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1. 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}, MARGINALMARK = {$\bullet$}, 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
2. 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}, MARGINALMARK = {$\bullet$}, DATE = {2016}, JOURNAL = {Nucleic Acids Research}, VOLUME = {44}, NUMBER = {W1/Web Server issue}, PAGES = {W581--W586}, }
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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 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
3. 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}, MARGINALMARK = {$\bullet$}, JOURNAL = {Faculty of 1000 Research}, VOLUME = {5}, EID = {1531}, }
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%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/
4. 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}, MARGINALMARK = {$\bullet$}, 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
5. 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}, MARGINALMARK = {$\bullet$}, 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
6. 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}, MARGINALMARK = {$\bullet$}, 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
7. 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}, MARGINALMARK = {$\bullet$}, 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
8. 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}, MARGINALMARK = {$\bullet$}, 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.sciencedirect.com/science/article/pii/S0167779916300233http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4959511/
9. 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}, MARGINALMARK = {$\bullet$}, 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)}, }
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%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
10. 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}, MARGINALMARK = {$\bullet$}, 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
11. 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}, MARGINALMARK = {$\bullet$}, 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
12. 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}, MARGINALMARK = {$\bullet$}, 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
13. 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}, MARGINALMARK = {$\bullet$}, 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
14. 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}, MARGINALMARK = {$\bullet$}, 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
15. 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}, MARGINALMARK = {$\bullet$}, 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
16. 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}, MARGINALMARK = {$\bullet$}, 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
17. 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}, MARGINALMARK = {$\bullet$}, 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
18. 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}, MARGINALMARK = {$\bullet$}, 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
19. 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}, MARGINALMARK = {$\bullet$}, 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
20. 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}, MARGINALMARK = {$\bullet$}, DATE = {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 %J Molecular Systems Biology %V 12 %N 8 %Z sequence number: 879 %I Nature Pub. Group %C London %@ false
21. 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}, MARGINALMARK = {$\bullet$}, 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
22. 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}, MARGINALMARK = {$\bullet$}, 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
23. 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}, MARGINALMARK = {$\bullet$}, 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
24. 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}, MARGINALMARK = {$\bullet$}, 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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%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
25. 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}, MARGINALMARK = {$\bullet$}, DATE = {2016}, }
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%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/doku/lic_ohne_pod.php?la=dehttp://scidok.sulb.uni-saarland.de/volltexte/2016/6587/
26. 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}, MARGINALMARK = {$\bullet$}, 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
27. 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}, MARGINALMARK = {$\bullet$}, 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
28. 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}, MARGINALMARK = {$\bullet$}, 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
29. 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}, MARGINALMARK = {$\bullet$}, DATE = {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
30. 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}, MARGINALMARK = {$\bullet$}, 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
31. 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}, MARGINALMARK = {$\bullet$}, 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
32. 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}, MARGINALMARK = {$\bullet$}, 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
33. 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}, MARGINALMARK = {$\bullet$}, 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
34. 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}, MARGINALMARK = {$\bullet$}, 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
35. 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}, MARGINALMARK = {$\bullet$}, 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
36. 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}, MARGINALMARK = {$\bullet$}, 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
37. 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}, MARGINALMARK = {$\bullet$}, 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
38. 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}, MARGINALMARK = {$\bullet$}, 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
39. 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}, MARGINALMARK = {$\bullet$}, 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
40. 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}, MARGINALMARK = {$\bullet$}, 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
41. Marschall T: Computational Pan-genomics: Status, Promises and Challenges. Briefings in Bioinformatics 2016, Online First.
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@article{Marschall2016, TITLE = {Computational Pan-genomics: Status, Promises and Challenges}, AUTHOR = {Marschall, Tobias and {The Computational Pan-Genomics Consortium}}, LANGUAGE = {eng}, ISSN = {1467-5463}, DOI = {10.1093/bib/bbw089}, PUBLISHER = {Oxford University Press}, ADDRESS = {London}, YEAR = {2016}, MARGINALMARK = {$\bullet$}, JOURNAL = {Briefings in Bioinformatics}, VOLUME = {Online First}, EID = {bbw089}, }
Endnote
%0 Journal Article %A Marschall, Tobias %A The Computational Pan-Genomics Consortium, %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %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 2016 %8 21.10.2016 %J Briefings in Bioinformatics %V Online First %Z sequence number: bbw089 %I Oxford University Press %C London %@ false
42. 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}, MARGINALMARK = {$\bullet$}, 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
43. 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}, MARGINALMARK = {$\bullet$}, 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
44. 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}, MARGINALMARK = {$\bullet$}, DATE = {2016}, }
Endnote
%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
45. 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}, MARGINALMARK = {$\bullet$}, DATE = {2016}, JOURNAL = {Bioinformatics}, VOLUME = {32}, NUMBER = {12}, PAGES = {1888--1890}, }
Endnote
%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
46. 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}, MARGINALMARK = {$\bullet$}, DATE = {2016}, JOURNAL = {Hepatology}, VOLUME = {63}, NUMBER = {1}, PAGES = {63--73}, }
Endnote
%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
47. 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}, MARGINALMARK = {$\bullet$}, 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
48. 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}, MARGINALMARK = {$\bullet$}, 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
49. 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}, MARGINALMARK = {$\bullet$}, 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
50. 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}, MARGINALMARK = {$\bullet$}, 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
51. 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}, MARGINALMARK = {$\bullet$}, 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
52. 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}, MARGINALMARK = {$\bullet$}, 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
53. 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}, MARGINALMARK = {$\bullet$}, 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
54. 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}, MARGINALMARK = {$\bullet$}, 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.
55. 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}, MARGINALMARK = {$\bullet$}, 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
56. 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}, MARGINALMARK = {$\bullet$}, 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
57. 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}, MARGINALMARK = {$\bullet$}, 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
58. 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}, MARGINALMARK = {$\bullet$}, 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
59. 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}, MARGINALMARK = {$\bullet$}, 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
60. 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}, MARGINALMARK = {$\bullet$}, 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