %A Gut, Ivo %A Bock, Christoph %A Schuringa, Jan Jacob %A Altucci, Lucia %A Vellenga, Edo %A Stunnenberg, Hendrik G. %A Martens, Joost %A H., A. %+ External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations %T Chromatin-Based Classification of Genetically Heterogeneous AMLs into Two Distinct Subtypes with Diverse Stemness Phenotypes : %G eng %U http://hdl.handle.net/21.11116/0000-0002-F6CB-4 %R 10.1016/j.celrep.2018.12.098 %7 2019 %D 2019 %J Cell Reports %V 26 %N 4 %& 1059 %P 1059 - 1069 %Z sequence number: e6 %I Cell Press %C Maryland Heights, MO %@ false
2018
41. Allison TF, Andrews PW, Avior Y, Barbaric I, Benvenisty N, Bock C, Brehm J, Bruestle O, Damjanov I, Elefanty A, Felkner D, Gokhale PJ, Halbritter F, Healy LE, Hu TX, Knowles BB, Loring JF, Ludwig TE, Mayberry R, Micallef S, Mohamed JS, Mueller F-J, Mummery CL, Nakatsuji N, Ng ES, Oh SKW, O’Shea O, Pera MF, Reubinoff B, Robson P, et al.: Assessment of Established Techniques to Determine Developmental and Malignant Potential of Human Pluripotent Stem Cells. Nature Communications 2018.
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@article{Allison2018, TITLE = {Assessment of Established Techniques to Determine Developmental and Malignant Potential of Human Pluripotent Stem Cells}, AUTHOR = {Allison, Thomas F. and Andrews, Peter W. and Avior, Yishai and Barbaric, Ivana and Benvenisty, Nissim and Bock, Christoph and Brehm, Jennifer and Bruestle, Oliver and Damjanov, Ivan and Elefanty, Andrew and Felkner, Daniel and Gokhale, Paul J. and Halbritter, Florian and Healy, Lyn E. and Hu, Tim X. and Knowles, Barbara B. and Loring, Jeanne F. and Ludwig, Tenneille E. and Mayberry, Robyn and Micallef, Suzanne and Mohamed, Jameelah S. and Mueller, Franz-Josef and Mummery, Christine L. and Nakatsuji, Norio and Ng, Elizabeth S. and Oh, Steve K. W. and O'Shea, Orla and Pera, Martin F. and Reubinoff, Benjamin and Robson, Paul and Rossant, Janet and Schuldt, Bernhard M. and Solter, Davor and Sourris, Koula and Stacey, Glyn and Stanley, Edouard G. and Suemori, Hirofumi and Takahashi, Kazutoshi and Yamanaka, Shinya}, LANGUAGE = {eng}, ISSN = {2041-1723}, DOI = {10.1038/s41467-018-04011-3}, PUBLISHER = {Nature Publishing Group}, ADDRESS = {London}, YEAR = {2018}, MARGINALMARK = {$\bullet$}, JOURNAL = {Nature Communications}, EID = {1925}, }
Endnote
%0 Journal Article %A Allison, Thomas F. %A Andrews, Peter W. %A Avior, Yishai %A Barbaric, Ivana %A Benvenisty, Nissim %A Bock, Christoph %A Brehm, Jennifer %A Bruestle, Oliver %A Damjanov, Ivan %A Elefanty, Andrew %A Felkner, Daniel %A Gokhale, Paul J. %A Halbritter, Florian %A Healy, Lyn E. %A Hu, Tim X. %A Knowles, Barbara B. %A Loring, Jeanne F. %A Ludwig, Tenneille E. %A Mayberry, Robyn %A Micallef, Suzanne %A Mohamed, Jameelah S. %A Mueller, Franz-Josef %A Mummery, Christine L. %A Nakatsuji, Norio %A Ng, Elizabeth S. %A Oh, Steve K. W. %A O'Shea, Orla %A Pera, Martin F. %A Reubinoff, Benjamin %A Robson, Paul %A Rossant, Janet %A Schuldt, Bernhard M. %A Solter, Davor %A Sourris, Koula %A Stacey, Glyn %A Stanley, Edouard G. %A Suemori, Hirofumi %A Takahashi, Kazutoshi %A Yamanaka, Shinya %+ External Organizations External Organizations External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations %T Assessment of Established Techniques to Determine Developmental and Malignant Potential of Human Pluripotent Stem Cells : %G eng %U http://hdl.handle.net/21.11116/0000-0001-66DB-6 %R 10.1038/s41467-018-04011-3 %7 2018 %D 2018 %J Nature Communications %O Nat. Commun. %Z sequence number: 1925 %I Nature Publishing Group %C London %@ false
42. Apweiler R, Beissbarth T, Berthold MR, Bluethgen N, Burmeister Y, Dammann O, Deutsch A, Feuerhake F, Franke A, Hasenauer J, Hoffmann S, Hoefer T, Jansen PLM, Kaderali L, Klingmueller U, Koch I, Kohlbacher O, Kuepfer L, Lammert F, Maier D, Pfeifer N, Radde N, Rehm M, Roeder I, Saez-Rodriguez J, Sax U, Schmeck B, Schuppert A, Seilheimer B, Theis FJ, et al.: Whither systems medicine?Experimental & Molecular Medicine 2018, 50.
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@article{Apweiler2018, TITLE = {Whither systems medicine?}, AUTHOR = {Apweiler, Rolf and Beissbarth, Tim and Berthold, Michael R. and Bluethgen, Nils and Burmeister, Yvonne and Dammann, Olaf and Deutsch, Andreas and Feuerhake, Friedrich and Franke, Andre and Hasenauer, Jan and Hoffmann, Steve and Hoefer, Thomas and Jansen, Peter L. M. and Kaderali, Lars and Klingmueller, Ursula and Koch, Ina and Kohlbacher, Oliver and Kuepfer, Lars and Lammert, Frank and Maier, Dieter and Pfeifer, Nico and Radde, Nicole and Rehm, Markus and Roeder, Ingo and Saez-Rodriguez, Julio and Sax, Ulrich and Schmeck, Bernd and Schuppert, Andreas and Seilheimer, Bernd and Theis, Fabian J. and Vera, Julio and Wolkenhauer, Olaf}, LANGUAGE = {eng}, ISSN = {2092-6413}, DOI = {10.1038/emm.2017.290}, PUBLISHER = {Korean Society of Medical Biochemistry and Molecular Biology}, ADDRESS = {Seoul}, YEAR = {2018}, MARGINALMARK = {$\bullet$}, DATE = {2018}, JOURNAL = {Experimental \& Molecular Medicine}, VOLUME = {50}, EID = {e453}, }
Endnote
%0 Journal Article %A Apweiler, Rolf %A Beissbarth, Tim %A Berthold, Michael R. %A Bluethgen, Nils %A Burmeister, Yvonne %A Dammann, Olaf %A Deutsch, Andreas %A Feuerhake, Friedrich %A Franke, Andre %A Hasenauer, Jan %A Hoffmann, Steve %A Hoefer, Thomas %A Jansen, Peter L. M. %A Kaderali, Lars %A Klingmueller, Ursula %A Koch, Ina %A Kohlbacher, Oliver %A Kuepfer, Lars %A Lammert, Frank %A Maier, Dieter %A Pfeifer, Nico %A Radde, Nicole %A Rehm, Markus %A Roeder, Ingo %A Saez-Rodriguez, Julio %A Sax, Ulrich %A Schmeck, Bernd %A Schuppert, Andreas %A Seilheimer, Bernd %A Theis, Fabian J. %A Vera, Julio %A Wolkenhauer, Olaf %+ External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations %T Whither systems medicine? : %G eng %U http://hdl.handle.net/21.11116/0000-0001-2D95-5 %R 10.1038/emm.2017.290 %7 2018 %D 2018 %J Experimental & Molecular Medicine %O EMM %V 50 %Z sequence number: e453 %I Korean Society of Medical Biochemistry and Molecular Biology %C Seoul %@ false
43. Barakat TS, Halbritter F, Zhang M, Rendeiro AF, Perenthaler E, Bock C, Chambers I: Functional Dissection of the Enhancer Repertoire in Human Embryonic Stem Cells. Cell Stem Cell 2018, 23.
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@article{Bakarat2018, TITLE = {Functional Dissection of the Enhancer Repertoire in Human Embryonic Stem Cells}, AUTHOR = {Barakat, Tahsin Stefan and Halbritter, Florian and Zhang, Man and Rendeiro, Andre F. and Perenthaler, Elena and Bock, Christoph and Chambers, Ian}, LANGUAGE = {eng}, ISSN = {1934-5909; 1875-9777}, DOI = {10.1016/j.stem.2018.06.014}, PUBLISHER = {Elsevier}, ADDRESS = {Amsterdam}, YEAR = {2018}, MARGINALMARK = {$\bullet$}, DATE = {2018}, JOURNAL = {Cell Stem Cell}, VOLUME = {23}, NUMBER = {2}, PAGES = {276--288}, EID = {e8}, }
Endnote
%0 Journal Article %A Barakat, Tahsin Stefan %A Halbritter, Florian %A Zhang, Man %A Rendeiro, Andre F. %A Perenthaler, Elena %A Bock, Christoph %A Chambers, Ian %+ External Organizations External Organizations External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations %T Functional Dissection of the Enhancer Repertoire in Human Embryonic Stem Cells : %G eng %U http://hdl.handle.net/21.11116/0000-0001-EE1A-7 %R 10.1016/j.stem.2018.06.014 %7 2018 %D 2018 %J Cell Stem Cell %V 23 %N 2 %& 276 %P 276 - 288 %Z sequence number: e8 %I Elsevier %C Amsterdam %@ false
44. Bar-On Y, Gruell H, Schoofs T, Pai JA, Nogueira L, Butler AL, Millard K, Lehmann C, Suarez I, Oliveira TY, Karagounis T, Cohen YZ, Wyen C, Scholten S, Handl L, Belblidia S, Dizon JP, Vehreschild JJ, Witmer-Pack M, Shimeliovich I, Jain K, Fiddike K, Seaton KE, Yates NL, Horowitz J, Gulick RM, Pfeifer N, Tomaras GD, Seaman MS, Faetkenheuer G, et al.: Safety and Antiviral Activity of Combination HIV-1 Broadly Neutralizing Antibodies in Viremic Individuals. Nature Medicine 2018, 24.
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@article{Bar-On_2018, TITLE = {Safety and antiviral activity of combination {HIV}-1 broadly neutralizing antibodies in viremic individuals}, AUTHOR = {Bar-On, Yotam and Gruell, Henning and Schoofs, Till and Pai, Joy A. and Nogueira, Lilian and Butler, Allison L. and Millard, Katrina and Lehmann, Clara and Suarez, Isabelle and Oliveira, Thiago Y. and Karagounis, Theodora and Cohen, Yehuda Z. and Wyen, Christoph and Scholten, Stefan and Handl, Lisa and Belblidia, Shiraz and Dizon, Juan P. and Vehreschild, Joerg J. and Witmer-Pack, Maggi and Shimeliovich, Irina and Jain, Kanika and Fiddike, Kerstin and Seaton, Kelly E. and Yates, Nicole L. and Horowitz, Jill and Gulick, Roy M. and Pfeifer, Nico and Tomaras, Georgia D. and Seaman, Michael S. and Faetkenheuer, Gerd and Caskey, Marina and Klein, Florian and Nussenzweig, Michel C.}, LANGUAGE = {eng}, ISSN = {1078-8956}, DOI = {10.1038/s41591-018-0186-4}, PUBLISHER = {Nature Pub. Co.}, ADDRESS = {New York, NY}, YEAR = {2018}, MARGINALMARK = {$\bullet$}, DATE = {2018}, JOURNAL = {Nature Medicine}, VOLUME = {24}, NUMBER = {1}, PAGES = {1701--1707}, }
Endnote
%0 Journal Article %A Bar-On, Yotam %A Gruell, Henning %A Schoofs, Till %A Pai, Joy A. %A Nogueira, Lilian %A Butler, Allison L. %A Millard, Katrina %A Lehmann, Clara %A Suarez, Isabelle %A Oliveira, Thiago Y. %A Karagounis, Theodora %A Cohen, Yehuda Z. %A Wyen, Christoph %A Scholten, Stefan %A Handl, Lisa %A Belblidia, Shiraz %A Dizon, Juan P. %A Vehreschild, Joerg J. %A Witmer-Pack, Maggi %A Shimeliovich, Irina %A Jain, Kanika %A Fiddike, Kerstin %A Seaton, Kelly E. %A Yates, Nicole L. %A Horowitz, Jill %A Gulick, Roy M. %A Pfeifer, Nico %A Tomaras, Georgia D. %A Seaman, Michael S. %A Faetkenheuer, Gerd %A Caskey, Marina %A Klein, Florian %A Nussenzweig, Michel C. %+ External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations %T Safety and Antiviral Activity of Combination HIV-1 Broadly Neutralizing Antibodies in Viremic Individuals : %G eng %U http://hdl.handle.net/21.11116/0000-0002-8636-A %R 10.1038/s41591-018-0186-4 %7 2018 %D 2018 %J Nature Medicine %O Nat. Med. %V 24 %N 1 %& 1701 %P 1701 - 1707 %I Nature Pub. Co. %C New York, NY %@ false
45. Bastys T: Analysis of the protein-Ligand and protein-peptide interactions using a combined sequence- and structure-based approach. Universität des Saarlandes; 2018.
Abstract
Proteins participate in most of the important processes in cells, and their ability to perform their function ultimately depends on their three-dimensional structure. They usually act in these processes through interactions with other molecules. Because of the importance of their role, proteins are also the common target for small molecule drugs that inhibit their activity, which may include targeting protein interactions. Understanding protein interactions and how they are affected by mutations is thus crucial for combating drug resistance and aiding drug design. This dissertation combines bioinformatics studies of protein interactions at both primary sequence and structural level. We analyse protein-protein interactions through linear motifs, as well as protein-small molecule interactions, and study how mutations affect them. This is done in the context of two systems. In the first study of drug resistance mutations in the protease of the human immunodeficiency virus type 1, we successfully apply molecular dynamics simulations to estimate the effects of known resistance-associated mutations on the free binding energy, also revealing molecular mechanisms of resistance. In the second study, we analyse consensus profiles of linear motifs that mediate the recognition by the mitogen-activated protein kinases of their target proteins. We thus gain insights into the cellular processes these proteins are involved in.
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@phdthesis{Bastysphd2013, TITLE = {Analysis of the protein-Ligand and protein-peptide interactions using a combined sequence- and structure-based approach}, AUTHOR = {Bastys, Tomas}, LANGUAGE = {eng}, DOI = {10.22028/D291-27920}, SCHOOL = {Universit{\"a}t des Saarlandes}, ADDRESS = {Saarbr{\"u}cken}, YEAR = {2018}, MARGINALMARK = {$\bullet$}, DATE = {2018}, ABSTRACT = {Proteins participate in most of the important processes in cells, and their ability to perform their function ultimately depends on their three-dimensional structure. They usually act in these processes through interactions with other molecules. Because of the importance of their role, proteins are also the common target for small molecule drugs that inhibit their activity, which may include targeting protein interactions. Understanding protein interactions and how they are affected by mutations is thus crucial for combating drug resistance and aiding drug design. This dissertation combines bioinformatics studies of protein interactions at both primary sequence and structural level. We analyse protein-protein interactions through linear motifs, as well as protein-small molecule interactions, and study how mutations affect them. This is done in the context of two systems. In the first study of drug resistance mutations in the protease of the human immunodeficiency virus type 1, we successfully apply molecular dynamics simulations to estimate the effects of known resistance-associated mutations on the free binding energy, also revealing molecular mechanisms of resistance. In the second study, we analyse consensus profiles of linear motifs that mediate the recognition by the mitogen-activated protein kinases of their target proteins. We thus gain insights into the cellular processes these proteins are involved in.}, }
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%0 Thesis %A Bastys, Tomas %Y Kalinina, Olga V. %A referee: Helms, Volkhard %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society International Max Planck Research School, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations %T Analysis of the protein-Ligand and protein-peptide interactions using a combined sequence- and structure-based approach : %G eng %U http://hdl.handle.net/21.11116/0000-0003-CE47-6 %R 10.22028/D291-27920 %I Universität des Saarlandes %C Saarbrücken %D 2018 %P 134 p. %V phd %9 phd %X Proteins participate in most of the important processes in cells, and their ability to perform their function ultimately depends on their three-dimensional structure. They usually act in these processes through interactions with other molecules. Because of the importance of their role, proteins are also the common target for small molecule drugs that inhibit their activity, which may include targeting protein interactions. Understanding protein interactions and how they are affected by mutations is thus crucial for combating drug resistance and aiding drug design. This dissertation combines bioinformatics studies of protein interactions at both primary sequence and structural level. We analyse protein-protein interactions through linear motifs, as well as protein-small molecule interactions, and study how mutations affect them. This is done in the context of two systems. In the first study of drug resistance mutations in the protease of the human immunodeficiency virus type 1, we successfully apply molecular dynamics simulations to estimate the effects of known resistance-associated mutations on the free binding energy, also revealing molecular mechanisms of resistance. In the second study, we analyse consensus profiles of linear motifs that mediate the recognition by the mitogen-activated protein kinases of their target proteins. We thus gain insights into the cellular processes these proteins are involved in. %U https://publikationen.sulb.uni-saarland.de/handle/20.500.11880/27455
46. Bastys T, Gapsys V, Doncheva NT, Kaiser R, de Groot BL, Kalinina OV: Consistent Prediction of Mutation Effect on Drug Binding in HIV-1 Protease Using Alchemical Calculations. Journal of Chemical Theory and Computation 2018, 14.
Abstract
Despite of a large number of antiretroviral drugs targeting HIV-1 protease for inhibition, mutations in this protein during the course of patient treatment can render them inefficient. This emerging resistance inspired numerous computational studies of the HIV-1 protease aimed at predicting the effect of mutations on drug binding in terms of free binding energy $\Delta G$, as well as in mechanistic terms. In this study, we analyse ten different protease-inhibitor complexes carrying major resistance-associated mutations (RAMs) G48V, I50V, and L90M using molecular dynamics simulations. We demonstrate that alchemical free energy calculations can consistently predict the effect of mutations on drug binding. By explicitly probing different protonation states of the catalytic aspartic dyad, we reveal the importance of the correct choice of protonation state for the accuracy of the result. We also provide insight into how different mutations affect drug binding in their specific ways, with the unifying theme of how all of them affect the crucial for drug binding regions of the protease.
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@article{Bastys2018, TITLE = {Consistent Prediction of Mutation Effect on Drug Binding in {HIV}-1 Protease Using Alchemical Calculations}, AUTHOR = {Bastys, Tomas and Gapsys, Vytautas and Doncheva, Nadezhda Tsankova and Kaiser, Rolf and de Groot, Bert L. and Kalinina, Olga V.}, LANGUAGE = {eng}, DOI = {10.1021/acs.jctc.7b01109}, PUBLISHER = {American Chemical Society}, ADDRESS = {Washington, D.C.}, YEAR = {2018}, MARGINALMARK = {$\bullet$}, DATE = {2018}, ABSTRACT = {Despite of a large number of antiretroviral drugs targeting HIV-1 protease for inhibition, mutations in this protein during the course of patient treatment can render them inefficient. This emerging resistance inspired numerous computational studies of the HIV-1 protease aimed at predicting the effect of mutations on drug binding in terms of free binding energy $\Delta G$, as well as in mechanistic terms. In this study, we analyse ten different protease-inhibitor complexes carrying major resistance-associated mutations (RAMs) G48V, I50V, and L90M using molecular dynamics simulations. We demonstrate that alchemical free energy calculations can consistently predict the effect of mutations on drug binding. By explicitly probing different protonation states of the catalytic aspartic dyad, we reveal the importance of the correct choice of protonation state for the accuracy of the result. We also provide insight into how different mutations affect drug binding in their specific ways, with the unifying theme of how all of them affect the crucial for drug binding regions of the protease.}, JOURNAL = {Journal of Chemical Theory and Computation}, VOLUME = {14}, NUMBER = {7}, PAGES = {3397--3408}, }
Endnote
%0 Journal Article %A Bastys, Tomas %A Gapsys, Vytautas %A Doncheva, Nadezhda Tsankova %A Kaiser, Rolf %A de Groot, Bert L. %A Kalinina, Olga V. %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T Consistent Prediction of Mutation Effect on Drug Binding in HIV-1 Protease Using Alchemical Calculations : %G eng %U http://hdl.handle.net/21.11116/0000-0001-E5BA-B %R 10.1021/acs.jctc.7b01109 %7 2018-05-30 %D 2018 %* Review method: peer-reviewed %X Despite of a large number of antiretroviral drugs targeting HIV-1 protease for inhibition, mutations in this protein during the course of patient treatment can render them inefficient. This emerging resistance inspired numerous computational studies of the HIV-1 protease aimed at predicting the effect of mutations on drug binding in terms of free binding energy $\Delta G$, as well as in mechanistic terms. In this study, we analyse ten different protease-inhibitor complexes carrying major resistance-associated mutations (RAMs) G48V, I50V, and L90M using molecular dynamics simulations. We demonstrate that alchemical free energy calculations can consistently predict the effect of mutations on drug binding. By explicitly probing different protonation states of the catalytic aspartic dyad, we reveal the importance of the correct choice of protonation state for the accuracy of the result. We also provide insight into how different mutations affect drug binding in their specific ways, with the unifying theme of how all of them affect the crucial for drug binding regions of the protease. %J Journal of Chemical Theory and Computation %O J. Chem. Theory Comput. %V 14 %N 7 %& 3397 %P 3397 - 3408 %I American Chemical Society %C Washington, D.C.
47. Baumgartner C, Toifl S, Farlik M, Halbritter F, Scheicher R, Fischer I, Sexl V, Bock C, Baccarini M: An ERK-Dependent Feedback Mechanism Prevents Hematopoietic Stem Cell Exhaustion. Cell Stem Cell 2018, 22.
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@article{Baumgartner2018, TITLE = {An {ERK}-Dependent Feedback Mechanism Prevents Hematopoietic Stem Cell Exhaustion}, AUTHOR = {Baumgartner, Christian and Toifl, Stefanie and Farlik, Matthias and Halbritter, Florian and Scheicher, Ruth and Fischer, Irmgard and Sexl, Veronika and Bock, Christoph and Baccarini, Manuela}, LANGUAGE = {eng}, ISSN = {1934-5909}, DOI = {10.1016/j.stem.2018.05.003}, PUBLISHER = {Cell Press}, ADDRESS = {Cambridge, Mass.}, YEAR = {2018}, MARGINALMARK = {$\bullet$}, DATE = {2018}, JOURNAL = {Cell Stem Cell}, VOLUME = {22}, NUMBER = {6}, PAGES = {879--892}, EID = {e6}, }
Endnote
%0 Journal Article %A Baumgartner, Christian %A Toifl, Stefanie %A Farlik, Matthias %A Halbritter, Florian %A Scheicher, Ruth %A Fischer, Irmgard %A Sexl, Veronika %A Bock, Christoph %A Baccarini, Manuela %+ External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations %T An ERK-Dependent Feedback Mechanism Prevents Hematopoietic Stem Cell Exhaustion : %G eng %U http://hdl.handle.net/21.11116/0000-0001-88D5-5 %R 10.1016/j.stem.2018.05.003 %7 2018 %D 2018 %J Cell Stem Cell %V 22 %N 6 %& 879 %P 879 - 892 %Z sequence number: e6 %I Cell Press %C Cambridge, Mass. %@ false
48. Behjati Ardakani F, Kattler K, Nordstroem K, Gasparoni N, Gasparoni G, Fuchs S, Sinha A, Barann M, Ebert P, Fischer J, Hutter B, Zipprich G, Imbusch CD, Felder B, Eils J, Brors B, Lengauer T, Manke T, Rosenstiel P, Walter J, Schulz MH: Integrative Analysis of Single-Cell Expression Data Reveals Distinct Regulatory States in Bidirectional Promoters. Epigenetics & Chromatin 2018, 11.
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@article{Ardakani2018, TITLE = {Integrative Analysis of Single-Cell Expression Data Reveals Distinct Regulatory States in Bidirectional Promoters}, AUTHOR = {Behjati Ardakani, Fatemeh and Kattler, Kathrin and Nordstroem, Karl and Gasparoni, Nina and Gasparoni, Gilles and Fuchs, Sarah and Sinha, Anupam and Barann, Matthias and Ebert, Peter and Fischer, Jonas and Hutter, Barbara and Zipprich, Gideon and Imbusch, Charles D. and Felder, Baerbel and Eils, Juergen and Brors, Benedikt and Lengauer, Thomas and Manke, Thomas and Rosenstiel, Philip and Walter, Joern and Schulz, Marcel Holger}, LANGUAGE = {eng}, DOI = {10.1186/s13072-018-0236-7}, PUBLISHER = {BioMed Central}, ADDRESS = {London}, YEAR = {2018}, MARGINALMARK = {$\bullet$}, JOURNAL = {Epigenetics \& Chromatin}, VOLUME = {11}, EID = {66}, }
Endnote
%0 Journal Article %A Behjati Ardakani, Fatemeh %A Kattler, Kathrin %A Nordstroem, Karl %A Gasparoni, Nina %A Gasparoni, Gilles %A Fuchs, Sarah %A Sinha, Anupam %A Barann, Matthias %A Ebert, Peter %A Fischer, Jonas %A Hutter, Barbara %A Zipprich, Gideon %A Imbusch, Charles D. %A Felder, Baerbel %A Eils, Juergen %A Brors, Benedikt %A Lengauer, Thomas %A Manke, Thomas %A Rosenstiel, Philip %A Walter, Joern %A Schulz, Marcel Holger %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T Integrative Analysis of Single-Cell Expression Data Reveals Distinct Regulatory States in Bidirectional Promoters : %G eng %U http://hdl.handle.net/21.11116/0000-0002-D61C-E %R 10.1186/s13072-018-0236-7 %7 2018 %D 2018 %J Epigenetics & Chromatin %V 11 %Z sequence number: 66 %I BioMed Central %C London
49. Chakraborty S, Canzar S, Marschall T, Schulz MH: Chromatyping: Reconstructing Nucleosome Profiles from NOMe Sequencing Data. In Research in Computational Molecular Biology (RECOMB 2018). Springer; 2018. [Lecture Notes in Bioinformatics, vol. 10812]
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@inproceedings{Chakraborty_RECOMB2018, TITLE = {Chromatyping: {R}econstructing Nucleosome Profiles from {NOMe} Sequencing Data}, AUTHOR = {Chakraborty, Shounak and Canzar, Stefan and Marschall, Tobias and Schulz, Marcel H.}, LANGUAGE = {eng}, ISBN = {978-3-319-89928-2}, DOI = {10.1007/978-3-319-89929-9_2}, PUBLISHER = {Springer}, YEAR = {2018}, MARGINALMARK = {$\bullet$}, DATE = {2018}, BOOKTITLE = {Research in Computational Molecular Biology (RECOMB 2018)}, EDITOR = {Raphael, Benjamin H.}, PAGES = {21--36}, SERIES = {Lecture Notes in Bioinformatics}, VOLUME = {10812}, ADDRESS = {Paris, France}, }
Endnote
%0 Conference Proceedings %A Chakraborty, Shounak %A Canzar, Stefan %A Marschall, Tobias %A Schulz, Marcel H. %+ External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T Chromatyping: Reconstructing Nucleosome Profiles from NOMe Sequencing Data : %G eng %U http://hdl.handle.net/21.11116/0000-0001-404B-3 %R 10.1007/978-3-319-89929-9_2 %D 2018 %B 22nd International Conference on Research in Computational Molecular Biology %Z date of event: 2018-04-21 - 2018-04-24 %C Paris, France %B Research in Computational Molecular Biology %E Raphael, Benjamin H. %P 21 - 36 %I Springer %@ 978-3-319-89928-2 %B Lecture Notes in Bioinformatics %N 10812
50. Dheghani Amirabad A, Ramasamy P, Wierz M, Nordstroem K, Kessler SM, Schulz MH, Simon M: Transgenic Expression of the RNA Binding Protein IMP2 Stabilizes miRNA Targets in Murine Microsteatosis. Biochimica et Biophysica Acta - Molecular Basis of Disease 2018, 1864.
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@article{Dheghani_2018, TITLE = {Transgenic expression of the {RNA} binding protein {IMP2} stabilizes {miRNA} targets in murine microsteatosis}, AUTHOR = {Dheghani Amirabad, Azim and Ramasamy, Pathmanaban and Wierz, Marina and Nordstroem, Karl and Kessler, Sonja M. and Schulz, Marcel H. and Simon, Martin}, LANGUAGE = {eng}, ISSN = {0925-4439}, DOI = {10.1016/j.bbadis.2018.05.024}, PUBLISHER = {Elsevier}, ADDRESS = {New York, NY}, YEAR = {2018}, MARGINALMARK = {$\bullet$}, DATE = {2018}, JOURNAL = {Biochimica et Biophysica Acta -- Molecular Basis of Disease}, VOLUME = {1864}, NUMBER = {10}, PAGES = {3099--3108}, }
Endnote
%0 Journal Article %A Dheghani Amirabad, Azim %A Ramasamy, Pathmanaban %A Wierz, Marina %A Nordstroem, Karl %A Kessler, Sonja M. %A Schulz, Marcel H. %A Simon, Martin %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations %T Transgenic Expression of the RNA Binding Protein IMP2 Stabilizes miRNA Targets in Murine Microsteatosis : %G eng %U http://hdl.handle.net/21.11116/0000-0002-576D-3 %R 10.1016/j.bbadis.2018.05.024 %7 2018 %D 2018 %J Biochimica et Biophysica Acta - Molecular Basis of Disease %O Biochim. Biophys. Acta-Mol. Basis Dis. %V 1864 %N 10 %& 3099 %P 3099 - 3108 %I Elsevier %C New York, NY %@ false
51. Döring M, Büch J, Friedrich G, Pironti A, Kalaghatgi P, Knops E, Heger E, Obermeier M, Däumer M, Thielen A, Kaiser R, Lengauer T, Pfeifer N: Geno2pheno[ngs-freq]: a Genotypic Interpretation System for Identifying Viral Drug Resistance using Next-Generation Sequencing Data. Nucleic Acids Research 2018, 46(Web Server issue).
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@article{Doering2018, TITLE = {Geno2pheno[ngs-freq]: a Genotypic Interpretation System for Identifying Viral Drug Resistance using Next-Generation Sequencing Data}, AUTHOR = {D{\"o}ring, Matthias and B{\"u}ch, Joachim and Friedrich, Georg and Pironti, Alejandro and Kalaghatgi, Prabhav and Knops, Elena and Heger, Eva and Obermeier, Martin and D{\"a}umer, Martin and Thielen, Alexander and Kaiser, Rolf and Lengauer, Thomas and Pfeifer, Nico}, LANGUAGE = {eng}, ISSN = {0305-1048}, DOI = {10.1093/nar/gky349}, PUBLISHER = {Oxford University Press}, ADDRESS = {Oxford}, YEAR = {2018}, MARGINALMARK = {$\bullet$}, DATE = {2018}, JOURNAL = {Nucleic Acids Research}, VOLUME = {46}, NUMBER = {Web Server issue}, PAGES = {W271--W277}, EID = {gky349}, }
Endnote
%0 Journal Article %A Döring, Matthias %A Büch, Joachim %A Friedrich, Georg %A Pironti, Alejandro %A Kalaghatgi, Prabhav %A Knops, Elena %A Heger, Eva %A Obermeier, Martin %A Däumer, Martin %A Thielen, Alexander %A Kaiser, Rolf %A Lengauer, Thomas %A Pfeifer, Nico %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T Geno2pheno[ngs-freq]: a Genotypic Interpretation System for Identifying Viral Drug Resistance using Next-Generation Sequencing Data : %G eng %U http://hdl.handle.net/21.11116/0000-0001-3F53-C %R 10.1093/nar/gky349 %2 PMC6031006 %7 2018 %D 2018 %J Nucleic Acids Research %O Nucleic Acids Res %V 46 %N Web Server issue %& W271 %P W271 - W277 %Z sequence number: gky349 %I Oxford University Press %C Oxford %@ false
52. Durai DA, Schulz MH: In silico Read Normalization using Set Multi-cover Optimization. Bioinformatics 2018, 34.
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@article{Durai2018, TITLE = {In silico Read Normalization using Set Multi-cover Optimization}, AUTHOR = {Durai, Dilip Ariyur and Schulz, Marcel Holger}, LANGUAGE = {eng}, ISSN = {1367-4803}, DOI = {10.1093/bioinformatics/bty307}, PUBLISHER = {Oxford University Press}, ADDRESS = {Oxford}, YEAR = {2018}, MARGINALMARK = {$\bullet$}, DATE = {2018}, JOURNAL = {Bioinformatics}, VOLUME = {34}, NUMBER = {19}, PAGES = {3273--3280}, }
Endnote
%0 Journal Article %A Durai, Dilip Ariyur %A Schulz, Marcel Holger %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T In silico Read Normalization using Set Multi-cover Optimization : %G eng %U http://hdl.handle.net/21.11116/0000-0002-5C51-C %R 10.1093/bioinformatics/bty307 %7 2018 %D 2018 %J Bioinformatics %V 34 %N 19 %& 3273 %P 3273 - 3280 %I Oxford University Press %C Oxford %@ false
53. Fröhlich H, Balling R, Beerenwinkel N, Kohlbacher O, Kumar S, Lengauer T, Maathuis MH, Moreau Y, Murphy SA, Przytycka TM, Rebhan M, Röst H, Schuppert A, Schwab M, Spang R, Stekhoven D, Sun J, Weber A, Ziemek D, Zupan B: From Hype to Reality: Data Science Enabling Personalized Medicine. BMC Medicine 2018, 16.
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@article{Froehlich2018, TITLE = {From Hype to Reality: Data Science Enabling Personalized Medicine}, AUTHOR = {Fr{\"o}hlich, Holger and Balling, Rudi and Beerenwinkel, Niko and Kohlbacher, Oliver and Kumar, Santosh and Lengauer, Thomas and Maathuis, Marloes H. and Moreau, Yves and Murphy, Susan A. and Przytycka, Teresa M. and Rebhan, Michael and R{\"o}st, Hannes and Schuppert, Andreas and Schwab, Matthias and Spang, Rainer and Stekhoven, Daniel and Sun, Jimeng and Weber, Andreas and Ziemek, Daniel and Zupan, Blaz}, LANGUAGE = {eng}, ISSN = {1741-7015}, DOI = {10.1186/s12916-018-1122-7}, PUBLISHER = {BioMed Central}, YEAR = {2018}, MARGINALMARK = {$\bullet$}, JOURNAL = {BMC Medicine}, VOLUME = {16}, EID = {150}, }
Endnote
%0 Journal Article %A Fröhlich, Holger %A Balling, Rudi %A Beerenwinkel, Niko %A Kohlbacher, Oliver %A Kumar, Santosh %A Lengauer, Thomas %A Maathuis, Marloes H. %A Moreau, Yves %A Murphy, Susan A. %A Przytycka, Teresa M. %A Rebhan, Michael %A Röst, Hannes %A Schuppert, Andreas %A Schwab, Matthias %A Spang, Rainer %A Stekhoven, Daniel %A Sun, Jimeng %A Weber, Andreas %A Ziemek, Daniel %A Zupan, Blaz %+ External Organizations External Organizations External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations %T From Hype to Reality: Data Science Enabling Personalized Medicine : %G eng %U http://hdl.handle.net/21.11116/0000-0002-09BD-0 %R 10.1186/s12916-018-1122-7 %7 2018 %D 2018 %J BMC Medicine %V 16 %Z sequence number: 150 %I BioMed Central %@ false
54. Fun A, Leitner T, Vandekerckhove L, Däumer M, Thielen A, Buchholz B, Hoepelman AIM, Gisolf EH, Schipper PJ, Wensing AMJ, Nijhuis M: Impact of the HIV-1 Genetic Background and HIV-1 Population Size on the Evolution of Raltegravir Resistance. Retrovirology 2018, 15.
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@article{Fun2018, TITLE = {Impact of the {HIV}-1 Genetic Background and {HIV}-1 Population Size on the Evolution of Raltegravir Resistance}, AUTHOR = {Fun, Axel and Leitner, Thomas and Vandekerckhove, Linos and D{\"a}umer, Martin and Thielen, Alexander and Buchholz, Bernd and Hoepelman, Andy I. M. and Gisolf, Elizabeth H. and Schipper, Pauline J. and Wensing, Annemarie M. J. and Nijhuis, Monique}, LANGUAGE = {eng}, ISSN = {1742-4690}, DOI = {10.1186/s12977-017-0384-z}, PUBLISHER = {BioMed Central}, ADDRESS = {London}, YEAR = {2018}, MARGINALMARK = {$\bullet$}, DATE = {2018}, JOURNAL = {Retrovirology}, VOLUME = {15}, EID = {1}, }
Endnote
%0 Journal Article %A Fun, Axel %A Leitner, Thomas %A Vandekerckhove, Linos %A Däumer, Martin %A Thielen, Alexander %A Buchholz, Bernd %A Hoepelman, Andy I. M. %A Gisolf, Elizabeth H. %A Schipper, Pauline J. %A Wensing, Annemarie M. J. %A Nijhuis, Monique %+ External Organizations External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations %T Impact of the HIV-1 Genetic Background and HIV-1 Population Size on the Evolution of Raltegravir Resistance : %G eng %U http://hdl.handle.net/21.11116/0000-0000-376A-C %R 10.1186/s12977-017-0384-z %7 2018 %D 2018 %J Retrovirology %V 15 %Z sequence number: 1 %I BioMed Central %C London %@ false
55. Garg S, Rautiainen M, Novak AM, Garrison E, Durbin R, Marschall T: A Graph-based Approach to Diploid Genome Assembly. Bioinformatics (Proc ISMB 2018) 2018, 34.
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@article{Garg_Bioinformatics2018, TITLE = {A Graph-based Approach to Diploid Genome Assembly}, AUTHOR = {Garg, Shilpa and Rautiainen, Mikko and Novak, Adam M. and Garrison, Erik and Durbin, Richard and Marschall, Tobias}, LANGUAGE = {eng}, ISSN = {1367-4803}, DOI = {10.1093/bioinformatics/bty279}, PUBLISHER = {Oxford University Press}, ADDRESS = {Oxford}, YEAR = {2018}, MARGINALMARK = {$\bullet$}, DATE = {2018}, JOURNAL = {Bioinformatics (Proc. ISMB)}, VOLUME = {34}, PAGES = {i105--i114}, BOOKTITLE = {ISMB 2018 Proceedings}, }
Endnote
%0 Journal Article %A Garg, Shilpa %A Rautiainen, Mikko %A Novak, Adam M. %A Garrison, Erik %A Durbin, Richard %A Marschall, Tobias %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T A Graph-based Approach to Diploid Genome Assembly : %G eng %U http://hdl.handle.net/21.11116/0000-0001-E5A6-1 %R 10.1093/bioinformatics/bty279 %7 2018 %D 2018 %J Bioinformatics %V 34 %& i105 %P i105 - i114 %I Oxford University Press %C Oxford %@ false %B ISMB 2018 Proceedings %O ISMB 2018 July 6 to July 10, 2018, Chicago, IL, United States
56. Garg S: Computational Haplotyping: Theory and Practice. Universität des Saarlandes; 2018.
Abstract
Genomics has paved a new way to comprehend life and its evolution, and also to investigate causes of diseases and their treatment. One of the important problems in genomic analyses is haplotype assembly. Constructing complete and accurate haplotypes plays an essential role in understanding population genetics and how species evolve. In this thesis, we focus on computational approaches to haplotype assembly from third generation sequencing technologies. This involves huge amounts of sequencing data, and such data contain errors due to the single molecule sequencing protocols employed. Taking advantage of combinatorial formulations helps to correct for these errors to solve the haplotyping problem. Various computational techniques such as dynamic programming, parameterized algorithms, and graph algorithms are used to solve this problem. This thesis presents several contributions concerning the area of haplotyping. First, a novel algorithm based on dynamic programming is proposed to provide approximation guarantees for phasing a single individual. Second, an integrative approach is introduced to combining multiple sequencing datasets to generating complete and accurate haplotypes. The effectiveness of this integrative approach is demonstrated on a real human genome. Third, we provide a novel efficient approach to phasing pedigrees and demonstrate its advantages in comparison to phasing a single individual. Fourth, we present a generalized graph-based framework for performing haplotype-aware de novo assembly. Specifically, this generalized framework consists of a hybrid pipeline for generating accurate and complete haplotypes from data stemming from multiple sequencing technologies, one that provides accurate reads and other that provides long reads.
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@phdthesis{gargphd2017, TITLE = {Computational Haplotyping: Theory and Practice}, AUTHOR = {Garg, Shilpa}, LANGUAGE = {eng}, DOI = {10.22028/D291-27252}, SCHOOL = {Universit{\"a}t des Saarlandes}, ADDRESS = {Saarbr{\"u}cken}, YEAR = {2018}, MARGINALMARK = {$\bullet$}, DATE = {2018}, ABSTRACT = {Genomics has paved a new way to comprehend life and its evolution, and also to investigate causes of diseases and their treatment. One of the important problems in genomic analyses is haplotype assembly. Constructing complete and accurate haplotypes plays an essential role in understanding population genetics and how species evolve. In this thesis, we focus on computational approaches to haplotype assembly from third generation sequencing technologies. This involves huge amounts of sequencing data, and such data contain errors due to the single molecule sequencing protocols employed. Taking advantage of combinatorial formulations helps to correct for these errors to solve the haplotyping problem. Various computational techniques such as dynamic programming, parameterized algorithms, and graph algorithms are used to solve this problem. This thesis presents several contributions concerning the area of haplotyping. First, a novel algorithm based on dynamic programming is proposed to provide approximation guarantees for phasing a single individual. Second, an integrative approach is introduced to combining multiple sequencing datasets to generating complete and accurate haplotypes. The effectiveness of this integrative approach is demonstrated on a real human genome. Third, we provide a novel efficient approach to phasing pedigrees and demonstrate its advantages in comparison to phasing a single individual. Fourth, we present a generalized graph-based framework for performing haplotype-aware de novo assembly. Specifically, this generalized framework consists of a hybrid pipeline for generating accurate and complete haplotypes from data stemming from multiple sequencing technologies, one that provides accurate reads and other that provides long reads.}, }
Endnote
%0 Thesis %A Garg, Shilpa %Y Marschall, Tobias %A referee: Helms, Volkhard %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society International Max Planck Research School, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations %T Computational Haplotyping: Theory and Practice : %G eng %U http://hdl.handle.net/21.11116/0000-0001-9D80-D %R 10.22028/D291-27252 %I Universität des Saarlandes %C Saarbrücken %D 2018 %P 119 p. %V phd %9 phd %X Genomics has paved a new way to comprehend life and its evolution, and also to investigate causes of diseases and their treatment. One of the important problems in genomic analyses is haplotype assembly. Constructing complete and accurate haplotypes plays an essential role in understanding population genetics and how species evolve. In this thesis, we focus on computational approaches to haplotype assembly from third generation sequencing technologies. This involves huge amounts of sequencing data, and such data contain errors due to the single molecule sequencing protocols employed. Taking advantage of combinatorial formulations helps to correct for these errors to solve the haplotyping problem. Various computational techniques such as dynamic programming, parameterized algorithms, and graph algorithms are used to solve this problem. This thesis presents several contributions concerning the area of haplotyping. First, a novel algorithm based on dynamic programming is proposed to provide approximation guarantees for phasing a single individual. Second, an integrative approach is introduced to combining multiple sequencing datasets to generating complete and accurate haplotypes. The effectiveness of this integrative approach is demonstrated on a real human genome. Third, we provide a novel efficient approach to phasing pedigrees and demonstrate its advantages in comparison to phasing a single individual. Fourth, we present a generalized graph-based framework for performing haplotype-aware de novo assembly. Specifically, this generalized framework consists of a hybrid pipeline for generating accurate and complete haplotypes from data stemming from multiple sequencing technologies, one that provides accurate reads and other that provides long reads. %U https://publikationen.sulb.uni-saarland.de/handle/20.500.11880/27102
57. Garrison E, Siren J, Novak AM, Hickey G, Eizenga JM, Dawson ET, Jones W, Garg S, Markello C, Lin MF, Paten B, Durbin R: Variation Graph Toolkit Improves Read Mapping by Representing Genetic Variation in the Reference. Nature Biotechnology 2018, 36.
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@article{Garrison_2018, TITLE = {Variation Graph Toolkit Improves Read Mapping by Representing Genetic Variation in the Reference}, AUTHOR = {Garrison, Erik and Siren, Jouni and Novak, Adam M. and Hickey, Glenn and Eizenga, Jordan M. and Dawson, Eric T. and Jones, William and Garg, Shilpa and Markello, Charles and Lin, Michael F. and Paten, Benedict and Durbin, Richard}, LANGUAGE = {eng}, ISSN = {1087-0156}, DOI = {10.1038/nbt.4227}, PUBLISHER = {NPG}, ADDRESS = {New York}, YEAR = {2018}, MARGINALMARK = {$\bullet$}, DATE = {2018}, JOURNAL = {Nature Biotechnology}, VOLUME = {36}, NUMBER = {9}, PAGES = {875--879}, }
Endnote
%0 Journal Article %A Garrison, Erik %A Siren, Jouni %A Novak, Adam M. %A Hickey, Glenn %A Eizenga, Jordan M. %A Dawson, Eric T. %A Jones, William %A Garg, Shilpa %A Markello, Charles %A Lin, Michael F. %A Paten, Benedict %A Durbin, Richard %+ External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations External Organizations %T Variation Graph Toolkit Improves Read Mapping by Representing Genetic Variation in the Reference : %G eng %U http://hdl.handle.net/21.11116/0000-0002-5761-F %R 10.1038/nbt.4227 %7 2018 %D 2018 %J Nature Biotechnology %V 36 %N 9 %& 875 %P 875 - 879 %I NPG %C New York %@ false
58. Ghareghani M, Porubsky D, Sanders AD, Meiers S, Eichler EE, Korbel JO, Marschall T: Strand-seq Enables Reliable Separation of Long Reads by Chromosome via Expectation Maximization. Bioinformatics (Proc ISMB 2018) 2018, 34.
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@article{Ghareghani_ISMB2018, TITLE = {Strand-seq Enables Reliable Separation of Long Reads by Chromosome via Expectation Maximization}, AUTHOR = {Ghareghani, Maryam and Porubsky, David and Sanders, Ashley D. and Meiers, Sascha and Eichler, Evan E. and Korbel, Jan O. and Marschall, Tobias}, LANGUAGE = {eng}, ISSN = {1367-4803}, DOI = {10.1093/bioinformatics/bty290}, PUBLISHER = {Oxford University Press}, ADDRESS = {Oxford}, YEAR = {2018}, MARGINALMARK = {$\bullet$}, DATE = {2018}, JOURNAL = {Bioinformatics (Proc. ISMB)}, VOLUME = {34}, NUMBER = {13}, PAGES = {i115--I123}, BOOKTITLE = {ISMB 2018 Proceedings}, }
Endnote
%0 Journal Article %A Ghareghani, Maryam %A Porubsky, David %A Sanders, Ashley D. %A Meiers, Sascha %A Eichler, Evan E. %A Korbel, Jan O. %A Marschall, Tobias %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T Strand-seq Enables Reliable Separation of Long Reads by Chromosome via Expectation Maximization : %G eng %U http://hdl.handle.net/21.11116/0000-0001-E5AA-D %R 10.1093/bioinformatics/bty290 %7 2018 %D 2018 %J Bioinformatics %V 34 %N 13 %& i115 %P i115 - I123 %I Oxford University Press %C Oxford %@ false %B ISMB 2018 Proceedings %O July 6 to July 10, 2018, Chicago, IL, United States ISMB 2018
59. Goeschl L, Preglej T, Hamminger P, Bonelli M, Andersen L, Boucheron N, Guelich AF, Mueller L, Saferding V, Mufazalov IA, Hirahara K, Seiser C, Matthias P, Penz T, Schuster M, Bock C, Waisman A, Steiner G, Ellmeier W: A T Cell-specific Deletion of HDAC1 Protects Against Experimental Autoimmune Encephalomyelitis. Journal of Autoimmunity 2018, 86.
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@article{Goeschl2018, TITLE = {A {T} Cell-specific Deletion of {HDAC}1 Protects Against Experimental Autoimmune Encephalomyelitis}, AUTHOR = {Goeschl, Lisa and Preglej, Teresa and Hamminger, Patricia and Bonelli, Michael and Andersen, Liisa and Boucheron, Nicole and Guelich, Alexandra F. and Mueller, Lena and Saferding, Victoria and Mufazalov, Ilgiz A. and Hirahara, Kiyoshi and Seiser, Christian and Matthias, Patrick and Penz, Thomas and Schuster, Michael and Bock, Christoph and Waisman, Ari and Steiner, Guenter and Ellmeier, Wilfried}, LANGUAGE = {eng}, ISSN = {0896-8411}, DOI = {10.1016/j.jaut.2017.09.008}, PUBLISHER = {Academic Press}, ADDRESS = {London}, YEAR = {2018}, MARGINALMARK = {$\bullet$}, DATE = {2018}, JOURNAL = {Journal of Autoimmunity}, VOLUME = {86}, PAGES = {51--61}, }
Endnote
%0 Journal Article %A Goeschl, Lisa %A Preglej, Teresa %A Hamminger, Patricia %A Bonelli, Michael %A Andersen, Liisa %A Boucheron, Nicole %A Guelich, Alexandra F. %A Mueller, Lena %A Saferding, Victoria %A Mufazalov, Ilgiz A. %A Hirahara, Kiyoshi %A Seiser, Christian %A Matthias, Patrick %A Penz, Thomas %A Schuster, Michael %A Bock, Christoph %A Waisman, Ari %A Steiner, Guenter %A Ellmeier, Wilfried %+ External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations %T A T Cell-specific Deletion of HDAC1 Protects Against Experimental Autoimmune Encephalomyelitis : %G eng %U http://hdl.handle.net/21.11116/0000-0000-8438-C %R 10.1016/j.jaut.2017.09.008 %7 2018 %D 2018 %J Journal of Autoimmunity %O J. Autoimmun. %V 86 %& 51 %P 51 - 61 %I Academic Press %C London %@ false
60. Grosser K, Ramasamy P, Dheghani Amirabad A, Schulz MH, Gasparoni G, Simon M, Schrallhammer M: More than the “Killer Trait”: Infection with the Bacterial Endosymbiont Caedibacter taeniospiralis Causes Transcriptomic Modulation in Paramecium Host. Genome Biology and Evolution 2018, 10.
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@article{Grosser2018, TITLE = {More than the “Killer Trait”: {I}nfection with the Bacterial Endosymbiont {C}aedibacter taeniospiralis Causes Transcriptomic Modulation in Paramecium Host}, AUTHOR = {Grosser, Katrin and Ramasamy, Pathmanaban and Dheghani Amirabad, Azim and Schulz, Marcel Holger and Gasparoni, Gilles and Simon, Martin and Schrallhammer, Martina}, LANGUAGE = {eng}, DOI = {10.1093/gbe/evy024}, PUBLISHER = {Oxford Univ. Press}, ADDRESS = {Oxford}, YEAR = {2018}, MARGINALMARK = {$\bullet$}, DATE = {2018}, JOURNAL = {Genome Biology and Evolution}, VOLUME = {10}, NUMBER = {2}, PAGES = {646--656}, }
Endnote
%0 Journal Article %A Grosser, Katrin %A Ramasamy, Pathmanaban %A Dheghani Amirabad, Azim %A Schulz, Marcel Holger %A Gasparoni, Gilles %A Simon, Martin %A Schrallhammer, Martina %+ External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations %T More than the “Killer Trait”: Infection with the Bacterial Endosymbiont Caedibacter taeniospiralis Causes Transcriptomic Modulation in Paramecium Host : %G eng %U http://hdl.handle.net/21.11116/0000-0000-C023-F %R 10.1093/gbe/evy024 %7 2018 %D 2018 %J Genome Biology and Evolution %O GBE Genome Biol Evol %V 10 %N 2 %& 646 %P 646 - 656 %I Oxford Univ. Press %C Oxford
61. Ha Thanh Pham T, Maurer B, Prchal-Murphy M, Grausenburger R, Grundschober E, Javaheri T, Nivarthi H, Boersma A, Kolbe T, Elabd M, Halbritter F, Pencik J, Kazemi Z, Grebien F, Hengstschlaeger M, Kenner L, Kubicek S, Farlik M, Bock C, Valent P, Mueller M, Ruelicke T, Sexl V, Moriggl R: STAT5B(N642H) is a Driver Mutation for T Cell Neoplasia. The Journal of Clinical Investigation 2018, 128.
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@article{Bock_JCI2018, TITLE = {{STAT5B}^({N642H)} is a Driver Mutation for {T} Cell Neoplasia}, AUTHOR = {Ha Thanh Pham, Thi and Maurer, Barbara and Prchal-Murphy, Michaela and Grausenburger, Reinhard and Grundschober, Eva and Javaheri, Tahereh and Nivarthi, Harini and Boersma, Auke and Kolbe, Thomas and Elabd, Mohamed and Halbritter, Florian and Pencik, Jan and Kazemi, Zahra and Grebien, Florian and Hengstschlaeger, Markus and Kenner, Lukas and Kubicek, Stefan and Farlik, Matthias and Bock, Christoph and Valent, Peter and Mueller, Mathias and Ruelicke, Thomas and Sexl, Veronika and Moriggl, Richard}, LANGUAGE = {eng}, ISSN = {0021-9738}, DOI = {10.1172/JCI94509}, PUBLISHER = {American Society for Clinical Investigation}, ADDRESS = {New York, NY}, YEAR = {2018}, MARGINALMARK = {$\bullet$}, DATE = {2018}, JOURNAL = {The Journal of Clinical Investigation}, VOLUME = {128}, NUMBER = {1}, PAGES = {387--401}, }
Endnote
%0 Journal Article %A Ha Thanh Pham, Thi %A Maurer, Barbara %A Prchal-Murphy, Michaela %A Grausenburger, Reinhard %A Grundschober, Eva %A Javaheri, Tahereh %A Nivarthi, Harini %A Boersma, Auke %A Kolbe, Thomas %A Elabd, Mohamed %A Halbritter, Florian %A Pencik, Jan %A Kazemi, Zahra %A Grebien, Florian %A Hengstschlaeger, Markus %A Kenner, Lukas %A Kubicek, Stefan %A Farlik, Matthias %A Bock, Christoph %A Valent, Peter %A Mueller, Mathias %A Ruelicke, Thomas %A Sexl, Veronika %A Moriggl, Richard %+ External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations External Organizations External Organizations %T STAT5B(N642H) is a Driver Mutation for T Cell Neoplasia : %G eng %U http://hdl.handle.net/21.11116/0000-0000-2DDC-7 %R 10.1172/JCI94509 %7 2018 %D 2018 %J The Journal of Clinical Investigation %O JCI %V 128 %N 1 %& 387 %P 387 - 401 %I American Society for Clinical Investigation %C New York, NY %@ false
62. Horňáková A, List M, Vreeken J, Schulz MH: JAMI: Fast Computation of Conditional Mutual Information for ceRNA Network Analysis. Bioinformatics 2018, 34.
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@article{Hornakova_Bioinformatics2018, TITLE = {{JAMI}: {F}ast Computation of Conditional Mutual Information for {ceRNA} Network Analysis}, AUTHOR = {Hor{\v n}{\'a}kov{\'a}, Andrea and List, Markus and Vreeken, Jilles and Schulz, Marcel H.}, LANGUAGE = {eng}, ISSN = {1367-4803}, DOI = {10.1093/bioinformatics/bty221}, PUBLISHER = {Oxford University Press}, ADDRESS = {Oxford}, YEAR = {2018}, MARGINALMARK = {$\bullet$}, DATE = {2018}, JOURNAL = {Bioinformatics}, VOLUME = {34}, NUMBER = {17}, PAGES = {3050--3051}, }
Endnote
%0 Journal Article %A Horňáková, Andrea %A List, Markus %A Vreeken, Jilles %A Schulz, Marcel H. %+ Computer Vision and Multimodal Computing, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Databases and Information Systems, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T JAMI: Fast Computation of Conditional Mutual Information for ceRNA Network Analysis : %G eng %U http://hdl.handle.net/21.11116/0000-0002-573A-C %R 10.1093/bioinformatics/bty221 %7 2018 %D 2018 %J Bioinformatics %V 34 %N 17 %& 3050 %P 3050 - 3051 %I Oxford University Press %C Oxford %@ false
63. Klughammer J, Kiesel B, Roetzer T, Fortelny N, Nemc A, Nenning K-H, Furtner J, Sheffield NC, Datlinger P, Peter N, Nowosielski M, Augustin M, Mischkulnig M, Stroebel T, Alpar D, Erguener B, Senekowitsch M, Moser P, Freyschlag CF, Kerschbaumer J, Thome C, Grams AE, Stockhammer G, Kitzwoegerer M, Oberndorfer S, Marhold F, Weis S, Trenkler J, Buchroithner J, Pichler J, et al.: The DNA Methylation Landscape of Glioblastoma Disease Progression Shows Extensive Heterogeneity in Time and Space. Nature Medicine 2018, 24.
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@article{Klughammer_2018, TITLE = {The {DNA} Methylation Landscape of Glioblastoma Disease Progression Shows Extensive Heterogeneity in Time and Space}, AUTHOR = {Klughammer, Johanna and Kiesel, Barbara and Roetzer, Thomas and Fortelny, Nikolaus and Nemc, Amelie and Nenning, Karl-Heinz and Furtner, Julia and Sheffield, Nathan C. and Datlinger, Paul and Peter, Nadine and Nowosielski, Martha and Augustin, Marco and Mischkulnig, Mario and Stroebel, Thomas and Alpar, Donat and Erguener, Bekir and Senekowitsch, Martin and Moser, Patrizia and Freyschlag, Christian F. and Kerschbaumer, Johannes and Thome, Claudius and Grams, Astrid E. and Stockhammer, Guenther and Kitzwoegerer, Melitta and Oberndorfer, Stefan and Marhold, Franz and Weis, Serge and Trenkler, Johannes and Buchroithner, Johanna and Pichler, Josef and Haybaeck, Johannes and Krassnig, Stefanie and Ali, Kariem Mahdy and von Campe, Gord and Payer, Franz and Sherif, Camillo and Preiser, Julius and Hauser, Thomas and Winkler, Peter A. and Kleindienst, Waltraud and Wuertz, Franz and Brandner-Kokalj, Tanisa and Stultschnig, Martin and Schweiger, Stefan and Dieckmann, Karin and Preusser, Matthias and Langs, Georg and Baumann, Bernhard and Knosp, Engelbert and Widhalm, Georg and Marosi, Christine and Hainfellner, Johannes A. and Woehrer, Adelheid and Bock, Christoph}, LANGUAGE = {eng}, ISSN = {1078-8956}, DOI = {10.1038/s41591-018-0156-x}, PUBLISHER = {Nature Pub. Co.}, ADDRESS = {New York, NY}, YEAR = {2018}, MARGINALMARK = {$\bullet$}, DATE = {2018}, JOURNAL = {Nature Medicine}, VOLUME = {24}, NUMBER = {10}, PAGES = {1611--1624}, }
Endnote
%0 Journal Article %A Klughammer, Johanna %A Kiesel, Barbara %A Roetzer, Thomas %A Fortelny, Nikolaus %A Nemc, Amelie %A Nenning, Karl-Heinz %A Furtner, Julia %A Sheffield, Nathan C. %A Datlinger, Paul %A Peter, Nadine %A Nowosielski, Martha %A Augustin, Marco %A Mischkulnig, Mario %A Stroebel, Thomas %A Alpar, Donat %A Erguener, Bekir %A Senekowitsch, Martin %A Moser, Patrizia %A Freyschlag, Christian F. %A Kerschbaumer, Johannes %A Thome, Claudius %A Grams, Astrid E. %A Stockhammer, Guenther %A Kitzwoegerer, Melitta %A Oberndorfer, Stefan %A Marhold, Franz %A Weis, Serge %A Trenkler, Johannes %A Buchroithner, Johanna %A Pichler, Josef %A Haybaeck, Johannes %A Krassnig, Stefanie %A Ali, Kariem Mahdy %A von Campe, Gord %A Payer, Franz %A Sherif, Camillo %A Preiser, Julius %A Hauser, Thomas %A Winkler, Peter A. %A Kleindienst, Waltraud %A Wuertz, Franz %A Brandner-Kokalj, Tanisa %A Stultschnig, Martin %A Schweiger, Stefan %A Dieckmann, Karin %A Preusser, Matthias %A Langs, Georg %A Baumann, Bernhard %A Knosp, Engelbert %A Widhalm, Georg %A Marosi, Christine %A Hainfellner, Johannes A. %A Woehrer, Adelheid %A Bock, Christoph %+ External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T The DNA Methylation Landscape of Glioblastoma Disease Progression Shows Extensive Heterogeneity in Time and Space : %G eng %U http://hdl.handle.net/21.11116/0000-0002-5F1F-3 %R 10.1038/s41591-018-0156-x %7 2018 %D 2018 %J Nature Medicine %O Nat. Med. %V 24 %N 10 %& 1611 %P 1611 - 1624 %I Nature Pub. Co. %C New York, NY %@ false
64. Knops E, Sierra S, Kalaghatgi P, Heger E, Kaiser R, Kalinina OV: Epistatic Interactions in NS5A of Hepatitis C Virus Suggest Drug Resistance Mechanisms. Genes 2018, 9.
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@article{Knops2018, TITLE = {Epistatic Interactions in {NS5A} of Hepatitis {C} Virus Suggest Drug Resistance Mechanisms}, AUTHOR = {Knops, Elena and Sierra, Saleta and Kalaghatgi, Prabhav and Heger, Eva and Kaiser, Rolf and Kalinina, Olga V.}, LANGUAGE = {eng}, ISSN = {2073-4425}, DOI = {10.3390/genes9070343}, PUBLISHER = {MDPI}, ADDRESS = {Basel}, YEAR = {2018}, MARGINALMARK = {$\bullet$}, JOURNAL = {Genes}, VOLUME = {9}, NUMBER = {7}, EID = {343}, }
Endnote
%0 Journal Article %A Knops, Elena %A Sierra, Saleta %A Kalaghatgi, Prabhav %A Heger, Eva %A Kaiser, Rolf %A Kalinina, Olga V. %+ External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T Epistatic Interactions in NS5A of Hepatitis C Virus Suggest Drug Resistance Mechanisms : %G eng %U http://hdl.handle.net/21.11116/0000-0002-09C6-5 %R 10.3390/genes9070343 %7 2018-07-06 %D 2018 %8 06.07.2018 %J Genes %V 9 %N 7 %Z sequence number: 343 %I MDPI %C Basel %@ false
65. Lowe R, Barton C, Jenkins CA, Ernst C, Forman O, Fernandez-Twinn DS, Bock C, Rossiter SJ, Faulkes CG, Ozanne SE, Walter L, Odom DT, Mellersh C, Rakyan VK: Ageing-associated DNA Methylation Dynamics are a Molecular Readout of Lifespan Variation among Mammalian Species. Genome Biology 2018, 19.
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@article{Lowe2018, TITLE = {Ageing-associated {DNA} Methylation Dynamics are a Molecular Readout of Lifespan Variation among Mammalian Species}, AUTHOR = {Lowe, Robert and Barton, Carl and Jenkins, Christopher A. and Ernst, Christina and Forman, Oliver and Fernandez-Twinn, Denise S. and Bock, Christoph and Rossiter, Stephen J. and Faulkes, Chris G. and Ozanne, Susan E. and Walter, Lutz and Odom, Duncan T. and Mellersh, Cathryn and Rakyan, Vardhman K.}, LANGUAGE = {eng}, ISSN = {1465-6906}, DOI = {10.1186/s13059-018-1397-1}, PUBLISHER = {BioMed Central Ltd.}, ADDRESS = {London}, YEAR = {2018}, MARGINALMARK = {$\bullet$}, JOURNAL = {Genome Biology}, VOLUME = {19}, EID = {22}, }
Endnote
%0 Journal Article %A Lowe, Robert %A Barton, Carl %A Jenkins, Christopher A. %A Ernst, Christina %A Forman, Oliver %A Fernandez-Twinn, Denise S. %A Bock, Christoph %A Rossiter, Stephen J. %A Faulkes, Chris G. %A Ozanne, Susan E. %A Walter, Lutz %A Odom, Duncan T. %A Mellersh, Cathryn %A Rakyan, Vardhman K. %+ External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations %T Ageing-associated DNA Methylation Dynamics are a Molecular Readout of Lifespan Variation among Mammalian Species : %G eng %U http://hdl.handle.net/21.11116/0000-0000-C8CF-6 %R 10.1186/s13059-018-1397-1 %7 2018 %D 2018 %J Genome Biology %V 19 %Z sequence number: 22 %I BioMed Central Ltd. %C London %@ false
66. Marschall T, Marz M, Abeel T, Dijkstra L, Dutilh BE, Ghaffaari A, Kersey P, Kloosterman WP, Makinen V, Novak AM, Paten B, Porubsky D, Rivals E, Alkan C, Baaijens JA, De Bakker PIW, Boeva V, Bonnal RJP, Chiaromonte F, Chikhi R, Ciccarelli FD, Cijvat R, Datema E, Van Duijn CM, Eichler EE, Ernst C, Eskin E, Garrison E, El-Kebir M, Klau GW, et al.: Computational Pan-genomics: Status, Promises and Challenges. Briefings in Bioinformatics 2018, 19.
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@article{Marschall2016, TITLE = {Computational Pan-genomics: Status, Promises and Challenges}, AUTHOR = {Marschall, Tobias and Marz, Manja and Abeel, Thomas and Dijkstra, Louis and Dutilh, Bas E. and Ghaffaari, Ali and Kersey, Paul and Kloosterman, Wigard P. and Makinen, Veli and Novak, Adam M. and Paten, Benedict and Porubsky, David and Rivals, Eric and Alkan, Can and Baaijens, Jasmijn A. and De Bakker, Paul I. W. and Boeva, Valentina and Bonnal, Raoul J. P. and Chiaromonte, Francesca and Chikhi, Rayan and Ciccarelli, Francesca D. and Cijvat, Robin and Datema, Erwin and Van Duijn, Cornelia M. and Eichler, Evan E. and Ernst, Corinna and Eskin, Eleazar and Garrison, Erik and El-Kebir, Mohammed and Klau, Gunnar W. and Korbel, Jan O. and Lameijer, Eric-Wubbo and Langmead, Benjamin and Martin, Marcel and Medvedev, Paul and Mu, John C. and Neerincx, Pieter and Ouwens, Klaasjan and Peterlongo, Pierre and Pisanti, Nadia and Rahmann, Sven and Raphael, Ben and Reinert, Knut and de Ridder, Dick and de Ridder, Jeroen and Schlesner, Matthias and Schulz-Trieglaff, Ole and Sanders, Ashley D. and Sheikhizadeh, Siavash and Shneider, Carl and Smit, Sandra and Valenzuela, Daniel and Wang, Jiayin and Wessels, Lodewyk and Zhang, Ying and Guryev, Victor and Vandin, Fabio and Ye, Kai and Schonhuth, Alexander}, LANGUAGE = {eng}, ISSN = {1467-5463}, DOI = {10.1093/bib/bbw089}, PUBLISHER = {Oxford University Press}, ADDRESS = {London}, YEAR = {2018}, MARGINALMARK = {$\bullet$}, DATE = {2018}, JOURNAL = {Briefings in Bioinformatics}, VOLUME = {19}, NUMBER = {1}, PAGES = {118--135}, EID = {bbw089}, }
Endnote
%0 Journal Article %A Marschall, Tobias %A Marz, Manja %A Abeel, Thomas %A Dijkstra, Louis %A Dutilh, Bas E. %A Ghaffaari, Ali %A Kersey, Paul %A Kloosterman, Wigard P. %A Makinen, Veli %A Novak, Adam M. %A Paten, Benedict %A Porubsky, David %A Rivals, Eric %A Alkan, Can %A Baaijens, Jasmijn A. %A De Bakker, Paul I. W. %A Boeva, Valentina %A Bonnal, Raoul J. P. %A Chiaromonte, Francesca %A Chikhi, Rayan %A Ciccarelli, Francesca D. %A Cijvat, Robin %A Datema, Erwin %A Van Duijn, Cornelia M. %A Eichler, Evan E. %A Ernst, Corinna %A Eskin, Eleazar %A Garrison, Erik %A El-Kebir, Mohammed %A Klau, Gunnar W. %A Korbel, Jan O. %A Lameijer, Eric-Wubbo %A Langmead, Benjamin %A Martin, Marcel %A Medvedev, Paul %A Mu, John C. %A Neerincx, Pieter %A Ouwens, Klaasjan %A Peterlongo, Pierre %A Pisanti, Nadia %A Rahmann, Sven %A Raphael, Ben %A Reinert, Knut %A de Ridder, Dick %A de Ridder, Jeroen %A Schlesner, Matthias %A Schulz-Trieglaff, Ole %A Sanders, Ashley D. %A Sheikhizadeh, Siavash %A Shneider, Carl %A Smit, Sandra %A Valenzuela, Daniel %A Wang, Jiayin %A Wessels, Lodewyk %A Zhang, Ying %A Guryev, Victor %A Vandin, Fabio %A Ye, Kai %A Schonhuth, Alexander %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations %T Computational Pan-genomics: Status, Promises and Challenges : %G eng %U http://hdl.handle.net/11858/00-001M-0000-002B-AF03-A %R 10.1093/bib/bbw089 %7 2016-10-21 %D 2018 %J Briefings in Bioinformatics %V 19 %N 1 %& 118 %P 118 - 135 %Z sequence number: bbw089 %I Oxford University Press %C London %@ false
67. Mendoza P, Gruell H, Nogueira L, Pai JA, Butler AL, Millard K, Lehmann C, Suarez I, Oliveira TY, Lorenzi JCC, Cohen YZ, Wyen C, Kuemmerle T, Karagounis T, Lu C-L, Handl L, Unson-O’Brien C, Patel R, Ruping C, Schlotz M, Witmer-Pack M, Shimeliovich I, Kremer G, Thomas E, Seaton KE, Horowitz J, West Jr. AP, Bjorkman PJ, Tomaras GD, Gulick RM, et al.: Combination Therapy with anti-HIV-1 Antibodies Maintains Viral Suppression. Nature 2018, 561.
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@article{Mendoza_2018, TITLE = {Combination therapy with anti-{HIV}-1 antibodies maintains viral suppression}, AUTHOR = {Mendoza, Pilar and Gruell, Henning and Nogueira, Lilian and Pai, Joy A. and Butler, Allison L. and Millard, Katrina and Lehmann, Clara and Suarez, Isabelle and Oliveira, Thiago Y. and Lorenzi, Julio C. C. and Cohen, Yehuda Z. and Wyen, Christoph and Kuemmerle, Tim and Karagounis, Theodora and Lu, Ching-Lan and Handl, Lisa and Unson-O'Brien, Cecilia and Patel, Roshni and Ruping, Carola and Schlotz, Maike and Witmer-Pack, Maggi and Shimeliovich, Irina and Kremer, Gisela and Thomas, Eleonore and Seaton, Kelly E. and Horowitz, Jill and West Jr., Anthony P. and Bjorkman, Pamela J. and Tomaras, Georgia D. and Gulick, Roy M. and Pfeifer, Nico and Faetkenheuer, Gerd and Seaman, Michael S. and Klein, Florian and Caskey, Marina and Nussenzweig, Michel C.}, LANGUAGE = {eng}, ISSN = {0028-0836}, DOI = {10.1038/s41586-018-0531-2}, PUBLISHER = {Nature Publishing Group}, ADDRESS = {London}, YEAR = {2018}, MARGINALMARK = {$\bullet$}, DATE = {2018}, JOURNAL = {Nature}, VOLUME = {561}, PAGES = {479--484}, }
Endnote
%0 Journal Article %A Mendoza, Pilar %A Gruell, Henning %A Nogueira, Lilian %A Pai, Joy A. %A Butler, Allison L. %A Millard, Katrina %A Lehmann, Clara %A Suarez, Isabelle %A Oliveira, Thiago Y. %A Lorenzi, Julio C. C. %A Cohen, Yehuda Z. %A Wyen, Christoph %A Kuemmerle, Tim %A Karagounis, Theodora %A Lu, Ching-Lan %A Handl, Lisa %A Unson-O'Brien, Cecilia %A Patel, Roshni %A Ruping, Carola %A Schlotz, Maike %A Witmer-Pack, Maggi %A Shimeliovich, Irina %A Kremer, Gisela %A Thomas, Eleonore %A Seaton, Kelly E. %A Horowitz, Jill %A West Jr., Anthony P. %A Bjorkman, Pamela J. %A Tomaras, Georgia D. %A Gulick, Roy M. %A Pfeifer, Nico %A Faetkenheuer, Gerd %A Seaman, Michael S. %A Klein, Florian %A Caskey, Marina %A Nussenzweig, Michel C. %+ External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations External Organizations External Organizations %T Combination Therapy with anti-HIV-1 Antibodies Maintains Viral Suppression : %G eng %U http://hdl.handle.net/21.11116/0000-0002-5770-E %R 10.1038/s41586-018-0531-2 %7 2018 %D 2018 %J Nature %O Nature %V 561 %& 479 %P 479 - 484 %I Nature Publishing Group %C London %@ false
68. Nazarieh M: Understanding Regulatory Mechanisms Underlying Stem Cells Helps to Identify Cancer Biomarkers. Universität des Saarlandes; 2018.
Abstract
Detection of biomarker genes play a crucial role in disease detection and treatment. Bioinformatics offers a variety of approaches for identification of biomarker genes which play key roles in complex diseases. These computational approaches enhance the insight derived from experiments and reduce the efforts of biologists and experimentalists. This is essentially achieved through prioritizing a set of genes with certain attributes. In this thesis, we show that understanding the regulatory mechanisms underlying stem cells helps to identify cancer biomarkers. We got inspired by the regulatory mechanisms of the pluripotency network in mouse embryonic stem cells and formulated the problem where a set of master regulatory genes in regulatory networks is identified with two combinatorial optimization problems namely as minimum dominating set and minimum connected dominating set in weakly and strongly connected components. Then we applied the developed methods to regulatory cancer networks to identify disease-associated genes and anti-cancer drug targets in breast cancer and hepatocellular carcinoma. As not all the nodes in the solutions are critical, we developed a prioritization method to rank a set of candidate genes which are related to a certain disease based on systematic analysis of the genes that are differentially expressed in tumor and normal conditions. Moreover, we demonstrated that the topological features in regulatory networks surrounding differentially expressed genes are highly consistent in terms of using the output of several analysis tools. We compared two randomization strategies for TF-miRNA co-regulatory networks to infer significant network motifs underlying cellular identity. We showed that the edge-type conserving method surpasses the non-conserving method in terms of biological relevance and centrality overlap. We presented several web servers and software packages that are publicly available at no cost. The Cytoscape plugin of minimum connected dominating set identifies a set of key regulatory genes in a user provided regulatory network based on a heuristic approach. The ILP formulations of minimum dominating set and minimum connected dominating set return the optimal solutions for the aforementioned problems. Our source code is publicly available. The web servers TFmiR and TFmiR2 construct disease-, tissue-, process-specific networks for the sets of deregulated genes and miRNAs provided by a user. They highlight topological hotspots and offer detection of three- and four-node FFL motifs as a separate web service for both organisms mouse and human.
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@phdthesis{nazariehphd2017, TITLE = {Understanding Regulatory Mechanisms Underlying Stem Cells Helps to Identify Cancer Biomarkers}, AUTHOR = {Nazarieh, Maryam}, LANGUAGE = {eng}, DOI = {10.22028/D291-27265}, SCHOOL = {Universit{\"a}t des Saarlandes}, ADDRESS = {Saarbr{\"u}cken}, YEAR = {2018}, MARGINALMARK = {$\bullet$}, DATE = {2018}, ABSTRACT = {Detection of biomarker genes play a crucial role in disease detection and treatment. Bioinformatics offers a variety of approaches for identification of biomarker genes which play key roles in complex diseases. These computational approaches enhance the insight derived from experiments and reduce the efforts of biologists and experimentalists. This is essentially achieved through prioritizing a set of genes with certain attributes. In this thesis, we show that understanding the regulatory mechanisms underlying stem cells helps to identify cancer biomarkers. We got inspired by the regulatory mechanisms of the pluripotency network in mouse embryonic stem cells and formulated the problem where a set of master regulatory genes in regulatory networks is identified with two combinatorial optimization problems namely as minimum dominating set and minimum connected dominating set in weakly and strongly connected components. Then we applied the developed methods to regulatory cancer networks to identify disease-associated genes and anti-cancer drug targets in breast cancer and hepatocellular carcinoma. As not all the nodes in the solutions are critical, we developed a prioritization method to rank a set of candidate genes which are related to a certain disease based on systematic analysis of the genes that are differentially expressed in tumor and normal conditions. Moreover, we demonstrated that the topological features in regulatory networks surrounding differentially expressed genes are highly consistent in terms of using the output of several analysis tools. We compared two randomization strategies for TF-miRNA co-regulatory networks to infer significant network motifs underlying cellular identity. We showed that the edge-type conserving method surpasses the non-conserving method in terms of biological relevance and centrality overlap. We presented several web servers and software packages that are publicly available at no cost. The Cytoscape plugin of minimum connected dominating set identifies a set of key regulatory genes in a user provided regulatory network based on a heuristic approach. The ILP formulations of minimum dominating set and minimum connected dominating set return the optimal solutions for the aforementioned problems. Our source code is publicly available. The web servers TFmiR and TFmiR2 construct disease-, tissue-, process-specific networks for the sets of deregulated genes and miRNAs provided by a user. They highlight topological hotspots and offer detection of three- and four-node FFL motifs as a separate web service for both organisms mouse and human.}, }
Endnote
%0 Thesis %A Nazarieh, Maryam %Y Helms, Volker %A referee: Lengauer, Thomas %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T Understanding Regulatory Mechanisms Underlying Stem Cells Helps to Identify Cancer Biomarkers : %G eng %U http://hdl.handle.net/21.11116/0000-0001-9D69-9 %R 10.22028/D291-27265 %I Universität des Saarlandes %C Saarbrücken %D 2018 %P 139 p. %V phd %9 phd %X Detection of biomarker genes play a crucial role in disease detection and treatment. Bioinformatics offers a variety of approaches for identification of biomarker genes which play key roles in complex diseases. These computational approaches enhance the insight derived from experiments and reduce the efforts of biologists and experimentalists. This is essentially achieved through prioritizing a set of genes with certain attributes. In this thesis, we show that understanding the regulatory mechanisms underlying stem cells helps to identify cancer biomarkers. We got inspired by the regulatory mechanisms of the pluripotency network in mouse embryonic stem cells and formulated the problem where a set of master regulatory genes in regulatory networks is identified with two combinatorial optimization problems namely as minimum dominating set and minimum connected dominating set in weakly and strongly connected components. Then we applied the developed methods to regulatory cancer networks to identify disease-associated genes and anti-cancer drug targets in breast cancer and hepatocellular carcinoma. As not all the nodes in the solutions are critical, we developed a prioritization method to rank a set of candidate genes which are related to a certain disease based on systematic analysis of the genes that are differentially expressed in tumor and normal conditions. Moreover, we demonstrated that the topological features in regulatory networks surrounding differentially expressed genes are highly consistent in terms of using the output of several analysis tools. We compared two randomization strategies for TF-miRNA co-regulatory networks to infer significant network motifs underlying cellular identity. We showed that the edge-type conserving method surpasses the non-conserving method in terms of biological relevance and centrality overlap. We presented several web servers and software packages that are publicly available at no cost. The Cytoscape plugin of minimum connected dominating set identifies a set of key regulatory genes in a user provided regulatory network based on a heuristic approach. The ILP formulations of minimum dominating set and minimum connected dominating set return the optimal solutions for the aforementioned problems. Our source code is publicly available. The web servers TFmiR and TFmiR2 construct disease-, tissue-, process-specific networks for the sets of deregulated genes and miRNAs provided by a user. They highlight topological hotspots and offer detection of three- and four-node FFL motifs as a separate web service for both organisms mouse and human. %U https://publikationen.sulb.uni-saarland.de/handle/20.500.11880/27104
69. Palanisamy N, Kalaghatgi P, Akaberi D, Lundkvist Å, Chen Z, Hu P, Lennerstrand J: Worldwide Prevalence of Baseline Resistance-associated Polymorphisms and Resistance Mutations in HCV against Current Direct-Acting Antivirals. Antiviral Therapy 2018, 23.
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@article{Palanisamy2018, TITLE = {Worldwide prevalence of baseline resistance-associated polymorphisms and resistance mutations in {HCV} against current direct-acting antivirals}, AUTHOR = {Palanisamy, Navaneethan and Kalaghatgi, Prabhav and Akaberi, Dario and Lundkvist, {\AA}ke and Chen, Zhi-wei and Hu, Peng and Lennerstrand, Johan}, LANGUAGE = {eng}, ISSN = {1359-6535}, DOI = {10.3851/IMP3237 2018}, PUBLISHER = {International Medical Press}, ADDRESS = {London}, YEAR = {2018}, MARGINALMARK = {$\bullet$}, JOURNAL = {Antiviral Therapy}, VOLUME = {23}, PAGES = {485--493}, }
Endnote
%0 Journal Article %A Palanisamy, Navaneethan %A Kalaghatgi, Prabhav %A Akaberi, Dario %A Lundkvist, Åke %A Chen, Zhi-wei %A Hu, Peng %A Lennerstrand, Johan %+ External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations External Organizations External Organizations %T Worldwide Prevalence of Baseline Resistance-associated Polymorphisms and Resistance Mutations in HCV against Current Direct-Acting Antivirals : %G eng %U http://hdl.handle.net/21.11116/0000-0002-CB09-0 %R 10.3851/IMP3237 2018 %7 2018 %D 2018 %J Antiviral Therapy %V 23 %& 485 %P 485 - 493 %I International Medical Press %C London %@ false
70. Pan W-H, Sommer F, Falk-Paulsen M, Ulas T, Best P, Fazio A, Kachroo P, Luzius A, Jentzsch M, Rehman A, Müller F, Lengauer T, Walter J, Kuenzel S, Baines JF, Schreiber S, Franke A, Schultze JL, Backhed F, Rosenstiel P: Exposure to the Gut Microbiota Drives Distinct Methylome and Transcriptome Changes in Intestinal Epithelial Cells during Postnatal Development. Genome Medicine 2018, 10.
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@article{Pan2018, TITLE = {Exposure to the Gut Microbiota Drives Distinct Methylome and Transcriptome Changes in Intestinal Epithelial Cells during Postnatal Development}, AUTHOR = {Pan, Wei-Hung and Sommer, Felix and Falk-Paulsen, Maren and Ulas, Thomas and Best, Philipp and Fazio, Antonella and Kachroo, Priyadarshini and Luzius, Anne and Jentzsch, Marlene and Rehman, Ateequr and M{\"u}ller, Fabian and Lengauer, Thomas and Walter, Joern and Kuenzel, Sven and Baines, John F. and Schreiber, Stefan and Franke, Andre and Schultze, Joachim L. and Backhed, Fredrik and Rosenstiel, Philip}, LANGUAGE = {eng}, DOI = {10.1186/s13073-018-0534-5}, PUBLISHER = {BioMed Central}, ADDRESS = {London}, YEAR = {2018}, MARGINALMARK = {$\bullet$}, JOURNAL = {Genome Medicine}, VOLUME = {10}, EID = {27}, }
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%0 Journal Article %A Pan, Wei-Hung %A Sommer, Felix %A Falk-Paulsen, Maren %A Ulas, Thomas %A Best, Philipp %A Fazio, Antonella %A Kachroo, Priyadarshini %A Luzius, Anne %A Jentzsch, Marlene %A Rehman, Ateequr %A Müller, Fabian %A Lengauer, Thomas %A Walter, Joern %A Kuenzel, Sven %A Baines, John F. %A Schreiber, Stefan %A Franke, Andre %A Schultze, Joachim L. %A Backhed, Fredrik %A Rosenstiel, Philip %+ External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations %T Exposure to the Gut Microbiota Drives Distinct Methylome and Transcriptome Changes in Intestinal Epithelial Cells during Postnatal Development : %G eng %U http://hdl.handle.net/21.11116/0000-0001-37F8-A %R 10.1186/s13073-018-0534-5 %7 2018 %D 2018 %J Genome Medicine %V 10 %Z sequence number: 27 %I BioMed Central %C London
71. Pirritano M, Goetz U, Karunanithi S, Nordstroem K, Schulz MH, Simon M: Environmental Temperature Controls Accumulation of Transacting siRNAs Involved in Heterochromatin Formation. Genes 2018, 9.
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@article{Pirritano2018, TITLE = {Environmental Temperature Controls Accumulation of Transacting {siRNAs} Involved in Heterochromatin Formation}, AUTHOR = {Pirritano, Marcello and Goetz, Ulrike and Karunanithi, Sivarajan and Nordstroem, Karl and Schulz, Marcel H. and Simon, Martin}, LANGUAGE = {eng}, ISSN = {2073-4425}, DOI = {10.3390/genes9020117}, PUBLISHER = {MPDI}, ADDRESS = {Basel}, YEAR = {2018}, MARGINALMARK = {$\bullet$}, JOURNAL = {Genes}, VOLUME = {9}, NUMBER = {2}, EID = {117}, }
Endnote
%0 Journal Article %A Pirritano, Marcello %A Goetz, Ulrike %A Karunanithi, Sivarajan %A Nordstroem, Karl %A Schulz, Marcel H. %A Simon, Martin %+ External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations %T Environmental Temperature Controls Accumulation of Transacting siRNAs Involved in Heterochromatin Formation : %G eng %U http://hdl.handle.net/21.11116/0000-0001-1F9E-C %R 10.3390/genes9020117 %2 PMC5852613 %7 2018 %D 2018 %J Genes %V 9 %N 2 %Z sequence number: 117 %I MPDI %C Basel %@ false
72. Salhab A, Nordstroem K, Gasparoni G, Kattler K, Ebert P, Ramirez F, Arrigoni L, Mueller F, Polansky JK, Cadenas C, Hengstler JG, Lengauer T, Manke T, Walter J: A Comprehensive Analysis of 195 DNA Methylomes Reveals Shared and Cell-specific Features of Partially Methylated Domains. Genome Biology 2018, 19.
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@article{Salhab_2018, TITLE = {A comprehensive analysis of 195 {DNA} methylomes reveals shared and cell-specific features of partially methylated domains}, AUTHOR = {Salhab, Abdulrahman and Nordstroem, Karl and Gasparoni, Gilles and Kattler, Kathrin and Ebert, Peter and Ramirez, Fidel and Arrigoni, Laura and Mueller, Fabian and Polansky, Julia K. and Cadenas, Cristina and Hengstler, Jan G. and Lengauer, Thomas and Manke, Thomas and Walter, Joern}, LANGUAGE = {eng}, ISSN = {1465-6906}, DOI = {10.1186/s13059-018-1510-5}, PUBLISHER = {BioMed Central Ltd.}, ADDRESS = {London}, YEAR = {2018}, MARGINALMARK = {$\bullet$}, JOURNAL = {Genome Biology}, VOLUME = {19}, EID = {150}, }
Endnote
%0 Journal Article %A Salhab, Abdulrahman %A Nordstroem, Karl %A Gasparoni, Gilles %A Kattler, Kathrin %A Ebert, Peter %A Ramirez, Fidel %A Arrigoni, Laura %A Mueller, Fabian %A Polansky, Julia K. %A Cadenas, Cristina %A Hengstler, Jan G. %A Lengauer, Thomas %A Manke, Thomas %A Walter, Joern %+ External Organizations External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations %T A Comprehensive Analysis of 195 DNA Methylomes Reveals Shared and Cell-specific Features of Partially Methylated Domains : %G eng %U http://hdl.handle.net/21.11116/0000-0002-5F29-7 %R 10.1186/s13059-018-1510-5 %7 2018 %D 2018 %J Genome Biology %V 19 %Z sequence number: 150 %I BioMed Central Ltd. %C London %@ false
73. Schmidt F, List M, Cukuroglu E, Koehler S, Goke J, Schulz MH: An Ontology-based Method for Assessing Batch Effect Adjustment Approaches in Heterogeneous Datasets. Bioinformatics (Proc ECCB 2018) 2018, 34.
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@article{Schmidt_Bioinformatics2018, TITLE = {An Ontology-based Method for Assessing Batch Effect Adjustment Approaches in Heterogeneous Datasets}, AUTHOR = {Schmidt, Florian and List, Markus and Cukuroglu, Engin and Koehler, Sebastian and Goke, Jonathan and Schulz, Marcel H.}, LANGUAGE = {eng}, ISSN = {1367-4803}, DOI = {10.1093/bioinformatics/bty553}, PUBLISHER = {Oxford University Press}, ADDRESS = {Oxford}, YEAR = {2018}, MARGINALMARK = {$\bullet$}, DATE = {2018}, JOURNAL = {Bioinformatics (Proc. ECCB)}, VOLUME = {34}, NUMBER = {17}, PAGES = {i908--i916}, BOOKTITLE = {The 17th European Conference on Computational Biology (ECCB 2018)}, }
Endnote
%0 Journal Article %A Schmidt, Florian %A List, Markus %A Cukuroglu, Engin %A Koehler, Sebastian %A Goke, Jonathan %A Schulz, Marcel H. %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T An Ontology-based Method for Assessing Batch Effect Adjustment Approaches in Heterogeneous Datasets : %G eng %U http://hdl.handle.net/21.11116/0000-0002-5732-4 %R 10.1093/bioinformatics/bty553 %7 2018 %D 2018 %J Bioinformatics %V 34 %N 17 %& i908 %P i908 - i916 %I Oxford University Press %C Oxford %@ false %B The 17th European Conference on Computational Biology %O ECCB 2018 Athens, Greece, 8 - 12 September 2018
74. Sikandar A, Cirnski K, Testolin G, Volz C, Broenstrup M, Kalinina OV, Müller R, Koehnke J: Adaptation of a Bacterial Multidrug Resistance System Revealed by the Structure and Function of AlbA. Journal of the American Chemical Society 2018, 140.
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@article{Sikandar2018, TITLE = {Adaptation of a Bacterial Multidrug Resistance System Revealed by the Structure and Function of {AlbA}}, AUTHOR = {Sikandar, Asfandyar and Cirnski, Katarina and Testolin, Giambattista and Volz, Carsten and Broenstrup, Mark and Kalinina, Olga V. and M{\"u}ller, Rolf and Koehnke, Jesko}, LANGUAGE = {eng}, ISSN = {0002-7863}, DOI = {10.1021/jacs.8b08895}, PUBLISHER = {American Chemical Society}, ADDRESS = {Washington, DC}, YEAR = {2018}, MARGINALMARK = {$\bullet$}, DATE = {2018}, JOURNAL = {Journal of the American Chemical Society}, VOLUME = {140}, NUMBER = {48}, PAGES = {16641--16649}, }
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%0 Journal Article %A Sikandar, Asfandyar %A Cirnski, Katarina %A Testolin, Giambattista %A Volz, Carsten %A Broenstrup, Mark %A Kalinina, Olga V. %A Müller, Rolf %A Koehnke, Jesko %+ External Organizations External Organizations External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations %T Adaptation of a Bacterial Multidrug Resistance System Revealed by the Structure and Function of AlbA : %G eng %U http://hdl.handle.net/21.11116/0000-0002-BA2F-9 %R 10.1021/jacs.8b08895 %7 2018 %D 2018 %J Journal of the American Chemical Society %O J. Am. Chem. Soc. JACS %V 140 %N 48 %& 16641 %P 16641 - 16649 %I American Chemical Society %C Washington, DC %@ false
75. Simovski B, Kanduri C, Gundersen S, Titov D, Domanska D, Bock C, Bossini-Castillo L, Chikina M, Favorov A, Layer RM, Mironov AA, Quinlan AR, Sheffield NC, Trynka G, Sandve GK: Coloc-stats: A Unified Web Interface to Perform Colocalization Analysis of Genomic Features. Nucleic Acids Research 2018, 46(Web Server issue).
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@article{Simovski_2018, TITLE = {Coloc-stats: A Unified Web Interface to Perform Colocalization Analysis of Genomic Features}, AUTHOR = {Simovski, Boris and Kanduri, Chakravarthi and Gundersen, Sveinung and Titov, Dmytro and Domanska, Diana and Bock, Christoph and Bossini-Castillo, Lara and Chikina, Maria and Favorov, Alexander and Layer, Ryan M. and Mironov, Andrey A. and Quinlan, Aaron R. and Sheffield, Nathan C. and Trynka, Gosia and Sandve, Geir K.}, LANGUAGE = {eng}, ISSN = {0301-5610}, DOI = {10.1093/nar/gky474}, PUBLISHER = {Oxford University Press}, ADDRESS = {Oxford, UK}, YEAR = {2018}, MARGINALMARK = {$\bullet$}, DATE = {2018}, JOURNAL = {Nucleic Acids Research}, VOLUME = {46}, NUMBER = {Web Server issue}, PAGES = {W186--W193}, }
Endnote
%0 Journal Article %A Simovski, Boris %A Kanduri, Chakravarthi %A Gundersen, Sveinung %A Titov, Dmytro %A Domanska, Diana %A Bock, Christoph %A Bossini-Castillo, Lara %A Chikina, Maria %A Favorov, Alexander %A Layer, Ryan M. %A Mironov, Andrey A. %A Quinlan, Aaron R. %A Sheffield, Nathan C. %A Trynka, Gosia %A Sandve, Geir K. %+ External Organizations External Organizations External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations %T Coloc-stats: A Unified Web Interface to Perform Colocalization Analysis of Genomic Features : %G eng %U http://hdl.handle.net/21.11116/0000-0001-E5C6-D %R 10.1093/nar/gky474 %7 2018 %D 2018 %J Nucleic Acids Research %O Nucleic Acids Res. %V 46 %N Web Server issue %& W186 %P W186 - W193 %I Oxford University Press %C Oxford, UK %@ false
2017
76. Ahmad M, Helms V, Kalinina OV, Lengauer T: Elucidating the Energetic Contributions to the Binding Free Energy. The Journal of Chemical Physics 2017, 146.
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@article{Ahmad2017, TITLE = {Elucidating the Energetic Contributions to the Binding Free Energy}, AUTHOR = {Ahmad, Mazen and Helms, Volkhard and Kalinina, Olga V. and Lengauer, Thomas}, LANGUAGE = {eng}, ISSN = {0021-9606}, DOI = {10.1063/1.4973349}, PUBLISHER = {American Institute of Physics}, ADDRESS = {Woodbury, N.Y.}, YEAR = {2017}, MARGINALMARK = {$\bullet$}, DATE = {2017}, JOURNAL = {The Journal of Chemical Physics}, VOLUME = {146}, NUMBER = {1}, EID = {014105}, }
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%0 Journal Article %A Ahmad, Mazen %A Helms, Volkhard %A Kalinina, Olga V. %A Lengauer, Thomas %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T Elucidating the Energetic Contributions to the Binding Free Energy : %G eng %U http://hdl.handle.net/11858/00-001M-0000-002C-3A74-2 %R 10.1063/1.4973349 %7 2017 %D 2017 %J The Journal of Chemical Physics %O J. Chem. Phys. %V 146 %N 1 %Z sequence number: 014105 %I American Institute of Physics %C Woodbury, N.Y. %@ false
77. Albrecht F, List M, Bock C, Lengauer T: DeepBlueR: Large-scale Epigenomic Analysis in R. Bioinformatics 2017, 33.
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@article{AlbrechtBioinformatics2017, TITLE = {{DeepBlueR}: {L}arge-scale Epigenomic Analysis in {R}}, AUTHOR = {Albrecht, Felipe and List, Markus and Bock, Christoph and Lengauer, Thomas}, LANGUAGE = {eng}, ISSN = {1367-4803}, DOI = {10.1093/bioinformatics/btx099}, PUBLISHER = {Oxford University Press}, ADDRESS = {Oxford}, YEAR = {2017}, MARGINALMARK = {$\bullet$}, DATE = {2017}, JOURNAL = {Bioinformatics}, VOLUME = {33}, NUMBER = {13}, PAGES = {2063--2064}, EID = {btx099}, }
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%0 Journal Article %A Albrecht, Felipe %A List, Markus %A Bock, Christoph %A Lengauer, Thomas %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T DeepBlueR: Large-scale Epigenomic Analysis in R : %G eng %U http://hdl.handle.net/11858/00-001M-0000-002C-8AB4-4 %R 10.1093/bioinformatics/btx099 %2 PMC5870546 %7 2017-02-22 %D 2017 %J Bioinformatics %V 33 %N 13 %& 2063 %P 2063 - 2064 %Z sequence number: btx099 %I Oxford University Press %C Oxford %@ false
78. Alcaraz N, List M, Batra R, Vandin F, Ditzel HJ, Baumbach J: De novo Pathway-based Biomarker Identification. Nucleic Acids Research 2017, 45.
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@article{Alcaraz2017, TITLE = {\textit{De novo} pathway-based biomarker identification}, AUTHOR = {Alcaraz, Nicolas and List, Markus and Batra, Richa and Vandin, Fabio and Ditzel, Henrik J. and Baumbach, Jan}, LANGUAGE = {eng}, ISSN = {0305-1048}, DOI = {10.1093/nar/gkx642}, PUBLISHER = {Oxford University Press}, ADDRESS = {Oxford}, YEAR = {2017}, MARGINALMARK = {$\bullet$}, DATE = {2017}, JOURNAL = {Nucleic Acids Research}, VOLUME = {45}, NUMBER = {16}, EID = {e151}, }
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%0 Journal Article %A Alcaraz, Nicolas %A List, Markus %A Batra, Richa %A Vandin, Fabio %A Ditzel, Henrik J. %A Baumbach, Jan %+ External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T De novo Pathway-based Biomarker Identification : %G eng %U http://hdl.handle.net/11858/00-001M-0000-002D-DDE0-C %R 10.1093/nar/gkx642 %7 2017 %D 2017 %J Nucleic Acids Research %O Nucleic Acids Res %V 45 %N 16 %Z sequence number: e151 %I Oxford University Press %C Oxford %@ false
79. Almeida D, Skov I, Silva A, Vandin F, Tan Q, Röttger R, Baumbach J: Efficient Detection of Differentially Methylated Regions using DiMmeR. Bioinformatics 2017, 33.
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@article{Almeida2017, TITLE = {Efficient Detection of Differentially Methylated Regions using {DiMmeR}}, AUTHOR = {Almeida, Diogo and Skov, Ida and Silva, Artur and Vandin, Fabio and Tan, Qihua and R{\"o}ttger, Richard and Baumbach, Jan}, LANGUAGE = {eng}, ISSN = {1367-4803}, DOI = {10.1093/bioinformatics/btw657}, PUBLISHER = {Oxford University Press}, ADDRESS = {Oxford}, YEAR = {2017}, MARGINALMARK = {$\bullet$}, DATE = {2017}, JOURNAL = {Bioinformatics}, VOLUME = {33}, NUMBER = {4}, PAGES = {549--551}, }
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%0 Journal Article %A Almeida, Diogo %A Skov, Ida %A Silva, Artur %A Vandin, Fabio %A Tan, Qihua %A Röttger, Richard %A Baumbach, Jan %+ External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T Efficient Detection of Differentially Methylated Regions using DiMmeR : %G eng %U http://hdl.handle.net/11858/00-001M-0000-002C-ECA5-7 %R 10.1093/bioinformatics/btw657 %7 2016 %D 2017 %J Bioinformatics %V 33 %N 4 %& 549 %P 549 - 551 %I Oxford University Press %C Oxford %@ false
80. Bader J, Däumer M, Schöni-Affolter F, Böni J, Gorgievski-Hrisoho M, Martinetti G, Thielen A, Klimkait T: Therapeutic Immune Recovery and Reduction of CXCR4-Tropic HIV-1. Clinical Infectious Diseases 2017, 64.
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@article{Bader2017, TITLE = {Therapeutic Immune Recovery and Reduction of {CXCR4}-Tropic {HIV}-1}, AUTHOR = {Bader, Jo{\"e}lle and D{\"a}umer, Martin and Sch{\"o}ni-Affolter, Franziska and B{\"o}ni, J{\"u}rg and Gorgievski-Hrisoho, Meri and Martinetti, Gladys and Thielen, Alexander and Klimkait, Thomas}, LANGUAGE = {eng}, ISSN = {1058-4838}, DOI = {10.1093/cid/ciw737}, PUBLISHER = {The University of Chicago Press}, ADDRESS = {Chicago, IL}, YEAR = {2017}, MARGINALMARK = {$\bullet$}, DATE = {2017}, JOURNAL = {Clinical Infectious Diseases}, VOLUME = {64}, NUMBER = {3}, PAGES = {295--300}, }
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%0 Journal Article %A Bader, Joëlle %A Däumer, Martin %A Schöni-Affolter, Franziska %A Böni, Jürg %A Gorgievski-Hrisoho, Meri %A Martinetti, Gladys %A Thielen, Alexander %A Klimkait, Thomas %+ External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations %T Therapeutic Immune Recovery and Reduction of CXCR4-Tropic HIV-1 : %G eng %U http://hdl.handle.net/11858/00-001M-0000-002C-ECAE-6 %R 10.1093/cid/ciw737 %7 2016 %D 2017 %J Clinical Infectious Diseases %V 64 %N 3 %& 295 %P 295 - 300 %I The University of Chicago Press %C Chicago, IL %@ false
81. Batra R, Alcaraz N, Gitzhofer K, Pauling J, Ditzel HJ, Hellmuth M, Baumbach J, List M: On the Performance of De Novo Pathway Enrichment. njp Systems Biology and Applications 2017, 3.
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@article{Baumbachnjp2016, TITLE = {On the Performance of De Novo Pathway Enrichment}, AUTHOR = {Batra, Richa and Alcaraz, Nicolas and Gitzhofer, Kevin and Pauling, Josch and Ditzel, Henrik J. and Hellmuth, Marc and Baumbach, Jan and List, Markus}, LANGUAGE = {eng}, DOI = {10.1038/s41540-017-0007-2}, PUBLISHER = {Nature Publishing Group}, ADDRESS = {London}, YEAR = {2017}, MARGINALMARK = {$\bullet$}, JOURNAL = {njp Systems Biology and Applications}, VOLUME = {3}, PAGES = {1--8}, EID = {6}, }
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%0 Journal Article %A Batra, Richa %A Alcaraz, Nicolas %A Gitzhofer, Kevin %A Pauling, Josch %A Ditzel, Henrik J. %A Hellmuth, Marc %A Baumbach, Jan %A List, Markus %+ External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T On the Performance of De Novo Pathway Enrichment : %G eng %U http://hdl.handle.net/11858/00-001M-0000-002C-2039-6 %R 10.1038/s41540-017-0007-2 %7 2017 %D 2017 %J njp Systems Biology and Applications %V 3 %& 1 %P 1 - 8 %Z sequence number: 6 %I Nature Publishing Group %C London
82. Berger B, Gaasterland T, Lengauer T, Orengo C, Gaeta B, Markel S, Valencia A: ISCB’s Initial Reaction to The New England Journal of Medicine Editorial on Data Sharing. Bioinformatics 2017, 33.
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@article{Berger2017, TITLE = {{ISCB}'s Initial Reaction to {The New England Journal of Medicine} Editorial on Data Sharing}, AUTHOR = {Berger, Bonnie and Gaasterland, Terry and Lengauer, Thomas and Orengo, Christine and Gaeta, Bruno and Markel, Scott and Valencia, Alfonso}, LANGUAGE = {eng}, ISSN = {1367-4803}, DOI = {10.1093/bioinformatics/btw090}, PUBLISHER = {Oxford University Press}, ADDRESS = {Oxford}, YEAR = {2017}, MARGINALMARK = {$\bullet$}, DATE = {2017}, JOURNAL = {Bioinformatics}, VOLUME = {33}, NUMBER = {18}, PAGES = {2968--2968}, }
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%0 Journal Article %A Berger, Bonnie %A Gaasterland, Terry %A Lengauer, Thomas %A Orengo, Christine %A Gaeta, Bruno %A Markel, Scott %A Valencia, Alfonso %+ External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations External Organizations %T ISCB’s Initial Reaction to The New England Journal of Medicine Editorial on Data Sharing : %G eng %U http://hdl.handle.net/21.11116/0000-0000-39C4-3 %R 10.1093/bioinformatics/btw090 %7 2017 %D 2017 %J Bioinformatics %V 33 %N 18 %& 2968 %P 2968 - 2968 %I Oxford University Press %C Oxford %@ false
83. Busch CJ-L, Hendrikx T, Weismann D, Jäckel S, Walenbergh SMA, Rendeiro AF, Weißer J, Puhm F, Hladik A, Göderle L, Papac-Milicevic N, Haas G, Millischer V, Subramaniam S, Knapp S, Bennett KL, Bock C, Reinhardt C, Shiri-Sverdlov R, Binder CJ: Malondialdehyde Epitopes Are Sterile Mediators of Hepatic Inflammation in Hypercholesterolemic Mice. Hepatology 2017, 65.
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@article{Busch2017, TITLE = {Malondialdehyde Epitopes Are Sterile Mediators of Hepatic Inflammation in Hypercholesterolemic Mice}, AUTHOR = {Busch, Clara Jana-Lui and Hendrikx, Tim and Weismann, David and J{\"a}ckel, Sven and Walenbergh, Sofie M. A. and Rendeiro, Andr{\'e} F. and Wei{\ss}er, Juliane and Puhm, Florian and Hladik, Anastasiya and G{\"o}derle, Laura and Papac-Milicevic, Nikolina and Haas, Gerald and Millischer, Vincent and Subramaniam, Saravanan and Knapp, Sylvia and Bennett, Keiryn L. and Bock, Christoph and Reinhardt, Christoph and Shiri-Sverdlov, Ronit and Binder, Christoph J.}, LANGUAGE = {eng}, ISSN = {0270-9139}, DOI = {10.1002/hep.28970}, PUBLISHER = {AASLD}, ADDRESS = {Alexandria, VA}, YEAR = {2017}, MARGINALMARK = {$\bullet$}, JOURNAL = {Hepatology}, VOLUME = {65}, NUMBER = {4}, PAGES = {1181--1195}, }
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%0 Journal Article %A Busch, Clara Jana-Lui %A Hendrikx, Tim %A Weismann, David %A Jäckel, Sven %A Walenbergh, Sofie M. A. %A Rendeiro, André F. %A Weißer, Juliane %A Puhm, Florian %A Hladik, Anastasiya %A Göderle, Laura %A Papac-Milicevic, Nikolina %A Haas, Gerald %A Millischer, Vincent %A Subramaniam, Saravanan %A Knapp, Sylvia %A Bennett, Keiryn L. %A Bock, Christoph %A Reinhardt, Christoph %A Shiri-Sverdlov, Ronit %A Binder, Christoph J. %+ External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations %T Malondialdehyde Epitopes Are Sterile Mediators of Hepatic Inflammation in Hypercholesterolemic Mice : %G eng %U http://hdl.handle.net/11858/00-001M-0000-002C-576B-C %R 10.1002/hep.28970 %2 PMC5892702 %7 2017 %D 2017 %J Hepatology %V 65 %N 4 %& 1181 %P 1181 - 1195 %I AASLD %C Alexandria, VA %@ false
84. Caskey M, Schoofs T, Gruell H, Settler A, Karagounis T, Kreider EF, Murrell B, Pfeifer N, Nogueira L, Oliveira TY, Learn GH, Cohen YZ, Lehmann C, Gillor D, Shimeliovich I, Unson-O’Brien C, Weiland D, Robles A, Kümmerle T, Wyen C, Levin R, Witmer-Pack M, Eren K, Ignacio C, Kiss S, Jr APW, Mouquet H, Zingman BS, Gulick RM, Keler T, et al.: Antibody 10-1074 Suppresses Viremia in HIV-1-infected Individuals. Nature Medicine 2017, 23.
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@article{Pfeifernature2017, TITLE = {Antibody 10-1074 Suppresses Viremia in {HIV}-1-infected Individuals}, AUTHOR = {Caskey, Marina and Schoofs, Till and Gruell, Henning and Settler, Allison and Karagounis, Theodora and Kreider, Edward F and Murrell, Ben and Pfeifer, Nico and Nogueira, Lilian and Oliveira, Thiago Y and Learn, Gerald H and Cohen, Yehuda Z and Lehmann, Clara and Gillor, Daniel and Shimeliovich, Irina and Unson-O{\textquoteright}Brien, Cecilia and Weiland, Daniela and Robles, Alexander and K{\"u}mmerle, Tim and Wyen, Christoph and Levin, Rebeka and Witmer-Pack, Maggi and Eren, Kemal and Ignacio, Caroline and Kiss, Szilard and Jr, Anthony P West and Mouquet, Hugo and Zingman, Barry S and Gulick, Roy M and Keler, Tibor and Bjorkman, Pamela J and Seaman, Michael S and Hahn, Beatrice H and F{\"a}tkenheuer, Gerd and Schlesinger, Sarah J and Nussenzweig, Michel C and Klein, Florian}, LANGUAGE = {eng}, ISSN = {1078-8956}, DOI = {10.1038/nm.4268}, PUBLISHER = {Nature Pub. Co.}, ADDRESS = {New York, NY}, YEAR = {2017}, MARGINALMARK = {$\bullet$}, DATE = {2017}, JOURNAL = {Nature Medicine}, VOLUME = {23}, NUMBER = {2}, PAGES = {185--191}, }
Endnote
%0 Journal Article %A Caskey, Marina %A Schoofs, Till %A Gruell, Henning %A Settler, Allison %A Karagounis, Theodora %A Kreider, Edward F %A Murrell, Ben %A Pfeifer, Nico %A Nogueira, Lilian %A Oliveira, Thiago Y %A Learn, Gerald H %A Cohen, Yehuda Z %A Lehmann, Clara %A Gillor, Daniel %A Shimeliovich, Irina %A Unson-O’Brien, Cecilia %A Weiland, Daniela %A Robles, Alexander %A Kümmerle, Tim %A Wyen, Christoph %A Levin, Rebeka %A Witmer-Pack, Maggi %A Eren, Kemal %A Ignacio, Caroline %A Kiss, Szilard %A Jr, Anthony P West %A Mouquet, Hugo %A Zingman, Barry S %A Gulick, Roy M %A Keler, Tibor %A Bjorkman, Pamela J %A Seaman, Michael S %A Hahn, Beatrice H %A Fätkenheuer, Gerd %A Schlesinger, Sarah J %A Nussenzweig, Michel C %A Klein, Florian %+ External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations %T Antibody 10-1074 Suppresses Viremia in HIV-1-infected Individuals : %G eng %U http://hdl.handle.net/11858/00-001M-0000-002C-7F0C-8 %R 10.1038/nm.4268 %7 2017-01-16 %D 2017 %J Nature Medicine %O Nat. Med. %V 23 %N 2 %& 185 %P 185 - 191 %I Nature Pub. Co. %C New York, NY %@ false
85. Datlinger P, Rendeiro AF, Schmidl C, Krausgruber T, Traxler P, Klughammer J, Schuster LC, Kuchler A, Alpar D, Bock C: Pooled CRISPR Screening with Single-cell Transcriptome Readout. Nature Methods 2017, 14.
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@article{Bocknature2017, TITLE = {Pooled {CRISPR} Screening with Single-cell Transcriptome Readout}, AUTHOR = {Datlinger, Paul and Rendeiro, Andr{\'e} F and Schmidl, Christian and Krausgruber, Thomas and Traxler, Peter and Klughammer, Johanna and Schuster, Linda C and Kuchler, Amelie and Alpar, Donat and Bock, Christoph}, LANGUAGE = {eng}, ISSN = {1548-7091}, DOI = {10.1038/nmeth.4177}, PUBLISHER = {Nature Pub. Group}, ADDRESS = {New York, NY}, YEAR = {2017}, MARGINALMARK = {$\bullet$}, DATE = {2017}, JOURNAL = {Nature Methods}, VOLUME = {14}, NUMBER = {3}, PAGES = {297--301}, }
Endnote
%0 Journal Article %A Datlinger, Paul %A Rendeiro, André F %A Schmidl, Christian %A Krausgruber, Thomas %A Traxler, Peter %A Klughammer, Johanna %A Schuster, Linda C %A Kuchler, Amelie %A Alpar, Donat %A Bock, Christoph %+ External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T Pooled CRISPR Screening with Single-cell Transcriptome Readout : %G eng %U http://hdl.handle.net/11858/00-001M-0000-002C-532B-2 %R 10.1038/nmeth.4177 %7 2017 %D 2017 %J Nature Methods %O Nature methods %V 14 %N 3 %& 297 %P 297 - 301 %I Nature Pub. Group %C New York, NY %@ false
86. Demirci MDS, Baumbach J, Allmer J: On the Performance of pre-microRNA Detection Algorithms. Nature Communications 2017, 8.
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@article{Demirci2017, TITLE = {On the performance of pre-micro{RNA} detection algorithms}, AUTHOR = {Demirci, M{\"u}{\c s}erref Duygu Sa{\c c}ar and Baumbach, Jan and Allmer, Jens}, LANGUAGE = {eng}, ISSN = {2041-1723}, DOI = {10.1038/s41467-017-00403-z}, PUBLISHER = {Nature Publishing Group}, ADDRESS = {London}, YEAR = {2017}, MARGINALMARK = {$\bullet$}, JOURNAL = {Nature Communications}, VOLUME = {8}, EID = {330}, }
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%0 Journal Article %A Demirci, Müşerref Duygu Saçar %A Baumbach, Jan %A Allmer, Jens %+ External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations %T On the Performance of pre-microRNA Detection Algorithms : %G eng %U http://hdl.handle.net/11858/00-001M-0000-002D-DC7E-1 %R 10.1038/s41467-017-00403-z %2 PMC5571158 %7 2017-08-24 %D 2017 %8 24.08.2017 %J Nature Communications %O Nat. Commun. %V 8 %Z sequence number: 330 %I Nature Publishing Group %C London %@ false
87. Ebler J, Schönhuth A, Marschall T: Genotyping of Inversions and Tandem Duplications. Bioinformatics 2017, 33.
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@article{Marshallbio17, TITLE = {Genotyping of Inversions and Tandem Duplications}, AUTHOR = {Ebler, Jana and Sch{\"o}nhuth, Alexander and Marschall, Tobias}, LANGUAGE = {eng}, ISSN = {1367-4803}, DOI = {10.1093/bioinformatics/btx020}, PUBLISHER = {Oxford University Press}, ADDRESS = {Oxford}, YEAR = {2017}, MARGINALMARK = {$\bullet$}, DATE = {2017}, JOURNAL = {Bioinformatics}, VOLUME = {33}, NUMBER = {24}, PAGES = {4015--4023}, EID = {btx020}, }
Endnote
%0 Journal Article %A Ebler, Jana %A Schönhuth, Alexander %A Marschall, Tobias %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T Genotyping of Inversions and Tandem Duplications : %G eng %U http://hdl.handle.net/11858/00-001M-0000-002C-468F-7 %R 10.1093/bioinformatics/btx020 %7 2017-02-07 %D 2017 %J Bioinformatics %V 33 %N 24 %& 4015 %P 4015 - 4023 %Z sequence number: btx020 %I Oxford University Press %C Oxford %@ false
88. Gress A, Ramensky V, Kalinina OV: Spatial Distribution of Disease-associated Variants in Three-dimensional Structures of Protein Complexes. Oncogenesis 2017, 6.
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@article{Gress_2017, TITLE = {Spatial Distribution of Disease-associated Variants in Three-dimensional Structures of Protein Complexes}, AUTHOR = {Gress, Alexander and Ramensky, V. and Kalinina, Olga V.}, LANGUAGE = {eng}, ISSN = {2157-9024}, DOI = {10.1038/oncsis.2017.79}, PUBLISHER = {Nature Publishing}, YEAR = {2017}, MARGINALMARK = {$\bullet$}, JOURNAL = {Oncogenesis}, VOLUME = {6}, NUMBER = {9}, EID = {e380}, }
Endnote
%0 Journal Article %A Gress, Alexander %A Ramensky, V. %A Kalinina, Olga V. %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T Spatial Distribution of Disease-associated Variants in Three-dimensional Structures of Protein Complexes : %G eng %U http://hdl.handle.net/11858/00-001M-0000-002E-24CF-8 %R 10.1038/oncsis.2017.79 %2 PMC5623905 %7 2017 %D 2017 %J Oncogenesis %V 6 %N 9 %Z sequence number: e380 %I Nature Publishing %@ false
89. Hake A, Pfeifer N: Prediction of HIV-1 Sensitivity to Broadly Neutralizing Antibodies Shows a Trend towards Resistance over Time. PLoS Computational Biology 2017, 13.
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@article{HakePfeifer2017, TITLE = {Prediction of {HIV}-1 Sensitivity to Broadly Neutralizing Antibodies Shows a Trend towards Resistance over Time}, AUTHOR = {Hake, Anna and Pfeifer, Nico}, LANGUAGE = {eng}, ISSN = {1553-734X}, DOI = {10.1371/journal.pcbi.1005789}, PUBLISHER = {Public Library of Science}, ADDRESS = {San Francisco, CA}, YEAR = {2017}, MARGINALMARK = {$\bullet$}, JOURNAL = {PLoS Computational Biology}, VOLUME = {13}, NUMBER = {10}, EID = {e1005789}, }
Endnote
%0 Journal Article %A Hake, Anna %A Pfeifer, Nico %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T Prediction of HIV-1 Sensitivity to Broadly Neutralizing Antibodies Shows a Trend towards Resistance over Time : %G eng %U http://hdl.handle.net/11858/00-001M-0000-002E-3127-A %R 10.1371/journal.pcbi.1005789 %2 PMC5669501 %7 2017 %D 2017 %J PLoS Computational Biology %V 13 %N 10 %Z sequence number: e1005789 %I Public Library of Science %C San Francisco, CA %@ false
90. Hashemi S, Dalini AN, Jalali A, Banaei-Moghaddam AM, Razaghi-Moghadam Z: Cancerouspdomains: Comprehensive Analysis of Cancer Type-specific Recurrent Somatic Mutations in Proteins and Domains. BMC Bioinformatics 2017, 18.
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@article{Hashemi2017, TITLE = {Cancerouspdomains: {C}omprehensive analysis of cancer type-specific recurrent somatic mutations in proteins and domains}, AUTHOR = {Hashemi, Seirana and Dalini, Abbas Nowzari and Jalali, Adrin and Banaei-Moghaddam, Ali Mohammad and Razaghi-Moghadam, Zahra}, LANGUAGE = {eng}, ISSN = {1471-2105}, DOI = {10.1186/s12859-017-1779-5}, PUBLISHER = {BioMed Central}, YEAR = {2017}, MARGINALMARK = {$\bullet$}, JOURNAL = {BMC Bioinformatics}, VOLUME = {18}, EID = {370}, }
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%0 Journal Article %A Hashemi, Seirana %A Dalini, Abbas Nowzari %A Jalali, Adrin %A Banaei-Moghaddam, Ali Mohammad %A Razaghi-Moghadam, Zahra %+ External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations %T Cancerouspdomains: Comprehensive Analysis of Cancer Type-specific Recurrent Somatic Mutations in Proteins and Domains : %G eng %U http://hdl.handle.net/11858/00-001M-0000-002D-DDC4-C %R 10.1186/s12859-017-1779-5 %7 2017 %D 2017 %J BMC Bioinformatics %V 18 %Z sequence number: 370 %I BioMed Central %@ false
91. Heger E, Kaiser R, Knops E, Neumann-Fraune M, Pironti A, Lengauer T, Walter H, Sierra S: Results of the First International HIV-1 Coreceptor Proficiency Panel Test. Journal of Clinical Virology 2017, 93.
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@article{Heger2017, TITLE = {Results of the First International {HIV}-1 Coreceptor Proficiency Panel Test}, AUTHOR = {Heger, Eva and Kaiser, Rolf and Knops, Elena and Neumann-Fraune, Maria and Pironti, Alejandro and Lengauer, Thomas and Walter, Hauke and Sierra, Saleta}, LANGUAGE = {eng}, ISSN = {1386-6532}, DOI = {10.1016/j.jcv.2017.06.002}, PUBLISHER = {Elsevier}, ADDRESS = {Amsterdam}, YEAR = {2017}, MARGINALMARK = {$\bullet$}, DATE = {2017}, JOURNAL = {Journal of Clinical Virology}, VOLUME = {93}, PAGES = {53--56}, }
Endnote
%0 Journal Article %A Heger, Eva %A Kaiser, Rolf %A Knops, Elena %A Neumann-Fraune, Maria %A Pironti, Alejandro %A Lengauer, Thomas %A Walter, Hauke %A Sierra, Saleta %+ External Organizations External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations %T Results of the First International HIV-1 Coreceptor Proficiency Panel Test : %G eng %U http://hdl.handle.net/11858/00-001M-0000-002E-0189-7 %R 10.1016/j.jcv.2017.06.002 %7 2017 %D 2017 %J Journal of Clinical Virology %V 93 %& 53 %P 53 - 56 %I Elsevier %C Amsterdam %@ false
92. Jühling F, Bandiera S, Hamdane N, Thumann C, Durand SC, Saghire H. E, Davidson I, Habersetzer F, Pessaux P, Bardeesy N, Schmidl C, Bock C, Hoshida Y, Zeisel MB, Baumert TF: Hepatitis C Virus-induced Epigenetic and Transcriptional Changes Persist Post Cure. Journal of Hepatology 2017, 66.
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@article{Juehling2017, TITLE = {Hepatitis {C} Virus-induced Epigenetic and Transcriptional Changes Persist Post Cure}, AUTHOR = {J{\"u}hling, F. and Bandiera, S. and Hamdane, N. and Thumann, C. and Durand, S. C. and Saghire, H .E. and Davidson, I. and Habersetzer, F. and Pessaux, P. and Bardeesy, N. and Schmidl, C. and Bock, Christoph and Hoshida, Y. and Zeisel, M. B. and Baumert, T. F.}, LANGUAGE = {eng}, ISBN = {0168-8278}, URL = {http://dx.doi.org/10.1016/S0168-8278(17)30304-5}, DOI = {10.1016/S0168-8278(17)30304-5}, PUBLISHER = {Elsevier}, ADDRESS = {Amsterdam}, YEAR = {2017}, MARGINALMARK = {$\bullet$}, DATE = {2017}, JOURNAL = {Journal of Hepatology}, VOLUME = {66}, NUMBER = {1}, PAGES = {S21--S21}, }
Endnote
%0 Journal Article %A Jühling, F. %A Bandiera, S. %A Hamdane, N. %A Thumann, C. %A Durand, S. C. %A Saghire, H .E. %A Davidson, I. %A Habersetzer, F. %A Pessaux, P. %A Bardeesy, N. %A Schmidl, C. %A Bock, Christoph %A Hoshida, Y. %A Zeisel, M. B. %A Baumert, T. F. %+ external external external external external external external external external external external Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society external external external %T Hepatitis C Virus-induced Epigenetic and Transcriptional Changes Persist Post Cure : %G eng %U http://hdl.handle.net/11858/00-001M-0000-002D-7861-8 %U http://dx.doi.org/10.1016/S0168-8278(17)30304-5 %R 10.1016/S0168-8278(17)30304-5 %7 2017 %D 2017 %J Journal of Hepatology %V 66 %N 1 %& S21 %P S21 - S21 %I Elsevier %C Amsterdam %@ 0168-8278
93. Kalaghatgi P, Lengauer T: Computing Phylogenetic Trees Using Topologically Related Minimum Spanning Trees. Journal of Graph Algorithms and Applications 2017, 21.
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@article{Kalaghatgi2017a, TITLE = {Computing Phylogenetic Trees Using Topologically Related Minimum Spanning Trees}, AUTHOR = {Kalaghatgi, Prabhav and Lengauer, Thomas}, LANGUAGE = {eng}, ISSN = {1526-1719}, DOI = {10.7155/jgaa.00447}, PUBLISHER = {Brown University, Dept. of Computer Science}, ADDRESS = {Providence, R.I.}, YEAR = {2017}, MARGINALMARK = {$\bullet$}, JOURNAL = {Journal of Graph Algorithms and Applications}, VOLUME = {21}, NUMBER = {6}, PAGES = {1003--1025}, }
Endnote
%0 Journal Article %A Kalaghatgi, Prabhav %A Lengauer, Thomas %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T Computing Phylogenetic Trees Using Topologically Related Minimum Spanning Trees : %G eng %U http://hdl.handle.net/21.11116/0000-0000-39A9-2 %R 10.7155/jgaa.00447 %7 2017 %D 2017 %J Journal of Graph Algorithms and Applications %V 21 %N 6 %& 1003 %P 1003 - 1025 %I Brown University, Dept. of Computer Science %C Providence, R.I. %@ false
94. Selecting Optimal Minimum Spanning Trees that Share a Topological Correspondence with Phylogenetic Trees [http://arxiv.org/abs/1701.02844]
(arXiv: 1701.02844)
Abstract
Choi et. al (2011) introduced a minimum spanning tree (MST)-based method called CLGrouping, for constructing tree-structured probabilistic graphical models, a statistical framework that is commonly used for inferring phylogenetic trees. While CLGrouping works correctly if there is a unique MST, we observe an indeterminacy in the method in the case that there are multiple MSTs. In this work we remove this indeterminacy by introducing so-called vertex-ranked MSTs. We note that the effectiveness of CLGrouping is inversely related to the number of leaves in the MST. This motivates the problem of finding a vertex-ranked MST with the minimum number of leaves (MLVRMST). We provide a polynomial time algorithm for the MLVRMST problem, and prove its correctness for graphs whose edges are weighted with tree-additive distances.
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@online{Kalaghatgi2017, TITLE = {Selecting Optimal Minimum Spanning Trees that Share a Topological Correspondence with Phylogenetic Trees}, AUTHOR = {Kalaghatgi, Prabhav and Lengauer, Thomas}, LANGUAGE = {eng}, URL = {http://arxiv.org/abs/1701.02844}, EPRINT = {1701.02844}, EPRINTTYPE = {arXiv}, YEAR = {2017}, MARGINALMARK = {$\bullet$}, ABSTRACT = {Choi et. al (2011) introduced a minimum spanning tree (MST)-based method called CLGrouping, for constructing tree-structured probabilistic graphical models, a statistical framework that is commonly used for inferring phylogenetic trees. While CLGrouping works correctly if there is a unique MST, we observe an indeterminacy in the method in the case that there are multiple MSTs. In this work we remove this indeterminacy by introducing so-called vertex-ranked MSTs. We note that the effectiveness of CLGrouping is inversely related to the number of leaves in the MST. This motivates the problem of finding a vertex-ranked MST with the minimum number of leaves (MLVRMST). We provide a polynomial time algorithm for the MLVRMST problem, and prove its correctness for graphs whose edges are weighted with tree-additive distances.}, }
Endnote
%0 Report %A Kalaghatgi, Prabhav %A Lengauer, Thomas %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T Selecting Optimal Minimum Spanning Trees that Share a Topological Correspondence with Phylogenetic Trees : %G eng %U http://hdl.handle.net/11858/00-001M-0000-002C-3E81-2 %U http://arxiv.org/abs/1701.02844 %D 2017 %X Choi et. al (2011) introduced a minimum spanning tree (MST)-based method called CLGrouping, for constructing tree-structured probabilistic graphical models, a statistical framework that is commonly used for inferring phylogenetic trees. While CLGrouping works correctly if there is a unique MST, we observe an indeterminacy in the method in the case that there are multiple MSTs. In this work we remove this indeterminacy by introducing so-called vertex-ranked MSTs. We note that the effectiveness of CLGrouping is inversely related to the number of leaves in the MST. This motivates the problem of finding a vertex-ranked MST with the minimum number of leaves (MLVRMST). We provide a polynomial time algorithm for the MLVRMST problem, and prove its correctness for graphs whose edges are weighted with tree-additive distances. %K Mathematics, Combinatorics, math.CO,Computer Science, Data Structures and Algorithms, cs.DS
95. Kehl T, Schneider L, Schmidt F, Stöckel D, Gerstner N, Backes C, Meese E, Keller A, Schulz MH, Lenhof H-P: RegulatorTrail: A Web Service for the Identification of Key Transcriptional Regulators. Nucleic Acids Research 2017, 45.
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@article{Kehl2017, TITLE = {{RegulatorTrail}: {A} Web Service for the Identification of Key Transcriptional Regulators}, AUTHOR = {Kehl, Tim and Schneider, Lara and Schmidt, Florian and St{\"o}ckel, Daniel and Gerstner, Nico and Backes, Christina and Meese, Eckart and Keller, Andreas and Schulz, Marcel Holger and Lenhof, Hans-Peter}, LANGUAGE = {eng}, ISSN = {0305-1048}, DOI = {10.1093/nar/gkx350}, PUBLISHER = {Oxford University Press}, ADDRESS = {Oxford}, YEAR = {2017}, MARGINALMARK = {$\bullet$}, DATE = {2017}, JOURNAL = {Nucleic Acids Research}, VOLUME = {45}, NUMBER = {W1}, PAGES = {W146--W153}, }
Endnote
%0 Journal Article %A Kehl, Tim %A Schneider, Lara %A Schmidt, Florian %A Stöckel, Daniel %A Gerstner, Nico %A Backes, Christina %A Meese, Eckart %A Keller, Andreas %A Schulz, Marcel Holger %A Lenhof, Hans-Peter %+ External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations %T RegulatorTrail: A Web Service for the Identification of Key Transcriptional Regulators : %G eng %U http://hdl.handle.net/11858/00-001M-0000-002D-C393-D %R 10.1093/nar/gkx350 %2 PMC5570139 %7 2017 %D 2017 %J Nucleic Acids Research %O Nucleic Acids Res %V 45 %N W1 %& W146 %P W146 - W153 %I Oxford University Press %C Oxford %@ false
96. Klau GW, Marschall T: A Guided Tour to Computational Haplotyping. In Unveiling Dynamics and Complexity (CiE 2017). Springer; 2017. [Lecture Notes in Computer Science, vol. 10307]
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@inproceedings{Klau_CiE2017, TITLE = {A Guided Tour to Computational Haplotyping}, AUTHOR = {Klau, Gunnar W. and Marschall, Tobias}, LANGUAGE = {eng}, ISBN = {978-3-319-58740-0}, DOI = {10.1007/978-3-319-58741-7_6}, PUBLISHER = {Springer}, YEAR = {2017}, MARGINALMARK = {$\bullet$}, DATE = {2017}, BOOKTITLE = {Unveiling Dynamics and Complexity (CiE 2017)}, EDITOR = {Kari, Jarkko and Manea, Florin and Petre, Ion}, PAGES = {50-63}, SERIES = {Lecture Notes in Computer Science}, VOLUME = {10307}, ADDRESS = {Turku, Finland}, }
Endnote
%0 Conference Proceedings %A Klau, Gunnar W. %A Marschall, Tobias %+ External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T A Guided Tour to Computational Haplotyping : %G eng %U http://hdl.handle.net/21.11116/0000-0001-4053-9 %R 10.1007/978-3-319-58741-7_6 %D 2017 %B 13th Conference on Computability in Europe %Z date of event: 2017-06-12 - 2017-06-16 %C Turku, Finland %B Unveiling Dynamics and Complexity %E Kari, Jarkko; Manea, Florin; Petre, Ion %P 50-63 %I Springer %@ 978-3-319-58740-0 %B Lecture Notes in Computer Science %N 10307
97. Knops E, Schübel N, Heger E, Neumann-Fraune M, Kaiser R, Inden S, Kalaghatgi P, Sierra S: HCV Resistance Profile Evolution in a GT1b, DAA-Naive Patient Before, On, and After Failing Triple DAA Therapy. Clinical Gastroenterology and Hepatology 2017, 15.
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@article{Knops2017, TITLE = {{HCV} Resistance Profile Evolution in a {GT1b}, {DAA}-Naive Patient Before, On, and After Failing Triple {DAA} Therapy}, AUTHOR = {Knops, Elena and Sch{\"u}bel, Niels and Heger, Eva and Neumann-Fraune, Maria and Kaiser, Rolf and Inden, Stephanie and Kalaghatgi, Prabhav and Sierra, Saleta}, LANGUAGE = {eng}, DOI = {10.1016/j.cgh.2016.09.139}, PUBLISHER = {Elsevier}, ADDRESS = {Amsterdam}, YEAR = {2017}, MARGINALMARK = {$\bullet$}, DATE = {2017}, JOURNAL = {Clinical Gastroenterology and Hepatology}, VOLUME = {15}, NUMBER = {2}, PAGES = {307--309}, }
Endnote
%0 Journal Article %A Knops, Elena %A Schübel, Niels %A Heger, Eva %A Neumann-Fraune, Maria %A Kaiser, Rolf %A Inden, Stephanie %A Kalaghatgi, Prabhav %A Sierra, Saleta %+ External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations %T HCV Resistance Profile Evolution in a GT1b, DAA-Naive Patient Before, On, and After Failing Triple DAA Therapy : %G eng %U http://hdl.handle.net/11858/00-001M-0000-002C-ECB2-B %R 10.1016/j.cgh.2016.09.139 %7 2017 %D 2017 %J Clinical Gastroenterology and Hepatology %V 15 %N 2 %& 307 %P 307 - 309 %I Elsevier %C Amsterdam
98. Licciardello MP, Ringler A, Markt P, Klepsch F, Lardeau C-H, Sdelci S, Schirghuber E, Müller AC, Caldera M, Wagner A, Herzog R, Penz T, Schuster M, Boidol B, Dürnberger G, Folkvaljon Y, Stattin P, Ivanov V, Colinge J, Bock C, Kratochwill K, Menche J, Bennett KL, Kubicek S: A Combinatorial Screen of the CLOUD Uncovers a Synergy Targeting the Androgen Receptor. Nature Chemical Biology 2017, 13.
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@article{Licciardello2017, TITLE = {A Combinatorial Screen of the {CLOUD} Uncovers a Synergy Targeting the Androgen Receptor}, AUTHOR = {Licciardello, Marco P. and Ringler, Anna and Markt, Patrick and Klepsch, Freya and Lardeau, Charles-Hugues and Sdelci, Sara and Schirghuber, Erika and M{\"u}ller, Andr{\'e} C. and Caldera, Michael and Wagner, Anja and Herzog, Rebecca and Penz, Thomas and Schuster, Michael and Boidol, Bernd and D{\"u}rnberger, Gerhard and Folkvaljon, Yasin and Stattin, P{\"a}r and Ivanov, Vladimir and Colinge, Jacques and Bock, Christoph and Kratochwill, Klaus and Menche, J{\"o}rg and Bennett, Keiryn L. and Kubicek, Stefan}, LANGUAGE = {eng}, ISSN = {1552-4450}, DOI = {10.1038/nchembio.2382}, PUBLISHER = {Nature Pub. Group}, ADDRESS = {New York, NY}, YEAR = {2017}, MARGINALMARK = {$\bullet$}, DATE = {2017}, JOURNAL = {Nature Chemical Biology}, VOLUME = {13}, PAGES = {771--778}, }
Endnote
%0 Journal Article %A Licciardello, Marco P. %A Ringler, Anna %A Markt, Patrick %A Klepsch, Freya %A Lardeau, Charles-Hugues %A Sdelci, Sara %A Schirghuber, Erika %A Müller, André C. %A Caldera, Michael %A Wagner, Anja %A Herzog, Rebecca %A Penz, Thomas %A Schuster, Michael %A Boidol, Bernd %A Dürnberger, Gerhard %A Folkvaljon, Yasin %A Stattin, Pär %A Ivanov, Vladimir %A Colinge, Jacques %A Bock, Christoph %A Kratochwill, Klaus %A Menche, Jörg %A Bennett, Keiryn L. %A Kubicek, Stefan %+ External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations External Organizations %T A Combinatorial Screen of the CLOUD Uncovers a Synergy Targeting the Androgen Receptor : %G eng %U http://hdl.handle.net/11858/00-001M-0000-002D-8F17-5 %R 10.1038/nchembio.2382 %7 2017-05-22 %D 2017 %J Nature Chemical Biology %O Nat. Chem. Biol. %V 13 %& 771 %P 771 - 778 %I Nature Pub. Group %C New York, NY %@ false
99. Li J, Casteels T, Frogne T, Ingvorsen C, Honoré C, Courtney M, Huber KVM, Schmitner N, Kimmel RA, Romanov RA, Sturtzel C, Lardeau C-H, Klughammer J, Farlik M, Sdelci S, Vieira A, Avolio F, Briand F, Baburin I, Májek P, Pauler FM, Penz T, Stukalov A, Gridling M, Parapatics K, Barbieux C, Berishvili E, Spittler A, Colinge J, Bennett KL, et al.: Artemisinins Target GABA A Receptor Signaling and Impair α Cell Identity. Cell 2017, 168.
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@article{Li2017, TITLE = {Artemisinins Target {GABA$_{\mathrm A}$} Receptor Signaling and Impair $\alpha$ Cell Identity}, AUTHOR = {Li, Jin and Casteels, Tamara and Frogne, Thomas and Ingvorsen, Camilla and Honor{\'e}, Christian and Courtney, Monica and Huber, Kilian V. M. and Schmitner, Nicole and Kimmel, Robin A. and Romanov, Roman A. and Sturtzel, Caterina and Lardeau, Charles-Hugues and Klughammer, Johanna and Farlik, Matthias and Sdelci, Sara and Vieira, Andhira and Avolio, Fabio and Briand, Fran{\c c}ois and Baburin, Igor and M{\'a}jek, Peter and Pauler, Florian M. and Penz, Thomas and Stukalov, Alexey and Gridling, Manuela and Parapatics, Katja and Barbieux, Charlotte and Berishvili, Ekaterine and Spittler, Andreas and Colinge, Jacques and Bennett, Keiryn L. and Hering, Steffen and Sulpice, Thierry and Bock, Christoph and Distel, Martin and Harkany, Tibor and Meyer, Dirk and Superti-Furga, Giulio and Collombat, Patrick and Hecksher-S{\o}rensen, Jacob and Kubicek, Stefan}, LANGUAGE = {eng}, ISSN = {0092-8674}, DOI = {10.1016/j.cell.2016.11.010}, PUBLISHER = {Elsevier}, ADDRESS = {Amsterdam}, YEAR = {2017}, MARGINALMARK = {$\bullet$}, DATE = {2017}, JOURNAL = {Cell}, VOLUME = {168}, NUMBER = {1-2}, PAGES = {86--100}, EID = {e15}, }
Endnote
%0 Journal Article %A Li, Jin %A Casteels, Tamara %A Frogne, Thomas %A Ingvorsen, Camilla %A Honoré, Christian %A Courtney, Monica %A Huber, Kilian V. M. %A Schmitner, Nicole %A Kimmel, Robin A. %A Romanov, Roman A. %A Sturtzel, Caterina %A Lardeau, Charles-Hugues %A Klughammer, Johanna %A Farlik, Matthias %A Sdelci, Sara %A Vieira, Andhira %A Avolio, Fabio %A Briand, François %A Baburin, Igor %A Májek, Peter %A Pauler, Florian M. %A Penz, Thomas %A Stukalov, Alexey %A Gridling, Manuela %A Parapatics, Katja %A Barbieux, Charlotte %A Berishvili, Ekaterine %A Spittler, Andreas %A Colinge, Jacques %A Bennett, Keiryn L. %A Hering, Steffen %A Sulpice, Thierry %A Bock, Christoph %A Distel, Martin %A Harkany, Tibor %A Meyer, Dirk %A Superti-Furga, Giulio %A Collombat, Patrick %A Hecksher-Sørensen, Jacob %A Kubicek, Stefan %+ External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations %T Artemisinins Target GABA A Receptor Signaling and Impair α Cell Identity : %G eng %U http://hdl.handle.net/11858/00-001M-0000-002C-5C72-1 %2 PMC5236063 %R 10.1016/j.cell.2016.11.010 %7 2017 %D 2017 %J Cell %V 168 %N 1-2 %& 86 %P 86 - 100 %Z sequence number: e15 %I Elsevier %C Amsterdam %@ false
100. List M, Elnegaard MP, Schmidt S, Christiansen H, Tan Q, Mollenhauer J, Baumbach J: Efficient Management of High-Throughput Screening Libraries with SAVANAH. Journal of Biomolecular Screening 2017, 22.
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@article{List2016b, TITLE = {Efficient Management of High-Throughput Screening Libraries with {SAVANAH}}, AUTHOR = {List, Markus and Elnegaard, Marlene Pedersen and Schmidt, Steffen and Christiansen, Helle and Tan, Qihua and Mollenhauer, Jan and Baumbach, Jan}, LANGUAGE = {eng}, ISSN = {1087-0571}, DOI = {10.1177/1087057116673607}, PUBLISHER = {Sage Publications, Inc.}, ADDRESS = {Larchmont, NY}, YEAR = {2017}, MARGINALMARK = {$\bullet$}, DATE = {2017}, JOURNAL = {Journal of Biomolecular Screening}, VOLUME = {22}, NUMBER = {2}, PAGES = {196--202}, }
Endnote
%0 Journal Article %A List, Markus %A Elnegaard, Marlene Pedersen %A Schmidt, Steffen %A Christiansen, Helle %A Tan, Qihua %A Mollenhauer, Jan %A Baumbach, Jan %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T Efficient Management of High-Throughput Screening Libraries with SAVANAH : %G eng %U http://hdl.handle.net/11858/00-001M-0000-002C-202F-D %R 10.1177/1087057116673607 %7 2016-10-11 %D 2017 %J Journal of Biomolecular Screening %V 22 %N 2 %& 196 %P 196 - 202 %I Sage Publications, Inc. %C Larchmont, NY %@ false
101. List M, Ebert P, Albrecht F: Ten Simple Rules for Developing Usable Software in Computational Biology. PLoS Computational Biology 2017, 13.
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@article{ListPloSCompBiol2016, TITLE = {Ten Simple Rules for Developing Usable Software in Computational Biology}, AUTHOR = {List, Markus and Ebert, Peter and Albrecht, Felipe}, LANGUAGE = {eng}, ISSN = {1553-734X}, DOI = {10.1371/journal.pcbi.1005265}, PUBLISHER = {Public Library of Science}, ADDRESS = {San Francisco, CA}, YEAR = {2017}, MARGINALMARK = {$\bullet$}, JOURNAL = {PLoS Computational Biology}, VOLUME = {13}, NUMBER = {1}, EID = {e1005265}, }
Endnote
%0 Journal Article %A List, Markus %A Ebert, Peter %A Albrecht, Felipe %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T Ten Simple Rules for Developing Usable Software in Computational Biology : %G eng %U http://hdl.handle.net/11858/00-001M-0000-002C-203B-2 %R 10.1371/journal.pcbi.1005265 %7 2017-01-05 %D 2017 %8 05.01.2017 %J PLoS Computational Biology %V 13 %N 1 %Z sequence number: e1005265 %I Public Library of Science %C San Francisco, CA %@ false
102. List M: Using Docker Compose for the Simple Deployment of an Integrated Drug Target Screening Platform. Journal of Integrative Bioinformatics 2017, 14.
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@article{ListJIB2017, TITLE = {Using {Docker} Compose for the Simple Deployment of an Integrated Drug Target Screening Platform}, AUTHOR = {List, Markus}, LANGUAGE = {eng}, ISSN = {1613-4516}, DOI = {10.1515/jib-2017-0016}, PUBLISHER = {de Gruyter}, ADDRESS = {Berlin}, YEAR = {2017}, MARGINALMARK = {$\bullet$}, JOURNAL = {Journal of Integrative Bioinformatics}, VOLUME = {14}, NUMBER = {2}, EID = {20170016}, }
Endnote
%0 Journal Article %A List, Markus %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T Using Docker Compose for the Simple Deployment of an Integrated Drug Target Screening Platform : %G eng %U http://hdl.handle.net/11858/00-001M-0000-002D-DDE3-6 %R 10.1515/jib-2017-0016 %7 2017 %D 2017 %J Journal of Integrative Bioinformatics %V 14 %N 2 %Z sequence number: 20170016 %I de Gruyter %C Berlin %@ false
103. Lund JB, List M, Baumbach J: Interactive Microbial Distribution Analysis using BioAtlas. Nucleic Acids Research 2017, 45.
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@article{LundListBaumbach2017, TITLE = {Interactive microbial distribution analysis using {BioAtlas}}, AUTHOR = {Lund, Jesper Beltoft and List, Markus and Baumbach, Jan}, LANGUAGE = {eng}, ISSN = {0305-1048}, DOI = {10.1093/nar/gkx304}, PUBLISHER = {Oxford University Press}, ADDRESS = {Oxford}, YEAR = {2017}, MARGINALMARK = {$\bullet$}, DATE = {2017}, JOURNAL = {Nucleic Acids Research}, VOLUME = {45}, NUMBER = {W1}, PAGES = {W509--W513}, }
Endnote
%0 Journal Article %A Lund, Jesper Beltoft %A List, Markus %A Baumbach, Jan %+ External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T Interactive Microbial Distribution Analysis using BioAtlas : %G eng %U http://hdl.handle.net/11858/00-001M-0000-002D-C387-9 %R 10.1093/nar/gkx304 %2 PMC5570126 %7 2017 %D 2017 %J Nucleic Acids Research %O Nucleic Acids Res %V 45 %N W1 %& W509 %P W509 - W513 %I Oxford University Press %C Oxford %@ false
104. Müller F: Analyzing DNA Methylation Signatures of Cell Identity. Universität des Saarlandes; 2017.
Abstract
Although virtually all cells in an organism share the same genome, regulatory mechanisms give rise to hundreds of different, highly specialized cell types. Understanding these mechanisms has been in the limelight of epigenomic research. It is now evident that cellular identity is inscribed in the epigenome of each individual cell. Nonetheless, the precise mechanisms by which different epigenomic marks are involved in regulating gene expression are just beginning to be unraveled. Furthermore, epigenomic patterns are highly dynamic and subject to environmental influences. Any given cell type is defined by cell populations exhibiting epigenetic heterogeneity at different levels. Characterizing this heterogeneity is paramount in understanding the regulatory role of the epigenome. Different epigenomic marks can be profiled using high-throughput sequencing, and global initiatives have started to provide a comprehensive picture of the human epigenome by assaying a multitude of marks across a broad panel of cell types and conditions. In particular, DNA methylation has been extensively studied for its gene-regulatory role in health and disease. This thesis describes computational methods and pipelines for the analysis of DNA methylation data. It provides concepts for addressing bioinformatic challenges such as the processing of large, epigenome-wide datasets and integrating multiple levels of information in an interpretable manner. We developed RnBeads, an R package that facilitates comprehensive, interpretable analysis of large-scale DNA methylation datasets at the level of single CpGs or genomic regions of interest. With the epiRepeatR pipeline, we introduced additional tools for studying global patterns of epigenomic marks in transposons and other repetitive regions of the genome. Blood-cell differentiation represents a useful model for studying trajectories of cellular differentiation. We developed and applied bioinformatic methods to dissect the DNA methylation landscape of the hematopoietic system. Here, we provide a broad outline of cell-type-specific DNA methylation signatures and phenotypic diversity reflected in the epigenomes of human mature blood cells. We also describe the DNA methylation dynamics in the process of immune memory formation in T helper cells. Moreover, we portrayed epigenetic fingerprints of defined progenitor cell types and derived computational models that were capable of accurately inferring cell identity. We used these models in order to characterize heterogeneity in progenitor cell populations, to identify DNA methylation signatures of hematopoietic differentiation and to infer the epigenomic similarities of blood cell types. Finally, by interpreting DNA methylation patterns in leukemia and derived pluripotent cells, we started to discern how epigenomic patterns are altered in disease and explored how reprogramming of these patterns could potentially be used to restore a non-malignant state. In summary, this work showcases novel methods and computational tools for the identification and interpretation of epigenetic signatures of cell identity. It provides a detailed view on the epigenomic landscape spanned by DNA methylation patterns in hematopoietic cells that enhances our understanding of epigenetic regulation in cell differentiation and disease.
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@phdthesis{muellerphd17, TITLE = {Analyzing {DNA} Methylation Signatures of Cell Identity}, AUTHOR = {M{\"u}ller, Fabian}, LANGUAGE = {eng}, URL = {urn:nbn:de:bsz:291-scidok-69432}, DOI = {10.17617/2.2474737}, SCHOOL = {Universit{\"a}t des Saarlandes}, ADDRESS = {Saarbr{\"u}cken}, YEAR = {2017}, MARGINALMARK = {$\bullet$}, DATE = {2017}, ABSTRACT = {Although virtually all cells in an organism share the same genome, regulatory mechanisms give rise to hundreds of different, highly specialized cell types. Understanding these mechanisms has been in the limelight of epigenomic research. It is now evident that cellular identity is inscribed in the epigenome of each individual cell. Nonetheless, the precise mechanisms by which different epigenomic marks are involved in regulating gene expression are just beginning to be unraveled. Furthermore, epigenomic patterns are highly dynamic and subject to environmental influences. Any given cell type is defined by cell populations exhibiting epigenetic heterogeneity at different levels. Characterizing this heterogeneity is paramount in understanding the regulatory role of the epigenome. Different epigenomic marks can be profiled using high-throughput sequencing, and global initiatives have started to provide a comprehensive picture of the human epigenome by assaying a multitude of marks across a broad panel of cell types and conditions. In particular, DNA methylation has been extensively studied for its gene-regulatory role in health and disease. This thesis describes computational methods and pipelines for the analysis of DNA methylation data. It provides concepts for addressing bioinformatic challenges such as the processing of large, epigenome-wide datasets and integrating multiple levels of information in an interpretable manner. We developed RnBeads, an R package that facilitates comprehensive, interpretable analysis of large-scale DNA methylation datasets at the level of single CpGs or genomic regions of interest. With the epiRepeatR pipeline, we introduced additional tools for studying global patterns of epigenomic marks in transposons and other repetitive regions of the genome. Blood-cell differentiation represents a useful model for studying trajectories of cellular differentiation. We developed and applied bioinformatic methods to dissect the DNA methylation landscape of the hematopoietic system. Here, we provide a broad outline of cell-type-specific DNA methylation signatures and phenotypic diversity reflected in the epigenomes of human mature blood cells. We also describe the DNA methylation dynamics in the process of immune memory formation in T helper cells. Moreover, we portrayed epigenetic fingerprints of defined progenitor cell types and derived computational models that were capable of accurately inferring cell identity. We used these models in order to characterize heterogeneity in progenitor cell populations, to identify DNA methylation signatures of hematopoietic differentiation and to infer the epigenomic similarities of blood cell types. Finally, by interpreting DNA methylation patterns in leukemia and derived pluripotent cells, we started to discern how epigenomic patterns are altered in disease and explored how reprogramming of these patterns could potentially be used to restore a non-malignant state. In summary, this work showcases novel methods and computational tools for the identification and interpretation of epigenetic signatures of cell identity. It provides a detailed view on the epigenomic landscape spanned by DNA methylation patterns in hematopoietic cells that enhances our understanding of epigenetic regulation in cell differentiation and disease.}, }
Endnote
%0 Thesis %A Müller, Fabian %Y Lengauer, Thomas %A referee: Bock, Christoph %A referee: Brors, Benedikt %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society International Max Planck Research School, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations %T Analyzing DNA Methylation Signatures of Cell Identity : %G eng %U http://hdl.handle.net/11858/00-001M-0000-002D-D9AA-6 %U urn:nbn:de:bsz:291-scidok-69432 %R 10.17617/2.2474737 %I Universität des Saarlandes %C Saarbrücken %D 2017 %P 177 p. %V phd %9 phd %X Although virtually all cells in an organism share the same genome, regulatory mechanisms give rise to hundreds of different, highly specialized cell types. Understanding these mechanisms has been in the limelight of epigenomic research. It is now evident that cellular identity is inscribed in the epigenome of each individual cell. Nonetheless, the precise mechanisms by which different epigenomic marks are involved in regulating gene expression are just beginning to be unraveled. Furthermore, epigenomic patterns are highly dynamic and subject to environmental influences. Any given cell type is defined by cell populations exhibiting epigenetic heterogeneity at different levels. Characterizing this heterogeneity is paramount in understanding the regulatory role of the epigenome. Different epigenomic marks can be profiled using high-throughput sequencing, and global initiatives have started to provide a comprehensive picture of the human epigenome by assaying a multitude of marks across a broad panel of cell types and conditions. In particular, DNA methylation has been extensively studied for its gene-regulatory role in health and disease. This thesis describes computational methods and pipelines for the analysis of DNA methylation data. It provides concepts for addressing bioinformatic challenges such as the processing of large, epigenome-wide datasets and integrating multiple levels of information in an interpretable manner. We developed RnBeads, an R package that facilitates comprehensive, interpretable analysis of large-scale DNA methylation datasets at the level of single CpGs or genomic regions of interest. With the epiRepeatR pipeline, we introduced additional tools for studying global patterns of epigenomic marks in transposons and other repetitive regions of the genome. Blood-cell differentiation represents a useful model for studying trajectories of cellular differentiation. We developed and applied bioinformatic methods to dissect the DNA methylation landscape of the hematopoietic system. Here, we provide a broad outline of cell-type-specific DNA methylation signatures and phenotypic diversity reflected in the epigenomes of human mature blood cells. We also describe the DNA methylation dynamics in the process of immune memory formation in T helper cells. Moreover, we portrayed epigenetic fingerprints of defined progenitor cell types and derived computational models that were capable of accurately inferring cell identity. We used these models in order to characterize heterogeneity in progenitor cell populations, to identify DNA methylation signatures of hematopoietic differentiation and to infer the epigenomic similarities of blood cell types. Finally, by interpreting DNA methylation patterns in leukemia and derived pluripotent cells, we started to discern how epigenomic patterns are altered in disease and explored how reprogramming of these patterns could potentially be used to restore a non-malignant state. In summary, this work showcases novel methods and computational tools for the identification and interpretation of epigenetic signatures of cell identity. It provides a detailed view on the epigenomic landscape spanned by DNA methylation patterns in hematopoietic cells that enhances our understanding of epigenetic regulation in cell differentiation and disease. %U http://scidok.sulb.uni-saarland.de/volltexte/2017/6943/http://scidok.sulb.uni-saarland.de/doku/lic_ohne_pod.php?la=de
105. Müller H, Jimenez-Heredia R, Krolo A, Hirschmugl T, Dmytrus J, Boztug K, Bock C: VCF.Filter: Interactive Prioritization of Disease-linked Genetic Variants from Sequencing Data. Nucleic Acids Research 2017, 45.
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@article{BockVCF2017, TITLE = {{VCF}.{Filter}: {I}nteractive Prioritization of Disease-linked Genetic Variants from Sequencing Data}, AUTHOR = {M{\"u}ller, Heiko and Jimenez-Heredia, Raul and Krolo, Ana and Hirschmugl, Tatjana and Dmytrus, Jasmin and Boztug, Kaan and Bock, Christoph}, LANGUAGE = {eng}, ISSN = {0305-1048}, DOI = {10.1093/nar/gkx425}, PUBLISHER = {Oxford University Press}, ADDRESS = {Oxford}, YEAR = {2017}, MARGINALMARK = {$\bullet$}, DATE = {2017}, JOURNAL = {Nucleic Acids Research}, VOLUME = {45}, NUMBER = {W1}, PAGES = {W567--W572}, }
Endnote
%0 Journal Article %A Müller, Heiko %A Jimenez-Heredia, Raul %A Krolo, Ana %A Hirschmugl, Tatjana %A Dmytrus, Jasmin %A Boztug, Kaan %A Bock, Christoph %+ External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T VCF.Filter: Interactive Prioritization of Disease-linked Genetic Variants from Sequencing Data : %G eng %U http://hdl.handle.net/11858/00-001M-0000-002D-C37D-1 %R 10.1093/nar/gkx425 %2 PMC5570181 %7 2017 %D 2017 %J Nucleic Acids Research %O Nucleic Acids Res %V 45 %N W1 %& W567 %P W567 - W572 %I Oxford University Press %C Oxford %@ false
106. Neogi U, Siddik AB, Kalaghatgi P, Gisslén M, Bratt G, Marrone G, Sönnerborg A: Recent Increased Identification and Transmission of HIV-1 unique Recombinant Forms in Sweden. Scientific Reports 2017, 7.
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@article{Neogi2017, TITLE = {Recent Increased Identification and Transmission of {HIV}-1 unique Recombinant Forms in {Sweden}}, AUTHOR = {Neogi, Ujjwal and Siddik, Abu Bakar and Kalaghatgi, Prabhav and Gissl{\'e}n, Magnus and Bratt, G{\"o}ran and Marrone, Gaetano and S{\"o}nnerborg, Anders}, LANGUAGE = {eng}, ISSN = {2045-2322}, DOI = {10.1038/s41598-017-06860-2}, PUBLISHER = {Nature Publishing Group}, ADDRESS = {London, UK}, YEAR = {2017}, MARGINALMARK = {$\bullet$}, JOURNAL = {Scientific Reports}, VOLUME = {7}, EID = {6371}, }
Endnote
%0 Journal Article %A Neogi, Ujjwal %A Siddik, Abu Bakar %A Kalaghatgi, Prabhav %A Gisslén, Magnus %A Bratt, Göran %A Marrone, Gaetano %A Sönnerborg, Anders %+ External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations External Organizations %T Recent Increased Identification and Transmission of HIV-1 unique Recombinant Forms in Sweden : %G eng %U http://hdl.handle.net/11858/00-001M-0000-002D-BC30-F %2 PMC5527090 %R 10.1038/s41598-017-06860-2 %7 2017 %D 2017 %J Scientific Reports %O Sci. Rep. %V 7 %Z sequence number: 6371 %I Nature Publishing Group %C London, UK %@ false
107. Nikumbh S, Ebert P, Pfeifer N: All Fingers Are Not the Same: Handling Variable-Length Sequences in a Discriminative Setting Using Conformal Multi-Instance Kernels. In 17th International Workshop on Algorithms in Bioinformatics (WABI 2017). Schloss Dagstuhl; 2017. [Leibniz International Proceedings in Informatics, vol. 88]
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@inproceedings{nikumbh_et_al:LIPIcs:2017:7645, TITLE = {All Fingers Are Not the Same: {H}andling Variable-Length Sequences in a Discriminative Setting Using Conformal Multi-Instance Kernels}, AUTHOR = {Nikumbh, Sarvesh and Ebert, Peter and Pfeifer, Nico}, LANGUAGE = {eng}, ISSN = {1868-8969}, ISBN = {978-3-95977-050-7}, DOI = {10.4230/LIPIcs.WABI.2017.16}, PUBLISHER = {Schloss Dagstuhl}, YEAR = {2017}, MARGINALMARK = {$\bullet$}, BOOKTITLE = {17th International Workshop on Algorithms in Bioinformatics (WABI 2017)}, EDITOR = {Schwartz, Russell and Reinert, Knut}, PAGES = {1--14}, EID = {16}, SERIES = {Leibniz International Proceedings in Informatics}, VOLUME = {88}, ADDRESS = {Boston, MA, USA}, }
Endnote
%0 Conference Proceedings %A Nikumbh, Sarvesh %A Ebert, Peter %A Pfeifer, Nico %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T All Fingers Are Not the Same: Handling Variable-Length Sequences in a Discriminative Setting Using Conformal Multi-Instance Kernels : %G eng %U http://hdl.handle.net/11858/00-001M-0000-002D-BC17-7 %R 10.4230/LIPIcs.WABI.2017.16 %D 2017 %B 17th International Workshop on Algorithms in Bioinformatics %Z date of event: 2017-08-21 - 2017-08-23 %C Boston, MA, USA %B 17th International Workshop on Algorithms in Bioinformatics %E Schwartz, Russell; Reinert, Knut %P 1 - 14 %Z sequence number: 16 %I Schloss Dagstuhl %@ 978-3-95977-050-7 %B Leibniz International Proceedings in Informatics %N 88 %@ false %U http://drops.dagstuhl.de/opus/volltexte/2017/7645/http://drops.dagstuhl.de/doku/urheberrecht1.html
108. Nikumbh S, Pfeifer N: Genetic Sequence-based Prediction of Long-range Chromatin Interactions Suggests a Potential Role of Short Tandem Repeat Sequences in Genome Organization. BMC Bioinformatics 2017, 18.
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@article{Nikumbh2017, TITLE = {Genetic Sequence-based Prediction of Long-range Chromatin Interactions Suggests a Potential Role of Short Tandem Repeat Sequences in Genome Organization}, AUTHOR = {Nikumbh, Sarvesh and Pfeifer, Nico}, LANGUAGE = {eng}, ISSN = {1471-2105}, DOI = {10.1186/s12859-017-1624-x}, PUBLISHER = {BioMed Central}, ADDRESS = {London}, YEAR = {2017}, MARGINALMARK = {$\bullet$}, JOURNAL = {BMC Bioinformatics}, VOLUME = {18}, PAGES = {1--16}, EID = {218}, }
Endnote
%0 Journal Article %A Nikumbh, Sarvesh %A Pfeifer, Nico %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T Genetic Sequence-based Prediction of Long-range Chromatin Interactions Suggests a Potential Role of Short Tandem Repeat Sequences in Genome Organization : %G eng %U http://hdl.handle.net/11858/00-001M-0000-002D-26AD-4 %R 10.1186/s12859-017-1624-x %7 2017-04-18 %D 2017 %8 18.04.2017 %J BMC Bioinformatics %V 18 %& 1 %P 1 - 16 %Z sequence number: 218 %I BioMed Central %C London %@ false
109. Pironti A, Walter H, Pfeifer N, Knops E, Lübke N, Büch J, Di Giambenedetto S, Kaiser R, Lengauer T: Determination of Phenotypic Resistance Cutoffs from Routine Clinical Data. Journal of Acquired Immune Deficiency Syndromes 2017, 74.
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@article{Pironti_Pfeifer_Lengauer2017, TITLE = {Determination of Phenotypic Resistance Cutoffs from Routine Clinical Data}, AUTHOR = {Pironti, Alejandro and Walter, Hauke and Pfeifer, Nico and Knops, Elena and L{\"u}bke, Nadine and B{\"u}ch, Joachim and Di Giambenedetto, Simona and Kaiser, Rolf and Lengauer, Thomas}, LANGUAGE = {eng}, DOI = {10.1097/QAI.0000000000001198}, PUBLISHER = {Lippincott Williams \& Wilkins}, ADDRESS = {Philadelphia, PA}, YEAR = {2017}, MARGINALMARK = {$\bullet$}, JOURNAL = {Journal of Acquired Immune Deficiency Syndromes}, VOLUME = {74}, NUMBER = {5}, PAGES = {e129--e137}, }
Endnote
%0 Journal Article %A Pironti, Alejandro %A Walter, Hauke %A Pfeifer, Nico %A Knops, Elena %A Lübke, Nadine %A Büch, Joachim %A Di Giambenedetto, Simona %A Kaiser, Rolf %A Lengauer, Thomas %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T Determination of Phenotypic Resistance Cutoffs from Routine Clinical Data : %G eng %U http://hdl.handle.net/11858/00-001M-0000-002C-3F1D-D %R 10.1097/QAI.0000000000001198 %7 2017 %D 2017 %J Journal of Acquired Immune Deficiency Syndromes %O JAIDS %V 74 %N 5 %& e129 %P e129 - e137 %I Lippincott Williams & Wilkins %C Philadelphia, PA
110. Pironti A, Pfeifer N, Walter H, Jensen B-EO, Zazzi M, Gomes P, Kaiser R, Lengauer T: Using Drug Exposure for Predicting Drug Resistance – A data-driven Genotypic Interpretation Tool. PLoS One 2017, 12.
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@article{Pironti_Pfeifer_Lengauer_2017, TITLE = {Using Drug Exposure for Predicting Drug Resistance -- A data-driven Genotypic Interpretation Tool}, AUTHOR = {Pironti, Alejandro and Pfeifer, Nico and Walter, Hauke and Jensen, Bj{\"o}rn-Erik O. and Zazzi, Maurizio and Gomes, Perp{\'e}tua and Kaiser, Rolf and Lengauer, Thomas}, LANGUAGE = {eng}, ISSN = {1932-6203}, DOI = {10.1371/journal.pone.0174992}, PUBLISHER = {Public Library of Science}, ADDRESS = {San Francisco, CA}, YEAR = {2017}, MARGINALMARK = {$\bullet$}, JOURNAL = {PLoS One}, VOLUME = {12}, NUMBER = {4}, EID = {e0174992}, }
Endnote
%0 Journal Article %A Pironti, Alejandro %A Pfeifer, Nico %A Walter, Hauke %A Jensen, Björn-Erik O. %A Zazzi, Maurizio %A Gomes, Perpétua %A Kaiser, Rolf %A Lengauer, Thomas %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T Using Drug Exposure for Predicting Drug Resistance – A data-driven Genotypic Interpretation Tool : %G eng %U http://hdl.handle.net/11858/00-001M-0000-002D-48E5-0 %R 10.1371/journal.pone.0174992 %2 PMC5386274 %7 2017-04-10 %D 2017 %8 10.04.2017 %J PLoS One %V 12 %N 4 %Z sequence number: e0174992 %I Public Library of Science %C San Francisco, CA %@ false
111. Porubsky D, Garg S, Sanders AD, Korbel JO, Guryev V, Lansdorp PM, Marschall T: Dense and Accurate Whole-chromosome Haplotyping of Individual Genomes. Nature Communications 2017, 8.
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@article{Porubsky2017, TITLE = {Dense and Accurate Whole-chromosome Haplotyping of Individual Genomes}, AUTHOR = {Porubsky, David and Garg, Shilpa and Sanders, Ashley D. and Korbel, Jan O. and Guryev, Victor and Lansdorp, Peter M. and Marschall, Tobias}, LANGUAGE = {eng}, ISSN = {2041-1723}, DOI = {10.1038/s41467-017-01389-4}, PUBLISHER = {Nature Publishing Group}, ADDRESS = {London}, YEAR = {2017}, MARGINALMARK = {$\bullet$}, JOURNAL = {Nature Communications}, VOLUME = {8}, EID = {1293}, }
Endnote
%0 Journal Article %A Porubsky, David %A Garg, Shilpa %A Sanders, Ashley D. %A Korbel, Jan O. %A Guryev, Victor %A Lansdorp, Peter M. %A Marschall, Tobias %+ External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T Dense and Accurate Whole-chromosome Haplotyping of Individual Genomes : %G eng %U http://hdl.handle.net/11858/00-001M-0000-002E-3109-E %R 10.1038/s41467-017-01389-4 %2 PMC5670131 %7 2017 %D 2017 %J Nature Communications %O Nat. Commun. %V 8 %Z sequence number: 1293 %I Nature Publishing Group %C London %@ false
112. Schmidt F, Gasparoni N, Gasparoni G, Gianmoena K, Cadenas C, Polansky JK, Ebert P, Nordström K, Barann M, Sinha A, Fröhler S, Xiong J, Dheghani Amirabad A, Behjati Ardakani F, Hutter B, Zipprich G, Felder B, Eils J, Brors B, Chen W, Hengstler JG, Hamann A, Lengauer T, Rosenstiel P, Walter J, Schulz MH: Combining Transcription Factor Binding Affinities with Open-Chromatin Data for Accurate Gene Expression Prediction. Nucleic Acids Research 2017, 45.
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@article{pmid27899623, TITLE = {Combining Transcription Factor Binding Affinities with Open-Chromatin Data for Accurate Gene Expression Prediction}, AUTHOR = {Schmidt, Florian and Gasparoni, Nina and Gasparoni, Gilles and Gianmoena, Kathrin and Cadenas, Cristina and Polansky, Julia K. and Ebert, Peter and Nordstr{\"o}m, Karl and Barann, Matthias and Sinha, Anupam and Fr{\"o}hler, Sebastian and Xiong, Jieyi and Dheghani Amirabad, Azim and Behjati Ardakani, Fatemeh and Hutter, Barbara and Zipprich, Gideon and Felder, B{\"a}rbel and Eils, J{\"u}rgen and Brors, Benedikt and Chen, Wei and Hengstler, Jan G. and Hamann, Alf and Lengauer, Thomas and Rosenstiel, Philip and Walter, J{\"o}rn and Schulz, Marcel H.}, LANGUAGE = {eng}, ISSN = {0305-1048}, DOI = {10.1093/nar/gkw1061}, PUBLISHER = {Oxford University Press}, ADDRESS = {Oxford}, YEAR = {2017}, MARGINALMARK = {$\bullet$}, DATE = {2017}, JOURNAL = {Nucleic Acids Research}, VOLUME = {45}, NUMBER = {1}, PAGES = {54--66}, }
Endnote
%0 Journal Article %A Schmidt, Florian %A Gasparoni, Nina %A Gasparoni, Gilles %A Gianmoena, Kathrin %A Cadenas, Cristina %A Polansky, Julia K. %A Ebert, Peter %A Nordström, Karl %A Barann, Matthias %A Sinha, Anupam %A Fröhler, Sebastian %A Xiong, Jieyi %A Dheghani Amirabad, Azim %A Behjati Ardakani, Fatemeh %A Hutter, Barbara %A Zipprich, Gideon %A Felder, Bärbel %A Eils, Jürgen %A Brors, Benedikt %A Chen, Wei %A Hengstler, Jan G. %A Hamann, Alf %A Lengauer, Thomas %A Rosenstiel, Philip %A Walter, Jörn %A Schulz, Marcel H. %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T Combining Transcription Factor Binding Affinities with Open-Chromatin Data for Accurate Gene Expression Prediction : %G eng %U http://hdl.handle.net/11858/00-001M-0000-002C-378F-F %R 10.1093/nar/gkw1061 %7 2016 %D 2017 %J Nucleic Acids Research %O Nucleic Acids Res %V 45 %N 1 %& 54 %P 54 - 66 %I Oxford University Press %C Oxford %@ false
113. Schultheiss CS, Laggai S, Czepukojc B, Hussein UK, List M, Barghash A, Tierling S, Hosseini K, Golob-Schwarzl N, Pokorny J, Hachenthal N, Schulz MH, Helms V, Walter J, Zimmer V, Lammert F, Bohle RM, Dandolo L, Haybaeck J, Kiemer AK, Kessler SM: The Long Non-coding RNA H19 Suppresses Carcinogenesis and Chemoresistance in Hepatocellular Carcinoma. Cell Stress 2017, 1.
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@article{Schultheiss2019, TITLE = {The long non-coding {RNA} {H19} suppresses carcinogenesis and chemoresistance in hepatocellular carcinoma}, AUTHOR = {Schultheiss, Christina S. and Laggai, Stephan and Czepukojc, Beate and Hussein, Usama K. and List, Markus and Barghash, Ahmad and Tierling, Sascha and Hosseini, Kevan and Golob-Schwarzl, Nicole and Pokorny, Juliane and Hachenthal, Nina and Schulz, Marcel Holger and Helms, Volkhard and Walter, J{\"o}rn and Zimmer, Vincent and Lammert, Frank and Bohle, Rainer M. and Dandolo, Luisa and Haybaeck, Johannes and Kiemer, Alexandra K. and Kessler, Sonja M.}, LANGUAGE = {eng}, ISSN = {2523-0204}, DOI = {10.15698/cst2017.10.105}, PUBLISHER = {Shared Science Publishers}, ADDRESS = {Graz}, YEAR = {2017}, MARGINALMARK = {$\bullet$}, JOURNAL = {Cell Stress}, VOLUME = {1}, NUMBER = {1}, PAGES = {37--54}, }
Endnote
%0 Journal Article %A Schultheiss, Christina S. %A Laggai, Stephan %A Czepukojc, Beate %A Hussein, Usama K. %A List, Markus %A Barghash, Ahmad %A Tierling, Sascha %A Hosseini, Kevan %A Golob-Schwarzl, Nicole %A Pokorny, Juliane %A Hachenthal, Nina %A Schulz, Marcel Holger %A Helms, Volkhard %A Walter, Jörn %A Zimmer, Vincent %A Lammert, Frank %A Bohle, Rainer M. %A Dandolo, Luisa %A Haybaeck, Johannes %A Kiemer, Alexandra K. %A Kessler, Sonja M. %+ External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations %T The Long Non-coding RNA H19 Suppresses Carcinogenesis and Chemoresistance in Hepatocellular Carcinoma : %G eng %U http://hdl.handle.net/21.11116/0000-0003-EBF6-F %R 10.15698/cst2017.10.105 %2 PMC6551655 %7 2017 %D 2017 %J Cell Stress %V 1 %N 1 %& 37 %P 37 - 54 %I Shared Science Publishers %C Graz %@ false
114. Sheffield NC, Pierron G, Klughammer J, Datlinger P, Schönegger A, Schuster M, Hadler J, Surdez D, Guillemot D, Lapouble E, Freneaux P, Champigneulle J, Bouvier R, Walder D, Ambros IM, Hutter C, Sorz E, Amaral AT, de Álava E, Schallmoser K, Strunk D, Rinner B, Liegl-Atzwanger B, Huppertz B, Leithner A, de Pinieux G, Terrier P, Laurence V, Michon J, Ladenstein R, et al.: DNA Methylation Heterogeneity Defines a Disease Spectrum in Ewing Sarcoma. Nature Medicine 2017, 23.
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@article{Sheffield2017, TITLE = {{DNA} methylation heterogeneity defines a disease spectrum in {Ewing} sarcoma}, AUTHOR = {Sheffield, Nathan C. and Pierron, Gaelle and Klughammer, Johanna and Datlinger, Paul and Sch{\"o}negger, Andreas and Schuster, Michael and Hadler, Johanna and Surdez, Didier and Guillemot, Delphine and Lapouble, Eve and Freneaux, Paul and Champigneulle, Jacqueline and Bouvier, Raymonde and Walder, Diana and Ambros, Ingeborg M. and Hutter, Caroline and Sorz, Eva and Amaral, Ana T. and de {\'A}lava, Enrique and Schallmoser, Katharina and Strunk, Dirk and Rinner, Beate and Liegl-Atzwanger, Bernadette and Huppertz, Berthold and Leithner, Andreas and de Pinieux, Gonzague and Terrier, Philippe and Laurence, Val{\'e}rie and Michon, Jean and Ladenstein, Ruth and Holter, Wolfgang and Windhager, Reinhard and Dirksen, Uta and Ambros, Peter F. and Delattre, Olivier and Kovar, Heinrich and Bock, Christoph and Tomazou, Eleni M.}, LANGUAGE = {eng}, ISSN = {1078-8956}, DOI = {10.1038/nm.4273}, PUBLISHER = {Nature Publishing Group}, ADDRESS = {New York, NY}, YEAR = {2017}, MARGINALMARK = {$\bullet$}, DATE = {2017}, JOURNAL = {Nature Medicine}, VOLUME = {23}, NUMBER = {3}, PAGES = {386--395}, }
Endnote
%0 Journal Article %A Sheffield, Nathan C. %A Pierron, Gaelle %A Klughammer, Johanna %A Datlinger, Paul %A Schönegger, Andreas %A Schuster, Michael %A Hadler, Johanna %A Surdez, Didier %A Guillemot, Delphine %A Lapouble, Eve %A Freneaux, Paul %A Champigneulle, Jacqueline %A Bouvier, Raymonde %A Walder, Diana %A Ambros, Ingeborg M. %A Hutter, Caroline %A Sorz, Eva %A Amaral, Ana T. %A de Álava, Enrique %A Schallmoser, Katharina %A Strunk, Dirk %A Rinner, Beate %A Liegl-Atzwanger, Bernadette %A Huppertz, Berthold %A Leithner, Andreas %A de Pinieux, Gonzague %A Terrier, Philippe %A Laurence, Valérie %A Michon, Jean %A Ladenstein, Ruth %A Holter, Wolfgang %A Windhager, Reinhard %A Dirksen, Uta %A Ambros, Peter F. %A Delattre, Olivier %A Kovar, Heinrich %A Bock, Christoph %A Tomazou, Eleni M. %+ External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations %T DNA Methylation Heterogeneity Defines a Disease Spectrum in Ewing Sarcoma : %G eng %U http://hdl.handle.net/11858/00-001M-0000-002C-CBE6-E %R 10.1038/nm.4273 %7 2017-01-30 %D 2017 %J Nature Medicine %O Nat. Med. %V 23 %N 3 %& 386 %P 386 - 395 %I Nature Publishing Group %C New York, NY %@ false
115. Siu A: Knowledge-driven Entity Recognition and Disambiguation in Biomedical Text. Universität des Saarlandes; 2017.
Abstract
Entity recognition and disambiguation (ERD) for the biomedical domain are notoriously difficult problems due to the variety of entities and their often long names in many variations. Existing works focus heavily on the molecular level in two ways. First, they target scientific literature as the input text genre. Second, they target single, highly specialized entity types such as chemicals, genes, and proteins. However, a wealth of biomedical information is also buried in the vast universe of Web content. In order to fully utilize all the information available, there is a need to tap into Web content as an additional input. Moreover, there is a need to cater for other entity types such as symptoms and risk factors since Web content focuses on consumer health. The goal of this thesis is to investigate ERD methods that are applicable to all entity types in scientific literature as well as Web content. In addition, we focus on under-explored aspects of the biomedical ERD problems -- scalability, long noun phrases, and out-of-knowledge base (OOKB) entities. This thesis makes four main contributions, all of which leverage knowledge in UMLS (Unified Medical Language System), the largest and most authoritative knowledge base (KB) of the biomedical domain. The first contribution is a fast dictionary lookup method for entity recognition that maximizes throughput while balancing the loss of precision and recall. The second contribution is a semantic type classification method targeting common words in long noun phrases. We develop a custom set of semantic types to capture word usages; besides biomedical usage, these types also cope with non-biomedical usage and the case of generic, non-informative usage. The third contribution is a fast heuristics method for entity disambiguation in MEDLINE abstracts, again maximizing throughput but this time maintaining accuracy. The fourth contribution is a corpus-driven entity disambiguation method that addresses OOKB entities. The method first captures the entities expressed in a corpus as latent representations that comprise in-KB and OOKB entities alike before performing entity disambiguation.
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@phdthesis{siuphd17, TITLE = {Knowledge-driven Entity Recognition and Disambiguation in Biomedical Text}, AUTHOR = {Siu, Amy}, LANGUAGE = {eng}, DOI = {10.22028/D291-26790}, SCHOOL = {Universit{\"a}t des Saarlandes}, ADDRESS = {Saarbr{\"u}cken}, YEAR = {2017}, MARGINALMARK = {$\bullet$}, DATE = {2017}, ABSTRACT = {Entity recognition and disambiguation (ERD) for the biomedical domain are notoriously difficult problems due to the variety of entities and their often long names in many variations. Existing works focus heavily on the molecular level in two ways. First, they target scientific literature as the input text genre. Second, they target single, highly specialized entity types such as chemicals, genes, and proteins. However, a wealth of biomedical information is also buried in the vast universe of Web content. In order to fully utilize all the information available, there is a need to tap into Web content as an additional input. Moreover, there is a need to cater for other entity types such as symptoms and risk factors since Web content focuses on consumer health. The goal of this thesis is to investigate ERD methods that are applicable to all entity types in scientific literature as well as Web content. In addition, we focus on under-explored aspects of the biomedical ERD problems -- scalability, long noun phrases, and out-of-knowledge base (OOKB) entities. This thesis makes four main contributions, all of which leverage knowledge in UMLS (Unified Medical Language System), the largest and most authoritative knowledge base (KB) of the biomedical domain. The first contribution is a fast dictionary lookup method for entity recognition that maximizes throughput while balancing the loss of precision and recall. The second contribution is a semantic type classification method targeting common words in long noun phrases. We develop a custom set of semantic types to capture word usages; besides biomedical usage, these types also cope with non-biomedical usage and the case of generic, non-informative usage. The third contribution is a fast heuristics method for entity disambiguation in MEDLINE abstracts, again maximizing throughput but this time maintaining accuracy. The fourth contribution is a corpus-driven entity disambiguation method that addresses OOKB entities. The method first captures the entities expressed in a corpus as latent representations that comprise in-KB and OOKB entities alike before performing entity disambiguation.}, }
Endnote
%0 Thesis %A Siu, Amy %Y Weikum, Gerhard %A referee: Berberich, Klaus %A referee: Leser, Ulf %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society International Max Planck Research School, MPI for Informatics, Max Planck Society Databases and Information Systems, MPI for Informatics, Max Planck Society Databases and Information Systems, MPI for Informatics, Max Planck Society External Organizations %T Knowledge-driven Entity Recognition and Disambiguation in Biomedical Text : %G eng %U http://hdl.handle.net/11858/00-001M-0000-002D-DD18-E %R 10.22028/D291-26790 %I Universität des Saarlandes %C Saarbrücken %D 2017 %P 169 p. %V phd %9 phd %X Entity recognition and disambiguation (ERD) for the biomedical domain are notoriously difficult problems due to the variety of entities and their often long names in many variations. Existing works focus heavily on the molecular level in two ways. First, they target scientific literature as the input text genre. Second, they target single, highly specialized entity types such as chemicals, genes, and proteins. However, a wealth of biomedical information is also buried in the vast universe of Web content. In order to fully utilize all the information available, there is a need to tap into Web content as an additional input. Moreover, there is a need to cater for other entity types such as symptoms and risk factors since Web content focuses on consumer health. The goal of this thesis is to investigate ERD methods that are applicable to all entity types in scientific literature as well as Web content. In addition, we focus on under-explored aspects of the biomedical ERD problems -- scalability, long noun phrases, and out-of-knowledge base (OOKB) entities. This thesis makes four main contributions, all of which leverage knowledge in UMLS (Unified Medical Language System), the largest and most authoritative knowledge base (KB) of the biomedical domain. The first contribution is a fast dictionary lookup method for entity recognition that maximizes throughput while balancing the loss of precision and recall. The second contribution is a semantic type classification method targeting common words in long noun phrases. We develop a custom set of semantic types to capture word usages; besides biomedical usage, these types also cope with non-biomedical usage and the case of generic, non-informative usage. The third contribution is a fast heuristics method for entity disambiguation in MEDLINE abstracts, again maximizing throughput but this time maintaining accuracy. The fourth contribution is a corpus-driven entity disambiguation method that addresses OOKB entities. The method first captures the entities expressed in a corpus as latent representations that comprise in-KB and OOKB entities alike before performing entity disambiguation. %U https://publikationen.sulb.uni-saarland.de/handle/20.500.11880/26803
116. Towards Multiple Kernel Principal Component Analysis for Integrative Analysis of Tumor Samples [http://arxiv.org/abs/1701.00422]
(arXiv: 1701.00422)
Abstract
Personalized treatment of patients based on tissue-specific cancer subtypes has strongly increased the efficacy of the chosen therapies. Even though the amount of data measured for cancer patients has increased over the last years, most cancer subtypes are still diagnosed based on individual data sources (e.g. gene expression data). We propose an unsupervised data integration method based on kernel principal component analysis. Principal component analysis is one of the most widely used techniques in data analysis. Unfortunately, the straight-forward multiple-kernel extension of this method leads to the use of only one of the input matrices, which does not fit the goal of gaining information from all data sources. Therefore, we present a scoring function to determine the impact of each input matrix. The approach enables visualizing the integrated data and subsequent clustering for cancer subtype identification. Due to the nature of the method, no free parameters have to be set. We apply the methodology to five different cancer data sets and demonstrate its advantages in terms of results and usability.
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@online{SpeicherarXiv2017, TITLE = {Towards Multiple Kernel Principal Component Analysis for Integrative Analysis of Tumor Samples}, AUTHOR = {Speicher, Nora K. and Pfeifer, Nico}, LANGUAGE = {eng}, URL = {http://arxiv.org/abs/1701.00422}, EPRINT = {1701.00422}, EPRINTTYPE = {arXiv}, YEAR = {2017}, MARGINALMARK = {$\bullet$}, ABSTRACT = {Personalized treatment of patients based on tissue-specific cancer subtypes has strongly increased the efficacy of the chosen therapies. Even though the amount of data measured for cancer patients has increased over the last years, most cancer subtypes are still diagnosed based on individual data sources (e.g. gene expression data). We propose an unsupervised data integration method based on kernel principal component analysis. Principal component analysis is one of the most widely used techniques in data analysis. Unfortunately, the straight-forward multiple-kernel extension of this method leads to the use of only one of the input matrices, which does not fit the goal of gaining information from all data sources. Therefore, we present a scoring function to determine the impact of each input matrix. The approach enables visualizing the integrated data and subsequent clustering for cancer subtype identification. Due to the nature of the method, no free parameters have to be set. We apply the methodology to five different cancer data sets and demonstrate its advantages in terms of results and usability.}, }
Endnote
%0 Report %A Speicher, Nora K. %A Pfeifer, Nico %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T Towards Multiple Kernel Principal Component Analysis for Integrative Analysis of Tumor Samples : %G eng %U http://hdl.handle.net/11858/00-001M-0000-002C-4D68-3 %U http://arxiv.org/abs/1701.00422 %D 2017 %X Personalized treatment of patients based on tissue-specific cancer subtypes has strongly increased the efficacy of the chosen therapies. Even though the amount of data measured for cancer patients has increased over the last years, most cancer subtypes are still diagnosed based on individual data sources (e.g. gene expression data). We propose an unsupervised data integration method based on kernel principal component analysis. Principal component analysis is one of the most widely used techniques in data analysis. Unfortunately, the straight-forward multiple-kernel extension of this method leads to the use of only one of the input matrices, which does not fit the goal of gaining information from all data sources. Therefore, we present a scoring function to determine the impact of each input matrix. The approach enables visualizing the integrated data and subsequent clustering for cancer subtype identification. Due to the nature of the method, no free parameters have to be set. We apply the methodology to five different cancer data sets and demonstrate its advantages in terms of results and usability. %K Statistics, Machine Learning, stat.ML
117. Speicher NK, Pfeifer N: Towards Multiple Kernel Principal Component Analysis for Integrative Analysis of Tumor Samples. Journal of Integrative Bioinformatics 2017, 14.
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@article{Speicher2017, TITLE = {Towards Multiple Kernel Principal Component Analysis for Integrative Analysis of Tumor Samples}, AUTHOR = {Speicher, Nora K. and Pfeifer, Nico}, LANGUAGE = {eng}, ISSN = {1613-4516}, DOI = {10.1515/jib-2017-0019}, PUBLISHER = {Walter de Gruyter GmbH}, ADDRESS = {Berlin}, YEAR = {2017}, MARGINALMARK = {$\bullet$}, JOURNAL = {Journal of Integrative Bioinformatics}, VOLUME = {14}, NUMBER = {2}, EID = {20170019}, }
Endnote
%0 Journal Article %A Speicher, Nora K. %A Pfeifer, Nico %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T Towards Multiple Kernel Principal Component Analysis for Integrative Analysis of Tumor Samples : %G eng %U http://hdl.handle.net/21.11116/0000-0002-F720-3 %R 10.1515/jib-2017-0019 %2 PMC6042822 %7 2017 %D 2017 %J Journal of Integrative Bioinformatics %V 14 %N 2 %Z sequence number: 20170019 %I Walter de Gruyter GmbH %C Berlin %@ false
118. Stancu MC, van Roosmalen MJ, Renkens I, Nieboer MM, Middelkamp S, de Ligt J, Pregno G, Giachino D, Mandrile G, Valle-Inclan JE, Korzelius J, de Bruijn E, Cuppen E, Talkowski ME, Marschall T, de Ridder J, Kloosterman WP: Mapping and Phasing of Structural Variation in Patient Genomes Using Nanopore Sequencing. Nature Communications 2017, 8.
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@article{Stancu2017, TITLE = {Mapping and Phasing of Structural Variation in Patient Genomes Using Nanopore Sequencing}, AUTHOR = {Stancu, Mircea Cretu and van Roosmalen, Markus J. and Renkens, Ivo and Nieboer, Marleen M. and Middelkamp, Sjors and de Ligt, Joep and Pregno, Giulia and Giachino, Daniela and Mandrile, Giorgia and Valle-Inclan, Jose Espejo and Korzelius, Jerome and de Bruijn, Ewart and Cuppen, Edwin and Talkowski, Michael E. and Marschall, Tobias and de Ridder, Jeroen and Kloosterman, Wigard P.}, LANGUAGE = {eng}, ISSN = {2041-1723}, DOI = {10.1038/s41467-017-01343-4}, PUBLISHER = {Nature Publishing Group}, ADDRESS = {London}, YEAR = {2017}, MARGINALMARK = {$\bullet$}, JOURNAL = {Nature Communications}, VOLUME = {8}, EID = {1326}, }
Endnote
%0 Journal Article %A Stancu, Mircea Cretu %A van Roosmalen, Markus J. %A Renkens, Ivo %A Nieboer, Marleen M. %A Middelkamp, Sjors %A de Ligt, Joep %A Pregno, Giulia %A Giachino, Daniela %A Mandrile, Giorgia %A Valle-Inclan, Jose Espejo %A Korzelius, Jerome %A de Bruijn, Ewart %A Cuppen, Edwin %A Talkowski, Michael E. %A Marschall, Tobias %A de Ridder, Jeroen %A Kloosterman, Wigard P. %+ External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations %T Mapping and Phasing of Structural Variation in Patient Genomes Using Nanopore Sequencing : %G eng %U http://hdl.handle.net/11858/00-001M-0000-002E-55B2-A %R 10.1038/s41467-017-01343-4 %7 2017 %D 2017 %J Nature Communications %O Nat. Commun. %V 8 %Z sequence number: 1326 %I Nature Publishing Group %C London %@ false
119. Sun P: Bi-(N-) cluster editing and its biomedical applications. Universität des Saarlandes; 2017.
Abstract
he extremely fast advances in wet-lab techniques lead to an exponential growth of heterogeneous and unstructured biological data, posing a great challenge to data integration in nowadays system biology. The traditional clustering approach, although widely used to divide the data into groups sharing common features, is less powerful in the analysis of heterogeneous data from n different sources (n _ 2). The co-clustering approach has been widely used for combined analyses of multiple networks to address the challenge of heterogeneity. In this thesis, novel methods for the co-clustering of large scale heterogeneous data sets are presented in the software package n-CluE: one exact algorithm and two heuristic algorithms based on the model of bi-/n-cluster editing by modeling the input as n-partite graphs and solving the clustering problem with various strategies. In the first part of the thesis, the complexity and the fixed-parameter tractability of the extended bicluster editing model with relaxed constraints are investigated, namely the ?-bicluster editing model and its NP-hardness is proven. Based on the results of this analysis, three strategies within the n-CluE software package are then established and discussed, together with the evaluations on performances and the systematic comparisons against other algorithms of the same type in solving bi-/n-cluster editing problem. To demonstrate the practical impact, three real-world analyses using n-CluE are performed, including (a) prediction of novel genotype-phenotype associations by clustering the data from Genome-Wide Association Studies; (b) comparison between n-CluE and eight other biclustering tools on GEO Omnibus microarray data sets; (c) drug repositioning predictions by co-clustering on drug, gene and disease networks. The outstanding performance of n-CluE in the real-world applications shows its strength and flexibility in integrating heterogeneous data and extracting biological relevant information in bioinformatic analyses.
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@phdthesis{Sunphd17, TITLE = {Bi-(N-) cluster editing and its biomedical applications}, AUTHOR = {Sun, Peng}, LANGUAGE = {eng}, URL = {urn:nbn:de:bsz:291-scidok-69309}, SCHOOL = {Universit{\"a}t des Saarlandes}, ADDRESS = {Saarbr{\"u}cken}, YEAR = {2017}, MARGINALMARK = {$\bullet$}, DATE = {2017}, ABSTRACT = {he extremely fast advances in wet-lab techniques lead to an exponential growth of heterogeneous and unstructured biological data, posing a great challenge to data integration in nowadays system biology. The traditional clustering approach, although widely used to divide the data into groups sharing common features, is less powerful in the analysis of heterogeneous data from n different sources (n _ 2). The co-clustering approach has been widely used for combined analyses of multiple networks to address the challenge of heterogeneity. In this thesis, novel methods for the co-clustering of large scale heterogeneous data sets are presented in the software package n-CluE: one exact algorithm and two heuristic algorithms based on the model of bi-/n-cluster editing by modeling the input as n-partite graphs and solving the clustering problem with various strategies. In the first part of the thesis, the complexity and the fixed-parameter tractability of the extended bicluster editing model with relaxed constraints are investigated, namely the ?-bicluster editing model and its NP-hardness is proven. Based on the results of this analysis, three strategies within the n-CluE software package are then established and discussed, together with the evaluations on performances and the systematic comparisons against other algorithms of the same type in solving bi-/n-cluster editing problem. To demonstrate the practical impact, three real-world analyses using n-CluE are performed, including (a) prediction of novel genotype-phenotype associations by clustering the data from Genome-Wide Association Studies; (b) comparison between n-CluE and eight other biclustering tools on GEO Omnibus microarray data sets; (c) drug repositioning predictions by co-clustering on drug, gene and disease networks. The outstanding performance of n-CluE in the real-world applications shows its strength and flexibility in integrating heterogeneous data and extracting biological relevant information in bioinformatic analyses.}, }
Endnote
%0 Thesis %A Sun, Peng %Y Baumbach, Jan %A referee: Guo, Jiong %A referee: Lengauer, Thomas %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society International Max Planck Research School, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T Bi-(N-) cluster editing and its biomedical applications : %G eng %U http://hdl.handle.net/11858/00-001M-0000-002D-A65E-F %U urn:nbn:de:bsz:291-scidok-69309 %I Universität des Saarlandes %C Saarbrücken %D 2017 %P 192 p. %V phd %9 phd %X he extremely fast advances in wet-lab techniques lead to an exponential growth of heterogeneous and unstructured biological data, posing a great challenge to data integration in nowadays system biology. The traditional clustering approach, although widely used to divide the data into groups sharing common features, is less powerful in the analysis of heterogeneous data from n different sources (n _ 2). The co-clustering approach has been widely used for combined analyses of multiple networks to address the challenge of heterogeneity. In this thesis, novel methods for the co-clustering of large scale heterogeneous data sets are presented in the software package n-CluE: one exact algorithm and two heuristic algorithms based on the model of bi-/n-cluster editing by modeling the input as n-partite graphs and solving the clustering problem with various strategies. In the first part of the thesis, the complexity and the fixed-parameter tractability of the extended bicluster editing model with relaxed constraints are investigated, namely the ?-bicluster editing model and its NP-hardness is proven. Based on the results of this analysis, three strategies within the n-CluE software package are then established and discussed, together with the evaluations on performances and the systematic comparisons against other algorithms of the same type in solving bi-/n-cluster editing problem. To demonstrate the practical impact, three real-world analyses using n-CluE are performed, including (a) prediction of novel genotype-phenotype associations by clustering the data from Genome-Wide Association Studies; (b) comparison between n-CluE and eight other biclustering tools on GEO Omnibus microarray data sets; (c) drug repositioning predictions by co-clustering on drug, gene and disease networks. The outstanding performance of n-CluE in the real-world applications shows its strength and flexibility in integrating heterogeneous data and extracting biological relevant information in bioinformatic analyses. %U http://scidok.sulb.uni-saarland.de/volltexte/2017/6930/http://scidok.sulb.uni-saarland.de/doku/lic_ohne_pod.php?la=de
120. Sun P, Guo J, Winnenburg R, Baumbach J: Drug Repurposing by Integrated Literature Mining and Drug–Gene–Disease Triangulation. Drug Discovery Today 2017, 22.
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@article{Sun_Baumbach2017, TITLE = {Drug Repurposing by Integrated Literature Mining and Drug--Gene--Disease Triangulation}, AUTHOR = {Sun, Peng and Guo, Jiong and Winnenburg, Rainer and Baumbach, Jan}, LANGUAGE = {eng}, ISSN = {1359-6446}, DOI = {10.1016/j.drudis.2016.10.008}, PUBLISHER = {Elsevier}, ADDRESS = {Amsterdam}, YEAR = {2017}, MARGINALMARK = {$\bullet$}, DATE = {2017}, JOURNAL = {Drug Discovery Today}, VOLUME = {22}, NUMBER = {4}, PAGES = {615--619}, }
Endnote
%0 Journal Article %A Sun, Peng %A Guo, Jiong %A Winnenburg, Rainer %A Baumbach, Jan %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T Drug Repurposing by Integrated Literature Mining and Drug–Gene–Disease Triangulation : %G eng %U http://hdl.handle.net/11858/00-001M-0000-002D-6E09-3 %R 10.1016/j.drudis.2016.10.008 %7 2016-10-22 %D 2017 %J Drug Discovery Today %V 22 %N 4 %& 615 %P 615 - 619 %I Elsevier %C Amsterdam %@ false
2016
121. Ahmad M, Helms V, Kalinina OV, Lengauer T: The Role of Conformational Changes in Molecular Recognition. The Journal of Physical Chemistry B 2016, 120.
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@article{AhmadJPhysChem2016, TITLE = {The Role of Conformational Changes in Molecular Recognition}, AUTHOR = {Ahmad, Mazen and Helms, Volkhard and Kalinina, Olga V. and Lengauer, Thomas}, LANGUAGE = {eng}, ISSN = {1520-6106}, DOI = {10.1021/acs.jpcb.5b11593}, PUBLISHER = {American Chemical Society}, ADDRESS = {Washington, D.C.}, YEAR = {2016}, DATE = {2016}, JOURNAL = {The Journal of Physical Chemistry B}, VOLUME = {120}, NUMBER = {9}, PAGES = {2138--2144}, }
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%0 Journal Article %A Ahmad, Mazen %A Helms, Volkhard %A Kalinina, Olga V. %A Lengauer, Thomas %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T The Role of Conformational Changes in Molecular Recognition : %G eng %U http://hdl.handle.net/11858/00-001M-0000-002A-2962-8 %R 10.1021/acs.jpcb.5b11593 %7 2016 %D 2016 %J The Journal of Physical Chemistry B %O J. Phys. Chem. B %V 120 %N 9 %& 2138 %P 2138 - 2144 %I American Chemical Society %C Washington, D.C. %@ false
122. Albrecht F, List M, Bock C, Lengauer T: DeepBlue Epigenomic Data Server: Programmatic Data Retrieval and Analysis of Epigenome Region Sets. Nucleic Acids Research 2016, 44(W1/Web Server issue).
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@article{Albrecht:List:Bock:Lengauer2016, TITLE = {{DeepBlue} Epigenomic Data Server: {P}rogrammatic Data Retrieval and Analysis of Epigenome Region Sets}, AUTHOR = {Albrecht, Felipe and List, Markus and Bock, Christoph and Lengauer, Thomas}, LANGUAGE = {eng}, DOI = {10.1093/nar/gkw211}, PUBLISHER = {Oxford University Press}, ADDRESS = {Oxford, UK}, YEAR = {2016}, DATE = {2016}, JOURNAL = {Nucleic Acids Research}, VOLUME = {44}, NUMBER = {W1/Web Server issue}, PAGES = {W581--W586}, }
Endnote
%0 Journal Article %A Albrecht, Felipe %A List, Markus %A Bock, Christoph %A Lengauer, Thomas %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T DeepBlue Epigenomic Data Server: Programmatic Data Retrieval and Analysis of Epigenome Region Sets : %G eng %U http://hdl.handle.net/11858/00-001M-0000-002B-42AD-0 %R 10.1093/nar/gkw211 %2 PMC4987868 %7 2016 %D 2016 %* Review method: peer-reviewed %J Nucleic Acids Research %V 44 %N W1/Web Server issue %& W581 %P W581 - W586 %I Oxford University Press %C Oxford, UK
123. Alcaraz N, List M, Dissing-Hansen M, Rehmsmeier M, Tan Q, Mollenhauer J, Ditzel HJ, Baumbach J: Robust de novo pathway enrichment with KeyPathwayMiner 5. Faculty of 1000 Research 2016, 5.
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@article{ListF1000Research2016, TITLE = {Robust de novo pathway enrichment with {KeyPathwayMiner} 5}, AUTHOR = {Alcaraz, Nicolas and List, Markus and Dissing-Hansen, Martin and Rehmsmeier, Marc and Tan, Qihua and Mollenhauer, Jan and Ditzel, Henrik J. and Baumbach, Jan}, LANGUAGE = {eng}, DOI = {10.12688/f1000research.9054.1}, PUBLISHER = {BioMed Central}, ADDRESS = {London}, YEAR = {2016}, JOURNAL = {Faculty of 1000 Research}, VOLUME = {5}, EID = {1531}, }
Endnote
%0 Journal Article %A Alcaraz, Nicolas %A List, Markus %A Dissing-Hansen, Martin %A Rehmsmeier, Marc %A Tan, Qihua %A Mollenhauer, Jan %A Ditzel, Henrik J. %A Baumbach, Jan %+ External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T Robust de novo pathway enrichment with KeyPathwayMiner 5 : %G eng %U http://hdl.handle.net/11858/00-001M-0000-002B-4656-5 %R 10.12688/f1000research.9054.1 %2 PMC4965696 %7 2016 %D 2016 %J Faculty of 1000 Research %O F1000Research %V 5 %Z sequence number: 1531 %I BioMed Central %C London %U http://f1000research.com/articles/5-1531/
124. Auffray C, Balling R, Barroso I, Bencze L, Blomberg N, Bock C, Conesa A, Del Signore S, Delogne C, Deyilee P, Di Meglio A, Eijkemans M, Flicek P, Graf N, Grimm V, Guchelaar H-J, Guo Y-K, Gut IG, Hanbury A, Hanif S, Hilgers R-D, Honrado Á, Hose DR, Houwing-Duistermaat J, Hubbard T, Janacek SH, Karanikas H, Kievits T, Kohler M, Kremer A, et al.: Erratum to: Making Sense of Big Data in Health Research: Towards an EU Action Plan. Genome Medicine 2016, 8.
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@article{Auffray2016Erratum, TITLE = {Erratum to: Making sense of big data in health research: {T}owards an {EU} action plan}, AUTHOR = {Auffray, Charles and Balling, Rudi and Barroso, In{\^e}s and Bencze, L{\'a}szl{\'o} and Blomberg, Niklas and Bock, Christoph and Conesa, Anna and Del Signore, Susanna and Delogne, Christophe and Deyilee, Peter and Di Meglio, Alberto and Eijkemans, Marinus and Flicek, Paul and Graf, Norbert and Grimm, Vera and Guchelaar, Henk-Jan and Guo, Yi-Ke and Gut, Ivo Glynne and Hanbury, Allan and Hanif, Shahid and Hilgers, Ralf-Dieter and Honrado, {\'A}ngel and Hose, D. Rod and Houwing-Duistermaat, Jeanine and Hubbard, Tim and Janacek, Sophie Helen and Karanikas, Haralampos and Kievits, Tim and Kohler, Manfred and Kremer, Andreas and Lanfear, Jerry and Lengauer, Thomas and Maes, Edith and Meert, Theo and M{\"u}ller, Werner and Nickel, D{\"o}rthe and Oledzki, Peter and Pedersen, Bertrand and Petkovic, Milan and Pliakos, Konstantinos and Rattray, Magnus and Red{\'o}n i M{\`a}s, Josep and Schneider, Reinhard and Sengstag, Thierry and Serra-Picamal, Xavier and Spek, Wouter and Vaas, Lea A. I. and van Batenburg, Okker and Vandelaer, Marc and Varnai, Peter and Villoslada, Pablo and Vizca{\'i}no, Juan Antonio and Wubbe, John Peter Mary and Zanetti, Gianluigi}, LANGUAGE = {eng}, DOI = {10.1186/s13073-016-0376-y}, PUBLISHER = {BioMedCentral}, ADDRESS = {London}, YEAR = {2016}, JOURNAL = {Genome Medicine}, VOLUME = {8}, EID = {118}, }
Endnote
%0 Journal Article %A Auffray, Charles %A Balling, Rudi %A Barroso, Inês %A Bencze, László %A Blomberg, Niklas %A Bock, Christoph %A Conesa, Anna %A Del Signore, Susanna %A Delogne, Christophe %A Deyilee, Peter %A Di Meglio, Alberto %A Eijkemans, Marinus %A Flicek, Paul %A Graf, Norbert %A Grimm, Vera %A Guchelaar, Henk-Jan %A Guo, Yi-Ke %A Gut, Ivo Glynne %A Hanbury, Allan %A Hanif, Shahid %A Hilgers, Ralf-Dieter %A Honrado, Ángel %A Hose, D. Rod %A Houwing-Duistermaat, Jeanine %A Hubbard, Tim %A Janacek, Sophie Helen %A Karanikas, Haralampos %A Kievits, Tim %A Kohler, Manfred %A Kremer, Andreas %A Lanfear, Jerry %A Lengauer, Thomas %A Maes, Edith %A Meert, Theo %A Müller, Werner %A Nickel, Dörthe %A Oledzki, Peter %A Pedersen, Bertrand %A Petkovic, Milan %A Pliakos, Konstantinos %A Rattray, Magnus %A Redón i Màs, Josep %A Schneider, Reinhard %A Sengstag, Thierry %A Serra-Picamal, Xavier %A Spek, Wouter %A Vaas, Lea A. I. %A van Batenburg, Okker %A Vandelaer, Marc %A Varnai, Peter %A Villoslada, Pablo %A Vizcaíno, Juan Antonio %A Wubbe, John Peter Mary %A Zanetti, Gianluigi %+ External Organizations External Organizations External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations %T Erratum to: Making Sense of Big Data in Health Research: Towards an EU Action Plan : %G eng %U http://hdl.handle.net/11858/00-001M-0000-002C-1D02-C %R 10.1186/s13073-016-0376-y %2 PMC5100330 %7 2016-11-07 %D 2016 %8 07.11.2016 %J Genome Medicine %V 8 %Z sequence number: 118 %I BioMedCentral %C London
125. Auffray C, Balling R, Barroso I, Bencze L, Blomberg N, Bock C, Conesa A, Del Signore S, Delogne C, Deyilee P, Di Meglio A, Eijkemans M, Flicek P, Graf N, Grimm V, Guchelaar H-J, Guo Y-K, Gut IG, Hanbury A, Hanif S, Hilgers R-D, Honrado Á, Hose DR, Houwing-Duistermaat J, Hubbard T, Janacek SH, Karanikas H, Kievits T, Kohler M, Kremer A, et al.: Making Sense of Big Data in Health Research: Towards an EU Action Plan. Genome Medicine 2016, 8.
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@article{Auffray2016, TITLE = {Making sense of big data in health research: {T}owards an {EU} action plan}, AUTHOR = {Auffray, Charles and Balling, Rudi and Barroso, In{\^e}s and Bencze, L{\'a}szl{\'o} and Blomberg, Niklas and Bock, Christoph and Conesa, Anna and Del Signore, Susanna and Delogne, Christophe and Deyilee, Peter and Di Meglio, Alberto and Eijkemans, Marinus and Flicek, Paul and Graf, Norbert and Grimm, Vera and Guchelaar, Henk-Jan and Guo, Yi-Ke and Gut, Ivo Glynne and Hanbury, Allan and Hanif, Shahid and Hilgers, Ralf-Dieter and Honrado, {\'A}ngel and Hose, D. Rod and Houwing-Duistermaat, Jeanine and Hubbard, Tim and Janacek, Sophie Helen and Karanikas, Haralampos and Kievits, Tim and Kohler, Manfred and Kremer, Andreas and Lanfear, Jerry and Lengauer, Thomas and Maes, Edith and Meert, Theo and M{\"u}ller, Werner and Nickel, D{\"o}rthe and Oledzki, Peter and Pedersen, Bertrand and Petkovic, Milan and Pliakos, Konstantinos and Rattray, Magnus and Red{\'o}n i M{\`a}s, Josep and Schneider, Reinhard and Sengstag, Thierry and Serra-Picamal, Xavier and Spek, Wouter and Vaas, Lea A. I. and van Batenburg, Okker and Vandelaer, Marc and Varnai, Peter and Villoslada, Pablo and Vizca{\'i}no, Juan Antonio and Wubbe, John Peter Mary and Zanetti, Gianluigi}, LANGUAGE = {eng}, DOI = {10.1186/s13073-016-0323-y}, PUBLISHER = {BioMedCentral}, ADDRESS = {London}, YEAR = {2016}, JOURNAL = {Genome Medicine}, VOLUME = {8}, EID = {71}, }
Endnote
%0 Journal Article %A Auffray, Charles %A Balling, Rudi %A Barroso, Inês %A Bencze, László %A Blomberg, Niklas %A Bock, Christoph %A Conesa, Anna %A Del Signore, Susanna %A Delogne, Christophe %A Deyilee, Peter %A Di Meglio, Alberto %A Eijkemans, Marinus %A Flicek, Paul %A Graf, Norbert %A Grimm, Vera %A Guchelaar, Henk-Jan %A Guo, Yi-Ke %A Gut, Ivo Glynne %A Hanbury, Allan %A Hanif, Shahid %A Hilgers, Ralf-Dieter %A Honrado, Ángel %A Hose, D. Rod %A Houwing-Duistermaat, Jeanine %A Hubbard, Tim %A Janacek, Sophie Helen %A Karanikas, Haralampos %A Kievits, Tim %A Kohler, Manfred %A Kremer, Andreas %A Lanfear, Jerry %A Lengauer, Thomas %A Maes, Edith %A Meert, Theo %A Müller, Werner %A Nickel, Dörthe %A Oledzki, Peter %A Pedersen, Bertrand %A Petkovic, Milan %A Pliakos, Konstantinos %A Rattray, Magnus %A Redón i Màs, Josep %A Schneider, Reinhard %A Sengstag, Thierry %A Serra-Picamal, Xavier %A Spek, Wouter %A Vaas, Lea A. I. %A van Batenburg, Okker %A Vandelaer, Marc %A Varnai, Peter %A Villoslada, Pablo %A Vizcaíno, Juan Antonio %A Wubbe, John Peter Mary %A Zanetti, Gianluigi %+ External Organizations External Organizations External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations %T Making Sense of Big Data in Health Research: Towards an EU Action Plan : %G eng %U http://hdl.handle.net/11858/00-001M-0000-002A-F908-8 %R 10.1186/s13073-016-0323-y %2 PMC4919856 %7 2016 %D 2016 %J Genome Medicine %V 8 %Z sequence number: 71 %I BioMedCentral %C London
126. Berger B, Gaasterland T, Lengauer T, Orengo C, Gaeta B, Markel S, Valencia A: ISCB’s Initial Reaction to The New England Journal of Medicine Editorial on Data Sharing. PLoS Computational Biology 2016, 12.
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@article{Berger2016, TITLE = {{ISCB}'s Initial Reaction to {The New England Journal of Medicine} Editorial on Data Sharing}, AUTHOR = {Berger, Bonnie and Gaasterland, Terry and Lengauer, Thomas and Orengo, Christine and Gaeta, Bruno and Markel, Scott and Valencia, Alfonso}, LANGUAGE = {eng}, ISSN = {1553-734X}, DOI = {10.1371/journal.pcbi.1004816}, PUBLISHER = {Public Library of Science}, ADDRESS = {San Francisco, CA}, YEAR = {2016}, JOURNAL = {PLoS Computational Biology}, VOLUME = {12}, NUMBER = {3}, EID = {e1004816}, }
Endnote
%0 Journal Article %A Berger, Bonnie %A Gaasterland, Terry %A Lengauer, Thomas %A Orengo, Christine %A Gaeta, Bruno %A Markel, Scott %A Valencia, Alfonso %+ External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations External Organizations %T ISCB’s Initial Reaction to The New England Journal of Medicine Editorial on Data Sharing : %G eng %U http://hdl.handle.net/11858/00-001M-0000-002A-FD6F-D %R 10.1371/journal.pcbi.1004816 %7 2016 %D 2016 %J PLoS Computational Biology %V 12 %N 3 %Z sequence number: e1004816 %I Public Library of Science %C San Francisco, CA %@ false
127. Bock C, Halbritter F, Carmona FJ, Tierling S, Datlinger P, Assenov Y, Berdasco M, Bergmann AK, Booher K, Busato F, Campan M, Dahl C, Dahmcke CM, Diep D, Fernández AF, Gerhauser C, Haake A, Heilmann K, Holcomb T, Hussmann D, Ito M, Kläver R, Kreutz M, Kulis M, Lopez V, Nair SS, Paul DS, Plongthongkum N, Qu W, Queirós AC, et al.: Quantitative Comparison of DNA Methylation Assays for Biomarker Development and Clinical Applications. Nature Biotechnology 2016, 34.
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@article{BockNatureBiotechn2016, TITLE = {Quantitative comparison of {DNA} methylation assays for biomarker development and clinical applications}, AUTHOR = {Bock, Christoph and Halbritter, Florian and Carmona, Francisco J. and Tierling, Sascha and Datlinger, Paul and Assenov, Yassen and Berdasco, Maria and Bergmann, Anke K. and Booher, Keith and Busato, Florance and Campan, Mihaela and Dahl, Christina and Dahmcke, Christina M. and Diep, Dinh and Fern{\'a}ndez, Agust{\'i}n F. and Gerhauser, Clarissa and Haake, Andrea and Heilmann, Katharina and Holcomb, Thomas and Hussmann, Dianna and Ito, Mitsuteru and Kl{\"a}ver, Ruth and Kreutz, Martin and Kulis, Marta and Lopez, Virginia and Nair, Shalima S. and Paul, Dirk S. and Plongthongkum, Nongluk and Qu, Wenija and Queir{\'o}s, Ana C. and Reinicke, Frank and Sauter, Guido and Schlomm, Thorsten and Statham, Aaron and Stirzaker, Clare and Strogantsev, Ruslan and Urdinguio, Roc{\'i}o G. and Walter, Kimberly and Weichenhan, Dieter and Weisenberger, Daniel J. and Beck, Stephan and Clark, Susan J. and Esteller, Manel and Ferguson-Smith, Anne C. and Fraga, Mario F. and Guldberg, Per and Hansen, Lise Lotte and Laird, Peter W. and Mart{\'i}n-Subero, Jos{\'e} I. and Nygren, Anders O. H. and Peist, Ralf and Plass, Christoph and Shames, David S. and Siebert, Reiner and Sun, Xueguang and Tost, J{\"o}rg and Walter, J{\"o}rn and Zhan, Kun and {BLUEPRINT consortium}}, LANGUAGE = {eng}, ISSN = {1087-0156}, DOI = {10.1038/nbt.3605}, PUBLISHER = {Nature Publishing Group}, ADDRESS = {New York, NY}, YEAR = {2016}, DATE = {2016}, JOURNAL = {Nature Biotechnology}, VOLUME = {34}, PAGES = {726--737}, }
Endnote
%0 Journal Article %A Bock, Christoph %A Halbritter, Florian %A Carmona, Francisco J. %A Tierling, Sascha %A Datlinger, Paul %A Assenov, Yassen %A Berdasco, Maria %A Bergmann, Anke K. %A Booher, Keith %A Busato, Florance %A Campan, Mihaela %A Dahl, Christina %A Dahmcke, Christina M. %A Diep, Dinh %A Fernández, Agustín F. %A Gerhauser, Clarissa %A Haake, Andrea %A Heilmann, Katharina %A Holcomb, Thomas %A Hussmann, Dianna %A Ito, Mitsuteru %A Kläver, Ruth %A Kreutz, Martin %A Kulis, Marta %A Lopez, Virginia %A Nair, Shalima S. %A Paul, Dirk S. %A Plongthongkum, Nongluk %A Qu, Wenija %A Queirós, Ana C. %A Reinicke, Frank %A Sauter, Guido %A Schlomm, Thorsten %A Statham, Aaron %A Stirzaker, Clare %A Strogantsev, Ruslan %A Urdinguio, Rocío G. %A Walter, Kimberly %A Weichenhan, Dieter %A Weisenberger, Daniel J. %A Beck, Stephan %A Clark, Susan J. %A Esteller, Manel %A Ferguson-Smith, Anne C. %A Fraga, Mario F. %A Guldberg, Per %A Hansen, Lise Lotte %A Laird, Peter W. %A Martín-Subero, José I. %A Nygren, Anders O. H. %A Peist, Ralf %A Plass, Christoph %A Shames, David S. %A Siebert, Reiner %A Sun, Xueguang %A Tost, Jörg %A Walter, Jörn %A Zhan, Kun %A BLUEPRINT consortium, %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations %T Quantitative Comparison of DNA Methylation Assays for Biomarker Development and Clinical Applications : %G eng %U http://hdl.handle.net/11858/00-001M-0000-002B-6373-E %R 10.1038/nbt.3605 %7 2016 %D 2016 %K , Jörg Tost, Jörn Walter & Kun Zhang for The BLUEPRINT consortium %J Nature Biotechnology %V 34 %& 726 %P 726 - 737 %I Nature Publishing Group %C New York, NY %@ false
128. Bock C, Farlik M, Sheffield NC: Multi-Omics of Single Cells: Strategies and Applications. Trends in Biotechnology 2016, 34.
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@article{Bock_TrendsBiotech2016, TITLE = {Multi-Omics of Single Cells: {S}trategies and Applications}, AUTHOR = {Bock, Christoph and Farlik, Matthias and Sheffield, Nathan C.}, LANGUAGE = {eng}, ISSN = {0167-7799}, DOI = {10.1016/j.tibtech.2016.04.004}, PUBLISHER = {Elsevier}, ADDRESS = {Amsterdam, Netherlands}, YEAR = {2016}, DATE = {2016}, JOURNAL = {Trends in Biotechnology}, VOLUME = {34}, NUMBER = {8}, PAGES = {605--608}, }
Endnote
%0 Journal Article %A Bock, Christoph %A Farlik, Matthias %A Sheffield, Nathan C. %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations %T Multi-Omics of Single Cells: Strategies and Applications : %G eng %U http://hdl.handle.net/11858/00-001M-0000-002B-4789-D %R 10.1016/j.tibtech.2016.04.004 %2 PMC4959511 %7 2016 %D 2016 %J Trends in Biotechnology %O Trends Biotechnol. %V 34 %N 8 %& 605 %P 605 - 608 %I Elsevier %C Amsterdam, Netherlands %@ false %U http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4959511/http://www.sciencedirect.com/science/article/pii/S0167779916300233
129. Bracciali A, Aldinucci M, Patterson M, Marschall T, Pisanti N, Merelli I, Torquati M: PWHATSHAP: Efficient Haplotyping for Future Generation Sequencing. BMC Bioinformatics (Proc CIBB 2014) 2016, 17(Suppl. 11).
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@article{Bracciali2016, TITLE = {{PWHATSHAP}: {E}fficient Haplotyping for Future Generation Sequencing}, AUTHOR = {Bracciali, Andrea and Aldinucci, Marco and Patterson, Murray and Marschall, Tobias and Pisanti, Nadia and Merelli, Ivan and Torquati, Massimo}, LANGUAGE = {eng}, ISSN = {1471-2105}, DOI = {10.1186/s12859-016-1170-y}, PUBLISHER = {BioMed Central}, YEAR = {2016}, JOURNAL = {BMC Bioinformatics (Proc. CIBB)}, VOLUME = {17}, NUMBER = {Suppl. 11}, EID = {342}, BOOKTITLE = {Selected articles from the 11th International Meeting on Computational Intelligence Methods for Bioinformatics and Selected articles from the 11th International Meeting on Computational Intelligence Methods for Bioinformatics and Biostatistics (CIBB 2014)}, }
Endnote
%0 Journal Article %A Bracciali, Andrea %A Aldinucci, Marco %A Patterson, Murray %A Marschall, Tobias %A Pisanti, Nadia %A Merelli, Ivan %A Torquati, Massimo %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T PWHATSHAP: Efficient Haplotyping for Future Generation Sequencing : %G eng %U http://hdl.handle.net/11858/00-001M-0000-002B-AEFB-6 %R 10.1186/s12859-016-1170-y %2 PMC5046197 %7 2016 %D 2016 %J BMC Bioinformatics %V 17 %N Suppl. 11 %Z sequence number: 342 %I BioMed Central %@ false %B Selected articles from the 11th International Meeting on Computational Intelligence Methods for Bioinformatics and Selected articles from the 11th International Meeting on Computational Intelligence Methods for Bioinformatics and Biostatistics %O CIBB 2014
130. Carlson JM, Du VY, Pfeifer N, Bansal A, Tan VYF, Power K, Brumme CJ, Kreimer A, DeZiel CE, Fusi N, Schaefer M, Brockman MA, Gilmour J, Price MA, Kilembe W, Haubrich R, John M, Mallal S, Shapiro R, Frater J, Harrigan PR, Ndung’u T, Allen S, Heckerman D, Sidney J, Allen TM, Goulder PJR, Brumme ZL, Hunter E, Goepfert PA: Impact of Pre-adapted HIV Transmission. Nature Medicine 2016, 22.
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@article{Carlson2016, TITLE = {Impact of Pre-adapted {HIV} Transmission}, AUTHOR = {Carlson, Jonathan M. and Du, Victor Y. and Pfeifer, Nico and Bansal, Anju and Tan, Vincent Y. F. and Power, Karen and Brumme, Chanson J. and Kreimer, Anat and DeZiel, Charles E. and Fusi, Nicolo and Schaefer, Malinda and Brockman, Mark A. and Gilmour, Jil and Price, Matt A. and Kilembe, William and Haubrich, Richard and John, Mina and Mallal, Simon and Shapiro, Roger and Frater, John and Harrigan, P. Richard and Ndung'u, Thumbi and Allen, Susan and Heckerman, David and Sidney, John and Allen, Todd M. and Goulder, Philip J. R. and Brumme, Zabrina L. and Hunter, Eric and Goepfert, Paul A.}, LANGUAGE = {eng}, ISSN = {1078-8956}, DOI = {10.1038/nm.4100}, PUBLISHER = {Nature Pub. Co.}, ADDRESS = {New York, NY}, YEAR = {2016}, DATE = {2016}, JOURNAL = {Nature Medicine}, VOLUME = {22}, PAGES = {606--613}, }
Endnote
%0 Journal Article %A Carlson, Jonathan M. %A Du, Victor Y. %A Pfeifer, Nico %A Bansal, Anju %A Tan, Vincent Y. F. %A Power, Karen %A Brumme, Chanson J. %A Kreimer, Anat %A DeZiel, Charles E. %A Fusi, Nicolo %A Schaefer, Malinda %A Brockman, Mark A. %A Gilmour, Jil %A Price, Matt A. %A Kilembe, William %A Haubrich, Richard %A John, Mina %A Mallal, Simon %A Shapiro, Roger %A Frater, John %A Harrigan, P. Richard %A Ndung'u, Thumbi %A Allen, Susan %A Heckerman, David %A Sidney, John %A Allen, Todd M. %A Goulder, Philip J. R. %A Brumme, Zabrina L. %A Hunter, Eric %A Goepfert, Paul A. %+ External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations %T Impact of Pre-adapted HIV Transmission : %G eng %U http://hdl.handle.net/11858/00-001M-0000-002A-ED12-F %R 10.1038/nm.4100 %7 2016 %D 2016 %J Nature Medicine %O Nat. Med. %V 22 %& 606 %P 606 - 613 %I Nature Pub. Co. %C New York, NY %@ false
131. Christiansen A, Davidsen JR, Titlestad I, Vestbo J, Baumbach J: A Systematic Review of Breath Analysis and Detection of Volatile Organic Compounds in COPD. Journal of Breath Research 2016, 10.
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@article{Christiansen2016, TITLE = {A Systematic Review of Breath Analysis and Detection of Volatile Organic Compounds in {COPD}}, AUTHOR = {Christiansen, Anders and Davidsen, Jesper R{\o}mhild and Titlestad, Ingrid and Vestbo, J{\o}rgen and Baumbach, Jan}, LANGUAGE = {eng}, DOI = {10.1088/1752-7155/10/3/034002}, PUBLISHER = {IOP Publishing}, YEAR = {2016}, DATE = {2016}, JOURNAL = {Journal of Breath Research}, VOLUME = {10}, NUMBER = {3}, EID = {034002}, }
Endnote
%0 Journal Article %A Christiansen, Anders %A Davidsen, Jesper Rømhild %A Titlestad, Ingrid %A Vestbo, Jørgen %A Baumbach, Jan %+ External Organizations External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T A Systematic Review of Breath Analysis and Detection of Volatile Organic Compounds in COPD : %G eng %U http://hdl.handle.net/11858/00-001M-0000-002B-A5A2-E %R 10.1088/1752-7155/10/3/034002 %7 2016 %D 2016 %J Journal of Breath Research %V 10 %N 3 %Z sequence number: 034002 %I IOP Publishing
132. Dheghani Amirabad A, Schulz MH: Multitask Regression for Condition-specific Prioritization of miRNA Targets in Transcripts. PeerJ Preprints 2016, 4.
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@article{Amirabad2016, TITLE = {Multitask Regression for Condition-specific Prioritization of {miRNA} Targets in Transcripts}, AUTHOR = {Dheghani Amirabad, Azim and Schulz, Marcel Holger}, LANGUAGE = {eng}, DOI = {10.7287/peerj.preprints.2377v2}, YEAR = {2016}, JOURNAL = {PeerJ Preprints}, VOLUME = {4}, EID = {e2377v2}, }
Endnote
%0 Journal Article %A Dheghani Amirabad, Azim %A Schulz, Marcel Holger %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T Multitask Regression for Condition-specific Prioritization of miRNA Targets in Transcripts : %G eng %U http://hdl.handle.net/11858/00-001M-0000-002B-866A-8 %R 10.7287/peerj.preprints.2377v2 %7 2016-08-22 %D 2016 %8 22.08.2016 %J PeerJ Preprints %V 4 %Z sequence number: e2377v2
133. Doncheva NT: Network Biology Methods for Functional Characterization and Integrative Prioritization of Disease Genes and Proteins. Universität des Saarlandes; 2016.
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@phdthesis{DonchevaPhD2016, TITLE = {Network Biology Methods for Functional Characterization and Integrative Prioritization of Disease Genes and Proteins}, AUTHOR = {Doncheva, Nadezhda Tsankova}, LANGUAGE = {eng}, URL = {urn:nbn:de:bsz:291-scidok-65957}, SCHOOL = {Universit{\"a}t des Saarlandes}, ADDRESS = {Saarbr{\"u}cken}, YEAR = {2016}, DATE = {2016}, }
Endnote
%0 Thesis %A Doncheva, Nadezhda Tsankova %Y Albrecht, Mario %A referee: Lengauer, Thomas %A referee: Lenhof, Hans-Peter %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society International Max Planck Research School, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations %T Network Biology Methods for Functional Characterization and Integrative Prioritization of Disease Genes and Proteins : %G eng %U http://hdl.handle.net/11858/00-001M-0000-002B-1921-A %U urn:nbn:de:bsz:291-scidok-65957 %I Universität des Saarlandes %C Saarbrücken %D 2016 %P XII, 242 p. %V phd %9 phd %U http://scidok.sulb.uni-saarland.de/volltexte/2016/6595/http://scidok.sulb.uni-saarland.de/doku/lic_ohne_pod.php?la=de
134. Döring M, Borrego P, Büch J, Martins A, Friedrich G, Camacho RJ, Eberle J, Kaiser R, Lengauer T, Taveira N, Pfeifer N: A Genotypic Method for Determining HIV-2 Coreceptor Usage enables Epidemiological Studies and Clinical Decision Support. Retrovirology 2016, 13.
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@article{DoeringRetro16, TITLE = {A Genotypic Method for Determining {HIV-2} Coreceptor Usage enables Epidemiological Studies and Clinical Decision Support}, AUTHOR = {D{\"o}ring, Matthias and Borrego, Pedro and B{\"u}ch, Joachim and Martins, Andreia and Friedrich, Georg and Camacho, Ricardo Jorge and Eberle, Josef and Kaiser, Rolf and Lengauer, Thomas and Taveira, Nuno and Pfeifer, Nico}, LANGUAGE = {eng}, ISSN = {1742-4690}, DOI = {10.1186/s12977-016-0320-7}, PUBLISHER = {BioMed Central}, ADDRESS = {London}, YEAR = {2016}, JOURNAL = {Retrovirology}, VOLUME = {13}, EID = {85}, }
Endnote
%0 Journal Article %A Döring, Matthias %A Borrego, Pedro %A Büch, Joachim %A Martins, Andreia %A Friedrich, Georg %A Camacho, Ricardo Jorge %A Eberle, Josef %A Kaiser, Rolf %A Lengauer, Thomas %A Taveira, Nuno %A Pfeifer, Nico %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T A Genotypic Method for Determining HIV-2 Coreceptor Usage enables Epidemiological Studies and Clinical Decision Support : %G eng %U http://hdl.handle.net/11858/00-001M-0000-002C-298A-A %R 10.1186/s12977-016-0320-7 %7 2016-12-20 %D 2016 %8 20.12.2016 %K Human immunodeficiency virus type 2, HIV-2, Coreceptor, Chemokine receptor, Prediction, Statistical learning, V3, V1, V2, Coreceptor antagonists %J Retrovirology %V 13 %Z sequence number: 85 %I BioMed Central %C London %@ false
135. Durai DA, Schulz MH: Informed kmer Selection for de novo Transcriptome Assembly. Bioinformatics 2016, 32.
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@article{Durai2016, TITLE = {Informed $k$mer Selection for \textit{de novo} Transcriptome Assembly}, AUTHOR = {Durai, Dilip Ariyur and Schulz, Marcel H.}, LANGUAGE = {eng}, ISSN = {1367-4803}, DOI = {10.1093/bioinformatics/btw217}, PUBLISHER = {Oxford University Press}, ADDRESS = {Oxford}, YEAR = {2016}, DATE = {2016}, JOURNAL = {Bioinformatics}, VOLUME = {32}, NUMBER = {11}, PAGES = {1670--1677}, }
Endnote
%0 Journal Article %A Durai, Dilip Ariyur %A Schulz, Marcel H. %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T Informed kmer Selection for de novo Transcriptome Assembly : %G eng %U http://hdl.handle.net/11858/00-001M-0000-002A-F53A-5 %R 10.1093/bioinformatics/btw217 %2 PMC4892416 %7 2016 %D 2016 %J Bioinformatics %V 32 %N 11 %& 1670 %P 1670 - 1677 %I Oxford University Press %C Oxford %@ false
136. Durek P, Nordström K, Gasparoni G, Salhab A, Kressler C, de Almeida M, Bassler K, Ulas T, Schmidt F, Xiong J, Glažar P, Klironomos F, Sinha A, Kinkley S, Yang X, Arrigoni L, Dheghani Amirabad A, Behjati Ardakani F, Feuerbach L, Gorka O, Ebert P, Müller F, Li N, Frischbutter S, Schlickeiser S, Cendon C, Fröhler S, Felder B, Gasparoni N, Imbusch CD, et al.: Epigenomic Profiling of Human CD4+ T Cells Supports a Linear Differentiation Model and Highlights Molecular Regulators of Memory Development. Immunity 2016, 45.
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@article{Durek2016, TITLE = {Epigenomic Profiling of Human {CD4}+ {T} Cells Supports a Linear Differentiation Model and Highlights Molecular Regulators of Memory Development}, AUTHOR = {Durek, Pawel and Nordstr{\"o}m, Karl and Gasparoni, Gilles and Salhab, Abdulrahman and Kressler, Christopher and de Almeida, Melanie and Bassler, Kevin and Ulas, Thomas and Schmidt, Florian and Xiong, Jieyi and Gla{\v z}ar, Petar and Klironomos, Filippos and Sinha, Anupam and Kinkley, Sarah and Yang, Xinyi and Arrigoni, Laura and Dheghani Amirabad, Azim and Behjati Ardakani, Fatemeh and Feuerbach, Lars and Gorka, Oliver and Ebert, Peter and M{\"u}ller, Fabian and Li, Na and Frischbutter, Stefan and Schlickeiser, Stephan and Cendon, Carla and Fr{\"o}hler, Sebastian and Felder, B{\"a}rbel and Gasparoni, Nina and Imbusch, Charles D. and Hutter, Barbara and Zipprich, Gideon and Tauchmann, Yvonne and Reinke, Simon and Wassilew, Georgi and Hoffmann, Ute and Richter, Andreas S. and Sieverling, Lina and {DEEP Consortium} and Chang, Hyun-Dong and Syrbe, Uta and Kalus, Ulrich and Eils, J{\"u}rgen and Brors, Benedikt and Manke, Thomas and Ruland, J{\"u}rgen and Lengauer, Thomas and Rajewsky, Nikolaus and Chen, Wei and Dong, Jun and Sawitzki, Birgit and Chung, Ho-Ryun and Rosenstiel, Philip and Schulz, Marcel H. and Schultze, Joachim L. and Radbruch, Andreas and Walter, J{\"o}rn and Hamann, Alf and Polansky, Julia K.}, LANGUAGE = {eng}, ISSN = {1074-7613}, DOI = {10.1016/j.immuni.2016.10.022}, PUBLISHER = {Cell Press}, ADDRESS = {Cambridge, Mass.}, YEAR = {2016}, DATE = {2016}, JOURNAL = {Immunity}, VOLUME = {45}, NUMBER = {5}, PAGES = {1148--1161}, }
Endnote
%0 Journal Article %A Durek, Pawel %A Nordström, Karl %A Gasparoni, Gilles %A Salhab, Abdulrahman %A Kressler, Christopher %A de Almeida, Melanie %A Bassler, Kevin %A Ulas, Thomas %A Schmidt, Florian %A Xiong, Jieyi %A Glažar, Petar %A Klironomos, Filippos %A Sinha, Anupam %A Kinkley, Sarah %A Yang, Xinyi %A Arrigoni, Laura %A Dheghani Amirabad, Azim %A Behjati Ardakani, Fatemeh %A Feuerbach, Lars %A Gorka, Oliver %A Ebert, Peter %A Müller, Fabian %A Li, Na %A Frischbutter, Stefan %A Schlickeiser, Stephan %A Cendon, Carla %A Fröhler, Sebastian %A Felder, Bärbel %A Gasparoni, Nina %A Imbusch, Charles D. %A Hutter, Barbara %A Zipprich, Gideon %A Tauchmann, Yvonne %A Reinke, Simon %A Wassilew, Georgi %A Hoffmann, Ute %A Richter, Andreas S. %A Sieverling, Lina %A DEEP Consortium, %A Chang, Hyun-Dong %A Syrbe, Uta %A Kalus, Ulrich %A Eils, Jürgen %A Brors, Benedikt %A Manke, Thomas %A Ruland, Jürgen %A Lengauer, Thomas %A Rajewsky, Nikolaus %A Chen, Wei %A Dong, Jun %A Sawitzki, Birgit %A Chung, Ho-Ryun %A Rosenstiel, Philip %A Schulz, Marcel H. %A Schultze, Joachim L. %A Radbruch, Andreas %A Walter, Jörn %A Hamann, Alf %A Polansky, Julia K. %+ External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations External Organizations External Organizations %T Epigenomic Profiling of Human CD4+ T Cells Supports a Linear Differentiation Model and Highlights Molecular Regulators of Memory Development : %G eng %U http://hdl.handle.net/11858/00-001M-0000-002C-2DF6-1 %R 10.1016/j.immuni.2016.10.022 %7 2016 %D 2016 %J Immunity %V 45 %N 5 %& 1148 %P 1148 - 1161 %I Cell Press %C Cambridge, Mass. %@ false
137. Farlik M, Halbritter F, Müller F, Choudry FA, Ebert P, Klughammer J, Farrow S, Santoro A, Ciaurro V, Mathur A, Uppal R, Stunnenberg HG, Ouwehand WH, Laurenti E, Lengauer T, Frontini M, Bock C: DNA Methylation Dynamics of Human Hematopoietic Stem Cell Differentiation. Cell Stem Cell 2016, 19.
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@article{Farlik:2016ig, TITLE = {{DNA} Methylation Dynamics of Human Hematopoietic Stem Cell Differentiation}, AUTHOR = {Farlik, Matthias and Halbritter, Florian and M{\"u}ller, Fabian and Choudry, Fizzah A. and Ebert, Peter and Klughammer, Johanna and Farrow, Samantha and Santoro, Antonella and Ciaurro, Valerio and Mathur, Anthony and Uppal, Rakesh and Stunnenberg, Hendrik G. and Ouwehand, Willem H. and Laurenti, Elisa and Lengauer, Thomas and Frontini, Mattia and Bock, Christoph}, LANGUAGE = {eng}, ISSN = {1875-9777}, DOI = {10.1016/j.stem.2016.10.019}, PUBLISHER = {Elsevier}, ADDRESS = {Amsterdam}, YEAR = {2016}, DATE = {2016}, JOURNAL = {Cell Stem Cell}, VOLUME = {19}, NUMBER = {6}, PAGES = {808--822}, }
Endnote
%0 Journal Article %A Farlik, Matthias %A Halbritter, Florian %A Müller, Fabian %A Choudry, Fizzah A. %A Ebert, Peter %A Klughammer, Johanna %A Farrow, Samantha %A Santoro, Antonella %A Ciaurro, Valerio %A Mathur, Anthony %A Uppal, Rakesh %A Stunnenberg, Hendrik G. %A Ouwehand, Willem H. %A Laurenti, Elisa %A Lengauer, Thomas %A Frontini, Mattia %A Bock, Christoph %+ External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T DNA Methylation Dynamics of Human Hematopoietic Stem Cell Differentiation : %G eng %U http://hdl.handle.net/11858/00-001M-0000-002C-2094-5 %R 10.1016/j.stem.2016.10.019 %7 2016-11-17 %D 2016 %J Cell Stem Cell %V 19 %N 6 %& 808 %P 808 - 822 %I Elsevier %C Amsterdam %@ false
138. Fischer S: Selecting Reads for Haplotype Phasing. Universität des Saarlandes; 2016.
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@mastersthesis{FischerMSc2016, TITLE = {Selecting Reads for Haplotype Phasing}, AUTHOR = {Fischer, Sarah}, LANGUAGE = {eng}, SCHOOL = {Universit{\"a}t des Saarlandes}, ADDRESS = {Saarbr{\"u}cken}, YEAR = {2016}, DATE = {2016}, }
Endnote
%0 Thesis %A Fischer, Sarah %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T Selecting Reads for Haplotype Phasing : %G eng %U http://hdl.handle.net/11858/00-001M-0000-002C-4839-8 %I Universität des Saarlandes %C Saarbrücken %D 2016 %V master %9 master
139. Forster J: Inferring Horizontal Gene Transfer from NGS Data. Universität des Saarlandes; 2016.
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@mastersthesis{ForsterMSc2016, TITLE = {Inferring Horizontal Gene Transfer from {NGS} Data}, AUTHOR = {Forster, Jan}, LANGUAGE = {eng}, SCHOOL = {Universit{\"a}t des Saarlandes}, ADDRESS = {Saarbr{\"u}cken}, YEAR = {2016}, DATE = {2016}, }
Endnote
%0 Thesis %A Forster, Jan %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T Inferring Horizontal Gene Transfer from NGS Data : %G eng %U http://hdl.handle.net/11858/00-001M-0000-002C-4845-C %I Universität des Saarlandes %C Saarbrücken %D 2016 %V master %9 master
140. Gapp BV, Konopka T, Penz T, Dalal V, Bürckstümmer T, Bock C, Nijman SMB: Parallel Reverse Genetic Screening in Mutant Human Cells Using Transcriptomics. Molecular Systems Biology 2016, 12.
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@article{Gapp2016, TITLE = {Parallel Reverse Genetic Screening in Mutant Human Cells Using Transcriptomics}, AUTHOR = {Gapp, Bianca V. and Konopka, Tomasz and Penz, Thomas and Dalal, Vineet and B{\"u}rckst{\"u}mmer, Tilmann and Bock, Christoph and Nijman, Sebastian M. B.}, LANGUAGE = {eng}, ISSN = {1744-4292}, DOI = {10.15252/msb.20166890}, PUBLISHER = {Nature Pub. Group}, ADDRESS = {London}, YEAR = {2016}, JOURNAL = {Molecular Systems Biology}, VOLUME = {12}, NUMBER = {8}, EID = {879}, }
Endnote
%0 Journal Article %A Gapp, Bianca V. %A Konopka, Tomasz %A Penz, Thomas %A Dalal, Vineet %A Bürckstümmer, Tilmann %A Bock, Christoph %A Nijman, Sebastian M. B. %+ External Organizations External Organizations External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations %T Parallel Reverse Genetic Screening in Mutant Human Cells Using Transcriptomics : %G eng %U http://hdl.handle.net/11858/00-001M-0000-002B-5503-8 %R 10.15252/msb.20166890 %7 2016-08-01 %D 2016 %8 01.08.2016 %J Molecular Systems Biology %V 12 %N 8 %Z sequence number: 879 %I Nature Pub. Group %C London %@ false
141. Garg S, Martin M, Marschall T: Read-based Phasing of Related Individuals. Bioinformatics (Proc ISMB 2016) 2016, 32.
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@article{GargMarschall2016, TITLE = {Read-based Phasing of Related Individuals}, AUTHOR = {Garg, Shilpa and Martin, Marcel and Marschall, Tobias}, LANGUAGE = {eng}, ISSN = {1367-4803}, DOI = {10.1093/bioinformatics/btw276}, PUBLISHER = {Oxford University Press}, ADDRESS = {Oxford}, YEAR = {2016}, DATE = {2016}, JOURNAL = {Bioinformatics (Proc. ISMB)}, VOLUME = {32}, NUMBER = {12}, PAGES = {i234--i242}, BOOKTITLE = {ISMB 2016 Proceedings}, EDITOR = {Baldi, Pierre and Przytycka, Teresa}, }
Endnote
%0 Journal Article %A Garg, Shilpa %A Martin, Marcel %A Marschall, Tobias %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T Read-based Phasing of Related Individuals : %G eng %U http://hdl.handle.net/11858/00-001M-0000-002A-F931-A %R 10.1093/bioinformatics/btw276 %2 PMC4908360 %7 2016 %D 2016 %J Bioinformatics %V 32 %N 12 %& i234 %P i234 - i242 %I Oxford University Press %C Oxford %@ false %B ISMB 2016 Proceedings %O July 8 to July 12, 2016, Orlando, Florida 24th Annual Conference Intelligent Systems for Molecular Biology ISMB 2016
142. Götz U, Marker S, Cheaib M, Andresen K, Shrestha S, Durai DA, Nordström K, Schulz MH, Simon M: Two Sets of RNAi Components are Required for Heterochromatin Formation in Trans Triggered by Truncated Transgenes. Nucleic Acids Research 2016, 44.
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@article{Goetz2016, TITLE = {Two Sets of {RNA}i Components are Required for Heterochromatin Formation \textsl{in trans} Triggered by Truncated Transgenes}, AUTHOR = {G{\"o}tz, Ulrike and Marker, Simone and Cheaib, Miriam and Andresen, Karsten and Shrestha, Simon and Durai, Dilip Ariyur and Nordstr{\"o}m, Karl and Schulz, Marcel H. and Simon, Martin}, LANGUAGE = {eng}, ISSN = {0301-5610}, DOI = {10.1093/nar/gkw267}, YEAR = {2016}, DATE = {2016}, JOURNAL = {Nucleic Acids Research}, VOLUME = {44}, NUMBER = {12}, PAGES = {5908--5923}, }
Endnote
%0 Journal Article %A Götz, Ulrike %A Marker, Simone %A Cheaib, Miriam %A Andresen, Karsten %A Shrestha, Simon %A Durai, Dilip Ariyur %A Nordström, Karl %A Schulz, Marcel H. %A Simon, Martin %+ External Organizations External Organizations External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations %T Two Sets of RNAi Components are Required for Heterochromatin Formation in Trans Triggered by Truncated Transgenes : %G eng %U http://hdl.handle.net/11858/00-001M-0000-002B-16B8-E %R 10.1093/nar/gkw267 %7 2016 %D 2016 %J Nucleic Acids Research %O Nucleic Acids Res. %V 44 %N 12 %& 5908 %P 5908 - 5923 %@ false
143. Gress A, Ramensky V, Büch J, Keller A, Kalinina OV: StructMAn: Annotation of Single-nucleotide Polymorphisms in the Structural Context. Nucleic Acids Research 2016, 44(W1/Web Server issue).
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@article{Gress_Buech_Kalinina2016, TITLE = {{StructMAn}: {A}nnotation of Single-nucleotide Polymorphisms in the Structural Context}, AUTHOR = {Gress, Alexander and Ramensky, Vasily and B{\"u}ch, Joachim and Keller, Andreas and Kalinina, Olga V.}, LANGUAGE = {eng}, DOI = {10.1093/nar/gkw364}, PUBLISHER = {Oxford University Press}, ADDRESS = {Oxford, UK}, YEAR = {2016}, DATE = {2016}, JOURNAL = {Nucleic Acids Research}, VOLUME = {44}, NUMBER = {W1/Web Server issue}, PAGES = {W463--W468}, }
Endnote
%0 Journal Article %A Gress, Alexander %A Ramensky, Vasily %A Büch, Joachim %A Keller, Andreas %A Kalinina, Olga V. %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T StructMAn: Annotation of Single-nucleotide Polymorphisms in the Structural Context : %G eng %U http://hdl.handle.net/11858/00-001M-0000-002B-42A2-6 %R 10.1093/nar/gkw364 %2 PMC4987916 %7 2016 %D 2016 %* Review method: peer-reviewed %J Nucleic Acids Research %V 44 %N W1/Web Server issue %& W463 %P W463 - W468 %I Oxford University Press %C Oxford, UK
144. Partially Blind Domain Adaptation for Age Prediction from DNA Methylation Data [http://arxiv.org/abs/1612.06650]
(arXiv: 1612.06650)
Abstract
Over the last years, huge resources of biological and medical data have become available for research. This data offers great chances for machine learning applications in health care, e.g. for precision medicine, but is also challenging to analyze. Typical challenges include a large number of possibly correlated features and heterogeneity in the data. One flourishing field of biological research in which this is relevant is epigenetics. Here, especially large amounts of DNA methylation data have emerged. This epigenetic mark has been used to predict a donor's 'epigenetic age' and increased epigenetic aging has been linked to lifestyle and disease history. In this paper we propose an adaptive model which performs feature selection for each test sample individually based on the distribution of the input data. The method can be seen as partially blind domain adaptation. We apply the model to the problem of age prediction based on DNA methylation data from a variety of tissues, and compare it to a standard model, which does not take heterogeneity into account. The standard approach has particularly bad performance on one tissue type on which we show substantial improvement with our new adaptive approach even though no samples of that tissue were part of the training data.
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@online{HandlarXiv2016, TITLE = {Partially Blind Domain Adaptation for Age Prediction from {DNA} Methylation Data}, AUTHOR = {Handl, Lisa and Jalali, Adrin and Scherer, Michael and Pfeifer, Nico}, LANGUAGE = {eng}, URL = {http://arxiv.org/abs/1612.06650}, EPRINT = {1612.06650}, EPRINTTYPE = {arXiv}, YEAR = {2016}, ABSTRACT = {Over the last years, huge resources of biological and medical data have become available for research. This data offers great chances for machine learning applications in health care, e.g. for precision medicine, but is also challenging to analyze. Typical challenges include a large number of possibly correlated features and heterogeneity in the data. One flourishing field of biological research in which this is relevant is epigenetics. Here, especially large amounts of DNA methylation data have emerged. This epigenetic mark has been used to predict a donor's 'epigenetic age' and increased epigenetic aging has been linked to lifestyle and disease history. In this paper we propose an adaptive model which performs feature selection for each test sample individually based on the distribution of the input data. The method can be seen as partially blind domain adaptation. We apply the model to the problem of age prediction based on DNA methylation data from a variety of tissues, and compare it to a standard model, which does not take heterogeneity into account. The standard approach has particularly bad performance on one tissue type on which we show substantial improvement with our new adaptive approach even though no samples of that tissue were part of the training data.}, }
Endnote
%0 Report %A Handl, Lisa %A Jalali, Adrin %A Scherer, Michael %A Pfeifer, Nico %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T Partially Blind Domain Adaptation for Age Prediction from DNA Methylation Data : %G eng %U http://hdl.handle.net/11858/00-001M-0000-002C-4CDD-3 %U http://arxiv.org/abs/1612.06650 %D 2016 %X Over the last years, huge resources of biological and medical data have become available for research. This data offers great chances for machine learning applications in health care, e.g. for precision medicine, but is also challenging to analyze. Typical challenges include a large number of possibly correlated features and heterogeneity in the data. One flourishing field of biological research in which this is relevant is epigenetics. Here, especially large amounts of DNA methylation data have emerged. This epigenetic mark has been used to predict a donor's 'epigenetic age' and increased epigenetic aging has been linked to lifestyle and disease history. In this paper we propose an adaptive model which performs feature selection for each test sample individually based on the distribution of the input data. The method can be seen as partially blind domain adaptation. We apply the model to the problem of age prediction based on DNA methylation data from a variety of tissues, and compare it to a standard model, which does not take heterogeneity into account. The standard approach has particularly bad performance on one tissue type on which we show substantial improvement with our new adaptive approach even though no samples of that tissue were part of the training data. %K Quantitative Biology, Quantitative Methods, q-bio.QM,Statistics, Machine Learning, stat.ML
145. Hauschild A-C: Computational Methods for Breath Metabolomics in Clinical Diagnostics. Universität des Saarlandes; 2016.
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@phdthesis{Hauschild_PhD2016, TITLE = {Computational Methods for Breath Metabolomics in Clinical Diagnostics}, AUTHOR = {Hauschild, Anne-Christin}, LANGUAGE = {eng}, URL = {urn:nbn:de:bsz:291-scidok-65874}, SCHOOL = {Universit{\"a}t des Saarlandes}, ADDRESS = {Saarbr{\"u}cken}, YEAR = {2016}, DATE = {2016}, }
Endnote
%0 Thesis %A Hauschild, Anne-Christin %Y Helms, Volkhard %A referee: Baumbach, Jan %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society International Max Planck Research School, MPI for Informatics, Max Planck Society External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T Computational Methods for Breath Metabolomics in Clinical Diagnostics : %G eng %U http://hdl.handle.net/11858/00-001M-0000-002B-0C18-7 %U urn:nbn:de:bsz:291-scidok-65874 %I Universität des Saarlandes %C Saarbrücken %D 2016 %P 188 p. %V phd %9 phd %U http://scidok.sulb.uni-saarland.de/volltexte/2016/6587/http://scidok.sulb.uni-saarland.de/doku/lic_ohne_pod.php?la=de
146. Heger E, Theis AA, Remmel K, Walter H, Pironti A, Knops E, Cristanziano VD, Jensen B, Esser S, Kaiser R, Lübke N: Development of a Phenotypic Susceptibility Assay for HIV-1 Integrase Inhibitors. Journal of Virological Methods 2016, 238.
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@article{Heger_Theis2016, TITLE = {Development of a Phenotypic Susceptibility Assay for {HIV}-1 Integrase Inhibitors}, AUTHOR = {Heger, Eva and Theis, Alexandra Andr{\'e}e and Remmel, Klaus and Walter, Hauke and Pironti, Alejandro and Knops, Elena and Cristanziano, Veronica Di and Jensen, Bj{\"o}rn and Esser, Stefan and Kaiser, Rolf and L{\"u}bke, Nadine}, LANGUAGE = {eng}, ISSN = {0166-0934}, DOI = {10.1016/j.jviromet.2016.10.002}, PUBLISHER = {Elsevier}, ADDRESS = {Amsterdam}, YEAR = {2016}, DATE = {2016}, JOURNAL = {Journal of Virological Methods}, VOLUME = {238}, PAGES = {29--37}, }
Endnote
%0 Journal Article %A Heger, Eva %A Theis, Alexandra Andrée %A Remmel, Klaus %A Walter, Hauke %A Pironti, Alejandro %A Knops, Elena %A Cristanziano, Veronica Di %A Jensen, Björn %A Esser, Stefan %A Kaiser, Rolf %A Lübke, Nadine %+ External Organizations External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations %T Development of a Phenotypic Susceptibility Assay for HIV-1 Integrase Inhibitors : %G eng %U http://hdl.handle.net/11858/00-001M-0000-002C-2DCF-E %R 10.1016/j.jviromet.2016.10.002 %7 2016 %D 2016 %J Journal of Virological Methods %V 238 %& 29 %P 29 - 37 %I Elsevier %C Amsterdam %@ false
147. Hehir-Kwa JY, Marschall T, Kloosterman WP, Francioli LC, Baaijens JA, Dijkstra LJ, Abdellaoui A, Koval V, Thung DT, Wardenaar R, Renkens I, Coe BP, Deelen P, de Ligt J, Lameijer E-W, van Dijk F, Hormozdiari F, Uitterlinden AG, van Duijn CM, Eichler EE, de Bakker PIW, Swertz MA, Wijmenga C, van Ommen G-J, Slagboom E, Boomsma DI, Schönhuth A, Ye K, Guryev V: A High-quality Human Reference Panel Reveals the Complexity and Distribution of Genomic Structural Variants. Nature Communications 2016, 7.
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@article{Hehir-Kwa2016, TITLE = {A High-quality Human Reference Panel Reveals the Complexity and Distribution of Genomic Structural Variants}, AUTHOR = {Hehir-Kwa, Jayne Y. and Marschall, Tobias and Kloosterman, Wigard P. and Francioli, Laurent C. and Baaijens, Jasmijn A. and Dijkstra, Louis J. and Abdellaoui, Abdel and Koval, Vyacheslav and Thung, Dije Tiwan and Wardenaar, Ren{\'e} and Renkens, Ivo and Coe, Bradley P. and Deelen, Patrick and de Ligt, Joep and Lameijer, Eric-Wubbo and van Dijk, Freerk and Hormozdiari, Fereydoun and Uitterlinden, Andr{\'e} G. and van Duijn, Cornelia M. and Eichler, Evan E. and de Bakker, Paul I. W. and Swertz, Morris A. and Wijmenga, Cisca and van Ommen, Gert-Jan and Slagboom, Eline and Boomsma, Dorret I. and Sch{\"o}nhuth, Alexander and Ye, Kai and Guryev, Victor}, LANGUAGE = {eng}, ISSN = {2041-1723}, DOI = {10.1038/ncomms12989}, PUBLISHER = {Nature Publishing Group}, ADDRESS = {London}, YEAR = {2016}, JOURNAL = {Nature Communications}, VOLUME = {7}, EID = {12989}, }
Endnote
%0 Journal Article %A Hehir-Kwa, Jayne Y. %A Marschall, Tobias %A Kloosterman, Wigard P. %A Francioli, Laurent C. %A Baaijens, Jasmijn A. %A Dijkstra, Louis J. %A Abdellaoui, Abdel %A Koval, Vyacheslav %A Thung, Dije Tiwan %A Wardenaar, René %A Renkens, Ivo %A Coe, Bradley P. %A Deelen, Patrick %A de Ligt, Joep %A Lameijer, Eric-Wubbo %A van Dijk, Freerk %A Hormozdiari, Fereydoun %A Uitterlinden, André G. %A van Duijn, Cornelia M. %A Eichler, Evan E. %A de Bakker, Paul I. W. %A Swertz, Morris A. %A Wijmenga, Cisca %A van Ommen, Gert-Jan %A Slagboom, Eline %A Boomsma, Dorret I. %A Schönhuth, Alexander %A Ye, Kai %A Guryev, Victor %+ External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations %T A High-quality Human Reference Panel Reveals the Complexity and Distribution of Genomic Structural Variants : %G eng %U http://hdl.handle.net/11858/00-001M-0000-002B-AF0A-B %R 10.1038/ncomms12989 %7 2016 %D 2016 %J Nature Communications %O Nat. Commun. %V 7 %Z sequence number: 12989 %I Nature Publishing Group %C London %@ false
148. Heller G, Topakian T, Altenberger C, Cerny-Reiterer S, Herndlhofer S, Ziegler B, Datlinger P, Byrgazov K, Bock C, Mannhalter C, Hörmann G, Sperr WR, Lion T, Zielinski CC, Valent P, Zöchbauer-Müller S: Next-generation Sequencing Identifies Major DNA Methylation Changes during Progression of Ph+ Chronic Myeloid Leukemia. Leukemia 2016, 30.
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@article{Heller2016, TITLE = {Next-generation sequencing identifies major {DNA} methylation changes during progression of {Ph}+ chronic myeloid leukemia}, AUTHOR = {Heller, G. and Topakian, T. and Altenberger, C. and Cerny-Reiterer, S. and Herndlhofer, S. and Ziegler, B. and Datlinger, P. and Byrgazov, K. and Bock, Christoph and Mannhalter, C. and H{\"o}rmann, G. and Sperr, W. R. and Lion, T. and Zielinski, C. C. and Valent, P. and Z{\"o}chbauer-M{\"u}ller, S.}, LANGUAGE = {eng}, ISSN = {0887-6924}, DOI = {10.1038/leu.2016.143}, PUBLISHER = {NPG}, ADDRESS = {London}, YEAR = {2016}, DATE = {2016}, JOURNAL = {Leukemia}, VOLUME = {30}, PAGES = {1861--1868}, }
Endnote
%0 Journal Article %A Heller, G. %A Topakian, T. %A Altenberger, C. %A Cerny-Reiterer, S. %A Herndlhofer, S. %A Ziegler, B. %A Datlinger, P. %A Byrgazov, K. %A Bock, Christoph %A Mannhalter, C. %A Hörmann, G. %A Sperr, W. R. %A Lion, T. %A Zielinski, C. C. %A Valent, P. %A Zöchbauer-Müller, S. %+ External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations %T Next-generation Sequencing Identifies Major DNA Methylation Changes during Progression of Ph+ Chronic Myeloid Leukemia : %G eng %U http://hdl.handle.net/11858/00-001M-0000-002B-9AEC-3 %R 10.1038/leu.2016.143 %7 2016-06-17 %D 2016 %J Leukemia %V 30 %& 1861 %P 1861 - 1868 %I NPG %C London %@ false
149. Jalali A, Pfeifer N: Interpretable Per Case Weighted Ensemble Method for Cancer Associations. BMC Genomics 2016, 17.
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@article{JalaliPfeifer2016, TITLE = {Interpretable Per Case Weighted Ensemble Method for Cancer Associations}, AUTHOR = {Jalali, Adrin and Pfeifer, Nico}, LANGUAGE = {eng}, ISSN = {1471-2164}, DOI = {10.1186/s12864-016-2647-9}, PUBLISHER = {BioMed Central}, ADDRESS = {London}, YEAR = {2016}, JOURNAL = {BMC Genomics}, VOLUME = {17}, EID = {501}, }
Endnote
%0 Journal Article %A Jalali, Adrin %A Pfeifer, Nico %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T Interpretable Per Case Weighted Ensemble Method for Cancer Associations : %G eng %U http://hdl.handle.net/11858/00-001M-0000-002B-16A3-D %R 10.1186/s12864-016-2647-9 %7 2016 %D 2016 %J BMC Genomics %V 17 %Z sequence number: 501 %I BioMed Central %C London %@ false
150. Kalaghatgi P, Pfeifer N, Lengauer T: Family-Joining: A Fast Distance-Based Method for Constructing Generally Labeled Trees. Molecular Biology and Evolution 2016, 33.
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@article{Kalaghatgi2016, TITLE = {Family-Joining: A Fast Distance-Based Method for Constructing Generally Labeled Trees}, AUTHOR = {Kalaghatgi, Prabhav and Pfeifer, Nico and Lengauer, Thomas}, LANGUAGE = {eng}, ISSN = {0737-4038}, DOI = {10.1093/molbev/msw123}, PUBLISHER = {Oxford University Press}, ADDRESS = {Oxford}, YEAR = {2016}, DATE = {2016}, JOURNAL = {Molecular Biology and Evolution}, VOLUME = {33}, NUMBER = {10}, PAGES = {2720--2734}, }
Endnote
%0 Journal Article %A Kalaghatgi, Prabhav %A Pfeifer, Nico %A Lengauer, Thomas %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T Family-Joining: A Fast Distance-Based Method for Constructing Generally Labeled Trees : %G eng %U http://hdl.handle.net/11858/00-001M-0000-002B-8268-E %R 10.1093/molbev/msw123 %7 2016 %D 2016 %J Molecular Biology and Evolution %O Mol. Biol. Evol. %V 33 %N 10 %& 2720 %P 2720 - 2734 %I Oxford University Press %C Oxford %@ false %U http://mbe.oxfordjournals.org/content/33/10/2720/suppl/DC1
151. Kalaghatgi P, Sikorski AM, Knops E, Rupp D, Sierra S, Heger E, Neumann-Fraune M, Beggel B, Walker A, Timm J, Walter H, Obermeier M, Kaiser R, Bartenschlager R, Lengauer T: Geno2pheno [HCV] -- A Web-based Interpretation System to Support Hepatitis C Treatment Decisions in the Era of Direct-Acting Antiviral Agents. PLoS One 2016, 11.
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@article{KalaghatgiPLOSone2016, TITLE = {{Geno2pheno} [{HCV}] -- A Web-based Interpretation System to Support Hepatitis {C} Treatment Decisions in the Era of Direct-Acting Antiviral Agents}, AUTHOR = {Kalaghatgi, Prabhav and Sikorski, Anna Maria and Knops, Elena and Rupp, Daniel and Sierra, Saleta and Heger, Eva and Neumann-Fraune, Maria and Beggel, Bastian and Walker, Andreas and Timm, J{\"o}rg and Walter, Hauke and Obermeier, Martin and Kaiser, Rolf and Bartenschlager, Ralf and Lengauer, Thomas}, LANGUAGE = {eng}, ISSN = {1932-6203}, DOI = {10.1371/journal.pone.0155869}, PUBLISHER = {Public Library of Science}, ADDRESS = {San Francisco, CA}, YEAR = {2016}, JOURNAL = {PLoS One}, VOLUME = {11}, NUMBER = {5}, EID = {e0155869}, }
Endnote
%0 Journal Article %A Kalaghatgi, Prabhav %A Sikorski, Anna Maria %A Knops, Elena %A Rupp, Daniel %A Sierra, Saleta %A Heger, Eva %A Neumann-Fraune, Maria %A Beggel, Bastian %A Walker, Andreas %A Timm, Jörg %A Walter, Hauke %A Obermeier, Martin %A Kaiser, Rolf %A Bartenschlager, Ralf %A Lengauer, Thomas %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T Geno2pheno [HCV] -- A Web-based Interpretation System to Support Hepatitis C Treatment Decisions in the Era of Direct-Acting Antiviral Agents : %G eng %U http://hdl.handle.net/11858/00-001M-0000-002A-EB8A-2 %R 10.1371/journal.pone.0155869 %2 PMC4873220 %7 2016-05-19 %D 2016 %8 19.05.2016 %J PLoS One %V 11 %N 5 %Z sequence number: e0155869 %I Public Library of Science %C San Francisco, CA %@ false
152. Kartashev V, Döring M, Nieto L, Coletta E, Kaiser R, Sierra S: New Findings in HCV Genotype Distribution in Selected West European, Russian and Israeli Regions. Journal of Clinical Virology 2016, 81.
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@article{Kartashev2016, TITLE = {New findings in {HCV} genotype distribution in selected {West European}, {Russian} and {Israeli} regions}, AUTHOR = {Kartashev, Vladimir and D{\"o}ring, Matthias and Nieto, Leonardo and Coletta, Eleda and Kaiser, Rolf and Sierra, Saleta}, LANGUAGE = {eng}, ISSN = {1386-6532}, DOI = {10.1016/j.jcv.2016.05.010}, PUBLISHER = {Elsevier}, ADDRESS = {Amsterdam}, YEAR = {2016}, DATE = {2016}, JOURNAL = {Journal of Clinical Virology}, VOLUME = {81}, PAGES = {82--89}, }
Endnote
%0 Journal Article %A Kartashev, Vladimir %A Döring, Matthias %A Nieto, Leonardo %A Coletta, Eleda %A Kaiser, Rolf %A Sierra, Saleta %+ External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations External Organizations %T New Findings in HCV Genotype Distribution in Selected West European, Russian and Israeli Regions : %G eng %U http://hdl.handle.net/11858/00-001M-0000-002A-F8EB-0 %R 10.1016/j.jcv.2016.05.010 %7 2016-05-24 %D 2016 %J Journal of Clinical Virology %V 81 %& 82 %P 82 - 89 %I Elsevier %C Amsterdam %@ false
153. Keller S: Finding Common Substructures in Viral Proteins Using Frequent Subgraph Mining. Universität des Saarlandes; 2016.
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@mastersthesis{Keller2016, TITLE = {Finding Common Substructures in Viral Proteins Using Frequent Subgraph Mining}, AUTHOR = {Keller, Sebastian}, LANGUAGE = {eng}, SCHOOL = {Universit{\"a}t des Saarlandes}, ADDRESS = {Saarbr{\"u}cken}, YEAR = {2016}, DATE = {2016}, }
Endnote
%0 Thesis %A Keller, Sebastian %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T Finding Common Substructures in Viral Proteins Using Frequent Subgraph Mining : %G eng %U http://hdl.handle.net/11858/00-001M-0000-002C-2881-6 %I Universität des Saarlandes %C Saarbrücken %D 2016 %V master %9 master
154. Lawyer G: Measuring the Potential of Individual Airports for Pandemic Spread over the World Airline Network. BMC Infectious Diseases 2016, 16.
Abstract
ABSTRACT: BACKGROUND: Massive growth in human mobility has dramatically increased the risk and rate of pandemic spread. Macro-level descriptors of the topology of the World Airline Network (WAN) explains middle and late stage dynamics of pandemic spread mediated by this network, but necessarily regard early stage variation as stochastic. We propose that much of this early stage variation can be explained by appropriately characterizing the local network topology surrounding an outbreak’s debut location. METHODS: Based on a model of the WAN derived from public data, we measure for each airport the expected force of infection (AEF) which a pandemic originating at that airport would generate, assuming an epidemic process which transmits from airport to airport via scheduled commercial flights. We observe, for a subset of world airports, the minimum transmission rate at which a disease becomes pandemically competent at each airport. We also observe, for a larger subset, the time until a pandemically competent outbreak achieves pandemic status given its debut location. Observations are generated using a highly sophisticated metapopulation reaction-diffusion simulator under a disease model known to well replicate the 2009 influenza pandemic. The robustness of the AEF measure to model misspecification is examined by degrading the underlying model WAN. RESULTS: AEF powerfully explains pandemic risk, showing correlation of 0.90 to the transmission level needed to give a disease pandemic competence, and correlation of 0.85 to the delay until an outbreak becomes a pandemic. The AEF is robust to model misspecification. For 97 % of airports, removing 15 % of airports from the model changes their AEF metric by less than 1 %. CONCLUSIONS: Appropriately summarizing the size, shape, and diversity of an airport’s local neighborhood in the WAN accurately explains much of the macro-level stochasticity in pandemic outcomes.
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@article{Lawyer2016BMC, TITLE = {Measuring the Potential of Individual Airports for Pandemic Spread over the World Airline Network}, AUTHOR = {Lawyer, Glenn}, LANGUAGE = {eng}, ISSN = {1471-2334}, DOI = {10.1186/s12879-016-1350-4}, PUBLISHER = {BioMed Central Ltd.}, ADDRESS = {London, UK}, YEAR = {2016}, ABSTRACT = {ABSTRACT: BACKGROUND: Massive growth in human mobility has dramatically increased the risk and rate of pandemic spread. Macro-level descriptors of the topology of the World Airline Network (WAN) explains middle and late stage dynamics of pandemic spread mediated by this network, but necessarily regard early stage variation as stochastic. We propose that much of this early stage variation can be explained by appropriately characterizing the local network topology surrounding an outbreak{\textquoteright}s debut location. METHODS: Based on a model of the WAN derived from public data, we measure for each airport the expected force of infection (AEF) which a pandemic originating at that airport would generate, assuming an epidemic process which transmits from airport to airport via scheduled commercial flights. We observe, for a subset of world airports, the minimum transmission rate at which a disease becomes pandemically competent at each airport. We also observe, for a larger subset, the time until a pandemically competent outbreak achieves pandemic status given its debut location. Observations are generated using a highly sophisticated metapopulation reaction-diffusion simulator under a disease model known to well replicate the 2009 influenza pandemic. The robustness of the AEF measure to model misspecification is examined by degrading the underlying model WAN. RESULTS: AEF powerfully explains pandemic risk, showing correlation of 0.90 to the transmission level needed to give a disease pandemic competence, and correlation of 0.85 to the delay until an outbreak becomes a pandemic. The AEF is robust to model misspecification. For 97 % of airports, removing 15 % of airports from the model changes their AEF metric by less than 1 %. CONCLUSIONS: Appropriately summarizing the size, shape, and diversity of an airport{\textquoteright}s local neighborhood in the WAN accurately explains much of the macro-level stochasticity in pandemic outcomes.}, JOURNAL = {BMC Infectious Diseases}, VOLUME = {16}, NUMBER = {1}, EID = {70}, }
Endnote
%0 Journal Article %A Lawyer, Glenn %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T Measuring the Potential of Individual Airports for Pandemic Spread over the World Airline Network : %G eng %U http://hdl.handle.net/11858/00-001M-0000-0029-C693-A %R 10.1186/s12879-016-1350-4 %7 2016-02-09 %D 2016 %8 09.02.2016 %X ABSTRACT: BACKGROUND: Massive growth in human mobility has dramatically increased the risk and rate of pandemic spread. Macro-level descriptors of the topology of the World Airline Network (WAN) explains middle and late stage dynamics of pandemic spread mediated by this network, but necessarily regard early stage variation as stochastic. We propose that much of this early stage variation can be explained by appropriately characterizing the local network topology surrounding an outbreak’s debut location. METHODS: Based on a model of the WAN derived from public data, we measure for each airport the expected force of infection (AEF) which a pandemic originating at that airport would generate, assuming an epidemic process which transmits from airport to airport via scheduled commercial flights. We observe, for a subset of world airports, the minimum transmission rate at which a disease becomes pandemically competent at each airport. We also observe, for a larger subset, the time until a pandemically competent outbreak achieves pandemic status given its debut location. Observations are generated using a highly sophisticated metapopulation reaction-diffusion simulator under a disease model known to well replicate the 2009 influenza pandemic. The robustness of the AEF measure to model misspecification is examined by degrading the underlying model WAN. RESULTS: AEF powerfully explains pandemic risk, showing correlation of 0.90 to the transmission level needed to give a disease pandemic competence, and correlation of 0.85 to the delay until an outbreak becomes a pandemic. The AEF is robust to model misspecification. For 97 % of airports, removing 15 % of airports from the model changes their AEF metric by less than 1 %. CONCLUSIONS: Appropriately summarizing the size, shape, and diversity of an airport’s local neighborhood in the WAN accurately explains much of the macro-level stochasticity in pandemic outcomes. %J BMC Infectious Diseases %V 16 %N 1 %Z sequence number: 70 %I BioMed Central Ltd. %C London, UK %@ false
155. Li J, Klughammer J, Farlik M, Penz T, Spittler A, Barbieux C, Berishvili E, Bock C, Kubicek S: Single-cell Transcriptomes Reveal Characteristic Features of Human Pancreatic Islet Cell Types. EMBO Reports 2016, 17.
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@article{Li2015EMBO, TITLE = {Single-cell Transcriptomes Reveal Characteristic Features of Human Pancreatic Islet Cell Types}, AUTHOR = {Li, Jin and Klughammer, Johanna and Farlik, Matthias and Penz, Thomas and Spittler, Andreas and Barbieux, Charlotte and Berishvili, Ekaterine and Bock, Christoph and Kubicek, Stefan}, LANGUAGE = {eng}, ISSN = {1469-221X}, DOI = {10.15252/embr.201540946}, PUBLISHER = {Published for EMBO by Oxford University Press}, ADDRESS = {Oxford, UK}, YEAR = {2016}, DATE = {2016}, JOURNAL = {EMBO Reports}, VOLUME = {17}, NUMBER = {2}, PAGES = {178--187}, }
Endnote
%0 Journal Article %A Li, Jin %A Klughammer, Johanna %A Farlik, Matthias %A Penz, Thomas %A Spittler, Andreas %A Barbieux, Charlotte %A Berishvili, Ekaterine %A Bock, Christoph %A Kubicek, Stefan %+ External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations %T Single-cell Transcriptomes Reveal Characteristic Features of Human Pancreatic Islet Cell Types : %G eng %U http://hdl.handle.net/11858/00-001M-0000-0029-4243-A %R 10.15252/embr.201540946 %7 2015-12-21 %D 2016 %J EMBO Reports %O EMBO Rep. %V 17 %N 2 %& 178 %P 178 - 187 %I Published for EMBO by Oxford University Press %C Oxford, UK %@ false %U http://onlinelibrary.wiley.com/doi/10.15252/embr.201540946/pdf
156. List M, Schmidt S, Christiansen H, Rehmsmeier M, Tan O, Mollenhauer J, Baumbach J: Comprehensive Analysis of High-throughput Screens with HiTSeekR. Nucleic Acids Research 2016, 44.
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@article{ListNAR2016, TITLE = {Comprehensive analysis of high-throughput screens with {HiTSeekR}}, AUTHOR = {List, Markus and Schmidt, Steffen and Christiansen, Helle and Rehmsmeier, Marc and Tan, Oihua and Mollenhauer, Jan and Baumbach, Jan}, LANGUAGE = {eng}, ISSN = {0301-5610}, DOI = {10.1093/nar/gkw554}, YEAR = {2016}, DATE = {2016}, JOURNAL = {Nucleic Acids Research}, VOLUME = {44}, NUMBER = {14}, PAGES = {6639--6648}, }
Endnote
%0 Journal Article %A List, Markus %A Schmidt, Steffen %A Christiansen, Helle %A Rehmsmeier, Marc %A Tan, Oihua %A Mollenhauer, Jan %A Baumbach, Jan %+ External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T Comprehensive Analysis of High-throughput Screens with HiTSeekR : %G eng %U http://hdl.handle.net/11858/00-001M-0000-002B-4666-3 %R 10.1093/nar/gkw554 %7 2016 %D 2016 %J Nucleic Acids Research %O Nucleic Acids Res. %V 44 %N 14 %& 6639 %P 6639 - 6648 %@ false
157. List M, Alcaraz N, Dissing-Hansen M, Ditzel HJ, Mollenhauer J, Baumbach J: KeyPathwayMinerWeb: Online Multi-omics Network Enrichment. Nucleic Acids Research 2016, 44(W1/Web Server issue).
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@article{List:Baumbach2016, TITLE = {{KeyPathwayMinerWeb}: {O}nline Multi-omics Network Enrichment}, AUTHOR = {List, Markus and Alcaraz, Nicolas and Dissing-Hansen, Martin and Ditzel, Henrik J. and Mollenhauer, Jan and Baumbach, Jan}, LANGUAGE = {eng}, DOI = {10.1093/nar/gkw373}, PUBLISHER = {Oxford University Press}, ADDRESS = {Oxford, UK}, YEAR = {2016}, DATE = {2016}, JOURNAL = {Nucleic Acids Research}, VOLUME = {44}, NUMBER = {W1/Web Server issue}, PAGES = {W98--W104}, }
Endnote
%0 Journal Article %A List, Markus %A Alcaraz, Nicolas %A Dissing-Hansen, Martin %A Ditzel, Henrik J. %A Mollenhauer, Jan %A Baumbach, Jan %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T KeyPathwayMinerWeb: Online Multi-omics Network Enrichment : %G eng %U http://hdl.handle.net/11858/00-001M-0000-002B-42F8-8 %R 10.1093/nar/gkw373 %2 PMC4987922 %7 2016 %D 2016 %* Review method: peer-reviewed %J Nucleic Acids Research %V 44 %N W1/Web Server issue %& W98 %P W98 - W104 %I Oxford University Press %C Oxford, UK
158. Lüssem H: Identifying Structural Variants Using Variant Graphs. Universität des Saarlandes; 2016.
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@mastersthesis{LuessemBachelor2016, TITLE = {Identifying Structural Variants Using Variant Graphs}, AUTHOR = {L{\"u}ssem, Helene}, LANGUAGE = {eng}, SCHOOL = {Universit{\"a}t des Saarlandes}, ADDRESS = {Saarbr{\"u}cken}, YEAR = {2016}, DATE = {2016}, TYPE = {Bachelor's thesis}, }
Endnote
%0 Thesis %A Lüssem, Helene %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T Identifying Structural Variants Using Variant Graphs : %G eng %U http://hdl.handle.net/11858/00-001M-0000-002C-480F-A %I Universität des Saarlandes %C Saarbrücken %D 2016 %V bachelor %9 bachelor
159. Magiorkinis G, Angelis K, Mamais I, Katzourakis A, Hatzakis A, Albert J, Lawyer G, Hamouda O, Struck D, Vercauteren J, Wensing A, Alexiev I, Åsjö B, Balotta C, Gomes P, Camacho RJ, Coughlan S, Griskevicius A, Grossman Z, Horban A, Kostrikis LG, Lepej SJ, Liitsola K, Linka M, Nielsen C, Otelea D, Paredes R, Poljak M, Puchhammer-Stöckl E, Schmit JC, et al.: The Global Spread of HIV-1 Subtype B Epidemic. Infection, Genetics and Evolution 2016, 46.
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@article{Magiorkinis2016, TITLE = {The global spread of {HIV}-1 subtype {B} epidemic}, AUTHOR = {Magiorkinis, Gkikas and Angelis, Konstantinos and Mamais, Ioannis and Katzourakis, Aris and Hatzakis, Angelo and Albert, Jan and Lawyer, Glenn and Hamouda, Osamah and Struck, Daniel and Vercauteren, Jurgen and Wensing, Annemarie and Alexiev, Ivailo and {\AA}sj{\"o}, Birgitta and Balotta, Claudia and Gomes, Perp{\'e}tua and Camacho, Ricardo J. and Coughlan, Suzie and Griskevicius, Algirdas and Grossman, Zehava and Horban, Anders and Kostrikis, Leondios G. and Lepej, Snjezana J. and Liitsola, Kirsi and Linka, Marek and Nielsen, Claus and Otelea, Dan and Paredes, Roger and Poljak, Mario and Puchhammer-St{\"o}ckl, Elizabeth and Schmit, Jean Claude and S{\"o}nnerborg, Anders and Stanekov{\'a}, Danica and Stanojevic, Maja and Stylianou, Dora C. and Boucher, Charles A. B. and Nikolopoulos, Georgios and Vasylyeva, Tetyana and Friedman, Samuel R. and van de Vijver, David and Angarano, Gioacchino and Chaix, Marie-Laure and de Luca, Andrea and Korn, Klaus and Loveday, Clive and Soriano, Vincent and Yerly, Sabine and Zazzi, Mauricio and Vandamm, Anne-Mieke and Paraskevis, Dimitrios}, LANGUAGE = {eng}, DOI = {10.1016/j.meegid.2016.05.041}, PUBLISHER = {Elsevier}, ADDRESS = {Amsterdam}, YEAR = {2016}, DATE = {2016}, JOURNAL = {Infection, Genetics and Evolution}, VOLUME = {46}, PAGES = {169--179}, }
Endnote
%0 Journal Article %A Magiorkinis, Gkikas %A Angelis, Konstantinos %A Mamais, Ioannis %A Katzourakis, Aris %A Hatzakis, Angelo %A Albert, Jan %A Lawyer, Glenn %A Hamouda, Osamah %A Struck, Daniel %A Vercauteren, Jurgen %A Wensing, Annemarie %A Alexiev, Ivailo %A Åsjö, Birgitta %A Balotta, Claudia %A Gomes, Perpétua %A Camacho, Ricardo J. %A Coughlan, Suzie %A Griskevicius, Algirdas %A Grossman, Zehava %A Horban, Anders %A Kostrikis, Leondios G. %A Lepej, Snjezana J. %A Liitsola, Kirsi %A Linka, Marek %A Nielsen, Claus %A Otelea, Dan %A Paredes, Roger %A Poljak, Mario %A Puchhammer-Stöckl, Elizabeth %A Schmit, Jean Claude %A Sönnerborg, Anders %A Staneková, Danica %A Stanojevic, Maja %A Stylianou, Dora C. %A Boucher, Charles A. B. %A Nikolopoulos, Georgios %A Vasylyeva, Tetyana %A Friedman, Samuel R. %A van de Vijver, David %A Angarano, Gioacchino %A Chaix, Marie-Laure %A de Luca, Andrea %A Korn, Klaus %A Loveday, Clive %A Soriano, Vincent %A Yerly, Sabine %A Zazzi, Mauricio %A Vandamm, Anne-Mieke %A Paraskevis, Dimitrios %+ External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations %T The Global Spread of HIV-1 Subtype B Epidemic : %G eng %U http://hdl.handle.net/11858/00-001M-0000-002C-2F82-8 %R 10.1016/j.meegid.2016.05.041 %7 2016 %D 2016 %J Infection, Genetics and Evolution %V 46 %& 169 %P 169 - 179 %I Elsevier %C Amsterdam
160. Malek M, Ibragimov R, Albrecht M, Baumbach J: CytoGEDEVO-global Alignment of Biological Networks with Cytoscape. Bioinformatics 2016, 32.
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@article{Malek2016, TITLE = {{CytoGEDEVO}-global alignment of biological networks with {Cytoscape}}, AUTHOR = {Malek, Maximilian and Ibragimov, Rashid and Albrecht, Mario and Baumbach, Jan}, LANGUAGE = {eng}, ISSN = {1367-4803}, DOI = {10.1093/bioinformatics/btv732}, PUBLISHER = {Oxford University Press}, ADDRESS = {Oxford}, YEAR = {2016}, DATE = {2016}, JOURNAL = {Bioinformatics}, VOLUME = {32}, NUMBER = {8}, PAGES = {1259--1261}, }
Endnote
%0 Journal Article %A Malek, Maximilian %A Ibragimov, Rashid %A Albrecht, Mario %A Baumbach, Jan %+ External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations %T CytoGEDEVO-global Alignment of Biological Networks with Cytoscape : %G eng %U http://hdl.handle.net/11858/00-001M-0000-002A-C477-9 %R 10.1093/bioinformatics/btv732 %7 2015-12-14 %D 2016 %J Bioinformatics %V 32 %N 8 %& 1259 %P 1259 - 1261 %I Oxford University Press %C Oxford %@ false
161. Martínez-Cardús A, Moran S, Musulen E, Moutinho C, Manzano JL, Martinez-Balibrea E, Tierno M, Élez E, Landolfi S, Lorden P, Arribas C, Müller F, Bock C, Tabernero J, Esteller M: Epigenetic Homogeneity Within Colorectal Tumors Predicts Shorter Relapse-Free and Overall Survival Times for Patients With Locoregional Cancer. Gastroenterology 2016, 151.
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@article{MartinezCardus:2016jd, TITLE = {Epigenetic Homogeneity Within Colorectal Tumors Predicts Shorter Relapse-Free and Overall Survival Times for Patients With Locoregional Cancer}, AUTHOR = {Mart{\'i}nez-Card{\'u}s, Anna and Moran, Sebastian and Musulen, Eva and Moutinho, C{\'a}tia and Manzano, Jose L. and Martinez-Balibrea, Eva and Tierno, Montserrat and {\'E}lez, Elena and Landolfi, Stefania and Lorden, Patricia and Arribas, Carles and M{\"u}ller, Fabian and Bock, Christoph and Tabernero, Josep and Esteller, Manel}, LANGUAGE = {eng}, ISSN = {0016-5085}, DOI = {10.1053/j.gastro.2016.08.001}, PUBLISHER = {W.B. Saunders}, ADDRESS = {Philadelphia, Pa}, YEAR = {2016}, DATE = {2016}, JOURNAL = {Gastroenterology}, VOLUME = {151}, NUMBER = {5}, PAGES = {961--972}, }
Endnote
%0 Journal Article %A Martínez-Cardús, Anna %A Moran, Sebastian %A Musulen, Eva %A Moutinho, Cátia %A Manzano, Jose L. %A Martinez-Balibrea, Eva %A Tierno, Montserrat %A Élez, Elena %A Landolfi, Stefania %A Lorden, Patricia %A Arribas, Carles %A Müller, Fabian %A Bock, Christoph %A Tabernero, Josep %A Esteller, Manel %+ External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations %T Epigenetic Homogeneity Within Colorectal Tumors Predicts Shorter Relapse-Free and Overall Survival Times for Patients With Locoregional Cancer : %G eng %U http://hdl.handle.net/11858/00-001M-0000-002C-20AF-B %R 10.1053/j.gastro.2016.08.001 %7 2016 %D 2016 %J Gastroenterology %O Gastroenterology %V 151 %N 5 %& 961 %P 961 - 972 %I W.B. Saunders %C Philadelphia, Pa %@ false
162. Mass E, Ballestero I, Farlik M, Halbritter F, Günther P, Crozet L, Jacome-Galarza CE, Händler K, Klughammer J, Kobayashi Y, Gomez-Perdiguero E, Schultze JL, Beyer M, Bock C, Geissman F: Specification of Tissue-resident Macrophages During Organogenesis. Science 2016, 353.
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@article{Mass2016, TITLE = {Specification of Tissue-resident Macrophages During Organogenesis}, AUTHOR = {Mass, Elvira and Ballestero, Ivan and Farlik, Matthias and Halbritter, Florian and G{\"u}nther, Patrick and Crozet, Lucile and Jacome-Galarza, Christian E. and H{\"a}ndler, Kristian and Klughammer, Johanna and Kobayashi, Yasuhiro and Gomez-Perdiguero, Elisa and Schultze, Joachim L. and Beyer, Marc and Bock, Christoph and Geissman, Frederic}, LANGUAGE = {eng}, ISSN = {0036-8075}, DOI = {10.1126/science.aaf4238}, PUBLISHER = {American Association for the Advancement of Science}, ADDRESS = {Washington, D.C.}, YEAR = {2016}, DATE = {2016}, JOURNAL = {Science}, VOLUME = {353}, NUMBER = {6304}, EID = {aaf4238}, }
Endnote
%0 Journal Article %A Mass, Elvira %A Ballestero, Ivan %A Farlik, Matthias %A Halbritter, Florian %A Günther, Patrick %A Crozet, Lucile %A Jacome-Galarza, Christian E. %A Händler, Kristian %A Klughammer, Johanna %A Kobayashi, Yasuhiro %A Gomez-Perdiguero, Elisa %A Schultze, Joachim L. %A Beyer, Marc %A Bock, Christoph %A Geissman, Frederic %+ External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations %T Specification of Tissue-resident Macrophages During Organogenesis : %G eng %U http://hdl.handle.net/11858/00-001M-0000-002B-62AE-3 %R 10.1126/science.aaf4238 %7 2016 %D 2016 %J Science %V 353 %N 6304 %Z sequence number: aaf4238 %I American Association for the Advancement of Science %C Washington, D.C. %@ false
163. Meyerheim M: Viral Haplotype Assembly from HIV Patient Data. Universität des Saarlandes; 2016.
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@mastersthesis{Meyerheim_MSc2016, TITLE = {Viral Haplotype Assembly from {HIV} Patient Data}, AUTHOR = {Meyerheim, Marcel}, LANGUAGE = {eng}, SCHOOL = {Universit{\"a}t des Saarlandes}, ADDRESS = {Saarbr{\"u}cken}, YEAR = {2016}, DATE = {2016}, }
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%0 Thesis %A Meyerheim, Marcel %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T Viral Haplotype Assembly from HIV Patient Data : %G eng %U http://hdl.handle.net/11858/00-001M-0000-002C-484C-D %I Universität des Saarlandes %C Saarbrücken %D 2016 %V master %9 master
164. Mueller SC, Backes C, Gress A, Baumgarten N, Kalinina OV, Moll A, Kohlbacher O, Meese E, Keller A: BALL-SNPgp -- From Genetic Variants Toward Computational Diagnostics. Bioinformatics 2016, 32.
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@article{MuellerBioinformatics2016, TITLE = {{BALL}-{SNPgp} -- From Genetic Variants Toward Computational Diagnostics}, AUTHOR = {Mueller, Sabine C. and Backes, Christina and Gress, Alexander and Baumgarten, Nina and Kalinina, Olga V. and Moll, Andreas and Kohlbacher, Oliver and Meese, Eckart and Keller, Andreas}, LANGUAGE = {eng}, ISSN = {1367-4803}, DOI = {10.1093/bioinformatics/btw084}, PUBLISHER = {Oxford University Press}, ADDRESS = {Oxford}, YEAR = {2016}, DATE = {2016}, JOURNAL = {Bioinformatics}, VOLUME = {32}, NUMBER = {12}, PAGES = {1888--1890}, }
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%0 Journal Article %A Mueller, Sabine C. %A Backes, Christina %A Gress, Alexander %A Baumgarten, Nina %A Kalinina, Olga V. %A Moll, Andreas %A Kohlbacher, Oliver %A Meese, Eckart %A Keller, Andreas %+ External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations External Organizations %T BALL-SNPgp -- From Genetic Variants Toward Computational Diagnostics : %G eng %U http://hdl.handle.net/11858/00-001M-0000-002B-1954-5 %R 10.1093/bioinformatics/btw084 %7 2016 %D 2016 %J Bioinformatics %V 32 %N 12 %& 1888 %P 1888 - 1890 %I Oxford University Press %C Oxford %@ false
165. Peiffer K-H, Sommer L, Susser S, Vermehren J, Herrmann E, Döring M, Dietz J, Perner D, Berkowski C, Zeuzem S, Sarrazin C: Interferon Lambda 4 Genotypes and Resistance-associated Variants in Patients Infected with Hepatitis C Virus Genotypes 1 and 3. Hepatology 2016, 63.
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@article{Pfeiffer2015, TITLE = {Interferon Lambda 4 Genotypes and Resistance-associated Variants in Patients Infected with Hepatitis {C} Virus Genotypes 1 and 3}, AUTHOR = {Peiffer, Kai-Henrik and Sommer, Lisa and Susser, Simone and Vermehren, Johannes and Herrmann, Eva and D{\"o}ring, Matthias and Dietz, Julia and Perner, Dany and Berkowski, Caterina and Zeuzem, Stefan and Sarrazin, Christoph}, LANGUAGE = {eng}, ISSN = {1527-3350}, DOI = {10.1002/hep.28255}, PUBLISHER = {Wiley}, ADDRESS = {New York, NY}, YEAR = {2016}, DATE = {2016}, JOURNAL = {Hepatology}, VOLUME = {63}, NUMBER = {1}, PAGES = {63--73}, }
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%0 Journal Article %A Peiffer, Kai-Henrik %A Sommer, Lisa %A Susser, Simone %A Vermehren, Johannes %A Herrmann, Eva %A Döring, Matthias %A Dietz, Julia %A Perner, Dany %A Berkowski, Caterina %A Zeuzem, Stefan %A Sarrazin, Christoph %+ External Organizations External Organizations External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations External Organizations External Organizations %T Interferon Lambda 4 Genotypes and Resistance-associated Variants in Patients Infected with Hepatitis C Virus Genotypes 1 and 3 : %G eng %U http://hdl.handle.net/11858/00-001M-0000-0029-1864-F %R 10.1002/hep.28255 %7 2015-11-25 %D 2016 %J Hepatology %V 63 %N 1 %& 63 %P 63 - 73 %I Wiley %C New York, NY %@ false
166. Pironti A: Improving and Validating Data-driven Genotypic Interpretation Systems for the Selection of Antiretroviral Therapies. Universität des Saarlandes; 2016.
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@phdthesis{Pirontiphd16, TITLE = {Improving and Validating Data-driven Genotypic Interpretation Systems for the Selection of Antiretroviral Therapies}, AUTHOR = {Pironti, Alejandro}, LANGUAGE = {eng}, URL = {urn:nbn:de:bsz:291-scidok-67190}, SCHOOL = {Universit{\"a}t des Saarlandes}, ADDRESS = {Saarbr{\"u}cken}, YEAR = {2016}, DATE = {2016}, }
Endnote
%0 Thesis %A Pironti, Alejandro %Y Lengauer, Thomas %A referee: Lenhof, Hans-Peter %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society International Max Planck Research School, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations %T Improving and Validating Data-driven Genotypic Interpretation Systems for the Selection of Antiretroviral Therapies : %G eng %U http://hdl.handle.net/11858/00-001M-0000-002C-30D5-5 %U urn:nbn:de:bsz:291-scidok-67190 %I Universität des Saarlandes %C Saarbrücken %D 2016 %P x, 272 p. %V phd %9 phd %U http://scidok.sulb.uni-saarland.de/volltexte/2016/6719/http://scidok.sulb.uni-saarland.de/doku/lic_ohne_pod.php?la=de
167. Rendeiro AF, Schmidl C, Strefford JC, Walewska R, Davis Z, Farlik M, Oscier D, Bock C: Chromatin Accessibility Maps of Chronic Lymphocytic Leukaemia Identify Subtype-specific Epigenome Signatures and Transcription Regulatory networks. Nature Communications 2016, 7.
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@article{Rendeiro2016, TITLE = {Chromatin Accessibility Maps of Chronic Lymphocytic Leukaemia Identify Subtype-specific Epigenome Signatures and Transcription Regulatory networks}, AUTHOR = {Rendeiro, Andr{\'e} F. and Schmidl, Christian and Strefford, Jonathan C. and Walewska, Renata and Davis, Zadie and Farlik, Matthias and Oscier, David and Bock, Christoph}, LANGUAGE = {eng}, ISSN = {2041-1723}, DOI = {10.1038/ncomms11938}, PUBLISHER = {Nature Publishing Group}, ADDRESS = {London}, YEAR = {2016}, JOURNAL = {Nature Communications}, VOLUME = {7}, EID = {11938}, }
Endnote
%0 Journal Article %A Rendeiro, André F. %A Schmidl, Christian %A Strefford, Jonathan C. %A Walewska, Renata %A Davis, Zadie %A Farlik, Matthias %A Oscier, David %A Bock, Christoph %+ External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T Chromatin Accessibility Maps of Chronic Lymphocytic Leukaemia Identify Subtype-specific Epigenome Signatures and Transcription Regulatory networks : %G eng %U http://hdl.handle.net/11858/00-001M-0000-002B-133F-B %R 10.1038/ncomms11938 %7 2016 %D 2016 %J Nature Communications %O Nat. Commun. %V 7 %Z sequence number: 11938 %I Nature Publishing Group %C London %@ false
168. Rommes B: Genome-Wide Association Studies on Simulated Bacterial Genomes. Universität des Saarlandes; 2016.
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@mastersthesis{RommesBachelor2016, TITLE = {Genome-Wide Association Studies on Simulated Bacterial Genomes}, AUTHOR = {Rommes, Basile}, LANGUAGE = {eng}, SCHOOL = {Universit{\"a}t des Saarlandes}, ADDRESS = {Saarbr{\"u}cken}, YEAR = {2016}, DATE = {2016}, TYPE = {Bachelor's thesis}, }
Endnote
%0 Thesis %A Rommes, Basile %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T Genome-Wide Association Studies on Simulated Bacterial Genomes : %G eng %U http://hdl.handle.net/11858/00-001M-0000-002C-4807-9 %I Universität des Saarlandes %C Saarbrücken %D 2016 %V bachelor %9 bachelor
169. Scheid JF, Horwitz JA, Bar-On Y, Kreider EF, Lu C-L, Lorenzi JCC, Feldmann A, Braunschweig M, Nogueira L, Oliveira T, Shimeliovich I, Patel R, Burke L, Cohen YZ, Hadrigan S, Settler A, Witmer-Pack M, West AP, Juelg B, Keler T, Hawthorne T, Zingman B, Gulick RM, Pfeifer N, Learn GH, Seaman MS, Bjorkman PJ, Klein F, Schlesinger SJ, Walker BD, et al.: HIV-1 Antibody 3BNC117 Suppresses Viral Rebound in Humans During Treatment Interruption. Nature 2016, 535.
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@article{Scheid2016, TITLE = {{HIV}-1 antibody {3BNC117} suppresses viral rebound in humans during treatment interruption}, AUTHOR = {Scheid, Johannes F. and Horwitz, Joshua A. and Bar-On, Yotam and Kreider, Edward F. and Lu, Ching-Lan and Lorenzi, Julio C. C. and Feldmann, Anna and Braunschweig, Malte and Nogueira, Lilian and Oliveira, Thiago and Shimeliovich, Irina and Patel, Roshni and Burke, Leah and Cohen, Yehuda Z. and Hadrigan, Sonya and Settler, Allison and Witmer-Pack, Maggi and West, Anthony P. and Juelg, Boris and Keler, Tibor and Hawthorne, Thomas and Zingman, Barry and Gulick, Roy M. and Pfeifer, Nico and Learn, Gerald H. and Seaman, Michael S. and Bjorkman, Pamela J. and Klein, Florian and Schlesinger, Sarah J. and Walker, Bruce D. and Hahn, Beatrice H. and Nussenzweig, Michel C. and Caskey, Marina}, LANGUAGE = {eng}, ISSN = {0028-0836}, DOI = {10.1038/nature18929}, PUBLISHER = {Nature Publishing Group}, ADDRESS = {London}, YEAR = {2016}, DATE = {2016}, JOURNAL = {Nature}, VOLUME = {535}, NUMBER = {7613}, PAGES = {556--560}, }
Endnote
%0 Journal Article %A Scheid, Johannes F. %A Horwitz, Joshua A. %A Bar-On, Yotam %A Kreider, Edward F. %A Lu, Ching-Lan %A Lorenzi, Julio C. C. %A Feldmann, Anna %A Braunschweig, Malte %A Nogueira, Lilian %A Oliveira, Thiago %A Shimeliovich, Irina %A Patel, Roshni %A Burke, Leah %A Cohen, Yehuda Z. %A Hadrigan, Sonya %A Settler, Allison %A Witmer-Pack, Maggi %A West, Anthony P. %A Juelg, Boris %A Keler, Tibor %A Hawthorne, Thomas %A Zingman, Barry %A Gulick, Roy M. %A Pfeifer, Nico %A Learn, Gerald H. %A Seaman, Michael S. %A Bjorkman, Pamela J. %A Klein, Florian %A Schlesinger, Sarah J. %A Walker, Bruce D. %A Hahn, Beatrice H. %A Nussenzweig, Michel C. %A Caskey, Marina %+ External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations %T HIV-1 Antibody 3BNC117 Suppresses Viral Rebound in Humans During Treatment Interruption : %G eng %U http://hdl.handle.net/11858/00-001M-0000-002B-8264-5 %R 10.1038/nature18929 %7 2016 %D 2016 %J Nature %O Nature %V 535 %N 7613 %& 556 %P 556 - 560 %I Nature Publishing Group %C London %@ false
170. Scherer M: Dissecting DNA Methylation in Human Aging. Universität des Saarlandes; 2016.
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@mastersthesis{SchererMaster2016, TITLE = {Dissecting {DNA} Methylation in Human Aging}, AUTHOR = {Scherer, Michael}, LANGUAGE = {eng}, SCHOOL = {Universit{\"a}t des Saarlandes}, ADDRESS = {Saarbr{\"u}cken}, YEAR = {2016}, DATE = {2016}, }
Endnote
%0 Thesis %A Scherer, Michael %Y Lengauer, Thomas %A referee: Walter, Jörn %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T Dissecting DNA Methylation in Human Aging : %G eng %U http://hdl.handle.net/11858/00-001M-0000-002C-3B96-C %I Universität des Saarlandes %C Saarbrücken %D 2016 %V master %9 master
171. Schoofs T, Klein F, Braunschweig M, Kreider EF, Feldmann A, Nogueira L, Oliveira T, Lorenzi JCC, Parrish EH, Learn GH, West AP, Bjorkman PJ, Schlesinger S, Seaman MS, Czartoski J, McElrath MJ, Pfeifer N, Hahn BH, Caskey M, Nussenzweig MC: HIV-1 Therapy with Monoclonal Antibody 3BNC117 Elicits Host Immune Responses Against HIV-1. Science 2016, 352.
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@article{Schoofs2016, TITLE = {{HIV}-1 Therapy with Monoclonal Antibody {3BNC117} Elicits Host Immune Responses Against {HIV}-1}, AUTHOR = {Schoofs, Till and Klein, Florian and Braunschweig, Malte and Kreider, Edward F. and Feldmann, Anna and Nogueira, Lilian and Oliveira, Thiago and Lorenzi, Julio C. C. and Parrish, Erica H. and Learn, Gerald H. and West, Anthony P. and Bjorkman, Pamela J. and Schlesinger, Sarah and Seaman, Michael S. and Czartoski, Julie and McElrath, M. Juliana and Pfeifer, Nico and Hahn, Beatrice H. and Caskey, Marina and Nussenzweig, Michel C.}, LANGUAGE = {eng}, ISSN = {0036-8075}, DOI = {10.1126/science.aaf0972}, PUBLISHER = {AAAS}, ADDRESS = {Washington, DC}, YEAR = {2016}, DATE = {2016}, JOURNAL = {Science}, VOLUME = {352}, NUMBER = {6288}, PAGES = {997--1001}, }
Endnote
%0 Journal Article %A Schoofs, Till %A Klein, Florian %A Braunschweig, Malte %A Kreider, Edward F. %A Feldmann, Anna %A Nogueira, Lilian %A Oliveira, Thiago %A Lorenzi, Julio C. C. %A Parrish, Erica H. %A Learn, Gerald H. %A West, Anthony P. %A Bjorkman, Pamela J. %A Schlesinger, Sarah %A Seaman, Michael S. %A Czartoski, Julie %A McElrath, M. Juliana %A Pfeifer, Nico %A Hahn, Beatrice H. %A Caskey, Marina %A Nussenzweig, Michel C. %+ External Organizations External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations %T HIV-1 Therapy with Monoclonal Antibody 3BNC117 Elicits Host Immune Responses Against HIV-1 : %G eng %U http://hdl.handle.net/11858/00-001M-0000-002A-D9BC-3 %R 10.1126/science.aaf0972 %7 2016 %D 2016 %J Science %V 352 %N 6288 %& 997 %P 997 - 1001 %I AAAS %C Washington, DC %@ false
172. Sdelci S, Lardeau C-H, Tallant C, Klepsch F, Klaiber B, Bennett J, Rathert P, Schuster M, Penz T, Fedorov O, Superti-Furga G, Bock C, Zuber J, Huber KVM, Knapp S, Müller S, Kubicek S: Mapping the Chemical Chromatin Reactivation Landscape Identifies BRD4-TAF1 Cross-talk. Nature Chemical Biology 2016, 12.
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@article{Sdelci2016, TITLE = {Mapping the Chemical Chromatin Reactivation Landscape Identifies {BRD4}-{TAF1} Cross-talk}, AUTHOR = {Sdelci, Sara and Lardeau, Charles-Hugues and Tallant, Cynthia and Klepsch, Freya and Klaiber, Bj{\"o}rn and Bennett, James and Rathert, Philipp and Schuster, Michael and Penz, Thomas and Fedorov, Oleg and Superti-Furga, Guilio and Bock, Christoph and Zuber, Johannes and Huber, Kilan V. M. and Knapp, Stefan and M{\"u}ller, Susanne and Kubicek, Stefan}, LANGUAGE = {eng}, ISSN = {1552-4450}, DOI = {10.1038/nchembio.2080}, PUBLISHER = {Nature Pub. Group}, ADDRESS = {New York, NY}, YEAR = {2016}, DATE = {2016}, JOURNAL = {Nature Chemical Biology}, VOLUME = {12}, PAGES = {504--510}, }
Endnote
%0 Journal Article %A Sdelci, Sara %A Lardeau, Charles-Hugues %A Tallant, Cynthia %A Klepsch, Freya %A Klaiber, Björn %A Bennett, James %A Rathert, Philipp %A Schuster, Michael %A Penz, Thomas %A Fedorov, Oleg %A Superti-Furga, Guilio %A Bock, Christoph %A Zuber, Johannes %A Huber, Kilan V. M. %A Knapp, Stefan %A Müller, Susanne %A Kubicek, Stefan %+ External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations External Organizations External Organizations %T Mapping the Chemical Chromatin Reactivation Landscape Identifies BRD4-TAF1 Cross-talk : %G eng %U http://hdl.handle.net/11858/00-001M-0000-002A-FC88-C %R 10.1038/nchembio.2080 %7 2016 %D 2016 %J Nature Chemical Biology %O Nat. Chem. Biol. %V 12 %& 504 %P 504 - 510 %I Nature Pub. Group %C New York, NY %@ false
173. Sethi R: Evaluation of Population-Based Haplotype Phasing Algorithms. Universität des Saarlandes; 2016.
Abstract
The valuable information in correct order of alleles on the haplotypes has many applications in GWAS studies and population genetics. A considerable number of computational and statistical algorithms have been developed for haplotype phasing. Historically, these algorithms were compared using the simulated population data with less dense markers which was inspired by genotype data from the HapMap project. Currently due to the advancement and reduction in cost of NGS, thousands of individuals across the world have been sequenced in 1000 Genomes Project. This has generated the genotype information of individuals from different ethnicity along with much denser genetic variations in them. Here, we have developed a scalable approach to assess state-of-the-art population-based haplotype phasing algorithms with benchmark data designed by simulation of the population (unrelated and related individuals), NGS pipeline and genotype calling. The most accurate algorithm was MVNCall (v1) for phase inference in unrelated individuals while DuoHMM approach of Shapeit (v2) had lowest switch error rate of 0.298 %(with true genotype likelihoods) in the related individuals. Moreover, we also conducted a comprehensive assessment of algorithms for the imputation of missing genotypes in the population with a reference panel. For this metrics, Impute2 (v2.3.2) and Beagle (v4.1) both performed competitively under different imputation scenarios and had genotype concordance rate of >99%. However, Impute2 was better in imputation of genotypes with minor allele frequency of <0.025 in the reference panel.
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@mastersthesis{SethiMaster2016, TITLE = {Evaluation of Population-Based Haplotype Phasing Algorithms}, AUTHOR = {Sethi, Riccha}, LANGUAGE = {eng}, SCHOOL = {Universit{\"a}t des Saarlandes}, ADDRESS = {Saarbr{\"u}cken}, YEAR = {2016}, DATE = {2016-03-09}, ABSTRACT = {The valuable information in correct order of alleles on the haplotypes has many applications in GWAS studies and population genetics. A considerable number of computational and statistical algorithms have been developed for haplotype phasing. Historically, these algorithms were compared using the simulated population data with less dense markers which was inspired by genotype data from the HapMap project. Currently due to the advancement and reduction in cost of NGS, thousands of individuals across the world have been sequenced in 1000 Genomes Project. This has generated the genotype information of individuals from different ethnicity along with much denser genetic variations in them. Here, we have developed a scalable approach to assess state-of-the-art population-based haplotype phasing algorithms with benchmark data designed by simulation of the population (unrelated and related individuals), NGS pipeline and genotype calling. The most accurate algorithm was MVNCall (v1) for phase inference in unrelated individuals while DuoHMM approach of Shapeit (v2) had lowest switch error rate of 0.298 %(with true genotype likelihoods) in the related individuals. Moreover, we also conducted a comprehensive assessment of algorithms for the imputation of missing genotypes in the population with a reference panel. For this metrics, Impute2 (v2.3.2) and Beagle (v4.1) both performed competitively under different imputation scenarios and had genotype concordance rate of >99%. However, Impute2 was better in imputation of genotypes with minor allele frequency of <0.025 in the reference panel.}, }
Endnote
%0 Thesis %A Sethi, Riccha %Y Marschall, Tobias %A referee: Pfeifer, Nico %+ International Max Planck Research School, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T Evaluation of Population-Based Haplotype Phasing Algorithms : %G eng %U http://hdl.handle.net/11858/00-001M-0000-002C-41DA-7 %I Universit&#228;t des Saarlandes %C Saarbr&#252;cken %D 2016 %8 09.03.2016 %P 76 p. %V master %9 master %X The valuable information in correct order of alleles on the haplotypes has many applications in GWAS studies and population genetics. A considerable number of computational and statistical algorithms have been developed for haplotype phasing. Historically, these algorithms were compared using the simulated population data with less dense markers which was inspired by genotype data from the HapMap project. Currently due to the advancement and reduction in cost of NGS, thousands of individuals across the world have been sequenced in 1000 Genomes Project. This has generated the genotype information of individuals from different ethnicity along with much denser genetic variations in them. Here, we have developed a scalable approach to assess state-of-the-art population-based haplotype phasing algorithms with benchmark data designed by simulation of the population (unrelated and related individuals), NGS pipeline and genotype calling. The most accurate algorithm was MVNCall (v1) for phase inference in unrelated individuals while DuoHMM approach of Shapeit (v2) had lowest switch error rate of 0.298 %(with true genotype likelihoods) in the related individuals. Moreover, we also conducted a comprehensive assessment of algorithms for the imputation of missing genotypes in the population with a reference panel. For this metrics, Impute2 (v2.3.2) and Beagle (v4.1) both performed competitively under different imputation scenarios and had genotype concordance rate of >99%. However, Impute2 was better in imputation of genotypes with minor allele frequency of <0.025 in the reference panel.
174. Sheffield NC, Bock C: LOLA: Enrichment Analysis for Genomic Region Sets and Regulatory Elements in R and Bioconductor. Bioinformatics 2016, 32.
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@article{Sheffield2016, TITLE = {{LOLA}: enrichment analysis for genomic region sets and regulatory elements in {R} and {Bioconductor}}, AUTHOR = {Sheffield, Nathan C. and Bock, Christoph}, LANGUAGE = {eng}, ISSN = {1367-4803}, DOI = {10.1093/bioinformatics/btv612}, PUBLISHER = {Oxford University Press}, ADDRESS = {Oxford}, YEAR = {2016}, DATE = {2016}, JOURNAL = {Bioinformatics}, VOLUME = {32}, NUMBER = {4}, PAGES = {587--589}, }
Endnote
%0 Journal Article %A Sheffield, Nathan C. %A Bock, Christoph %+ External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T LOLA: Enrichment Analysis for Genomic Region Sets and Regulatory Elements in R and Bioconductor : %G eng %U http://hdl.handle.net/11858/00-001M-0000-002A-0530-B %R 10.1093/bioinformatics/btv612 %7 2015-10-27 %D 2016 %J Bioinformatics %V 32 %N 4 %& 587 %P 587 - 589 %I Oxford University Press %C Oxford %@ false
175. St. John EP, Simen BB, Turenchalk GS, Brayerman MS, Abhate I, Aerssens J, Bouchez O, Gabriel C, Izopet J, Meixenberger K, Giallonardo F, Metzner KJ, Schlapbach R, Paredes R, Sakwa J, Schmitz-Agheguian GG, Victor M, Thielen A, Däumer MP, Lengauer T: A Follow-Up of the Multicenter Collaborative Study on HIV-1 Drug Resistance and Tropism Testing Using 454 Ultra Deep Pyrosequencing. PLoS One 2016, 11.
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@article{Lengauer2016PLoSOne, TITLE = {A Follow-Up of the Multicenter Collaborative Study on {HIV}-1 Drug Resistance and Tropism Testing Using 454 Ultra Deep Pyrosequencing}, AUTHOR = {St. John, Elizabeth P. and Simen, Birgitte B. and Turenchalk, Gregory S. and Brayerman, Michael S. and Abhate, Isabella and Aerssens, Jeroen and Bouchez, Olivier and Gabriel, Christian and Izopet, Jacques and Meixenberger, Karolin and Giallonardo, Francesca and Metzner, Karin J. and Schlapbach, Ralph and Paredes, Roger and Sakwa, James and Schmitz-Agheguian, Gudrun G. and Victor, Martin and Thielen, Alexander and D{\"a}umer, Martin P. and Lengauer, Thomas}, LANGUAGE = {eng}, ISSN = {1932-6203}, DOI = {10.1371/journal.pone.0146687}, PUBLISHER = {Public Library of Science}, ADDRESS = {San Francisco, CA}, YEAR = {2016}, JOURNAL = {PLoS One}, VOLUME = {11}, NUMBER = {1}, EID = {e0146687}, }
Endnote
%0 Journal Article %A St. John, Elizabeth P. %A Simen, Birgitte B. %A Turenchalk, Gregory S. %A Brayerman, Michael S. %A Abhate, Isabella %A Aerssens, Jeroen %A Bouchez, Olivier %A Gabriel, Christian %A Izopet, Jacques %A Meixenberger, Karolin %A Giallonardo, Francesca %A Metzner, Karin J. %A Schlapbach, Ralph %A Paredes, Roger %A Sakwa, James %A Schmitz-Agheguian, Gudrun G. %A Victor, Martin %A Thielen, Alexander %A D&#228;umer, Martin P. %A Lengauer, Thomas %+ External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T A Follow-Up of the Multicenter Collaborative Study on HIV-1 Drug Resistance and Tropism Testing Using 454 Ultra Deep Pyrosequencing : %G eng %U http://hdl.handle.net/11858/00-001M-0000-002A-432C-1 %R 10.1371/journal.pone.0146687 %7 2016 %D 2016 %J PLoS One %V 11 %N 1 %Z sequence number: e0146687 %I Public Library of Science %C San Francisco, CA %@ false
176. Trappe K, Marschall T, Renard BJ: Detecting Horizontal Gene Transfer by Mapping Sequencing Reads Across Species Boundaries. Bioinformatics (Proc ECCB 2016) 2016, 32.
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@article{TrappeBioinformatics_2016, TITLE = {Detecting Horizontal Gene Transfer by Mapping Sequencing Reads Across Species Boundaries}, AUTHOR = {Trappe, Kathrin and Marschall, Tobias and Renard, Bernhard J.}, LANGUAGE = {eng}, ISSN = {1367-4803}, DOI = {10.1093/bioinformatics/btw423}, PUBLISHER = {Oxford University Press}, ADDRESS = {Oxford}, YEAR = {2016}, DATE = {2016}, JOURNAL = {Bioinformatics (Proc. ECCB)}, VOLUME = {32}, NUMBER = {17}, PAGES = {i595--i604}, BOOKTITLE = {ECCB 2016}, }
Endnote
%0 Journal Article %A Trappe, Kathrin %A Marschall, Tobias %A Renard, Bernhard J. %+ External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations %T Detecting Horizontal Gene Transfer by Mapping Sequencing Reads Across Species Boundaries : %G eng %U http://hdl.handle.net/11858/00-001M-0000-002B-8674-0 %R 10.1093/bioinformatics/btw423 %7 2016 %D 2016 %J Bioinformatics %V 32 %N 17 %& i595 %P i595 - i604 %I Oxford University Press %C Oxford %@ false %B ECCB 2016 %O ECCB 2016 The 15th European Conference on Computational Biology
177. Voitenko OS, Dhroso A, Feldmann A, Korkin D, Kalinina OV: Patterns of Amino Acid Conservation in Human and Animal Immunodeficiency Viruses. Bioinformatics (Proc ECCB 2016) 2016, 32.
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@article{VoitenkoBioinformatics2016, TITLE = {Patterns of Amino Acid Conservation in Human and Animal Immunodeficiency Viruses}, AUTHOR = {Voitenko, Olga S. and Dhroso, Andi and Feldmann, Anna and Korkin, Dmitry and Kalinina, Olga V.}, LANGUAGE = {eng}, ISSN = {1367-4803}, DOI = {10.1093/bioinformatics/btw441}, PUBLISHER = {Oxford University Press}, ADDRESS = {Oxford}, YEAR = {2016}, DATE = {2016}, JOURNAL = {Bioinformatics (Proc. ECCB)}, VOLUME = {32}, NUMBER = {17}, PAGES = {i685--i692}, BOOKTITLE = {ECCB 2016}, }
Endnote
%0 Journal Article %A Voitenko, Olga S. %A Dhroso, Andi %A Feldmann, Anna %A Korkin, Dmitry %A Kalinina, Olga V. %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T Patterns of Amino Acid Conservation in Human and Animal Immunodeficiency Viruses : %G eng %U http://hdl.handle.net/11858/00-001M-0000-002B-861E-1 %R 10.1093/bioinformatics/btw441 %7 2016 %D 2016 %J Bioinformatics %V 32 %N 17 %& i685 %P i685 - i692 %I Oxford University Press %C Oxford %@ false %B ECCB 2016 %O ECCB 2016 The 15th European Conference on Computational Biology
178. Wallner S, Schröder C, Leitão E, Berulava T, Haak C, Beißer D, Rahmann S, Richter AS, Manke T, Bönisch U, Arrigoni L, Fröhler S, Klironomos F, Chen W, Rajewsky N, Müller F, Ebert P, Lengauer T, Barann M, Rosenstiel P, Gasparoni G, Nordström K, Walter J, Brors B, Zipprich G, Felder B, Klein-Hitpass L, Attenberger C, Schmitz G, Horsthemke B: Epigenetic Dynamics of Monocyte-to-Macrophage Differentiation. Epigenetics & Chromatin 2016, 9.
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@article{Wallner2016, TITLE = {Epigenetic Dynamics of Monocyte-to-Macrophage Differentiation}, AUTHOR = {Wallner, Stefan and Schr{\"o}der, Christopher and Leit{\~a}o, Elsa and Berulava, Tea and Haak, Claudia and Bei{\ss}er, Daniela and Rahmann, Sven and Richter, Andreas S. and Manke, Thomas and B{\"o}nisch, Ulrike and Arrigoni, Laura and Fr{\"o}hler, Sebastian and Klironomos, Filippos and Chen, Wei and Rajewsky, Nikolaus and M{\"u}ller, Fabian and Ebert, Peter and Lengauer, Thomas and Barann, Matthias and Rosenstiel, Philip and Gasparoni, Gilles and Nordstr{\"o}m, Karl and Walter, J{\"o}rn and Brors, Benedikt and Zipprich, Gideon and Felder, B{\"a}rbel and Klein-Hitpass, Ludger and Attenberger, Corinna and Schmitz, Gerd and Horsthemke, Bernhard}, LANGUAGE = {eng}, DOI = {10.1186/s13072-016-0079-z}, PUBLISHER = {BioMed Central}, ADDRESS = {London}, YEAR = {2016}, JOURNAL = {Epigenetics \& Chromatin}, VOLUME = {9}, EID = {33}, }
Endnote
%0 Journal Article %A Wallner, Stefan %A Schr&#246;der, Christopher %A Leit&#227;o, Elsa %A Berulava, Tea %A Haak, Claudia %A Bei&#223;er, Daniela %A Rahmann, Sven %A Richter, Andreas S. %A Manke, Thomas %A B&#246;nisch, Ulrike %A Arrigoni, Laura %A Fr&#246;hler, Sebastian %A Klironomos, Filippos %A Chen, Wei %A Rajewsky, Nikolaus %A M&#252;ller, Fabian %A Ebert, Peter %A Lengauer, Thomas %A Barann, Matthias %A Rosenstiel, Philip %A Gasparoni, Gilles %A Nordstr&#246;m, Karl %A Walter, J&#246;rn %A Brors, Benedikt %A Zipprich, Gideon %A Felder, B&#228;rbel %A Klein-Hitpass, Ludger %A Attenberger, Corinna %A Schmitz, Gerd %A Horsthemke, Bernhard %+ External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations %T Epigenetic Dynamics of Monocyte-to-Macrophage Differentiation : %G eng %U http://hdl.handle.net/11858/00-001M-0000-002B-1691-6 %R 10.1186/s13072-016-0079-z %7 2016 %D 2016 %J Epigenetics & Chromatin %V 9 %Z sequence number: 33 %I BioMed Central %C London
179. Welsch C, Haselow K, Gouttenoire J, Schneider M, Morikawa K, Martinez Y, Susser S, Sarrazin C, Zeuzem S, Antes I, Moradpour D, Lange CM: Hepatitis C Virus Variants Resistant to Macrocyclic NS3-4A Inhibitors Subvert IFN-β Induction by Efficient MAVS Cleavage. Journal of Hepatology 2016, 62.
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@article{WelschJoH2016, TITLE = {Hepatitis {C} Virus Variants Resistant to Macrocyclic {NS3}-{4A} Inhibitors Subvert {IFN}-$\beta$ Induction by Efficient {MAVS} Cleavage Efficient {MAVS} Cleavage}, AUTHOR = {Welsch, Christoph and Haselow, Katrin and Gouttenoire, J{\'e}r{\^o}me and Schneider, Markus and Morikawa, Kenichi and Martinez, Yolanda and Susser, Simone and Sarrazin, Christoph and Zeuzem, Stefan and Antes, Iris and Moradpour, Darius and Lange, Christian M.}, LANGUAGE = {eng}, ISSN = {0168-8278}, DOI = {10.1016/j.jhep.2014.11.009}, PUBLISHER = {Elsevier}, ADDRESS = {Amsterdam}, YEAR = {2016}, DATE = {2016}, JOURNAL = {Journal of Hepatology}, VOLUME = {62}, NUMBER = {4}, PAGES = {779--784}, }
Endnote
%0 Journal Article %A Welsch, Christoph %A Haselow, Katrin %A Gouttenoire, J&#233;r&#244;me %A Schneider, Markus %A Morikawa, Kenichi %A Martinez, Yolanda %A Susser, Simone %A Sarrazin, Christoph %A Zeuzem, Stefan %A Antes, Iris %A Moradpour, Darius %A Lange, Christian M. %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations %T Hepatitis C Virus Variants Resistant to Macrocyclic NS3-4A Inhibitors Subvert IFN-&#946; Induction by Efficient MAVS Cleavage : %G eng %U http://hdl.handle.net/11858/00-001M-0000-002A-433B-0 %R 10.1016/j.jhep.2014.11.009 %7 2016 %D 2016 %J Journal of Hepatology %O J. Hepatol. %V 62 %N 4 %& 779 %P 779 - 784 %I Elsevier %C Amsterdam %@ false
2015
180. Abreu VAC, Almeida S, Tiwari S, Hassan SS, Mariano D, Silva A, Baumbach J, Azevedo V, Röttger R: CMRegNet -- An Interspecies Reference Database for Corynebacterial and Mycobacterial Regulatory Networks. BMC Genomics 2015, 16.
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@article{AbreuBMCGenomics2015, TITLE = {{CMRegNet} -- An Interspecies Reference Database for Corynebacterial and Mycobacterial Regulatory Networks}, AUTHOR = {Abreu, Vinicius A. C. and Almeida, Sintia and Tiwari, Sandeep and Hassan, Syed Shah and Mariano, Diego and Silva, Artur and Baumbach, Jan and Azevedo, Vasco and R{\"o}ttger, Richard}, LANGUAGE = {eng}, ISSN = {1471-2164}, URL = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=4464113&tool=pmcentrez&rendertype=abstract}, DOI = {10.1186/s12864-015-1631-0}, PUBLISHER = {BioMed Central}, ADDRESS = {London}, YEAR = {2015}, JOURNAL = {BMC Genomics}, VOLUME = {16}, NUMBER = {1}, EID = {452}, }
Endnote
%0 Journal Article %A Abreu, Vinicius A. C. %A Almeida, Sintia %A Tiwari, Sandeep %A Hassan, Syed Shah %A Mariano, Diego %A Silva, Artur %A Baumbach, Jan %A Azevedo, Vasco %A R&#246;ttger, Richard %+ External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T CMRegNet -- An Interspecies Reference Database for Corynebacterial and Mycobacterial Regulatory Networks : %! {CMRegNet} -- An Interspecies Reference Database for Corynebacterial and Mycobacterial Regulatory Networks %G eng %U http://hdl.handle.net/11858/00-001M-0000-0027-ACBB-E %F OTHER: accessionPMC4464113 %F OTHER: pmcidPMC4464113 %F OTHER: pmc-uid4464113 %F OTHER: publisher-id1631 %R 10.1186/s12864-015-1631-0 %U http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=4464113&tool=pmcentrez&rendertype=abstract %7 2015-06-11 %D 2015 %8 11.06.2015 %J BMC Genomics %V 16 %N 1 %Z sequence number: 452 %I BioMed Central %C London %@ false
181. Ahmad M, Helms V, Lengauer T, Kalinina OV: Enthalpy-entropy Compensation upon Molecular Conformational Changes. Journal of Chemical Theory and Computation 2015, 11.
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@article{Lengauer2015, TITLE = {Enthalpy-entropy Compensation upon Molecular Conformational Changes}, AUTHOR = {Ahmad, Mazen and Helms, Volkhard and Lengauer, Thomas and Kalinina, Olga V.}, LANGUAGE = {eng}, DOI = {10.1021/ct501161t}, PUBLISHER = {American Chemical Society}, ADDRESS = {Washington, D.C.}, YEAR = {2015}, DATE = {2015}, JOURNAL = {Journal of Chemical Theory and Computation}, VOLUME = {11}, NUMBER = {4}, PAGES = {1410--1418}, }
Endnote
%0 Journal Article %A Ahmad, Mazen %A Helms, Volkhard %A Lengauer, Thomas %A Kalinina, Olga V. %+ External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T Enthalpy-entropy Compensation upon Molecular Conformational Changes : %G eng %U http://hdl.handle.net/11858/00-001M-0000-0024-E34E-B %R 10.1021/ct501161t %7 2015 %D 2015 %J Journal of Chemical Theory and Computation %O J. Chem. Theory Comput. %V 11 %N 4 %& 1410 %P 1410 - 1418 %I American Chemical Society %C Washington, D.C.
182. Ahmad M, Helms V, Lengauer T, Kalinina OV: How Molecular Conformational Changes Affect Changes in Free Energy. Journal of Chemical Theory and Computation 2015, 11.
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@article{AhmadJCTC2015, TITLE = {How Molecular Conformational Changes Affect Changes in Free Energy}, AUTHOR = {Ahmad, Mazen and Helms, Volkhard and Lengauer, Thomas and Kalinina, Olga V.}, LANGUAGE = {eng}, DOI = {10.1021/acs.jctc.5b00235}, PUBLISHER = {American Chemical Society}, ADDRESS = {Washington, D.C.}, YEAR = {2015}, DATE = {2015}, JOURNAL = {Journal of Chemical Theory and Computation}, VOLUME = {11}, NUMBER = {7}, PAGES = {2945--2957}, }
Endnote
%0 Journal Article %A Ahmad, Mazen %A Helms, Volkhard %A Lengauer, Thomas %A Kalinina, Olga V. %+ External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T How Molecular Conformational Changes Affect Changes in Free Energy : %G eng %U http://hdl.handle.net/11858/00-001M-0000-0028-4CAF-6 %R 10.1021/acs.jctc.5b00235 %7 2015 %D 2015 %J Journal of Chemical Theory and Computation %O J. Chem. Theory Comput. %V 11 %N 7 %& 2945 %P 2945 - 2957 %I American Chemical Society %C Washington, D.C.
183. Aldinucci M, Bracciali A, Marschall T, Patterson M, Pisanti N, Torquati M: High-Performance Haplotype Assembly. In Computational Intelligence Methods for Bioinformatics and Biostatistics (CIBB 2014). Springer; 2015. [Lecture Notes in Computer Science, vol. 8623]
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@inproceedings{MarschallLNBI15, TITLE = {High-Performance Haplotype Assembly}, AUTHOR = {Aldinucci, Marco and Bracciali, Andrea and Marschall, Tobias and Patterson, Murray and Pisanti, Nadia and Torquati, Massimo}, LANGUAGE = {eng}, ISBN = {978-3-319-24461-7}, DOI = {10.1007/978-3-319-24462-4_21}, PUBLISHER = {Springer}, YEAR = {2014}, DATE = {2015}, BOOKTITLE = {Computational Intelligence Methods for Bioinformatics and Biostatistics (CIBB 2014)}, PAGES = {245--258}, SERIES = {Lecture Notes in Computer Science}, VOLUME = {8623}, ADDRESS = {Cambridge, UK}, }
Endnote
%0 Conference Proceedings %A Aldinucci, Marco %A Bracciali, Andrea %A Marschall, Tobias %A Patterson, Murray %A Pisanti, Nadia %A Torquati, Massimo %+ External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations %T High-Performance Haplotype Assembly : %G eng %U http://hdl.handle.net/11858/00-001M-0000-0029-5D10-1 %R 10.1007/978-3-319-24462-4_21 %D 2015 %B 11th International Meeting on Computational Intelligence Methods for Bioinformatics and Biostatistics %Z date of event: 2014-06-26 - 2014-06-28 %C Cambridge, UK %B Computational Intelligence Methods for Bioinformatics and Biostatistics %P 245 - 258 %I Springer %@ 978-3-319-24461-7 %B Lecture Notes in Computer Science %N 8623
184. Amabile G, Di Ruscio A, Müller F, Welner RS, Yang H, Ebralidze AK, Zhong H, Levantini E, Qi L, Martinelli G, Brummelkamp T, Le Beau MM, Figueroa ME, Bock C, Tenen DG: Dissecting the Role of Aberrant DNA Methylation in Human Leukaemia. Nature Communications 2015, 6.
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@article{MullerBock2015, TITLE = {Dissecting the Role of Aberrant {DNA} Methylation in Human Leukaemia}, AUTHOR = {Amabile, Giovanni and Di Ruscio, Annalisa and M{\"u}ller, Fabian and Welner, Robert S. and Yang, Henry and Ebralidze, Alexander K. and Zhong, Hong and Levantini, Elena and Qi, Lihua and Martinelli, Giovanni and Brummelkamp, Thijn and Le Beau, Michelle M. and Figueroa, Maria E. and Bock, Christoph and Tenen, Daniel G.}, LANGUAGE = {eng}, ISSN = {2041-1723}, DOI = {10.1038/ncomms8091}, PUBLISHER = {Nature Publishing Group}, ADDRESS = {London}, YEAR = {2015}, DATE = {2015}, JOURNAL = {Nature Communications}, VOLUME = {6}, EID = {7091}, }
Endnote
%0 Journal Article %A Amabile, Giovanni %A Di Ruscio, Annalisa %A M&#252;ller, Fabian %A Welner, Robert S. %A Yang, Henry %A Ebralidze, Alexander K. %A Zhong, Hong %A Levantini, Elena %A Qi, Lihua %A Martinelli, Giovanni %A Brummelkamp, Thijn %A Le Beau, Michelle M. %A Figueroa, Maria E. %A Bock, Christoph %A Tenen, Daniel G. %+ External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations %T Dissecting the Role of Aberrant DNA Methylation in Human Leukaemia : %G eng %U http://hdl.handle.net/11858/00-001M-0000-0027-AD30-B %R 10.1038/ncomms8091 %7 2015 %D 2015 %J Nature Communications %O Nat. Commun. %V 6 %Z sequence number: 7091 %I Nature Publishing Group %C London %@ false
185. Andreassen OA, Desikan RS, Wang Y, Thompson WK, Schork AJ, Zuber V, Doncheva NT, Ellinghaus E, Albrecht M, Mattingsdal M, Franke A, Lie BA, Mills I, Aukrust P, McEvoy LK, Djurovic S, Karlsen TH, Dale AM: Abundant Genetic Overlap between Blood Lipids and Immune-Mediated Diseases Indicates Shared Molecular Genetic Mechanisms. PLoS ONE 2015, 10.
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@article{Andreassen2015, TITLE = {Abundant Genetic Overlap between Blood Lipids and Immune-Mediated Diseases Indicates Shared Molecular Genetic Mechanisms}, AUTHOR = {Andreassen, Ole A. and Desikan, Rahul S. and Wang, Yunpeng and Thompson, Wesley K. and Schork, Andrew J. and Zuber, Verena and Doncheva, Nadezhda Tsankova and Ellinghaus, Eva and Albrecht, Mario and Mattingsdal, Morten and Franke, Andre and Lie, Benedicte A. and Mills, Ian and Aukrust, P{\aa}l and McEvoy, Linda K. and Djurovic, Srdjan and Karlsen, Tom H. and Dale, Anders M.}, LANGUAGE = {eng}, ISSN = {1932-6203}, URL = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=4390360&tool=pmcentrez&rendertype=abstract}, DOI = {10.1371/journal.pone.0123057}, PUBLISHER = {Public Library of Science}, ADDRESS = {San Francisco, CA}, YEAR = {2015}, JOURNAL = {PLoS ONE}, VOLUME = {10}, NUMBER = {4}, EID = {e0123057}, }
Endnote
%0 Journal Article %A Andreassen, Ole A. %A Desikan, Rahul S. %A Wang, Yunpeng %A Thompson, Wesley K. %A Schork, Andrew J. %A Zuber, Verena %A Doncheva, Nadezhda Tsankova %A Ellinghaus, Eva %A Albrecht, Mario %A Mattingsdal, Morten %A Franke, Andre %A Lie, Benedicte A. %A Mills, Ian %A Aukrust, P&#229;l %A McEvoy, Linda K. %A Djurovic, Srdjan %A Karlsen, Tom H. %A Dale, Anders M. %+ External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations %T Abundant Genetic Overlap between Blood Lipids and Immune-Mediated Diseases Indicates Shared Molecular Genetic Mechanisms : %G eng %U http://hdl.handle.net/11858/00-001M-0000-002A-3AB7-1 %2 PMC4390360 %F OTHER: pmc-uid4390360 %R 10.1371/journal.pone.0123057 %U http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=4390360&tool=pmcentrez&rendertype=abstract %7 2015-04-08 %D 2015 %8 08.04.2015 %J PLoS ONE %V 10 %N 4 %Z sequence number: e0123057 %I Public Library of Science %C San Francisco, CA %@ false
186. Baumbach J, Guo J, Ibragimov R: Covering Tree with Stars. Journal of Combinatorial Optimization 2015, 29.
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@article{BaumbachJCombOptim2015, TITLE = {Covering Tree with Stars}, AUTHOR = {Baumbach, Jan and Guo, Jiong and Ibragimov, Rashid}, LANGUAGE = {eng}, ISSN = {1382-6905}, DOI = {10.1007/s10878-013-9692-y}, PUBLISHER = {Springer}, ADDRESS = {New York, NY}, YEAR = {2015}, DATE = {2015}, JOURNAL = {Journal of Combinatorial Optimization}, VOLUME = {29}, NUMBER = {1}, PAGES = {141--152}, }
Endnote
%0 Journal Article %A Baumbach, Jan %A Guo, Jiong %A Ibragimov, Rashid %+ External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T Covering Tree with Stars : %G eng %U http://hdl.handle.net/11858/00-001M-0000-0026-BEEF-7 %R 10.1007/s10878-013-9692-y %7 2015 %D 2015 %J Journal of Combinatorial Optimization %V 29 %N 1 %& 141 %P 141 - 152 %I Springer %C New York, NY %@ false
187. Bellitto T, Marschall T, Schönhuth A, Klau GW: Next Generation Cluster Editing. PeerJ PrePrints (Proc GCB 2015) 2015, 3.
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@article{MarschallPeer15, TITLE = {Next Generation Cluster Editing}, AUTHOR = {Bellitto, Thomas and Marschall, Tobias and Sch{\"o}nhuth, Alexander and Klau, Gunnar W.}, LANGUAGE = {eng}, DOI = {10.7287/peerj.preprints.1301v1}, YEAR = {2015}, JOURNAL = {PeerJ PrePrints (Proc. GCB)}, VOLUME = {3}, EID = {e1599}, BOOKTITLE = {German Conference on Bioinformatics (GCB 2015)}, }
Endnote
%0 Journal Article %A Bellitto, Thomas %A Marschall, Tobias %A Sch&#246;nhuth, Alexander %A Klau, Gunnar W. %+ External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations %T Next Generation Cluster Editing : %G eng %U http://hdl.handle.net/11858/00-001M-0000-0029-5E4D-6 %R 10.7287/peerj.preprints.1301v1 %7 2015-08-13 %D 2015 %8 13.08.2015 %* Review method: peer-reviewed %J PeerJ PrePrints %O GCB 2015 %V 3 %Z sequence number: e1599 %B German Conference on Bioinformatics %O GCB 2015 Dortmund, Germany, 27.09. - 30.09.2015
188. Bock C, Bortolussi L, Krüger T, Mikeev L, Wolf V: Model-based Whole-genome Analysis of DNA Methylation Fidelity. In Hybrid Systems Biology (HSB 2015). Springer; 2015. [Lecture Notes in Bioinformatics, vol. 9271]
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@inproceedings{BockHSB2015, TITLE = {Model-Based Whole-Genome Analysis of {DNA} Methylation Fidelity}, AUTHOR = {Bock, Christoph and Bortolussi, Luca and Kr{\"u}ger, Thilo and Mikeev, Linar and Wolf, Verena}, LANGUAGE = {eng}, ISBN = {978-3-319-26915-3}, DOI = {10.1007/978-3-319-26916-0_8}, PUBLISHER = {Springer}, YEAR = {2015}, DATE = {2015}, BOOKTITLE = {Hybrid Systems Biology (HSB 2015)}, EDITOR = {Abate, Alessandro and {\v S}afr{\'a}nek, David}, PAGES = {141--155}, SERIES = {Lecture Notes in Bioinformatics}, VOLUME = {9271}, ADDRESS = {Madrid, Spain}, }
Endnote
%0 Conference Proceedings %A Bock, Christoph %A Bortolussi, Luca %A Kr&#252;ger, Thilo %A Mikeev, Linar %A Wolf, Verena %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations External Organizations %T Model-based Whole-genome Analysis of DNA Methylation Fidelity : %G eng %U http://hdl.handle.net/11858/00-001M-0000-002A-07ED-6 %R 10.1007/978-3-319-26916-0_8 %D 2015 %B 4th International Workshop on Hybrid Systems Biology %Z date of event: 2015-09-04 - 2015-09-05 %C Madrid, Spain %B Hybrid Systems Biology %E Abate, Alessandro; &#352;afr&#225;nek , David %P 141 - 155 %I Springer %@ 978-3-319-26915-3 %B Lecture Notes in Bioinformatics %N 9271
189. Caprari S, Metzler S, Lengauer T, Kalinina OV: Sequence and Structure Analysis of Distantly-Related Viruses Reveals Extensive Gene Transfer between Viruses and Hosts and among Viruses. Viruses 2015, 7.
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@article{Caprari2015, TITLE = {Sequence and Structure Analysis of Distantly-Related Viruses Reveals Extensive Gene Transfer between Viruses and Hosts and among Viruses}, AUTHOR = {Caprari, Silvia and Metzler, Saskia and Lengauer, Thomas and Kalinina, Olga V.}, LANGUAGE = {eng}, ISSN = {1999-4915}, DOI = {10.3390/v7102882}, PUBLISHER = {MDPI}, ADDRESS = {Basel}, YEAR = {2015}, JOURNAL = {Viruses}, VOLUME = {7}, NUMBER = {10}, PAGES = {5388--5409}, }
Endnote
%0 Journal Article %A Caprari, Silvia %A Metzler, Saskia %A Lengauer, Thomas %A Kalinina, Olga V. %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T Sequence and Structure Analysis of Distantly-Related Viruses Reveals Extensive Gene Transfer between Viruses and Hosts and among Viruses : %G eng %U http://hdl.handle.net/11858/00-001M-0000-0029-1A7E-5 %R 10.3390/v7102882 %2 PMC4632390 %7 2015 %D 2015 %J Viruses %V 7 %N 10 %& 5388 %P 5388 - 5409 %I MDPI %C Basel %@ false %U http://www.mdpi.com/1999-4915/7/10/2882
190. Charpentier C, Camacho R, Ruelle J, Eberle J, Gürtler L, Pironti A, Stürmer M, Brun-Vézinet F, Kaiser R, Descamps D, Obermeier M: HIV-2EU -- Supporting Standardized HIV-2 Drug-Resistance Interpretation in Europe: An Update. Clinical Infectious Diseases 2015, 61.
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@article{Charpentier2015, TITLE = {{HIV}-{2EU} -- {S}upporting Standardized {HIV}-2 Drug-Resistance Interpretation in {E}urope: {A}n Update}, AUTHOR = {Charpentier, Charlotte and Camacho, Ricardo and Ruelle, Jean and Eberle, Josef and G{\"u}rtler, Lutz and Pironti, Alejandro and St{\"u}rmer, Martin and Brun-V{\'e}zinet, Fran{\c c}oise and Kaiser, Rolf and Descamps, Diane and Obermeier, Martin}, LANGUAGE = {eng}, ISSN = {1058-4838}, DOI = {10.1093/cid/civ572}, PUBLISHER = {The University of Chicago Press}, ADDRESS = {Chicago, IL}, YEAR = {2015}, DATE = {2015}, JOURNAL = {Clinical Infectious Diseases}, VOLUME = {61}, NUMBER = {8}, PAGES = {1347--1349}, }
Endnote
%0 Journal Article %A Charpentier, Charlotte %A Camacho, Ricardo %A Ruelle, Jean %A Eberle, Josef %A G&#252;rtler, Lutz %A Pironti, Alejandro %A St&#252;rmer, Martin %A Brun-V&#233;zinet, Fran&#231;oise %A Kaiser, Rolf %A Descamps, Diane %A Obermeier, Martin %+ External Organizations External Organizations External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations External Organizations External Organizations %T HIV-2EU -- Supporting Standardized HIV-2 Drug-Resistance Interpretation in Europe: An Update : %G eng %U http://hdl.handle.net/11858/00-001M-0000-0028-F6CC-9 %R 10.1093/cid/civ572 %7 2015-07-17 %D 2015 %J Clinical Infectious Diseases %V 61 %N 8 %& 1347 %P 1347 - 1349 %I The University of Chicago Press %C Chicago, IL %@ false
191. Cheaib M, Dehghani Amirabad A, Nordström KJV, Schulz MH, Simon M: Epigenetic regulation of serotype expression antagonizes transcriptome dynamics in Paramecium tetraurelia. DNA Research 2015, 22.
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@article{Cheaib2015, TITLE = {Epigenetic regulation of serotype expression antagonizes transcriptome dynamics in {Paramecium} tetraurelia}, AUTHOR = {Cheaib, Miriam and Dehghani Amirabad, Azim and Nordstr{\"o}m, Karl J. V. and Schulz, Marcel Holger and Simon, Martin}, LANGUAGE = {eng}, ISSN = {1340-2838; 1756-1663}, URL = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=4535620&tool=pmcentrez&rendertype=abstract}, DOI = {10.1093/dnares/dsv014}, PUBLISHER = {Oxford University Press}, ADDRESS = {Oxford}, YEAR = {2015}, DATE = {2015-08}, JOURNAL = {DNA Research}, VOLUME = {22}, NUMBER = {4}, PAGES = {293--305}, }
Endnote
%0 Journal Article %A Cheaib, Miriam %A Dehghani Amirabad, Azim %A Nordstr&#246;m, Karl J. V. %A Schulz, Marcel Holger %A Simon, Martin %+ External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations %T Epigenetic regulation of serotype expression antagonizes transcriptome dynamics in Paramecium tetraurelia : %G eng %U http://hdl.handle.net/11858/00-001M-0000-0028-52A5-D %F OTHER: accessionPMC4535620 %F OTHER: pmcidPMC4535620 %F OTHER: pmc-uid4535620 %R 10.1093/dnares/dsv014 %F OTHER: publisher-iddsv014 %U http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=4535620&tool=pmcentrez&rendertype=abstract %2 PMC4535620 %7 2015-07-31 %D 2015 %K heat-shock %J DNA Research %V 22 %N 4 %& 293 %P 293 - 305 %I Oxford University Press %C Oxford %@ false
192. Cijvat R, Manegold S, Kersten M, Klau GW, Schönhuth A, Marschall T, Zhang Y: Genome Sequence Analysis with MonetDB. Datenbank-Spektrum 2015, 15.
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@article{MarschallMonetDB15, TITLE = {Genome Sequence Analysis with {M}onet{DB}}, AUTHOR = {Cijvat, Robin and Manegold, Stefan and Kersten, Martin and Klau, Gunnar W. and Sch{\"o}nhuth, Alexander and Marschall, Tobias and Zhang, Ying}, LANGUAGE = {eng}, ISSN = {1618-2162}, DOI = {10.1007/s13222-015-0198-x}, PUBLISHER = {Springer}, ADDRESS = {Berlin}, YEAR = {2015}, DATE = {2015}, JOURNAL = {Datenbank-Spektrum}, VOLUME = {15}, NUMBER = {3}, PAGES = {185--191}, }
Endnote
%0 Journal Article %A Cijvat, Robin %A Manegold, Stefan %A Kersten, Martin %A Klau, Gunnar W. %A Sch&#246;nhuth, Alexander %A Marschall, Tobias %A Zhang, Ying %+ External Organizations External Organizations External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations %T Genome Sequence Analysis with MonetDB : %G eng %U http://hdl.handle.net/11858/00-001M-0000-0029-5B50-E %R 10.1007/s13222-015-0198-x %7 2015-10-12 %D 2015 %J Datenbank-Spektrum %V 15 %N 3 %& 185 %P 185 - 191 %I Springer %C Berlin %@ false
193. Cijvat R, Manegold S, Kersten M, Klau GW, Schönhuth A, Marschall T, Zhang Y: Genome Sequence Analysis with MonetDB: A Case Study on Ebola virus diversity. In Joint Workshop on Data Management for Science (DMS 2015); 2015.
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@inproceedings{CijvatDMforLS2015, TITLE = {Genome Sequence Analysis with {MonetDB}: A Case Study on {Ebola} virus diversity}, AUTHOR = {Cijvat, Robin and Manegold, Stefan and Kersten, Martin and Klau, Gunnar W. and Sch{\"o}nhuth, Alexander and Marschall, Tobias and Zhang, Ying}, LANGUAGE = {eng}, YEAR = {2015}, BOOKTITLE = {Joint Workshop on Data Management for Science (DMS 2015)}, EDITOR = {Dorok, Sebastian and K{\"o}nig-Ries, Brigitta and Lange, Matthias and Rahm, Erhard and Saake, Gunter and Seeger, Bernhard}, ADDRESS = {Hamburg, Germany}, }
Endnote
%0 Conference Proceedings %A Cijvat, Robin %A Manegold, Stefan %A Kersten, Martin %A Klau, Gunnar W. %A Sch&#246;nhuth, Alexander %A Marschall, Tobias %A Zhang, Ying %+ External Organizations External Organizations External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations %T Genome Sequence Analysis with MonetDB: A Case Study on Ebola virus diversity : %G eng %U http://hdl.handle.net/11858/00-001M-0000-0029-5E85-6 %D 2015 %B Joint Workshop on Data Management for Science %Z date of event: 2015-03-03 - 2015-03-03 %C Hamburg, Germany %B Joint Workshop on Data Management for Science %E Dorok, Sebastian; K&#246;nig-Ries, Brigitta; Lange, Matthias; Rahm, Erhard; Saake, Gunter; Seeger, Bernhard %U http://www.btw-2015.de/res/proceedings/Workshops/DMS/Cijvat-Genome_sequence_analysis_wi.pdf
194. Deuber D: Visualisierung, Vergleich und Analyse genetischer Variationen. Universität des Saarlandes; 2015.
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@mastersthesis{DeuberBachelor2015, TITLE = {{Visualisierung, Vergleich und Analyse genetischer Variationen}}, AUTHOR = {Deuber, Dominic}, LANGUAGE = {deu}, SCHOOL = {Universit{\"a}t des Saarlandes}, ADDRESS = {Saarbr{\"u}cken}, YEAR = {2015}, DATE = {2015-07-31}, TYPE = {Bachelor's thesis}, }
Endnote
%0 Thesis %A Deuber, Dominic %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T Visualisierung, Vergleich und Analyse genetischer Variationen : %G deu %U http://hdl.handle.net/11858/00-001M-0000-002C-47E5-E %I Universit&#228;t des Saarlandes %C Saarbr&#252;cken %D 2015 %8 31.07.2015 %V bachelor %9 bachelor
195. Dietzen M, Kalinina OV, Taškova K, Kneissl B, Hildebrandt A-K, Jaenicke E, Decker H, Lengauer T, Hildebrandt A: Large Oligomeric Complex Structures Can Be Computationally Assembled by Efficiently Combining Docked Interfaces. Proteins: Structure, Function, and Bioinformatics 2015, 83.
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@article{Dietzenetal2015, TITLE = {Large Oligomeric Complex Structures Can Be Computationally Assembled by Efficiently Combining Docked Interfaces}, AUTHOR = {Dietzen, Matthias and Kalinina, Olga V. and Ta{\v s}kova, Katerina and Kneissl, Benny and Hildebrandt, Anna-Katharina and Jaenicke, Elmar and Decker, Heinz and Lengauer, Thomas and Hildebrandt, Andreas}, LANGUAGE = {eng}, ISSN = {0887-3585}, DOI = {10.1002/prot.24873}, PUBLISHER = {John Wiley \& Sons}, ADDRESS = {New York, NY}, YEAR = {2015}, DATE = {2015}, JOURNAL = {Proteins: Structure, Function, and Bioinformatics}, VOLUME = {83}, NUMBER = {10}, PAGES = {1887--1899}, }
Endnote
%0 Journal Article %A Dietzen, Matthias %A Kalinina, Olga V. %A Ta&#353;kova, Katerina %A Kneissl, Benny %A Hildebrandt, Anna-Katharina %A Jaenicke, Elmar %A Decker, Heinz %A Lengauer, Thomas %A Hildebrandt, Andreas %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations %T Large Oligomeric Complex Structures Can Be Computationally Assembled by Efficiently Combining Docked Interfaces : %G eng %U http://hdl.handle.net/11858/00-001M-0000-0028-5273-E %R 10.1002/prot.24873 %7 2015 %D 2015 %J Proteins: Structure, Function, and Bioinformatics %V 83 %N 10 %& 1887 %P 1887 - 1899 %I John Wiley & Sons %C New York, NY %@ false
196. Döring M, Gasparoni G, Gries J, Nordström K, Lutsik P, Walter J, Pfeifer N: Identification and Analysis of Methylation Call Differences Between Bisulfite Microarray and Bisulfite Sequencing Data with Statistical Learning Techniques. BMC Bioinformatics (Proc ISCB 2014) 2015, 16(Suppl 3).
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@article{doering2015, TITLE = {Identification and Analysis of Methylation Call Differences Between Bisulfite Microarray and Bisulfite Sequencing Data with Statistical Learning Techniques}, AUTHOR = {D{\"o}ring, Matthias and Gasparoni, Gilles and Gries, Jasmin and Nordstr{\"o}m, Karl and Lutsik, Pavlo and Walter, J{\"o}rn and Pfeifer, Nico}, LANGUAGE = {eng}, ISSN = {1471-2105}, URL = {http://www.biomedcentral.com/1471-2105/16/S3/A7}, DOI = {10.1186/1471-2105-16-S3-A7}, PUBLISHER = {BioMed Central}, ADDRESS = {London}, YEAR = {2015}, CONTENTS = {Background Methods Results Conclusion}, JOURNAL = {BMC Bioinformatics (Proc. ISCB)}, VOLUME = {16}, NUMBER = {Suppl 3}, EID = {A7}, BOOKTITLE = {Highlights from the Third International Society for Computational Biology (ISCB) European Student Council Symposium 2014}, }
Endnote
%0 Journal Article %A D&#246;ring, Matthias %A Gasparoni, Gilles %A Gries, Jasmin %A Nordstr&#246;m, Karl %A Lutsik, Pavlo %A Walter, J&#246;rn %A Pfeifer, Nico %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Affiliation External Affiliation External Affiliation External Affiliation External Affiliation Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T Identification and Analysis of Methylation Call Differences Between Bisulfite Microarray and Bisulfite Sequencing Data with Statistical Learning Techniques : %G eng %U http://hdl.handle.net/11858/00-001M-0000-0024-C7F7-B %U http://www.biomedcentral.com/1471-2105/16/S3/A7 %R 10.1186/1471-2105-16-S3-A7 %7 2015-02-13 %D 2015 %8 13.02.2015 %Z Background Methods Results Conclusion %J BMC Bioinformatics %V 16 %N Suppl 3 %Z sequence number: A7 %I BioMed Central %C London %@ false %B Highlights from the Third International Society for Computational Biology (ISCB) European Student Council Symposium 2014 %O ISCB 2014
197. Ebert P, Müller F, Nordström K, Lengauer T, Schulz MH: A General Concept for Consistent Documentation of Computational Analyses. Database 2015, 2015.
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@article{EbertDatabase2015, TITLE = {A General Concept for Consistent Documentation of Computational Analyses}, AUTHOR = {Ebert, Peter and M{\"u}ller, Fabian and Nordstr{\"o}m, Karl and Lengauer, Thomas and Schulz, Marcel Holger}, LANGUAGE = {eng}, ISSN = {1758-0463}, URL = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=4460408&tool=pmcentrez&rendertype=abstract}, DOI = {10.1093/database/bav050}, PUBLISHER = {Oxford University Press}, ADDRESS = {Oxford}, YEAR = {2015}, JOURNAL = {Database}, VOLUME = {2015}, EID = {bav050}, }
Endnote
%0 Journal Article %A Ebert, Peter %A M&#252;ller, Fabian %A Nordstr&#246;m, Karl %A Lengauer, Thomas %A Schulz, Marcel Holger %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T A General Concept for Consistent Documentation of Computational Analyses : %G eng %U http://hdl.handle.net/11858/00-001M-0000-0027-BD04-8 %F OTHER: accessionPMC4460408 %F OTHER: pmcidPMC4460408 %F OTHER: pmc-uid4460408 %R 10.1093/database/bav050 %F OTHER: publisher-idbav050 %U http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=4460408&tool=pmcentrez&rendertype=abstract %7 2015-06-08 %D 2015 %8 08.06.2015 %J Database %O The Journal of Biological Databases and Curation %V 2015 %Z sequence number: bav050 %I Oxford University Press %C Oxford %@ false
198. Ebert P, Bock C: Improving Reference Epigenome Catalogs by Computational Prediction. Nature Biotechnology 2015, 33.
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@article{Ebert2015, TITLE = {Improving Reference Epigenome Catalogs by Computational Prediction}, AUTHOR = {Ebert, Peter and Bock, Christoph}, LANGUAGE = {eng}, ISSN = {1087-0156}, DOI = {10.1038/nbt.3194}, PUBLISHER = {Nature Publishing Group}, ADDRESS = {New York, NY}, YEAR = {2015}, DATE = {2015}, JOURNAL = {Nature Biotechnology}, VOLUME = {33}, NUMBER = {4}, PAGES = {354--355}, }
Endnote
%0 Journal Article %A Ebert, Peter %A Bock, Christoph %+ External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T Improving Reference Epigenome Catalogs by Computational Prediction : %G eng %U http://hdl.handle.net/11858/00-001M-0000-0026-C911-B %R 10.1038/nbt.3194 %7 2015-04-07 %D 2015 %J Nature Biotechnology %V 33 %N 4 %& 354 %P 354 - 355 %I Nature Publishing Group %C New York, NY %@ false
199. Ebler J: Genotyping of Inversions and Tandem Duplications. Universität des Saarlandes; 2015.
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@mastersthesis{EblerBachelor2015, TITLE = {Genotyping of Inversions and Tandem Duplications}, AUTHOR = {Ebler, Jana}, LANGUAGE = {eng}, SCHOOL = {Universit{\"a}t des Saarlandes}, ADDRESS = {Saarbr{\"u}cken}, YEAR = {2015}, DATE = {2015}, TYPE = {Bachelor's thesis}, }
Endnote
%0 Thesis %A Ebler, Jana %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T Genotyping of Inversions and Tandem Duplications : %G eng %U http://hdl.handle.net/11858/00-001M-0000-002C-47FD-9 %I Universit&#228;t des Saarlandes %C Saarbr&#252;cken %D 2015 %V bachelor %9 bachelor
200. Farlik M, Sheffield NC, Nuzzo A, Datlinger P, Schönegger A, Klughammer J, Bock C: Single-Cell DNA Methylome Sequencing and Bioinformatic Inference of Epigenomic Cell-State Dynamics. Cell Reports 2015, 10.
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@article{BockCellReports2015, TITLE = {Single-Cell {DNA} Methylome Sequencing and Bioinformatic Inference of Epigenomic Cell-State Dynamics}, AUTHOR = {Farlik, Matthias and Sheffield, Nathan C. and Nuzzo, Angelo and Datlinger, Paul and Sch{\"o}negger, Andreas and Klughammer, Johanna and Bock, Christoph}, LANGUAGE = {eng}, DOI = {10.1016/j.celrep.2015.02.001}, PUBLISHER = {Elsevier}, ADDRESS = {Amsterdam}, YEAR = {2015}, JOURNAL = {Cell Reports}, VOLUME = {10}, NUMBER = {8}, PAGES = {1386--1397}, }
Endnote
%0 Journal Article %A Farlik, Matthias %A Sheffield, Nathan C. %A Nuzzo, Angelo %A Datlinger, Paul %A Sch&#246;negger, Andreas %A Klughammer, Johanna %A Bock, Christoph %+ External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T Single-Cell DNA Methylome Sequencing and Bioinformatic Inference of Epigenomic Cell-State Dynamics : %! Single-Cell {DNA} Methylome Sequencing and Bioinformatic Inference of Epigenomic Cell-State Dynamics %G eng %U http://hdl.handle.net/11858/00-001M-0000-0026-BEE0-5 %R 10.1016/j.celrep.2015.02.001 %7 2015 %D 2015 %J Cell Reports %V 10 %N 8 %& 1386 %P 1386 - 1397 %I Elsevier %C Amsterdam %U http://www.sciencedirect.com/science/article/pii/S2211124715001096
201. Feldmann A, Pfeifer N: From Predicting to Analyzing HIV-1 Resistance to Broadly Neutralizing Antibodies. PeerJ Preprints 2015, 3.
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@article{Feldmann2015, TITLE = {From predicting to analyzing {HIV}-1 resistance to broadly neutralizing antibodies}, AUTHOR = {Feldmann, Anna and Pfeifer, Nico}, LANGUAGE = {eng}, DOI = {10.7287/peerj.preprints.1304v1}, YEAR = {2015}, JOURNAL = {PeerJ Preprints}, VOLUME = {3}, EID = {e1304v1}, }
Endnote
%0 Journal Article %A Feldmann, Anna %A Pfeifer, Nico %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T From Predicting to Analyzing HIV-1 Resistance to Broadly Neutralizing Antibodies : %G eng %U http://hdl.handle.net/11858/00-001M-0000-002C-4CC9-F %R 10.7287/peerj.preprints.1304v1 %7 2015-08-13 %D 2015 %8 13.08.2015 %J PeerJ Preprints %V 3 %Z sequence number: e1304v1
202. Fink T, Wolf A, Maurer F, Albrecht FW, Heim N, Wolf B, Hauschild AC, Bödeker B, Baumbach JI, Volk T, Sessler DI, Kreuer S: Volatile Organic Compounds during Inflammation and Sepsis in Rats: A Potential Breath Test Using Ion-mobility Spectrometry. Anesthesiology 2015, 122.
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@article{BaumbachVolatile2015, TITLE = {Volatile Organic Compounds during Inflammation and Sepsis in Rats: {A} Potential Breath Test Using Ion-mobility Spectrometry}, AUTHOR = {Fink, Tobias and Wolf, Alexander and Maurer, Felix and Albrecht, Frederic W. and Heim, Nathalie and Wolf, Beate and Hauschild, Anne C. and B{\"o}deker, Bertram and Baumbach, J{\"o}rg I. and Volk, Thomas and Sessler, Daniel I. and Kreuer, Sascha}, LANGUAGE = {eng}, ISSN = {0003-3022}, DOI = {10.1097/ALN.0000000000000420}, PUBLISHER = {American Society of Anesthesiologists}, ADDRESS = {Philadelphia, Pa.}, YEAR = {2015}, DATE = {2015}, JOURNAL = {Anesthesiology}, VOLUME = {122}, NUMBER = {1}, PAGES = {117--126}, }
Endnote
%0 Journal Article %A Fink, Tobias %A Wolf, Alexander %A Maurer, Felix %A Albrecht, Frederic W. %A Heim, Nathalie %A Wolf, Beate %A Hauschild, Anne C. %A B&#246;deker, Bertram %A Baumbach, J&#246;rg I. %A Volk, Thomas %A Sessler, Daniel I. %A Kreuer, Sascha %+ External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations External Organizations External Organizations %T Volatile Organic Compounds during Inflammation and Sepsis in Rats: A Potential Breath Test Using Ion-mobility Spectrometry : %G eng %U http://hdl.handle.net/11858/00-001M-0000-0026-BF4B-2 %R 10.1097/ALN.0000000000000420 %7 2015 %D 2015 %J Anesthesiology %V 122 %N 1 %& 117 %P 117 - 126 %I American Society of Anesthesiologists %C Philadelphia, Pa. %@ false
203. Garg S: Towards Fewer Seeds for Network Discovery. In Modelling, Computation and Optimization in Information Systems and Management Sciences (MCO 2015). Springer; 2015. [Advances in Intelligent Systems and Computing, vol. 360]
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@inproceedings{GargMCO2015, TITLE = {Towards Fewer Seeds for Network Discovery}, AUTHOR = {Garg, Shilpa}, LANGUAGE = {eng}, ISSN = {2194-5357}, ISBN = {978-3-319-18166-0}, DOI = {10.1007/978-3-319-18167-7_8}, PUBLISHER = {Springer}, YEAR = {2015}, DATE = {2015}, BOOKTITLE = {Modelling, Computation and Optimization in Information Systems and Management Sciences (MCO 2015)}, EDITOR = {Thi, Hoai An Le and Dinh, Tao Pham and Nguyen, Ngoc Thanh}, PAGES = {81--89}, SERIES = {Advances in Intelligent Systems and Computing}, VOLUME = {360}, ADDRESS = {Metz, France}, }
Endnote
%0 Conference Proceedings %A Garg, Shilpa %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T Towards Fewer Seeds for Network Discovery : %G eng %U http://hdl.handle.net/11858/00-001M-0000-002A-FC95-E %R 10.1007/978-3-319-18167-7_8 %D 2015 %B 3rd International Conference on Modelling, Computation and Optimization in Information Systems and Management Sciences %Z date of event: 2015-05-11 - 2015-05-13 %C Metz, France %B Modelling, Computation and Optimization in Information Systems and Management Sciences %E Thi, Hoai An Le; Dinh, Tao Pham; Nguyen, Ngoc Thanh %P 81 - 89 %I Springer %@ 978-3-319-18166-0 %B Advances in Intelligent Systems and Computing %N 360 %@ false
204. Gress A: Automated Mutation Associated Protein Structure Prediction. Universität des Saarlandes; 2015.
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@mastersthesis{Gress2015, TITLE = {Automated Mutation Associated Protein Structure Prediction}, AUTHOR = {Gress, Alexander}, LANGUAGE = {eng}, SCHOOL = {Universit{\"a}t des Saarlandes}, ADDRESS = {Saarbr{\"u}cken}, YEAR = {2015}, DATE = {2015}, }
Endnote
%0 Thesis %A Gress, Alexander %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T Automated Mutation Associated Protein Structure Prediction : %G eng %U http://hdl.handle.net/11858/00-001M-0000-002C-287D-1 %I Universit&#228;t des Saarlandes %C Saarbr&#252;cken %D 2015 %V master %9 master
205. Grund S, Gkioule C, Termos T, Pfeifer N, Kobbe G, Verheyen J, Adams O: Primarily Oseltamivir-resistant Influenza A (H1N1pdm09) Virus Evolving into a Multidrug-resistant Virus Carrying H275Y and I223R Neuraminidase Substitutions. Antiviral Therapy 2015, 20.
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@article{Grund2015, TITLE = {Primarily Oseltamivir-resistant Influenza {A} ({H1N1pdm09}) Virus Evolving into a Multidrug-resistant Virus Carrying {H275Y} and {I223R} Neuraminidase Substitutions}, AUTHOR = {Grund, Sebastian and Gkioule, Charikleia and Termos, Tahani and Pfeifer, Nico and Kobbe, Guido and Verheyen, Jens and Adams, Ortwin}, LANGUAGE = {eng}, ISSN = {1359-6535}, DOI = {10.3851/IMP2811}, PUBLISHER = {International Medical Press}, ADDRESS = {London}, YEAR = {2015}, DATE = {2015}, JOURNAL = {Antiviral Therapy}, VOLUME = {20}, PAGES = {97--100}, }
Endnote
%0 Journal Article %A Grund, Sebastian %A Gkioule, Charikleia %A Termos, Tahani %A Pfeifer, Nico %A Kobbe, Guido %A Verheyen, Jens %A Adams, Ortwin %+ External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations %T Primarily Oseltamivir-resistant Influenza A (H1N1pdm09) Virus Evolving into a Multidrug-resistant Virus Carrying H275Y and I223R Neuraminidase Substitutions : %G eng %U http://hdl.handle.net/11858/00-001M-0000-0028-5380-8 %R 10.3851/IMP2811 %7 2014-06-18 %D 2015 %J Antiviral Therapy %V 20 %& 97 %P 97 - 100 %I International Medical Press %C London %@ false
206. Hauschild A-C, Frisch T, Baumbach JI, Baumbach J: Carotta: Revealing Hidden Confounder Markers in Metabolic Breath Profiles. Metabolites 2015, 5.
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@article{HauschildMetabolites2015, TITLE = {Carotta: {R}evealing Hidden Confounder Markers in Metabolic Breath Profiles}, AUTHOR = {Hauschild, Anne-Christin and Frisch, Tobias and Baumbach, J{\"o}rg Ingo and Baumbach, Jan}, LANGUAGE = {eng}, ISSN = {2218-1989}, URL = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=4495376&tool=pmcentrez&rendertype=abstract}, DOI = {10.3390/metabo5020344}, PUBLISHER = {MDPI}, YEAR = {2015}, JOURNAL = {Metabolites}, VOLUME = {5}, NUMBER = {2}, PAGES = {344--363}, }
Endnote
%0 Journal Article %A Hauschild, Anne-Christin %A Frisch, Tobias %A Baumbach, J&#246;rg Ingo %A Baumbach, Jan %A contributor: Kaleta, Christoph %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations %T Carotta: Revealing Hidden Confounder Markers in Metabolic Breath Profiles : %G eng %U http://hdl.handle.net/11858/00-001M-0000-0028-1B69-D %F OTHER: accessionPMC4495376 %F OTHER: pmcidPMC4495376 %F OTHER: pmc-uid4495376 %R 10.3390/metabo5020344 %F OTHER: publisher-idmetabolites-05-00344 %U http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=4495376&tool=pmcentrez&rendertype=abstract %7 2015-06-10 %D 2015 %8 10.06.2015 %K breath analysis %J Metabolites %V 5 %N 2 %& 344 %P 344 - 363 %I MDPI %@ false
207. Hauschild A-C, Maurer F, Fink T, Baumbach JI, Kreuer S, Eckel SP, Baumbach J: Analysis of Volatile Organic Compounds during Sepsis in Rats. In Metaboliten in Prozessabluft und Ausatemluft; 2015.
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@inproceedings{HauschildMetaboliten2015, TITLE = {Analysis of Volatile Organic Compounds during Sepsis in Rats}, AUTHOR = {Hauschild, Anne-Christin and Maurer, Felix and Fink, Tobias and Baumbach, J{\"o}rg Ingo and Kreuer, Sascha and Eckel, Sandrah P. and Baumbach, Jan}, LANGUAGE = {eng}, YEAR = {2015}, BOOKTITLE = {Metaboliten in Prozessabluft und Ausatemluft}, PAGES = {23--23}, ADDRESS = {Reutlingen, Germany}, }
Endnote
%0 Conference Proceedings %A Hauschild, Anne-Christin %A Maurer, Felix %A Fink, Tobias %A Baumbach, J&#246;rg Ingo %A Kreuer, Sascha %A Eckel, Sandrah P. %A Baumbach, Jan %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations %T Analysis of Volatile Organic Compounds during Sepsis in Rats : %G eng %U http://hdl.handle.net/11858/00-001M-0000-002A-06C9-B %D 2015 %B 6. Symposium Metaboliten in Prozessabluft und Ausatemluft %Z date of event: 2015-09-22 - 2015-09-23 %C Reutlingen, Germany %B Metaboliten in Prozessabluft und Ausatemluft %P 23 - 23 %U http://www.bs-analytik.de/pdf/150508_BoA_Anwedertreffen_v5.pdf
208. Hauschild A-C, Baumbach JI, Baumbach J: Bioinformatics Methods for Breath Analysis and Biomarker Detection. In Breath Research Topics from IABR 2015 Summit; 2015.
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@inproceedings{HauschildIABR2015, TITLE = {Bioinformatics Methods for Breath Analysis and Biomarker Detection}, AUTHOR = {Hauschild, Anne-Christin and Baumbach, J{\"o}rg Ingo and Baumbach, Jan}, LANGUAGE = {eng}, YEAR = {2015}, BOOKTITLE = {Breath Research Topics from IABR 2015 Summit}, EDITOR = {Baddour, Rafid}, ADDRESS = {Vienna, Austria}, }
Endnote
%0 Conference Proceedings %A Hauschild, Anne-Christin %A Baumbach, J&#246;rg Ingo %A Baumbach, Jan %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T Bioinformatics Methods for Breath Analysis and Biomarker Detection : %G eng %U http://hdl.handle.net/11858/00-001M-0000-002A-14B6-6 %D 2015 %B International Association of Breath Researchers 2015 Summit Conference %Z date of event: 2015-09-14 - 2015-09-16 %C Vienna, Austria %B Breath Research Topics from IABR 2015 Summit %E Baddour, Rafid
209. He X, Cicek AE, Wang Y, Schulz MH, Le H-S, Bar-Joseph Z: De Novo ChIP-seq Analysis. Genome Biology 2015, 16.
Abstract
ABSTRACT: Methods for the analysis of chromatin immunoprecipitation sequencing (ChIP-seq) data start by aligning the short reads to a reference genome. While often successful, they are not appropriate for cases where a reference genome is not available. Here we develop methods for de novo analysis of ChIP-seq data. Our methods combine de novo assembly with statistical tests enabling motif discovery without the use of a reference genome. We validate the performance of our method using human and mouse data. Analysis of fly data indicates that our method outperforms alignment based methods that utilize closely related species.
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@article{He2015, TITLE = {{\textit{De novo}} {ChIP}-seq analysis}, AUTHOR = {He, Xin and Cicek, A. Ercument and Wang, Yuhao and Schulz, Marcel H. and Le, Hai-Son and Bar-Joseph, Ziv}, LANGUAGE = {eng}, ISSN = {1474-760X}, DOI = {10.1186/s13059-015-0756-4}, PUBLISHER = {BioMed Central Ltd.}, ADDRESS = {London}, YEAR = {2015}, ABSTRACT = {ABSTRACT: Methods for the analysis of chromatin immunoprecipitation sequencing (ChIP-seq) data start by aligning the short reads to a reference genome. While often successful, they are not appropriate for cases where a reference genome is not available. Here we develop methods for de novo analysis of ChIP-seq data. Our methods combine de novo assembly with statistical tests enabling motif discovery without the use of a reference genome. We validate the performance of our method using human and mouse data. Analysis of fly data indicates that our method outperforms alignment based methods that utilize closely related species.}, JOURNAL = {Genome Biology}, VOLUME = {16}, NUMBER = {1}, EID = {205}, }
Endnote
%0 Journal Article %A He, Xin %A Cicek, A. Ercument %A Wang, Yuhao %A Schulz, Marcel H. %A Le, Hai-Son %A Bar-Joseph, Ziv %+ External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations %T De Novo ChIP-seq Analysis : %G eng %U http://hdl.handle.net/11858/00-001M-0000-0028-DD0C-3 %R 10.1186/s13059-015-0756-4 %7 2015-09-23 %D 2015 %8 23.09.2015 %X ABSTRACT: Methods for the analysis of chromatin immunoprecipitation sequencing (ChIP-seq) data start by aligning the short reads to a reference genome. While often successful, they are not appropriate for cases where a reference genome is not available. Here we develop methods for de novo analysis of ChIP-seq data. Our methods combine de novo assembly with statistical tests enabling motif discovery without the use of a reference genome. We validate the performance of our method using human and mouse data. Analysis of fly data indicates that our method outperforms alignment based methods that utilize closely related species. %J Genome Biology %V 16 %N 1 %Z sequence number: 205 %I BioMed Central Ltd. %C London %@ false %U http://www.genomebiology.com/2015/16/1/205
210. Ibragimov R: Exact and Heuristic Algorithms for Network Alignment using Graph Edit Distance Models. Universität des Saarlandes; 2015.
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@phdthesis{Ibragimovphd14, TITLE = {Exact and Heuristic Algorithms for Network Alignment using Graph Edit Distance Models}, AUTHOR = {Ibragimov, Rashid}, LANGUAGE = {eng}, SCHOOL = {Universit{\"a}t des Saarlandes}, ADDRESS = {Saarbr{\"u}cken}, YEAR = {2015}, DATE = {2015}, }
Endnote
%0 Thesis %A Ibragimov, Rashid %Y Baumbach, Jan %A referee: Guo, Jiong %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society International Max Planck Research School, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations %T Exact and Heuristic Algorithms for Network Alignment using Graph Edit Distance Models : %G eng %U http://hdl.handle.net/11858/00-001M-0000-0029-6E4C-7 %I Universit&#228;t des Saarlandes %C Saarbr&#252;cken %D 2015 %P 149 p. %V phd %9 phd %U http://scidok.sulb.uni-saarland.de/volltexte/2015/5999/http://scidok.sulb.uni-saarland.de/doku/urheberrecht.php?la=de
211. Karp PD, Berger B, Kovats D, Lengauer T, Linial M, Sabeti P, Hide W, Rost B: ISCB Ebola Award for Important Future Research on the Computational Biology of Ebola Virus. F1000Research 2015, 4.
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@article{LengauerF1000Research2015, TITLE = {{ISCB Ebola Award} for Important Future Research on the Computational Biology of {Ebola} Virus}, AUTHOR = {Karp, Peter D. and Berger, Bonnie and Kovats, Diane and Lengauer, Thomas and Linial, Michal and Sabeti, Pardis and Hide, Winston and Rost, Burkhard}, LANGUAGE = {eng}, ISSN = {2046-1402}, URL = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=4457108&tool=pmcentrez&rendertype=abstract}, DOI = {10.12688/f1000research.6038.1}, PUBLISHER = {F1000Research}, ADDRESS = {London, UK}, YEAR = {2015}, JOURNAL = {F1000Research}, VOLUME = {4}, EID = {12}, }
Endnote
%0 Journal Article %A Karp, Peter D. %A Berger, Bonnie %A Kovats, Diane %A Lengauer, Thomas %A Linial, Michal %A Sabeti, Pardis %A Hide, Winston %A Rost, Burkhard %+ External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations External Organizations %T ISCB Ebola Award for Important Future Research on the Computational Biology of Ebola Virus : %G eng %U http://hdl.handle.net/11858/00-001M-0000-0027-BD0D-5 %F OTHER: accessionPMC4457108 %F OTHER: pmcidPMC4457108 %F OTHER: pmc-uid4457108 %R 10.12688/f1000research.6038.1 %U http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=4457108&tool=pmcentrez&rendertype=abstract %7 2015-01-15 %D 2015 %8 15.01.2015 %J F1000Research %V 4 %Z sequence number: 12 %I F1000Research %C London, UK %@ false
212. Karp PD, Berger B, Kovats D, Lengauer T, Linial M, Sabeti P, Hide W, Rost B: ISCB Ebola Award for Important Future Research on the Computational Biology of Ebola Virus. PLoS Computational Biology 2015, 11.
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@article{KarpPLoS2015, TITLE = {{ISCB} {Ebola Award} for Important Future Research on the Computational Biology of {E}bola Virus}, AUTHOR = {Karp, Peter D. and Berger, Bonnie and Kovats, Diane and Lengauer, Thomas and Linial, Michal and Sabeti, Pardis and Hide, Winston and Rost, Burkhard}, LANGUAGE = {eng}, ISSN = {1553-734X; 1553-7358}, URL = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=4310586&tool=pmcentrez&rendertype=abstract}, DOI = {10.1371/journal.pcbi.1004087}, PUBLISHER = {Public Library of Science}, ADDRESS = {San Francisco, CA}, YEAR = {2015}, JOURNAL = {PLoS Computational Biology}, VOLUME = {11}, NUMBER = {1}, EID = {e1004087}, }
Endnote
%0 Journal Article %A Karp, Peter D. %A Berger, Bonnie %A Kovats, Diane %A Lengauer, Thomas %A Linial, Michal %A Sabeti, Pardis %A Hide, Winston %A Rost, Burkhard %+ External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations External Organizations %T ISCB Ebola Award for Important Future Research on the Computational Biology of Ebola Virus : %G eng %U http://hdl.handle.net/11858/00-001M-0000-0024-E54D-E %2 PMC4310586 %F OTHER: publisher-idPCOMPBIOL-D-14-02242 %R 10.1371/journal.pcbi.1004087 %U http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=4310586&tool=pmcentrez&rendertype=abstract %7 2015-01-29 %D 2015 %8 29.01.2015 %J PLoS Computational Biology %V 11 %N 1 %Z sequence number: e1004087 %I Public Library of Science %C San Francisco, CA %@ false
213. Karp PD, Berger B, Kovats D, Lengauer T, Linial M, Sabeti P, Hide W, Rost B: Message from the ISCB: ISCB Ebola award for important future research on the computational biology of Ebola virus. Bioinformatics 2015, 31.
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@article{LengauerBioinformatics2015, TITLE = {Message from the {ISCB}: {ISCB} {Ebola} award for important future research on the computational biology of {Ebola} virus}, AUTHOR = {Karp, Peter D. and Berger, Bonnie and Kovats, Diane and Lengauer, Thomas and Linial, Michal and Sabeti, Pardis and Hide, Winston and Rost, Burkhard}, ISSN = {1367-4803}, DOI = {10.1093/bioinformatics/btv019}, PUBLISHER = {Oxford University Press}, ADDRESS = {Oxford}, YEAR = {2015}, DATE = {2015}, JOURNAL = {Bioinformatics}, VOLUME = {31}, NUMBER = {4}, PAGES = {616--617}, }
Endnote
%0 Journal Article %A Karp, Peter D. %A Berger, Bonnie %A Kovats, Diane %A Lengauer, Thomas %A Linial, Michal %A Sabeti, Pardis %A Hide, Winston %A Rost, Burkhard %+ external external external Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society external external external external %T Message from the ISCB: ISCB Ebola award for important future research on the computational biology of Ebola virus : %U http://hdl.handle.net/11858/00-001M-0000-0026-A0E1-3 %F ISI: 000350059600029 %R 10.1093/bioinformatics/btv019 %D 2015 %J Bioinformatics %V 31 %N 4 %& 616 %P 616 - 617 %I Oxford University Press %C Oxford %@ false
214. Klughammer J, Datlinger P, Printz D, Sheffield NC, Farlik M, Hadler J, Fritsch G, Bock C: Differential DNA Methylation Analysis without a Reference Genome. Cell 2015, 11.
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@article{Klughammer2015, TITLE = {Differential {DNA} Methylation Analysis without a Reference Genome}, AUTHOR = {Klughammer, Johanna and Datlinger, Paul and Printz, Dieter and Sheffield, Nathan C. and Farlik, Matthias and Hadler, Johanna and Fritsch, Gerhard and Bock, Christoph}, LANGUAGE = {eng}, ISSN = {0092-8674}, DOI = {10.1016/j.celrep.2015.11.024}, PUBLISHER = {Cell Press}, ADDRESS = {Cambridge, Mass.}, YEAR = {2015}, DATE = {2015}, JOURNAL = {Cell}, VOLUME = {11}, PAGES = {2621--2633}, }
Endnote
%0 Journal Article %A Klughammer, Johanna %A Datlinger, Paul %A Printz, Dieter %A Sheffield, Nathan C. %A Farlik, Matthias %A Hadler, Johanna %A Fritsch, Gerhard %A Bock, Christoph %+ External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T Differential DNA Methylation Analysis without a Reference Genome : %G eng %U http://hdl.handle.net/11858/00-001M-0000-0029-5762-8 %R 10.1016/j.celrep.2015.11.024 %7 2015 %D 2015 %J Cell %V 11 %& 2621 %P 2621 - 2633 %I Cell Press %C Cambridge, Mass. %@ false %U http://www.sciencedirect.com/science/article/pii/S2211124715013248
215. Kouri V, Khouri R, Alemán Y, Abrahantes Y, Vercauteren J, Pineda-Peña A-C, Theys K, Megens S, Moutschen M, Pfeifer N, Van Weyenbergh J, Pérez AB, Pérez J, Pérez L, Van Laethem K, Vandamme A-M: CRF19_cpx is an Evolutionary Fit HIV-1 Variant Strongly Associated With Rapid Progression to AIDS in Cuba. EBioMedicine 2015, 2.
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@article{Kouri2015, TITLE = {{CRF19\_cpx} is an Evolutionary Fit {HIV}-1 Variant Strongly Associated With Rapid Progression to {AIDS} in {Cuba}}, AUTHOR = {Kouri, Vivian and Khouri, Ricardo and Alem{\'a}n, Yoan and Abrahantes, Yeissel and Vercauteren, Jurgen and Pineda-Pe{\~n}a, Andrea-Clemencia and Theys, Kristof and Megens, Sarah and Moutschen, Michel and Pfeifer, Nico and Van Weyenbergh, Johan and P{\'e}rez, Ana B. and P{\'e}rez, Jorge and P{\'e}rez, Lissette and Van Laethem, Kristel and Vandamme, Anne-Mieke}, LANGUAGE = {eng}, URL = {http://www.ebiomedicine.com/article/S2352-3964(15)00038-9/abstract}, DOI = {10.1016/j.ebiom.2015.01.015}, PUBLISHER = {Elsevier}, ADDRESS = {Amsterdam}, YEAR = {2015}, JOURNAL = {EBioMedicine}, VOLUME = {2}, NUMBER = {3}, PAGES = {244--254}, }
Endnote
%0 Journal Article %A Kouri, Vivian %A Khouri, Ricardo %A Alem&#225;n, Yoan %A Abrahantes, Yeissel %A Vercauteren, Jurgen %A Pineda-Pe&#241;a, Andrea-Clemencia %A Theys, Kristof %A Megens, Sarah %A Moutschen, Michel %A Pfeifer, Nico %A Van Weyenbergh, Johan %A P&#233;rez, Ana B. %A P&#233;rez, Jorge %A P&#233;rez, Lissette %A Van Laethem, Kristel %A Vandamme, Anne-Mieke %+ External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations %T CRF19_cpx is an Evolutionary Fit HIV-1 Variant Strongly Associated With Rapid Progression to AIDS in Cuba : %G eng %U http://hdl.handle.net/11858/00-001M-0000-0024-D01E-C %U http://www.ebiomedicine.com/article/S2352-3964(15)00038-9/abstract %R 10.1016/j.ebiom.2015.01.015 %7 2015-01-28 %D 2015 %8 28.01.2015 %J EBioMedicine %V 2 %N 3 %& 244 %P 244 - 254 %I Elsevier %C Amsterdam %U http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4484819/pdf/main.pdf
216. Lang B: Evaluation of Clique-Enumeration Algorithms with Application to Haplotype Reconstruction. Universität des Saarlandes; 2015.
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@mastersthesis{LangBachelor2015, TITLE = {Evaluation of Clique-Enumeration Algorithms with Application to Haplotype Reconstruction}, AUTHOR = {Lang, Bernhard}, LANGUAGE = {eng}, SCHOOL = {Universit{\"a}t des Saarlandes}, ADDRESS = {Saarbr{\"u}cken}, YEAR = {2015}, DATE = {2015}, TYPE = {Bachelor's thesis}, }
Endnote
%0 Thesis %A Lang, Bernhard %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T Evaluation of Clique-Enumeration Algorithms with Application to Haplotype Reconstruction : %G eng %U http://hdl.handle.net/11858/00-001M-0000-002C-47EF-9 %I Universit&#228;t des Saarlandes %C Saarbr&#252;cken %D 2015 %V bachelor %9 bachelor
217. Lawyer G: Understanding the Influence of All Nodes in a Network. Scientific Reports 2015, 5.
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@article{Lawyer2015, TITLE = {Understanding the Influence of All Nodes in a Network}, AUTHOR = {Lawyer, Glenn}, LANGUAGE = {eng}, DOI = {10.1038/srep08665}, PUBLISHER = {Nature Publishing Group}, ADDRESS = {London, UK}, YEAR = {2015}, JOURNAL = {Scientific Reports}, VOLUME = {5}, EID = {8665}, }
Endnote
%0 Journal Article %A Lawyer, Glenn %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T Understanding the Influence of All Nodes in a Network : %G eng %U http://hdl.handle.net/11858/00-001M-0000-0024-CAA9-3 %R 10.1038/srep08665 %7 2015-03-02 %D 2015 %8 02.03.2015 %J Scientific Reports %O Sci. Rep. %V 5 %Z sequence number: 8665 %I Nature Publishing Group %C London, UK
218. Lengauer T, Nussinov R: How to Write a Presubmission Inquiry. PLoS Computational Biology 2015, 11.
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@article{LengauerNussinov2015, TITLE = {How to Write a Presubmission Inquiry}, AUTHOR = {Lengauer, Thomas and Nussinov, Ruth}, LANGUAGE = {eng}, ISSN = {1553-734X}, DOI = {10.1371/journal.pcbi.1004098}, PUBLISHER = {Public Library of Science}, ADDRESS = {San Francisco, CA}, YEAR = {2015}, JOURNAL = {PLoS Computational Biology}, VOLUME = {11}, NUMBER = {2}, EID = {e1004098}, }
Endnote
%0 Journal Article %A Lengauer, Thomas %A Nussinov, Ruth %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations %T How to Write a Presubmission Inquiry : %G eng %U http://hdl.handle.net/11858/00-001M-0000-0026-C655-D %R 10.1371/journal.pcbi.1004098 %7 2015-02-26 %D 2015 %8 26.02.2015 %J PLoS Computational Biology %V 11 %N 2 %Z sequence number: e1004098 %I Public Library of Science %C San Francisco, CA %@ false %U http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004098
219. Leung WY, Marschall T, Paudel Y, Falquet L, Mei H, Schönhuth A, Maoz TY: SV-AUTOPILOT: Optimized, Automated Construction of Structural Variation Discovery and Benchmarking Pipelines. BMC Genomics 2015, 16.
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@article{Marschall2015, TITLE = {{SV}-{AUTOPILOT}: {O}ptimized, Automated Construction of Structural Variation Discovery and Benchmarking Pipelines}, AUTHOR = {Leung, Wai Yi and Marschall, Tobias and Paudel, Yogesh and Falquet, Laurent and Mei, Hailiang and Sch{\"o}nhuth, Alexander and Maoz, Tiffanie Yael}, LANGUAGE = {eng}, ISSN = {1471-2164}, URL = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=4520269&tool=pmcentrez&rendertype=abstract}, DOI = {10.1186/s12864-015-1376-9}, PUBLISHER = {BioMed Central}, ADDRESS = {London}, YEAR = {2015}, JOURNAL = {BMC Genomics}, VOLUME = {16}, NUMBER = {1}, EID = {238}, }
Endnote
%0 Journal Article %A Leung, Wai Yi %A Marschall, Tobias %A Paudel, Yogesh %A Falquet, Laurent %A Mei, Hailiang %A Sch&#246;nhuth, Alexander %A Maoz, Tiffanie Yael %+ External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations External Organizations External Organizations %T SV-AUTOPILOT: Optimized, Automated Construction of Structural Variation Discovery and Benchmarking Pipelines : %G eng %U http://hdl.handle.net/11858/00-001M-0000-0028-1B8C-0 %F OTHER: accessionPMC4520269 %F OTHER: pmcidPMC4520269 %F OTHER: pmc-uid4520269 %F OTHER: publisher-id1376 %R 10.1186/s12864-015-1376-9 %U http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=4520269&tool=pmcentrez&rendertype=abstract %7 2015-03-25 %D 2015 %8 25.03.2015 %K SV tool development %J BMC Genomics %V 16 %N 1 %Z sequence number: 238 %I BioMed Central %C London %@ false
220. List M, Franz M, Tan O, Mollenhauer J, Baumbach J: OpenLabNotes - An Electronic Laboratory Notebook Extension for OpenLabFramework. Journal of Integrative Bioinformatics 2015, 12.
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@article{List_jib274, TITLE = {{OpenLabNotes} -- An Electronic Laboratory Notebook Extension for {OpenLabFramework}}, AUTHOR = {List, Markus and Franz, Michael and Tan, Oihua and Mollenhauer, Jan and Baumbach, Jan}, LANGUAGE = {eng}, ISSN = {1613-4516}, DOI = {10.2390/biecoll-jib-2015-274}, YEAR = {2015}, JOURNAL = {Journal of Integrative Bioinformatics}, VOLUME = {12}, NUMBER = {3}, EID = {274}, }
Endnote
%0 Journal Article %A List, Markus %A Franz, Michael %A Tan, Oihua %A Mollenhauer, Jan %A Baumbach, Jan %+ External Organizations External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T OpenLabNotes - An Electronic Laboratory Notebook Extension for OpenLabFramework : %G eng %U http://hdl.handle.net/11858/00-001M-0000-002B-466F-2 %R 10.2390/biecoll-jib-2015-274 %7 2015 %D 2015 %J Journal of Integrative Bioinformatics %O JIB %V 12 %N 3 %Z sequence number: 274 %@ false
221. Lübke N, Di Cristanziano V, Sierra S, Knops E, Schülter E, Jensen B, Oette M, Lengauer T, Kaiser R: Proviral DNA as a Target for HIV-1 Resistance Analysis. Intervirology 2015, 58.
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@article{Lubke2015, TITLE = {Proviral {DNA} as a Target for {HIV}-1 Resistance Analysis}, AUTHOR = {L{\"u}bke, Nadine and Di Cristanziano, Veronica and Sierra, Saleta and Knops, Elena and Sch{\"u}lter, Eugen and Jensen, Bj{\"o}rn and Oette, Mark and Lengauer, Thomas and Kaiser, Rolf}, LANGUAGE = {eng}, DOI = {10.1159/000431093}, PUBLISHER = {Karger}, ADDRESS = {Basel}, YEAR = {2015}, DATE = {2015}, JOURNAL = {Intervirology}, VOLUME = {58}, NUMBER = {3}, PAGES = {184--189}, }
Endnote
%0 Journal Article %A L&#252;bke, Nadine %A Di Cristanziano, Veronica %A Sierra, Saleta %A Knops, Elena %A Sch&#252;lter, Eugen %A Jensen, Bj&#246;rn %A Oette, Mark %A Lengauer, Thomas %A Kaiser, Rolf %+ External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations %T Proviral DNA as a Target for HIV-1 Resistance Analysis : %G eng %U http://hdl.handle.net/11858/00-001M-0000-0028-5373-6 %R 10.1159/000431093 %7 2015 %D 2015 %K Kaiser, Rolf %J Intervirology %V 58 %N 3 %& 184 %P 184 - 189 %I Karger %C Basel
222. Mueller SC, Backes C, Kalinina OV, Meder B, Stöckel D, Lenhof H-P, Meese E, Keller A: BALL-SNP: Combining Genetic and Structural Information to Identify Candidate non-Synonymous Single Nucleotide Polymorphisms. Genome Medicine 2015, 7.
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@article{KalininaGenomeMed2015, TITLE = {{BALL}-{SNP}: {C}ombining Genetic and Structural Information to Identify Candidate non-Synonymous Single Nucleotide Polymorphisms}, AUTHOR = {Mueller, Sabine C. and Backes, Christina and Kalinina, Olga V. and Meder, Benjamin and St{\"o}ckel, Daniel and Lenhof, Hans-Peter and Meese, Eckart and Keller, Andreas}, LANGUAGE = {eng}, ISSN = {1756-994X}, URL = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=4506604&tool=pmcentrez&rendertype=abstract}, DOI = {10.1186/s13073-015-0190-y}, PUBLISHER = {BioMed Central}, ADDRESS = {London}, YEAR = {2015}, JOURNAL = {Genome Medicine}, VOLUME = {7}, NUMBER = {1}, EID = {65}, }
Endnote
%0 Journal Article %A Mueller, Sabine C. %A Backes, Christina %A Kalinina, Olga V. %A Meder, Benjamin %A St&#246;ckel, Daniel %A Lenhof, Hans-Peter %A Meese, Eckart %A Keller, Andreas %+ External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations External Organizations External Organizations %T BALL-SNP: Combining Genetic and Structural Information to Identify Candidate non-Synonymous Single Nucleotide Polymorphisms : %G eng %U http://hdl.handle.net/11858/00-001M-0000-0028-1B2E-4 %F OTHER: accessionPMC4506604 %F OTHER: pmcidPMC4506604 %F OTHER: pmc-uid4506604 %F OTHER: publisher-id190 %R 10.1186/s13073-015-0190-y %U http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=4506604&tool=pmcentrez&rendertype=abstract %7 2015-07-01 %D 2015 %8 01.07.2015 %J Genome Medicine %V 7 %N 1 %Z sequence number: 65 %I BioMed Central %C London %@ false
223. Passing NE: Advanced Runtime Analysis of Pattern Matching Algorithms. Universität des Saarlandes; 2015.
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@mastersthesis{PassingBachelor2015, TITLE = {Advanced Runtime Analysis of Pattern Matching Algorithms}, AUTHOR = {Passing, Noemi Estric}, LANGUAGE = {eng}, SCHOOL = {Universit{\"a}t des Saarlandes}, ADDRESS = {Saarbr{\"u}cken}, YEAR = {2015}, DATE = {2015}, TYPE = {Bachelor's thesis}, }
Endnote
%0 Thesis %A Passing, Noemi Estric %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T Advanced Runtime Analysis of Pattern Matching Algorithms : %G eng %U http://hdl.handle.net/11858/00-001M-0000-002C-47F6-8 %I Universit&#228;t des Saarlandes %C Saarbr&#252;cken %D 2015 %V bachelor %9 bachelor
224. Patterson M, Marschall T, Pisanti N, Iersel L, Stougie L, Klau GW, Schönhuth A: WhatsHap: Weighted Haplotype Assembly for Future-Generation Sequencing Reads. Journal of Computational Biology 2015, 22.
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@article{Patterson2015, TITLE = {{WhatsHap}: {W}eighted Haplotype Assembly for Future-Generation Sequencing Reads}, AUTHOR = {Patterson, Murray and Marschall, Tobias and Pisanti, Nadia and Iersel, Leo and Stougie, Leen and Klau, Gunnar W. and Sch{\"o}nhuth, Alexander}, LANGUAGE = {eng}, ISSN = {1066-5277}, DOI = {10.1089/cmb.2014.0157}, PUBLISHER = {Mary Ann Liebert}, ADDRESS = {New York, NY}, YEAR = {2015}, DATE = {2015}, JOURNAL = {Journal of Computational Biology}, VOLUME = {22}, NUMBER = {6}, PAGES = {498--509}, }
Endnote
%0 Journal Article %A Patterson, Murray %A Marschall, Tobias %A Pisanti, Nadia %A Iersel, Leo %A Stougie, Leen %A Klau, Gunnar W. %A Sch&#246;nhuth, Alexander %+ External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations External Organizations External Organizations %T WhatsHap: Weighted Haplotype Assembly for Future-Generation Sequencing Reads : %G eng %U http://hdl.handle.net/11858/00-001M-0000-0029-1A80-E %R 10.1089/cmb.2014.0157 %7 2015 %D 2015 %J Journal of Computational Biology %V 22 %N 6 %& 498 %P 498 - 509 %I Mary Ann Liebert %C New York, NY %@ false
225. Pironti A, Sierra S, Kaiser R, Lengauer T, Pfeifer N: Effects of Sequence Alterations on Results from Genotypic Tropism Testing. Journal of Clinical Virology 2015, 65.
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@article{Pironti2015, TITLE = {Effects of Sequence Alterations on Results from Genotypic Tropism Testing}, AUTHOR = {Pironti, Alejandro and Sierra, Saleta and Kaiser, Rolf and Lengauer, Thomas and Pfeifer, Nico}, LANGUAGE = {eng}, ISSN = {1386-6532}, DOI = {10.1016/j.jcv.2015.02.006}, PUBLISHER = {Elsevier}, ADDRESS = {Amsterdam}, YEAR = {2015}, JOURNAL = {Journal of Clinical Virology}, VOLUME = {65}, PAGES = {68--73}, }
Endnote
%0 Journal Article %A Pironti, Alejandro %A Sierra, Saleta %A Kaiser, Rolf %A Lengauer, Thomas %A Pfeifer, Nico %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T Effects of Sequence Alterations on Results from Genotypic Tropism Testing : %G eng %U http://hdl.handle.net/11858/00-001M-0000-0024-CFA4-1 %R 10.1016/j.jcv.2015.02.006 %7 2015-02-10 %D 2015 %8 10.02.2015 %J Journal of Clinical Virology %V 65 %& 68 %P 68 - 73 %I Elsevier %C Amsterdam %@ false
226. Poenisch M, Metz P, Blankenburg H, Ruggieri A, Lee J-Y, Rupp D, Rebhan I, Diederich K, Kaderali L, Domingues FS, Albrecht M, Lohmann V, Erfle H, Bartenschlager R: Identification of HNRNPK as Regulator of Hepatitis C Virus Particle Production. PLoS Pathogens 2015, 11.
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@article{PoenischPLoSPathog2015, TITLE = {Identification of {HNRNPK} as Regulator of Hepatitis {C} Virus Particle Production}, AUTHOR = {Poenisch, Marion and Metz, Philippe and Blankenburg, Hagen and Ruggieri, Alessia and Lee, Ji-Young and Rupp, Daniel and Rebhan, Ilka and Diederich, Kathrin and Kaderali, Lars and Domingues, Francisco S. and Albrecht, Mario and Lohmann, Volker and Erfle, Holger and Bartenschlager, Ralf}, LANGUAGE = {eng}, ISSN = {1553-7366; 1553-7374}, URL = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=4287573&tool=pmcentrez&rendertype=abstract}, DOI = {10.1371/journal.ppat.1004573}, PUBLISHER = {Public Library of Science}, ADDRESS = {San Francisco, CA}, YEAR = {2015}, JOURNAL = {PLoS Pathogens}, VOLUME = {11}, NUMBER = {1}, EID = {e1004573}, }
Endnote
%0 Journal Article %A Poenisch, Marion %A Metz, Philippe %A Blankenburg, Hagen %A Ruggieri, Alessia %A Lee, Ji-Young %A Rupp, Daniel %A Rebhan, Ilka %A Diederich, Kathrin %A Kaderali, Lars %A Domingues, Francisco S. %A Albrecht, Mario %A Lohmann, Volker %A Erfle, Holger %A Bartenschlager, Ralf %A contributor: Randall, Glenn %+ External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations External Organizations %T Identification of HNRNPK as Regulator of Hepatitis C Virus Particle Production : %G eng %U http://hdl.handle.net/11858/00-001M-0000-0024-9075-F %F OTHER: accessionPMC4287573 %F OTHER: pmcidPMC4287573 %F OTHER: pmc-uid4287573 %F OTHER: publisher-idPPATHOGENS-D-14-01626 %R 10.1371/journal.ppat.1004573 %U http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=4287573&tool=pmcentrez&rendertype=abstract %7 2015-01-08 %D 2015 %8 08.01.2015 %J PLoS Pathogens %V 11 %N 1 %Z sequence number: e1004573 %I Public Library of Science %C San Francisco, CA %@ false
227. Pohlmann T, Baumann S, Haag C, Albrecht M, Feldbrügge M: A FYVE Zinc Finger Domain Protein Specifically Links mRNA Transport to Endosome Trafficking. eLife 2015.
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@article{Pohlmann2015, TITLE = {A {FYVE} Zinc Finger Domain Protein Specifically Links {mRNA} Transport to Endosome Trafficking}, AUTHOR = {Pohlmann, Thomas and Baumann, Sebastian and Haag, Carl and Albrecht, Mario and Feldbr{\"u}gge, Michael}, LANGUAGE = {eng}, DOI = {10.7554/eLife.06041}, PUBLISHER = {eLife Sciences Publications}, ADDRESS = {Cambridge}, YEAR = {2015}, JOURNAL = {eLife}, EID = {e06041}, }
Endnote
%0 Journal Article %A Pohlmann, Thomas %A Baumann, Sebastian %A Haag, Carl %A Albrecht, Mario %A Feldbr&#252;gge, Michael %+ External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations %T A FYVE Zinc Finger Domain Protein Specifically Links mRNA Transport to Endosome Trafficking : %G eng %U http://hdl.handle.net/11858/00-001M-0000-002A-5A2D-6 %R 10.7554/eLife.06041 %7 2015 %D 2015 %J eLife %Z sequence number: e06041 %I eLife Sciences Publications %C Cambridge
228. Ramasamy P: Reconstruction of Phylogenetic Relationships between Nucleic Acid Polymerases of Viruses with RNA Genome. Universität des Saarlandes; 2015.
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@mastersthesis{Ramasamy2015, TITLE = {Reconstruction of Phylogenetic Relationships between Nucleic Acid Polymerases of Viruses with {RNA} Genome}, AUTHOR = {Ramasamy, Pathmanaban}, LANGUAGE = {eng}, SCHOOL = {Universit{\"a}t des Saarlandes}, ADDRESS = {Saarbr{\"u}cken}, YEAR = {2015}, DATE = {2015}, }
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%0 Thesis %A Ramasamy, Pathmanaban %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T Reconstruction of Phylogenetic Relationships between Nucleic Acid Polymerases of Viruses with RNA Genome : %G eng %U http://hdl.handle.net/11858/00-001M-0000-002C-287F-E %I Universit&#228;t des Saarlandes %C Saarbr&#252;cken %D 2015 %V master %9 master
229. Schmidl C, Rendeiro AF, Sheffield NC, Bock C: ChIPmentation: Fast, Robust, Low-input ChIP-seq for Histones and Transcription Factors. Nature Methods 2015, 12.
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@article{Schmidl2015, TITLE = {{ChIPmentation}: {Fast}, Robust, Low-input {ChIP}-seq for Histones and Transcription Factors}, AUTHOR = {Schmidl, Christian and Rendeiro, Andr{\'e} F. and Sheffield, Nathan C. and Bock, Christoph}, LANGUAGE = {eng}, ISSN = {1548-7091}, DOI = {10.1038/nmeth.3542}, PUBLISHER = {Nature Pub. Group}, ADDRESS = {New York, NY}, YEAR = {2015}, DATE = {2015}, JOURNAL = {Nature Methods}, VOLUME = {12}, NUMBER = {10}, PAGES = {963--965}, }
Endnote
%0 Journal Article %A Schmidl, Christian %A Rendeiro, Andr&#233; F. %A Sheffield, Nathan C. %A Bock, Christoph %+ External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T ChIPmentation: Fast, Robust, Low-input ChIP-seq for Histones and Transcription Factors : %G eng %U http://hdl.handle.net/11858/00-001M-0000-0028-F6FD-C %R 10.1038/nmeth.3542 %2 PMC4589892 %7 2015 %D 2015 %J Nature Methods %O Nature methods %V 12 %N 10 %& 963 %P 963 - 965 %I Nature Pub. Group %C New York, NY %@ false
230. Schneider E, El Hajj N, Müller F, Navarro B: Epigenetic Dysregulation in the Prefrontal Cortex of Suicide Completers. Cytogenetics and Genome Research 2015, 146.
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@article{Muellerfab2015, TITLE = {Epigenetic Dysregulation in the Prefrontal Cortex of Suicide Completers}, AUTHOR = {Schneider, Ebahard and El Hajj, Nady and M{\"u}ller, Fabian and Navarro, Bianca}, LANGUAGE = {eng}, ISSN = {0301-0171}, DOI = {10.1159/000435778}, PUBLISHER = {Karger}, ADDRESS = {Basel}, YEAR = {2015}, DATE = {2015}, JOURNAL = {Cytogenetics and Genome Research}, VOLUME = {146}, NUMBER = {1}, PAGES = {19--27}, }
Endnote
%0 Journal Article %A Schneider, Ebahard %A El Hajj, Nady %A M&#252;ller, Fabian %A Navarro, Bianca %+ External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations %T Epigenetic Dysregulation in the Prefrontal Cortex of Suicide Completers : %G eng %U http://hdl.handle.net/11858/00-001M-0000-0028-E0EF-0 %R 10.1159/000435778 %7 2015-09 %D 2015 %J Cytogenetics and Genome Research %O Cytogenet Genome Res. %V 146 %N 1 %& 19 %P 19 - 27 %I Karger %C Basel %@ false
231. Serra Mari R: Analyse von populationsbasiertem Haplotyp-Phasing mittels Sequenzierdaten. Universität des Saarlandes; 2015.
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@mastersthesis{SerraMariBachelor2015, TITLE = {{Analyse von populationsbasiertem Haplotyp-Phasing mittels Sequenzierdaten}}, AUTHOR = {Serra Mari, Rebecca}, LANGUAGE = {deu}, SCHOOL = {Universit{\"a}t des Saarlandes}, ADDRESS = {Saarbr{\"u}cken}, YEAR = {2015}, DATE = {2015}, TYPE = {Bachelor's thesis}, }
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%0 Thesis %A Serra Mari, Rebecca %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T Analyse von populationsbasiertem Haplotyp-Phasing mittels Sequenzierdaten : %G deu %U http://hdl.handle.net/11858/00-001M-0000-002C-47FF-5 %I Universit&#228;t des Saarlandes %C Saarbr&#252;cken %D 2015 %V bachelor %9 bachelor
232. Sierra S, Dybowski JN, Pironti A, Heider D, Güney L, Thielen A, Reuter S, Esser S, Fätkenheuer G, Lengauer T, Hoffmann D, Pfister H, Jensen B, Kaiser R: Parameters Influencing Baseline HIV-1 Genotypic Tropism Testing Related to Clinical Outcome in Patients on Maraviroc. PLoS ONE 2015, 10.
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@article{SierraPLoSONE2015, TITLE = {Parameters Influencing Baseline {HIV}-1 Genotypic Tropism Testing Related to Clinical Outcome in Patients on Maraviroc}, AUTHOR = {Sierra, Saleta and Dybowski, J. Nikolai and Pironti, Alejandro and Heider, Dominik and G{\"u}ney, Lisa and Thielen, Alexander and Reuter, Stefan and Esser, Stefan and F{\"a}tkenheuer, Gerd and Lengauer, Thomas and Hoffmann, Daniel and Pfister, Herbert and Jensen, Bj{\"o}rn and Kaiser, Rolf}, LANGUAGE = {eng}, ISSN = {1932-6203}, URL = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=4430318&tool=pmcentrez&rendertype=abstract}, DOI = {10.1371/journal.pone.0125502}, PUBLISHER = {Public Library of Science}, ADDRESS = {San Francisco, CA}, YEAR = {2015}, JOURNAL = {PLoS ONE}, VOLUME = {10}, NUMBER = {5}, EID = {e0125502}, }
Endnote
%0 Journal Article %A Sierra, Saleta %A Dybowski, J. Nikolai %A Pironti, Alejandro %A Heider, Dominik %A G&#252;ney, Lisa %A Thielen, Alexander %A Reuter, Stefan %A Esser, Stefan %A F&#228;tkenheuer, Gerd %A Lengauer, Thomas %A Hoffmann, Daniel %A Pfister, Herbert %A Jensen, Bj&#246;rn %A Kaiser, Rolf %A contributor: Ceccherini-Silberstein, Francesca %+ External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations External Organizations External Organizations %T Parameters Influencing Baseline HIV-1 Genotypic Tropism Testing Related to Clinical Outcome in Patients on Maraviroc : %G eng %U http://hdl.handle.net/11858/00-001M-0000-0027-7AC3-3 %F OTHER: accessionPMC4430318 %F OTHER: pmcidPMC4430318 %F OTHER: pmc-uid4430318 %R 10.1371/journal.pone.0125502 %F OTHER: publisher-idPONE-D-14-44999 %U http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=4430318&tool=pmcentrez&rendertype=abstract %7 2015-05-13 %D 2015 %8 13.05.2015 %J PLoS ONE %V 10 %N 5 %Z sequence number: e0125502 %I Public Library of Science %C San Francisco, CA %@ false
233. Speicher NK, Pfeifer N: Integrating Different Data Types by Regularized Unsupervised Multiple Kernel Learning with Application to Cancer Subtype Discovery. Bioinformatics (Proc ISMB/ECCB 2015) 2015, 31.
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@article{SpeicherPfeifer2015, TITLE = {Integrating Different Data Types by Regularized Unsupervised Multiple Kernel Learning with Application to Cancer Subtype Discovery}, AUTHOR = {Speicher, Nora K. and Pfeifer, Nico}, LANGUAGE = {eng}, ISSN = {1367-4803}, DOI = {10.1093/bioinformatics/btv244}, PUBLISHER = {Oxford University Press}, ADDRESS = {Oxford}, YEAR = {2015}, DATE = {2015}, JOURNAL = {Bioinformatics (Proc. ISMB/ECCB)}, VOLUME = {31}, NUMBER = {12}, PAGES = {i268--i275}, BOOKTITLE = {ISMB/ECCB 2015}, }
Endnote
%0 Journal Article %A Speicher, Nora K. %A Pfeifer, Nico %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T Integrating Different Data Types by Regularized Unsupervised Multiple Kernel Learning with Application to Cancer Subtype Discovery : %G eng %U http://hdl.handle.net/11858/00-001M-0000-0027-D2E9-9 %R 10.1093/bioinformatics/btv244 %7 2015 %D 2015 %J Bioinformatics %V 31 %N 12 %& i268 %P i268 - i275 %I Oxford University Press %C Oxford %@ false %B ISMB/ECCB 2015 %O ISMB/ECCB 2015
234. Stöckel D, Schmidt F, Trampert P, Lenhof H-P: CausalTrail: Testing Hypothesis Using Causal Bayesian Networks. Faculty of 1000 Research 2015, 4.
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@article{StoeckelF1000Research2015, TITLE = {CausalTrail: Testing Hypothesis Using Causal {Bayesian} Networks}, AUTHOR = {St{\"o}ckel, Daniel and Schmidt, Florian and Trampert, Patrick and Lenhof, Hans-Peter}, LANGUAGE = {eng}, DOI = {10.12688/f1000research.7647.1}, PUBLISHER = {BioMed Central}, ADDRESS = {London}, YEAR = {2015}, JOURNAL = {Faculty of 1000 Research}, VOLUME = {4}, EID = {1520}, }
Endnote
%0 Journal Article %A St&#246;ckel, Daniel %A Schmidt, Florian %A Trampert, Patrick %A Lenhof, Hans-Peter %+ External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations %T CausalTrail: Testing Hypothesis Using Causal Bayesian Networks : %G eng %U http://hdl.handle.net/11858/00-001M-0000-0028-F706-0 %R 10.12688/f1000research.7647.1 %7 2015 %D 2015 %J Faculty of 1000 Research %O F1000Research %V 4 %Z sequence number: 1520 %I BioMed Central %C London
235. Susser S, Flinders M, Reesink HW, Zeuzem S, Lawyer G, Ghys A, Van Eygen V, Witek J, De Meyer S, Sarrazin C: Evolution of Hepatitis C Virus Quasispecies during Repeated Treatment with the NS3/4A Protease Inhibitor Telaprevir. Antimicrobial Agents and Chemotherapy 2015, 59.
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@article{Susser2015, TITLE = {Evolution of Hepatitis {C }Virus Quasispecies during Repeated Treatment with the {NS3}/{4A} Protease Inhibitor Telaprevir}, AUTHOR = {Susser, Simone and Flinders, Mathieu and Reesink, Henk W. and Zeuzem, Stefan and Lawyer, Glenn and Ghys, Anne and Van Eygen, Veerle and Witek, James and De Meyer, Sandra and Sarrazin, Christoph}, LANGUAGE = {eng}, ISSN = {0066-4804}, DOI = {10.1128/AAC.04911-14}, PUBLISHER = {American Society for Microbiology (ASM)}, YEAR = {2015}, DATE = {2015}, JOURNAL = {Antimicrobial Agents and Chemotherapy}, VOLUME = {59}, NUMBER = {5}, PAGES = {2746--2755}, }
Endnote
%0 Journal Article %A Susser, Simone %A Flinders, Mathieu %A Reesink, Henk W. %A Zeuzem, Stefan %A Lawyer, Glenn %A Ghys, Anne %A Van Eygen, Veerle %A Witek, James %A De Meyer, Sandra %A Sarrazin, Christoph %+ External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations External Organizations External Organizations %T Evolution of Hepatitis C Virus Quasispecies during Repeated Treatment with the NS3/4A Protease Inhibitor Telaprevir : %G eng %U http://hdl.handle.net/11858/00-001M-0000-0028-1345-A %R 10.1128/AAC.04911-14 %7 2015 %D 2015 %J Antimicrobial Agents and Chemotherapy %V 59 %N 5 %& 2746 %P 2746 - 2755 %I American Society for Microbiology (ASM) %@ false
236. Tomazou EM, Sheffield NC, Schmidl C, Schuster M, Schoenegger A, Datlinger P, Kubicek S, Bock C, Kovar H: Epigenome Mapping Reveals Distinct Modes of Gene Regulation and Widespread Enhancer Reprogramming by the Oncogenic Fusion Protein EWS-FLI1. Cell Reports 2015, 10.
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@article{BockCellReports2015a, TITLE = {Epigenome Mapping Reveals Distinct Modes of Gene Regulation and Widespread Enhancer Reprogramming by the Oncogenic Fusion Protein {EWS}-{FLI1}}, AUTHOR = {Tomazou, Eleni M. and Sheffield, Nathan C. and Schmidl, Christian and Schuster, Michael and Schoenegger, Andreas and Datlinger, Paul and Kubicek, Stefan and Bock, Christoph and Kovar, Heinrich}, DOI = {10.1016/j.celrep.2015.01.042}, PUBLISHER = {Cell Press}, ADDRESS = {Cambridge, MA}, YEAR = {2015}, DATE = {2015}, JOURNAL = {Cell Reports}, VOLUME = {10}, NUMBER = {7}, PAGES = {1082--1095}, }
Endnote
%0 Journal Article %A Tomazou, Eleni M. %A Sheffield, Nathan C. %A Schmidl, Christian %A Schuster, Michael %A Schoenegger, Andreas %A Datlinger, Paul %A Kubicek, Stefan %A Bock, Christoph %A Kovar, Heinrich %+ external external external external external external external Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society external %T Epigenome Mapping Reveals Distinct Modes of Gene Regulation and Widespread Enhancer Reprogramming by the Oncogenic Fusion Protein EWS-FLI1 : %U http://hdl.handle.net/11858/00-001M-0000-0026-A0DB-4 %F ISI: 000349918700006 %R 10.1016/j.celrep.2015.01.042 %D 2015 %J Cell Reports %V 10 %N 7 %& 1082 %P 1082 - 1095 %I Cell Press %C Cambridge, MA
237. Wittler R, Marschall T, Schönhuth A, Mäkinen V: Repeat- and Error-aware Comparison of Deletions. Bioinformatics 2015, 31.
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@article{Marschall2015a, TITLE = {Repeat- and Error-aware Comparison of Deletions}, AUTHOR = {Wittler, Roland and Marschall, Tobias and Sch{\"o}nhuth, Alexander and M{\"a}kinen, Veli}, LANGUAGE = {eng}, ISSN = {1367-4803}, DOI = {10.1093/bioinformatics/btv304}, PUBLISHER = {Oxford University Press}, ADDRESS = {Oxford}, YEAR = {2015}, DATE = {2015}, JOURNAL = {Bioinformatics}, VOLUME = {31}, NUMBER = {18}, PAGES = {2947--2954}, }
Endnote
%0 Journal Article %A Wittler, Roland %A Marschall, Tobias %A Sch&#246;nhuth, Alexander %A M&#228;kinen, Veli %+ External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations %T Repeat- and Error-aware Comparison of Deletions : %G eng %U http://hdl.handle.net/11858/00-001M-0000-0028-E11C-4 %R 10.1093/bioinformatics/btv304 %7 2015 %D 2015 %J Bioinformatics %V 31 %N 18 %& 2947 %P 2947 - 2954 %I Oxford University Press %C Oxford %@ false
238. Wiwie C, Baumbach J, Röttger R: Comparing the Performance of Biomedical Clustering Methods. Nature Methods 2015, 12.
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@article{WiwieComparing2015, TITLE = {Comparing the Performance of Biomedical Clustering Methods}, AUTHOR = {Wiwie, Christian and Baumbach, Jan and R{\"o}ttger, Richard}, LANGUAGE = {eng}, ISSN = {1548-7091}, DOI = {10.1038/nmeth.3583}, PUBLISHER = {Nature Pub. Group}, ADDRESS = {New York, NY}, YEAR = {2015}, DATE = {2015}, JOURNAL = {Nature Methods}, VOLUME = {12}, PAGES = {1033--1038}, }
Endnote
%0 Journal Article %A Wiwie, Christian %A Baumbach, Jan %A R&#246;ttger, Richard %+ External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations %T Comparing the Performance of Biomedical Clustering Methods : %G eng %U http://hdl.handle.net/11858/00-001M-0000-0029-226E-A %R 10.1038/nmeth.3583 %7 2015 %D 2015 %J Nature Methods %O Nature methods %V 12 %& 1033 %P 1033 - 1038 %I Nature Pub. Group %C New York, NY %@ false
239. Zeke A, Bastys T, Alexa A, Garai Á, Mészáros B, Kirsch K, Dosztányi Z, Kalinina OV, Reményi A: Systematic Discovery of Linear Binding Motifs Targeting an Ancient Protein Interaction Surface on MAP Kinases. Molecular Systems Biology 2015, 11.
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@article{BastysKalinina15, TITLE = {Systematic Discovery of Linear Binding Motifs Targeting an Ancient Protein Interaction Surface on {MAP} Kinases}, AUTHOR = {Zeke, Andr{\'a}s and Bastys, Tomas and Alexa, Anita and Garai, {\'A}gnes and M{\'e}sz{\'a}ros, B{\'a}lint and Kirsch, Kl{\'a}ra and Doszt{\'a}nyi, Zsuzsanna and Kalinina, Olga V. and Rem{\'e}nyi, Attila}, LANGUAGE = {eng}, ISSN = {1744-4292}, DOI = {10.15252/msb.20156269}, PUBLISHER = {EMBO Press}, ADDRESS = {Heidelberg}, YEAR = {2015}, JOURNAL = {Molecular Systems Biology}, VOLUME = {11}, NUMBER = {11}, PAGES = {1--29}, EID = {837}, }
Endnote
%0 Journal Article %A Zeke, Andr&#225;s %A Bastys, Tomas %A Alexa, Anita %A Garai, &#193;gnes %A M&#233;sz&#225;ros, B&#225;lint %A Kirsch, Kl&#225;ra %A Doszt&#225;nyi, Zsuzsanna %A Kalinina, Olga V. %A Rem&#233;nyi, Attila %+ External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations %T Systematic Discovery of Linear Binding Motifs Targeting an Ancient Protein Interaction Surface on MAP Kinases : %G eng %U http://hdl.handle.net/11858/00-001M-0000-0028-F563-E %R 10.15252/msb.20156269 %7 2015-11-04 %D 2015 %8 04.11.2015 %J Molecular Systems Biology %V 11 %N 11 %& 1 %P 1 - 29 %Z sequence number: 837 %I EMBO Press %C Heidelberg %@ false %U http://msb.embopress.org/content/11/11/837
2014
240. Ahmad M, Kalinina O, Lengauer T: Entropy Gain Due to Water Release Upon Ligand Binding. Journal of Cheminformatics 2014, 6.
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@article{DBLP:journals/jcheminf/AhmadKL14, TITLE = {Entropy Gain Due to Water Release Upon Ligand Binding}, AUTHOR = {Ahmad, Mazen and Kalinina, Olga and Lengauer, Thomas}, LANGUAGE = {eng}, ISSN = {1758-2946}, DOI = {10.1186/1758-2946-6-S1-P35}, PUBLISHER = {Springer}, ADDRESS = {Berlin}, YEAR = {2014}, DATE = {2014}, JOURNAL = {Journal of Cheminformatics}, VOLUME = {6}, NUMBER = {S-1}, EID = {P35}, }
Endnote
%0 Journal Article %A Ahmad, Mazen %A Kalinina, Olga %A Lengauer, Thomas %+ External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T Entropy Gain Due to Water Release Upon Ligand Binding : %G eng %U http://hdl.handle.net/11858/00-001M-0000-0024-6154-3 %R 10.1186/1758-2946-6-S1-P35 %7 2014 %D 2014 %J Journal of Cheminformatics %V 6 %N S-1 %Z sequence number: P35 %I Springer %C Berlin %@ false
241. Alcaraz N, Pauling J, Batra R, Barbosa E, Junge A, Christensen AGL, Azevedo V, Ditzel HJ, Baumbach J: KeyPathwayMiner 4.0: Condition-specific Pathway Analysis by Combining Multiple Omics Studies and Networks with Cytoscape. BMC Systems Biology 2014, 8.
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@article{AlcarazBMC2014, TITLE = {{KeyPathwayMiner} 4.0: Condition-specific Pathway Analysis by Combining Multiple Omics Studies and Networks with {Cytoscape}}, AUTHOR = {Alcaraz, Nicolas and Pauling, Josch and Batra, Richa and Barbosa, Eudes and Junge, Alexander and Christensen, Anne G. L. and Azevedo, Vasco and Ditzel, Henrik J. and Baumbach, Jan}, LANGUAGE = {eng}, ISSN = {1752-0509}, DOI = {10.1186/s12918-014-0099-x}, PUBLISHER = {BioMedCentral}, ADDRESS = {London}, YEAR = {2014}, JOURNAL = {BMC Systems Biology}, VOLUME = {8}, EID = {99}, }
Endnote
%0 Journal Article %A Alcaraz, Nicolas %A Pauling, Josch %A Batra, Richa %A Barbosa, Eudes %A Junge, Alexander %A Christensen, Anne G. L. %A Azevedo, Vasco %A Ditzel, Henrik J. %A Baumbach, Jan %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T KeyPathwayMiner 4.0: Condition-specific Pathway Analysis by Combining Multiple Omics Studies and Networks with Cytoscape : %G eng %U http://hdl.handle.net/11858/00-001M-0000-0024-6C98-D %F ISI: 000340909700001 %R 10.1186/s12918-014-0099-x %2 PMC4236746 %7 2014 %D 2014 %J BMC Systems Biology %V 8 %Z sequence number: 99 %I BioMedCentral %C London %@ false %U http://www.biomedcentral.com/1752-0509/8/99
242. Amabile G, Di Ruscio A, Müller F, Welner RS, Yang H, Ebralidze AK, Zhang H, Qi L, Martinelli G, Brummelkamp T, Le Beau MM, Figueroa ME, Bock C, Tenen DG: Cellular Reprogramming Erases Aberrant DNA Methylation and the Malignant Phenotype in Chronic Myeloid Leukemia. Blood 2014, 124.
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@article{AmabileBLOOD2014, TITLE = {Cellular Reprogramming Erases Aberrant {DNA} Methylation and the Malignant Phenotype in {Chronic Myeloid Leukemia}}, AUTHOR = {Amabile, Giovanni and Di Ruscio, Annalisa and M{\"u}ller, Fabian and Welner, Robert S. and Yang, Henry and Ebralidze, Alexander K. and Zhang, Hong and Qi, Lihua and Martinelli, Giovanni and Brummelkamp, Thijn and Le Beau, Michelle M. and Figueroa, Maria E. and Bock, Christoph and Tenen, Daniel G.}, LANGUAGE = {eng}, ISSN = {0006-4971}, PUBLISHER = {American Society of Hematology}, ADDRESS = {Washington, DC}, YEAR = {2014}, DATE = {2014}, JOURNAL = {Blood}, VOLUME = {124}, NUMBER = {21}, PAGES = {4524--4524}, }
Endnote
%0 Journal Article %A Amabile, Giovanni %A Di Ruscio, Annalisa %A M&#252;ller, Fabian %A Welner, Robert S. %A Yang, Henry %A Ebralidze, Alexander K. %A Zhang, Hong %A Qi, Lihua %A Martinelli, Giovanni %A Brummelkamp, Thijn %A Le Beau, Michelle M. %A Figueroa, Maria E. %A Bock, Christoph %A Tenen, Daniel G. %+ External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations %T Cellular Reprogramming Erases Aberrant DNA Methylation and the Malignant Phenotype in Chronic Myeloid Leukemia : %G eng %U http://hdl.handle.net/11858/00-001M-0000-0025-ACB5-3 %F ISI: 000349243500052 %7 2014 %D 2014 %J Blood %O Blood %V 124 %N 21 %& 4524 %P 4524 - 4524 %I American Society of Hematology %C Washington, DC %@ false
243. Assenov Y, Müller F, Lutsik P, Walter J, Lengauer T, Bock C: Comprehensive Analysis of DNA Methylation Data with RnBeads. Nature Methods 2014, 11.
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@article{Assenov:2014kqa, TITLE = {Comprehensive Analysis of {DNA} Methylation Data with {RnBeads}}, AUTHOR = {Assenov, Yassen and M{\"u}ller, Fabian and Lutsik, Pavlo and Walter, J{\"o}rn and Lengauer, Thomas and Bock, Christoph}, LANGUAGE = {eng}, DOI = {10.1038/nmeth.3115}, PUBLISHER = {Nature Publishing Group}, ADDRESS = {London}, YEAR = {2014}, DATE = {2014}, JOURNAL = {Nature Methods}, VOLUME = {11}, NUMBER = {11}, PAGES = {1138--1140}, }
Endnote
%0 Journal Article %A Assenov, Yassen %A M&#252;ller, Fabian %A Lutsik, Pavlo %A Walter, J&#246;rn %A Lengauer, Thomas %A Bock, Christoph %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T Comprehensive Analysis of DNA Methylation Data with RnBeads : %G eng %U http://hdl.handle.net/11858/00-001M-0000-0024-5D25-A %2 PMC4216143 %R 10.1038/nmeth.3115 %7 2014 %D 2014 %J Nature Methods %V 11 %N 11 %& 1138 %P 1138 - 1140 %I Nature Publishing Group %C London %U http://www.ncbi.nlm.nih.gov/pubmed/25262207
244. Assenov Y: Identification and Prioritization of Genomic Loci with Disease-specific Methylation. Universität des Saarlandes; 2014.
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@phdthesis{AssenovPhD2014, TITLE = {Identification and Prioritization of Genomic Loci with Disease-specific Methylation}, AUTHOR = {Assenov, Yassen}, LANGUAGE = {eng}, URL = {urn:nbn:de:bsz:291-scidok-58865}, SCHOOL = {Universit{\"a}t des Saarlandes}, ADDRESS = {Saarbr{\"u}cken}, YEAR = {2014}, DATE = {2014}, }
Endnote
%0 Thesis %A Assenov, Yassen %Y Lengauer, Thomas %A referee: Bock, Christoph %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society International Max Planck Research School, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T Identification and Prioritization of Genomic Loci with Disease-specific Methylation : %G eng %U http://hdl.handle.net/11858/00-001M-0000-0024-E49E-D %U urn:nbn:de:bsz:291-scidok-58865 %I Universit&#228;t des Saarlandes %C Saarbr&#252;cken %D 2014 %P IX, 142 p. %V phd %9 phd %U http://scidok.sulb.uni-saarland.de/volltexte/2014/5886/http://scidok.sulb.uni-saarland.de/doku/lic_ohne_pod.php?la=de
245. Barbosa E, Röttger R, Hauschild A-C, Azevedo V, Baumbach J: On the Limits of Computational Functional Genomics for Bacterial Lifestyle Prediction. Briefings in Functional Genomics 2014, 13.
Abstract
We review the level of genomic specificity regarding actinobacterial pathogenicity. As they occupy various niches in diverse habitats, one may assume the existence of lifestyle-specific genomic features. We include 240 actinobacteria classified into four pathogenicity classes: human pathogens (HPs), broad-spectrum pathogens (BPs), opportunistic pathogens (OPs) and non-pathogenic (NP). We hypothesize: (H1) Pathogens (HPs and BPs) possess specific pathogenicity signature genes. (H2) The same holds for OPs. (H3) Broad-spectrum and exclusively HPs cannot be distinguished from each other because of an observation bias, i.e. many HPs might yet be unclassified BPs. (H4) There is no intrinsic genomic characteristic of OPs compared with pathogens, as small mutations are likely to play a more dominant role to survive the immune system. To study these hypotheses, we implemented a bioinformatics pipeline that combines evolutionary sequence analysis with statistical learning methods (Random Forest with feature selection, model tuning and robustness analysis). Essentially, we present orthologous gene sets that computationally distinguish pathogens from NPs (H1). We further show a clear limit in differentiating OPs from both NPs (H2) and pathogens (H4). HPs may also not be distinguished from bacteria annotated as BPs based only on a small set of orthologous genes (H3), as many HPs might as well target a broad range of mammals but have not been annotated accordingly. In conclusion, we illustrate that even in the post-genome era and despite next-generation sequencing technology, our ability to efficiently deduce real-world conclusions, such as pathogenicity classification, remains quite limited.
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@article{Barbosa2014, TITLE = {On the Limits of Computational Functional Genomics for Bacterial Lifestyle Prediction}, AUTHOR = {Barbosa, Eudes and R{\"o}ttger, Richard and Hauschild, Anne-Christin and Azevedo, Vasco and Baumbach, Jan}, LANGUAGE = {eng}, DOI = {10.1093/bfgp/elu014}, PUBLISHER = {Oxford University Press}, ADDRESS = {Oxford}, YEAR = {2014}, DATE = {2014-09-01}, ABSTRACT = {We review the level of genomic specificity regarding actinobacterial pathogenicity. As they occupy various niches in diverse habitats, one may assume the existence of lifestyle-specific genomic features. We include 240 actinobacteria classified into four pathogenicity classes: human pathogens (HPs), broad-spectrum pathogens (BPs), opportunistic pathogens (OPs) and non-pathogenic (NP). We hypothesize: (H1) Pathogens (HPs and BPs) possess specific pathogenicity signature genes. (H2) The same holds for OPs. (H3) Broad-spectrum and exclusively HPs cannot be distinguished from each other because of an observation bias, i.e. many HPs might yet be unclassified BPs. (H4) There is no intrinsic genomic characteristic of OPs compared with pathogens, as small mutations are likely to play a more dominant role to survive the immune system. To study these hypotheses, we implemented a bioinformatics pipeline that combines evolutionary sequence analysis with statistical learning methods (Random Forest with feature selection, model tuning and robustness analysis). Essentially, we present orthologous gene sets that computationally distinguish pathogens from NPs (H1). We further show a clear limit in differentiating OPs from both NPs (H2) and pathogens (H4). HPs may also not be distinguished from bacteria annotated as BPs based only on a small set of orthologous genes (H3), as many HPs might as well target a broad range of mammals but have not been annotated accordingly. In conclusion, we illustrate that even in the post-genome era and despite next-generation sequencing technology, our ability to efficiently deduce real-world conclusions, such as pathogenicity classification, remains quite limited.}, JOURNAL = {Briefings in Functional Genomics}, VOLUME = {13}, NUMBER = {5}, PAGES = {398--408}, }
Endnote
%0 Journal Article %A Barbosa, Eudes %A R&#246;ttger, Richard %A Hauschild, Anne-Christin %A Azevedo, Vasco %A Baumbach, Jan %+ External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T On the Limits of Computational Functional Genomics for Bacterial Lifestyle Prediction : %G eng %U http://hdl.handle.net/11858/00-001M-0000-0024-551D-2 %R 10.1093/bfgp/elu014 %7 2014-05-22 %D 2014 %8 01.09.2014 %X We review the level of genomic specificity regarding actinobacterial pathogenicity. As they occupy various niches in diverse habitats, one may assume the existence of lifestyle-specific genomic features. We include 240 actinobacteria classified into four pathogenicity classes: human pathogens (HPs), broad-spectrum pathogens (BPs), opportunistic pathogens (OPs) and non-pathogenic (NP). We hypothesize: (H1) Pathogens (HPs and BPs) possess specific pathogenicity signature genes. (H2) The same holds for OPs. (H3) Broad-spectrum and exclusively HPs cannot be distinguished from each other because of an observation bias, i.e. many HPs might yet be unclassified BPs. (H4) There is no intrinsic genomic characteristic of OPs compared with pathogens, as small mutations are likely to play a more dominant role to survive the immune system. To study these hypotheses, we implemented a bioinformatics pipeline that combines evolutionary sequence analysis with statistical learning methods (Random Forest with feature selection, model tuning and robustness analysis). Essentially, we present orthologous gene sets that computationally distinguish pathogens from NPs (H1). We further show a clear limit in differentiating OPs from both NPs (H2) and pathogens (H4). HPs may also not be distinguished from bacteria annotated as BPs based only on a small set of orthologous genes (H3), as many HPs might as well target a broad range of mammals but have not been annotated accordingly. In conclusion, we illustrate that even in the post-genome era and despite next-generation sequencing technology, our ability to efficiently deduce real-world conclusions, such as pathogenicity classification, remains quite limited. %J Briefings in Functional Genomics %V 13 %N 5 %& 398 %P 398 - 408 %I Oxford University Press %C Oxford %U http://bfgp.oxfordjournals.org/content/13/5/398.abstract
246. Bastys T, Doncheva NT, Walter H, Kaiser R, Albrecht M, Kalinina OV: Molecular Mechanisms of HIV-1 Protease Resistance and Resensitization towards Lopinavir and Saquinavir upon L76V Mutation. Antiviral Therapy 2014(Suppl. 1).
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@inproceedings{Bastys2014x, TITLE = {Molecular Mechanisms of {HIV}-1 Protease Resistance and Resensitization towards Lopinavir and Saquinavir upon {L76V} Mutation}, AUTHOR = {Bastys, Tomas and Doncheva, Nadezhda Tsankova and Walter, Hauke and Kaiser, R. and Albrecht, Mario and Kalinina, Olga V.}, LANGUAGE = {eng}, ISSN = {1359-6535}, PUBLISHER = {International Medical Press}, PUBLISHER = {International Medical Press}, YEAR = {2014}, DATE = {2014}, BOOKTITLE = {Abstracts presented at the International Workshop on Antiviral Drug Resistance: Meeting the Global Challenge}, JOURNAL = {Antiviral Therapy}, VOLUME = {19}, ISSUE = {Suppl. 1}, EID = {A154}, ADDRESS = {Berlin, Germany}, }
Endnote
%0 Generic %A Bastys, Tomas %A Doncheva, Nadezhda Tsankova %A Walter, Hauke %A Kaiser, R. %A Albrecht, Mario %A Kalinina, Olga V. %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T Molecular Mechanisms of HIV-1 Protease Resistance and Resensitization towards Lopinavir and Saquinavir upon L76V Mutation : %G eng %U http://hdl.handle.net/11858/00-001M-0000-0027-9CE8-7 %D 2014 %Z name of event: International Workshop on Antiviral Drug Resistance: Meeting the Global Challenge %Z date of event: 2014-06-03 - 2014-06-07 %Z place of event: Berlin, Germany %B Abstracts presented at the International Workshop on Antiviral Drug Resistance: Meeting the Global Challenge %J Antiviral Therapy %V 19 %N Suppl. 1 %Z sequence number: A154 %@ false
247. Becker D: BiQ Analyzer HiMod - an Interactive Software Tool for High-throughput Locus-specific Analysis of 5-Methylcyclosine and its Oxidized Derivatives. Universität des Saarlandes; 2014.
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@mastersthesis{Becker2014, TITLE = {{BiQ} Analyzer {HiMod} -- an Interactive Software Tool for High-throughput Locus-specific Analysis of 5-Methylcyclosine and its Oxidized Derivatives}, AUTHOR = {Becker, Daniel}, LANGUAGE = {eng}, SCHOOL = {Universit{\"a}t des Saarlandes}, ADDRESS = {Saarbr{\"u}cken}, YEAR = {2014}, DATE = {2014}, }
Endnote
%0 Thesis %A Becker, Daniel %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T BiQ Analyzer HiMod - an Interactive Software Tool for High-throughput Locus-specific Analysis of 5-Methylcyclosine and its Oxidized Derivatives : %G eng %U http://hdl.handle.net/11858/00-001M-0000-0024-C278-D %I Universit&#228;t des Saarlandes %C Saarbr&#252;cken %D 2014 %V master %9 master
248. Becker D, Lutsik P, Ebert P, Bock C, Lengauer T, Walter J: BiQ Analyzer HiMod: An Interactive Software Tool for High-throughput Locus-specific Analysis of 5-Methylcytosine and its Oxidized Derivatives. Nucleic Acids Research 2014, 42.
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@article{BeckerBiQ2014, TITLE = {{BiQ} Analyzer {HiMod}: An Interactive Software Tool for High-throughput Locus-specific Analysis of 5-Methylcytosine and its Oxidized Derivatives}, AUTHOR = {Becker, Daniel and Lutsik, Pavlo and Ebert, Peter and Bock, Christoph and Lengauer, Thomas and Walter, J{\"o}rn}, LANGUAGE = {eng}, ISSN = {0305-1048; 1362-4962}, URL = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=4086109&tool=pmcentrez&rendertype=abstract}, DOI = {10.1093/nar/gku457}, PUBLISHER = {Oxford University Press}, ADDRESS = {Oxford, UK}, YEAR = {2014}, DATE = {2014-07-01}, JOURNAL = {Nucleic Acids Research}, VOLUME = {42}, NUMBER = {W1}, PAGES = {W501--W507}, }
Endnote
%0 Journal Article %A Becker, Daniel %A Lutsik, Pavlo %A Ebert, Peter %A Bock, Christoph %A Lengauer, Thomas %A Walter, J&#246;rn %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations %T BiQ Analyzer HiMod: An Interactive Software Tool for High-throughput Locus-specific Analysis of 5-Methylcytosine and its Oxidized Derivatives : %G eng %U http://hdl.handle.net/11858/00-001M-0000-0024-6BE8-1 %F OTHER: accessionPMC4086109 %F OTHER: pmcidPMC4086109 %F OTHER: pmc-uid4086109 %R 10.1093/nar/gku457 %U http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=4086109&tool=pmcentrez&rendertype=abstract %7 2014-05-29 %D 2014 %8 01.07.2014 %J Nucleic Acids Research %V 42 %N W1 %& W501 %P W501 - W507 %I Oxford University Press %C Oxford, UK %@ false
249. Beggel B: Determining and Utilizing the Quasispecies of the Hepatitis B Virus in Clinical Applications. Universität des Saarlandes; 2014.
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@phdthesis{Beggeltheses2014, TITLE = {Determining and Utilizing the Quasispecies of the Hepatitis {B} Virus in Clinical Applications}, AUTHOR = {Beggel, Bastian}, LANGUAGE = {eng}, URL = {urn:nbn:de:bsz:291-scidok-58317}, SCHOOL = {Universit{\"a}t des Saarlandes}, ADDRESS = {Saarbr{\"u}cken}, YEAR = {2014}, DATE = {2014}, }
Endnote
%0 Thesis %A Beggel, Bastian %Y Lengauer, Thomas %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society International Max Planck Research School, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T Determining and Utilizing the Quasispecies of the Hepatitis B Virus in Clinical Applications : %G eng %U http://hdl.handle.net/11858/00-001M-0000-0024-5DFB-A %U urn:nbn:de:bsz:291-scidok-58317 %I Universit&#228;t des Saarlandes %C Saarbr&#252;cken %D 2014 %P 138 p. %V phd %9 phd %U http://scidok.sulb.uni-saarland.de/volltexte/2014/5831/http://scidok.sulb.uni-saarland.de/doku/lic_ohne_pod.php?la=de
250. Blankenburg H: Computational Methods for Integrating and Analyzing Human Systems Biology Data. Universität des Saarlandes; 2014.
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@phdthesis{Blankenburg2014, TITLE = {Computational Methods for Integrating and Analyzing Human Systems Biology Data}, AUTHOR = {Blankenburg, Hagen}, LANGUAGE = {eng}, URL = {urn:nbn:de:bsz:291-scidok-59329}, SCHOOL = {Universit{\"a}t des Saarlandes}, ADDRESS = {Saarbr{\"u}cken}, YEAR = {2014}, DATE = {2014}, }
Endnote
%0 Thesis %A Blankenburg, Hagen %Y Albrecht, Mario %A referee: Helms, Volkhard %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society International Max Planck Research School, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations %T Computational Methods for Integrating and Analyzing Human Systems Biology Data : %G eng %U http://hdl.handle.net/11858/00-001M-0000-0024-9671-3 %U urn:nbn:de:bsz:291-scidok-59329 %I Universit&#228;t des Saarlandes %C Saarbr&#252;cken %D 2014 %P 181 p. %V phd %9 phd %U http://scidok.sulb.uni-saarland.de/volltexte/2014/5932/http://scidok.sulb.uni-saarland.de/doku/lic_ohne_pod.php?la=de
251. Bock C: Synergy and Competition between Cancer Genome Sequencing and Epigenome Mapping Projects. Genome Medicine 2014, 6.
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@article{BockSynergy2014, TITLE = {Synergy and Competition between Cancer Genome Sequencing and Epigenome Mapping Projects}, AUTHOR = {Bock, Christoph}, LANGUAGE = {eng}, ISSN = {1756-994X}, DOI = {10.1186/gm557}, PUBLISHER = {BioMed Central}, ADDRESS = {London}, YEAR = {2014}, JOURNAL = {Genome Medicine}, VOLUME = {6}, NUMBER = {5}, EID = {41}, }
Endnote
%0 Journal Article %A Bock, Christoph %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T Synergy and Competition between Cancer Genome Sequencing and Epigenome Mapping Projects : %G eng %U http://hdl.handle.net/11858/00-001M-0000-0024-6BF1-D %R 10.1186/gm557 %2 PMC4062064 %7 2014 %D 2014 %J Genome Medicine %V 6 %N 5 %Z sequence number: 41 %I BioMed Central %C London %@ false %U http://genomemedicine.com/content/6/5/41
252. Deplus R, Blanchon L, Rajavelu A, Boukaba A, Defrance M, Luciani J, Rothe F, Dedeurwaerder S, Denis H, Brinkman AB, Simmer F, Müller F, Bertin B, Berdasco M, Putmans P, Calonne E, Litchfield DW, de Launoit Y, Jurkowski TP, Stunnenberg HG, Bock C, Sotiriou C, Fraga MF, Esteller M, Jeltsch A, Fuks F: Regulation of DNA Methylation Patterns by CK2-mediated Phosphorylation of Dnmt3a. Cell Reports 2014, 8.
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@article{Deplus2014, TITLE = {Regulation of {DNA} Methylation Patterns by {CK2}-mediated Phosphorylation of {Dnmt3a}}, AUTHOR = {Deplus, Rachel and Blanchon, Lo{\"i}c and Rajavelu, Arumugam and Boukaba, Abdelhalim and Defrance, Matthieu and Luciani, Judith and Rothe, Fran{\c c}oise and Dedeurwaerder, Sarah and Denis, H{\'e}l{\`e}ne and Brinkman, Arie B. and Simmer, Femke and M{\"u}ller, Fabian and Bertin, Benjamin and Berdasco, Maria and Putmans, Pascale and Calonne, Emilie and Litchfield, David W. and de Launoit, Yvan and Jurkowski, Tomasz P. and Stunnenberg, Hendrik G. and Bock, Christoph and Sotiriou, Christos and Fraga, Mario F. and Esteller, Manel and Jeltsch, Albert and Fuks, Fran{\c c}ois}, LANGUAGE = {eng}, DOI = {10.1016/j.celrep.2014.06.048}, PUBLISHER = {Elsevier}, ADDRESS = {Amsterdam}, YEAR = {2014}, DATE = {2014}, JOURNAL = {Cell Reports}, VOLUME = {8}, NUMBER = {3}, PAGES = {743--753}, }
Endnote
%0 Journal Article %A Deplus, Rachel %A Blanchon, Lo&#239;c %A Rajavelu, Arumugam %A Boukaba, Abdelhalim %A Defrance, Matthieu %A Luciani, Judith %A Rothe, Fran&#231;oise %A Dedeurwaerder, Sarah %A Denis, H&#233;l&#232;ne %A Brinkman, Arie B. %A Simmer, Femke %A M&#252;ller, Fabian %A Bertin, Benjamin %A Berdasco, Maria %A Putmans, Pascale %A Calonne, Emilie %A Litchfield, David W. %A de Launoit, Yvan %A Jurkowski, Tomasz P. %A Stunnenberg, Hendrik G. %A Bock, Christoph %A Sotiriou, Christos %A Fraga, Mario F. %A Esteller, Manel %A Jeltsch, Albert %A Fuks, Fran&#231;ois %+ External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations External Organizations External Organizations %T Regulation of DNA Methylation Patterns by CK2-mediated Phosphorylation of Dnmt3a : %G eng %U http://hdl.handle.net/11858/00-001M-0000-0024-6BE1-F %F ISI: 000341572200012 %R 10.1016/j.celrep.2014.06.048 %7 2014 %D 2014 %J Cell Reports %V 8 %N 3 %& 743 %P 743 - 753 %I Elsevier %C Amsterdam %U http://www.sciencedirect.com/science/article/pii/S2211124714005324
253. Dietzen M, Zotenko E, Hildebrandt A, Lengauer T: Correction to On the Applicability of Elastic Network Normal Modes in Small-molecule Docking. Journal of Chemical Information and Modeling 2014, 54.
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@article{doi:10.1021/ci5006788, TITLE = {Correction to {O}n the Applicability of Elastic Network Normal Modes in Small-molecule Docking}, AUTHOR = {Dietzen, Matthias and Zotenko, Elena and Hildebrandt, Andreas and Lengauer, Thomas}, LANGUAGE = {eng}, ISSN = {1549-9596}, DOI = {10.1021/ci5006788}, PUBLISHER = {American Chemical Society}, ADDRESS = {Washington, DC}, YEAR = {2014}, DATE = {2014}, JOURNAL = {Journal of Chemical Information and Modeling}, VOLUME = {54}, NUMBER = {12}, PAGES = {3453--3453}, }
Endnote
%0 Journal Article %A Dietzen, Matthias %A Zotenko, Elena %A Hildebrandt, Andreas %A Lengauer, Thomas %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T Correction to On the Applicability of Elastic Network Normal Modes in Small-molecule Docking : %G eng %U http://hdl.handle.net/11858/00-001M-0000-0024-925B-A %R 10.1021/ci5006788 %7 2014 %D 2014 %J Journal of Chemical Information and Modeling %V 54 %N 12 %& 3453 %P 3453 - 3453 %I American Chemical Society %C Washington, DC %@ false
254. Dietzen M: Modeling Protein Interactions in Protein Binding Sites and Oligomeric Protein Complexes. Universität des Saarlandes; 2014.
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@phdthesis{DietzenPhD2014, TITLE = {Modeling Protein Interactions in Protein Binding Sites and Oligomeric Protein Complexes}, AUTHOR = {Dietzen, Matthias}, LANGUAGE = {eng}, URL = {urn:nbn:de:bsz:291-scidok-59402}, SCHOOL = {Universit{\"a}t des Saarlandes}, ADDRESS = {Saarbr{\"u}cken}, YEAR = {2014}, DATE = {2014}, }
Endnote
%0 Thesis %A Dietzen, Matthias %Y Lengauer, Thomas %A referee: Hildebrandt, Andreas %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society International Max Planck Research School, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations %T Modeling Protein Interactions in Protein Binding Sites and Oligomeric Protein Complexes : %G eng %U http://hdl.handle.net/11858/00-001M-0000-0024-E4A2-1 %U urn:nbn:de:bsz:291-scidok-59402 %I Universit&#228;t des Saarlandes %C Saarbr&#252;cken %D 2014 %P XVIII, 259 p. %V phd %9 phd %U http://scidok.sulb.uni-saarland.de/volltexte/2014/5940/http://scidok.sulb.uni-saarland.de/doku/lic_ohne_pod.php?la=de
255. Dirks M, Pfeifer N, Schulter E, Esser S, Fatkenheuer G, Jenssen B, Kaiser R, Verheyen J: Insertions and Deletions in p6-gag Correlate with the Predicted Cellular Tropism of HIV-1 V3 Sequences. Antiviral Therapy 2014(Suppl. 1).
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@inproceedings{Dirks2014x, TITLE = {Insertions and Deletions in p6-gag Correlate with the Predicted Cellular Tropism of {HIV}-1 V3 Sequences}, AUTHOR = {Dirks, M. and Pfeifer, Nico and Schulter, E. and Esser, S. and Fatkenheuer, G. and Jenssen, B. and Kaiser, R. and Verheyen, J.}, LANGUAGE = {eng}, ISSN = {1359-6535}, PUBLISHER = {International Medical Press}, PUBLISHER = {International Medical Press}, YEAR = {2014}, DATE = {2014}, BOOKTITLE = {Abstracts presented at the International Workshop on Antiviral Drug Resistance: Meeting the Global Challenge}, JOURNAL = {Antiviral Therapy}, VOLUME = {19}, ISSUE = {Suppl. 1}, EID = {A116}, ADDRESS = {Berlin, Germany}, }
Endnote
%0 Generic %A Dirks, M. %A Pfeifer, Nico %A Schulter, E. %A Esser, S. %A Fatkenheuer, G. %A Jenssen, B. %A Kaiser, R. %A Verheyen, J. %+ External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations %T Insertions and Deletions in p6-gag Correlate with the Predicted Cellular Tropism of HIV-1 V3 Sequences : %G eng %U http://hdl.handle.net/11858/00-001M-0000-0027-9CF8-3 %D 2014 %Z name of event: International Workshop on Antiviral Drug Resistance: Meeting the Global Challenge %Z date of event: 2014-06-03 - 2014-06-07 %Z place of event: Berlin, Germany %B Abstracts presented at the International Workshop on Antiviral Drug Resistance: Meeting the Global Challenge %J Antiviral Therapy %V 19 %N Suppl. 1 %Z sequence number: A116 %@ false
256. Doncheva NT, Klein K, Morris JH, Wybrow M, Domingues FS, Albrecht M: Integrative Visual Analysis of Protein Sequence Mutations. BMC Proceedings (Proc BioVis 2013) 2014, 8(Suppl 2).
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@article{doncheva14a, TITLE = {Integrative Visual Analysis of Protein Sequence Mutations}, AUTHOR = {Doncheva, Nadezhda Tsankova and Klein, Karsten and Morris, John H. and Wybrow, Michael and Domingues, Francisco S. and Albrecht, Mario}, LANGUAGE = {eng}, ISSN = {1753-6561}, DOI = {10.1186/1753-6561-8-S2-S2}, PUBLISHER = {BioMed Central}, ADDRESS = {London}, YEAR = {2014}, JOURNAL = {BMC Proceedings (Proc. BioVis)}, VOLUME = {8}, NUMBER = {Suppl 2}, EID = {S2}, BOOKTITLE = {Proceedings of the 3rd Annual Symposium on Biological Data Visualization: Data Analysis and Redesign Contests (BioVis 2013)}, }
Endnote
%0 Journal Article %A Doncheva, Nadezhda Tsankova %A Klein, Karsten %A Morris, John H. %A Wybrow, Michael %A Domingues, Francisco S. %A Albrecht, Mario %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations External Organizations External Organizations %T Integrative Visual Analysis of Protein Sequence Mutations : %G eng %U http://hdl.handle.net/11858/00-001M-0000-0024-5D70-D %R 10.1186/1753-6561-8-S2-S2 %7 2014-08-28 %D 2014 %8 28.08.2014 %J BMC Proceedings %V 8 %N Suppl 2 %Z sequence number: S2 %I BioMed Central %C London %@ false %B Proceedings of the 3rd Annual Symposium on Biological Data Visualization: Data Analysis and Redesign Contests %O 3rd IEEE Symposium on Biological Data Visualization ; Atlanta, GA, USA ; 13-14 October 2013 BioVis 2013 %U http://www.biomedcentral.com/1753-6561/8/S2/S2
257. Döring M: Identification and Analysis of Methylation Call Differences Between Bisulphite Microarray and Bisulphite Sequencing Data With Statistical Learning Techniques. Universität des Saarlandes; 2014.
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@mastersthesis{Doering2014, TITLE = {Identification and Analysis of Methylation Call Differences Between Bisulphite Microarray and Bisulphite Sequencing Data With Statistical Learning Techniques}, AUTHOR = {D{\"o}ring, Matthias}, LANGUAGE = {eng}, SCHOOL = {Universit{\"a}t des Saarlandes}, ADDRESS = {Saarbr{\"u}cken}, YEAR = {2014}, DATE = {2014}, }
Endnote
%0 Thesis %A D&#246;ring, Matthias %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T Identification and Analysis of Methylation Call Differences Between Bisulphite Microarray and Bisulphite Sequencing Data With Statistical Learning Techniques : %G eng %U http://hdl.handle.net/11858/00-001M-0000-0024-C276-2 %I Universit&#228;t des Saarlandes %C Saarbr&#252;cken %D 2014 %V master %9 master
258. Eckel SP, Baumbach J, Hauschild A-C: On the Importance of Statistics in Breath Analysis -- Hope or Curse?Journal of Breath Research 2014, 8.
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@article{Eckel2014, TITLE = {On the Importance of Statistics in Breath Analysis -- Hope or Curse?}, AUTHOR = {Eckel, Sandrah P. and Baumbach, Jan and Hauschild, Anne-Christin}, LANGUAGE = {eng}, ISSN = {1752-7155}, DOI = {10.1088/1752-7155/8/1/012001}, PUBLISHER = {IOP Publ.}, ADDRESS = {Bristol, UK}, YEAR = {2014}, JOURNAL = {Journal of Breath Research}, VOLUME = {8}, NUMBER = {1}, PAGES = {1--4}, EID = {012001}, }
Endnote
%0 Journal Article %A Eckel, Sandrah P. %A Baumbach, Jan %A Hauschild, Anne-Christin %+ External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T On the Importance of Statistics in Breath Analysis -- Hope or Curse? : %G eng %U http://hdl.handle.net/11858/00-001M-0000-0024-3DF7-0 %F ISI: 000332654800001 %R 10.1088/1752-7155/8/1/012001 %2 PMC4014528 %7 2014-02-24 %D 2014 %8 24.02.2014 %J Journal of Breath Research %V 8 %N 1 %& 1 %P 1 - 4 %Z sequence number: 012001 %I IOP Publ. %C Bristol, UK %@ false
259. Feldmann A: Predicting HIV-1 Susceptibility to Broadly Neutralizing Antibodies. Universität des Saarlandes; 2014.
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@mastersthesis{Feldmann2014, TITLE = {Predicting {HIV}-1 Susceptibility to Broadly Neutralizing Antibodies}, AUTHOR = {Feldmann, Anna}, LANGUAGE = {eng}, SCHOOL = {Universit{\"a}t des Saarlandes}, ADDRESS = {Saarbr{\"u}cken}, YEAR = {2014}, DATE = {2014}, }
Endnote
%0 Thesis %A Feldmann, Anna %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T Predicting HIV-1 Susceptibility to Broadly Neutralizing Antibodies : %G eng %U http://hdl.handle.net/11858/00-001M-0000-0024-C27F-0 %I Universit&#228;t des Saarlandes %C Saarbr&#252;cken %D 2014 %V master %9 master
260. Feuerbach L: Evolutionary Epigenomics - Identifying Functional Genome Elements by Epigenetic Footprints in the DNA. Universität des Saarlandes; 2014.
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@phdthesis{Feuerbach2014, TITLE = {Evolutionary Epigenomics -- Identifying Functional Genome Elements by Epigenetic Footprints in the {DNA}}, AUTHOR = {Feuerbach, Lars}, LANGUAGE = {eng}, SCHOOL = {Universit{\"a}t des Saarlandes}, ADDRESS = {Saarbr{\"u}cken}, YEAR = {2014}, DATE = {2014}, }
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%0 Thesis %A Feuerbach, Lars %Y Lengauer, Thomas %A referee: Jotun, Hein %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society International Max Planck Research School, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations %T Evolutionary Epigenomics - Identifying Functional Genome Elements by Epigenetic Footprints in the DNA : %G eng %U http://hdl.handle.net/11858/00-001M-0000-0024-9676-A %I Universit&#228;t des Saarlandes %C Saarbr&#252;cken %D 2014 %P 205 p. %V phd %9 phd %U http://scidok.sulb.uni-saarland.de/volltexte/2014/5888/http://scidok.sulb.uni-saarland.de/doku/lic_ohne_pod.php?la=de
261. Halachev K: Exploratory Visualizations and Statistical Analysis of Large, Heterogeneous Epigenetic Datasets. Universität des Saarlandes; 2014.
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@phdthesis{Halachev2014, TITLE = {Exploratory Visualizations and Statistical Analysis of Large, Heterogeneous Epigenetic Datasets}, AUTHOR = {Halachev, Konstantin}, LANGUAGE = {eng}, SCHOOL = {Universit{\"a}t des Saarlandes}, ADDRESS = {Saarbr{\"u}cken}, YEAR = {2014}, DATE = {2014}, }
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%0 Thesis %A Halachev, Konstantin %Y Lengauer, Thomas %A referee: Bock, Christoph %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society International Max Planck Research School, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T Exploratory Visualizations and Statistical Analysis of Large, Heterogeneous Epigenetic Datasets : %G eng %U http://hdl.handle.net/11858/00-001M-0000-0024-96A8-9 %I Universit&#228;t des Saarlandes %C Saarbr&#252;cken %D 2014 %P 163 p. %V phd %9 phd %U http://scidok.sulb.uni-saarland.de/volltexte/2014/5911/http://scidok.sulb.uni-saarland.de/doku/lic_ohne_pod.php?la=de
262. Hauschild A-C, Baumbach JI, Baumbach J: Novel Developments In Computational Clinical Breath Analysis and Biomarker Detection. In ECCB’14 Highlight Papers Abstracts; 2014.
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@inproceedings{HauschildECCB2014, TITLE = {Novel Developments In Computational Clinical Breath Analysis and Biomarker Detection}, AUTHOR = {Hauschild, Anne-Christin and Baumbach, J{\"o}rg Ingo and Baumbach, Jan}, LANGUAGE = {eng}, YEAR = {2014}, BOOKTITLE = {ECCB'14 Highlight Papers Abstracts}, EID = {HP09}, ADDRESS = {Strasbourg, France}, }
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%0 Conference Proceedings %A Hauschild, Anne-Christin %A Baumbach, J&#246;rg Ingo %A Baumbach, Jan %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations %T Novel Developments In Computational Clinical Breath Analysis and Biomarker Detection : %G eng %U http://hdl.handle.net/11858/00-001M-0000-002A-06CD-3 %D 2014 %B The 13th European Conference on Computational Biology %Z date of event: 2014-09-07 - 2014-09-10 %C Strasbourg, France %B ECCB'14 Highlight Papers Abstracts %Z sequence number: HP09 %U http://www.ebi.ac.uk/eccb/2014/eccb14.loria.fr/program/highlight-papers.html
263. Hildebrandt AK, Dietzen M, Lengauer T, Lenhof H-P, Althaus E, Hildebrandt A: Efficient Computation of Root Mean Square Deviations Under Rigid Transformations. Journal of Computational Chemistry 2014, 35.
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@article{HildebrandtJCC2014, TITLE = {Efficient Computation of Root Mean Square Deviations Under Rigid Transformations}, AUTHOR = {Hildebrandt, Anna K. and Dietzen, Matthias and Lengauer, Thomas and Lenhof, Hans-Peter and Althaus, Ernst and Hildebrandt, Andreas}, LANGUAGE = {eng}, ISSN = {0192-8651}, DOI = {10.1002/jcc.23513}, PUBLISHER = {Wiley}, ADDRESS = {New York, NY}, YEAR = {2014}, DATE = {2014}, JOURNAL = {Journal of Computational Chemistry}, VOLUME = {35}, NUMBER = {10}, PAGES = {765--771}, }
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%0 Journal Article %A Hildebrandt, Anna K. %A Dietzen, Matthias %A Lengauer, Thomas %A Lenhof, Hans-Peter %A Althaus, Ernst %A Hildebrandt, Andreas %+ External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations %T Efficient Computation of Root Mean Square Deviations Under Rigid Transformations : %G eng %U http://hdl.handle.net/11858/00-001M-0000-0024-3E35-B %F ISI: 000332446300001 %R 10.1002/jcc.23513 %7 2013-12-19 %D 2014 %J Journal of Computational Chemistry %O J. Comput. Chem. %V 35 %N 10 %& 765 %P 765 - 771 %I Wiley %C New York, NY %@ false
264. Jalali A, Pfeifer N: Interpretable Per Case Weighted Ensemble Method for Cancer Associations. In Algorithms in Bioinformatics (WABI 2014). Springer; 2014. [Lecture Notes in Bioinformatics, vol. 8701]
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@inproceedings{JalaliPfeifer2014, TITLE = {Interpretable Per Case Weighted Ensemble Method for Cancer Associations}, AUTHOR = {Jalali, Adrin and Pfeifer, Nico}, LANGUAGE = {eng}, ISBN = {978-3-662-44752-9}, DOI = {10.1007/978-3-662-44753-6_26}, PUBLISHER = {Springer}, YEAR = {2014}, DATE = {2014}, BOOKTITLE = {Algorithms in Bioinformatics (WABI 2014)}, EDITOR = {Brown, Dan and Morgenstern, Burkhard}, PAGES = {352--353}, SERIES = {Lecture Notes in Bioinformatics}, VOLUME = {8701}, ADDRESS = {Wroclaw, Poland}, }
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%0 Conference Proceedings %A Jalali, Adrin %A Pfeifer, Nico %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T Interpretable Per Case Weighted Ensemble Method for Cancer Associations : %G eng %U http://hdl.handle.net/11858/00-001M-0000-0024-901E-8 %R 10.1007/978-3-662-44753-6_26 %D 2014 %B 14th International Workshop on Algorithms in Bioinformatic %Z date of event: 2014-09-08 - 2014-09-10 %C Wroclaw, Poland %B Algorithms in Bioinformatics %E Brown, Dan; Morgenstern, Burkhard %P 352 - 353 %I Springer %@ 978-3-662-44752-9 %B Lecture Notes in Bioinformatics %N 8701
265. Kalaghatgi P, Lawyer G, Lengauer T: Estimating HIV Epidemic Characteristics from a Dated Transmission Network. In Reviews in Antiviral Therapy & Infectious Diseases. Volume 14-2. Virology Education; 2014.
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@inproceedings{Kalaghatgi2014Talk, TITLE = {Estimating {HIV} epidemic characteristics from a dated transmission network}, AUTHOR = {Kalaghatgi, Prabhav and Lawyer, Glenn and Lengauer, Thomas}, LANGUAGE = {eng}, PUBLISHER = {Virology Education}, YEAR = {2014}, DATE = {2014}, BOOKTITLE = {Abstract Book 12th European Workshop on HIV \& Hepatitis Treatment Strategies \& Antiviral Drug Resistance}, PAGES = {3--3}, EID = {O-01}, JOURNAL = {Reviews in Antiviral Therapy \& Infectious Diseases}, VOLUME = {14-2}, ADDRESS = {Barcelona, Spain}, }
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%0 Conference Proceedings %A Kalaghatgi, Prabhav %A Lawyer, Glenn %A Lengauer, Thomas %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T Estimating HIV Epidemic Characteristics from a Dated Transmission Network : %G eng %U http://hdl.handle.net/11858/00-001M-0000-0024-6F33-C %D 2014 %B 12th European HIV & Hepatitis Workshop %Z date of event: 2014-03-26 - 2014-03-28 %C Barcelona, Spain %B Abstract Book 12th European Workshop on HIV & Hepatitis Treatment Strategies & Antiviral Drug Resistance %P 3 - 3 %Z sequence number: O-01 %I Virology Education %J Reviews in Antiviral Therapy & Infectious Diseases %V 14-2
266. Kalinina OV, Lengauer T: Protein Structure Prediction and Databases. eLS 2014.
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@article{Kalinina2014, TITLE = {Protein Structure Prediction and Databases}, AUTHOR = {Kalinina, Olga V. and Lengauer, Thomas}, LANGUAGE = {eng}, DOI = {10.1002/9780470015902.a0006214.pub2}, PUBLISHER = {Wiley}, ADDRESS = {Chichester}, YEAR = {2014}, JOURNAL = {eLS}, PAGES = {1--5}, }
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%0 Journal Article %A Kalinina, Olga V. %A Lengauer, Thomas %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T Protein Structure Prediction and Databases : %G eng %U http://hdl.handle.net/11858/00-001M-0000-0024-6169-6 %R 10.1002/9780470015902.a0006214.pub2 %7 2014-09-15 %D 2014 %8 15.09.2014 %J eLS %& 1 %P 1 - 5 %I Wiley %C Chichester
267. Kreuer S, Hauschild A-C, Fink T, Baumbach JI, Maddula S, Volk T: Two Different Approaches for Pharmacokinetic Modeling of Exhaled Drug Concentrations. Scientific Reports 2014, 4.
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@article{HauschildScientificReports2014, TITLE = {Two Different Approaches for Pharmacokinetic Modeling of Exhaled Drug Concentrations}, AUTHOR = {Kreuer, S. and Hauschild, Anne-Christin