Publications: Journal articles, conference papers and theses from department members
2024
1. Bernett J, Blumenthal DB, List M: Cracking the Black Box of Deep Sequence-based Protein–Protein Interaction Prediction. Briefings in Bioinformatics 2024, 25.
Export
BibTeX
@article{Bernett24,
TITLE = {Cracking the Black Box of Deep Sequence-based Protein--Protein Interaction Prediction},
AUTHOR = {Bernett, Judith and Blumenthal, David B. and List, Markus},
LANGUAGE = {eng},
ISSN = {1467-5463},
DOI = {10.1093/bib/bbae076},
PUBLISHER = {H. Stewart Publications},
ADDRESS = {London},
YEAR = {2024},
MARGINALMARK = {$\bullet$},
DATE = {2024},
JOURNAL = {Briefings in Bioinformatics},
VOLUME = {25},
NUMBER = {2},
EID = {bbae076},
}
Endnote
%0 Journal Article
%A Bernett, Judith
%A Blumenthal, David B.
%A List, Markus
%+ External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
%T Cracking the Black Box of Deep Sequence-based Protein–Protein Interaction Prediction :
%G eng
%U http://hdl.handle.net/21.11116/0000-000F-BA97-5
%R 10.1093/bib/bbae076
%7 2024
%D 2024
%J Briefings in Bioinformatics
%V 25
%N 2
%Z sequence number: bbae076
%I H. Stewart Publications
%C London
%@ false
2. Teodoro GD, Pirkl M, Incardona F, Vicenti I, Sönnerborg A, Kaiser R, Palagi L, Zazzi M, Lengauer T: Incorporating temporal dynamics of mutations to enhance the prediction capability of antiretroviral therapy’s outcome for {HIV}-1. Bioinformatics 2024, 40.
Export
BibTeX
@article{Teodoro24,
TITLE = {Incorporating temporal dynamics of mutations to enhance the prediction capability of antiretroviral therapy{\textquoteright}s outcome for {\textbraceleft}{HIV}{\textbraceright}-1},
AUTHOR = {Teodoro, Giulia Di and Pirkl, Martin and Incardona, Francesca and Vicenti, Ilaria and S{\"o}nnerborg, Anders and Kaiser, Rolf and Palagi, Laura and Zazzi, Maurizio and Lengauer, Thomas},
LANGUAGE = {eng},
ISSN = {1367-4803},
DOI = {10.1093/bioinformatics/btae327},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford},
YEAR = {2024},
MARGINALMARK = {$\bullet$},
DATE = {2024},
JOURNAL = {Bioinformatics},
VOLUME = {40},
NUMBER = {6},
PAGES = {1--10},
EID = {btae327},
}
Endnote
%0 Journal Article
%A Teodoro, Giulia Di
%A Pirkl, Martin
%A Incardona, Francesca
%A Vicenti, Ilaria
%A Sönnerborg, Anders
%A Kaiser, Rolf
%A Palagi, Laura
%A Zazzi, Maurizio
%A Lengauer, Thomas
%+ External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
%T Incorporating temporal dynamics of mutations to enhance
the prediction capability of antiretroviral therapy’s
outcome for {HIV}-1 :
%G eng
%U http://hdl.handle.net/21.11116/0000-000F-9833-C
%R 10.1093/bioinformatics/btae327
%2 PMC11153833
%7 2024
%D 2024
%J Bioinformatics
%V 40
%N 6
%& 1
%P 1 - 10
%Z sequence number: btae327
%I Oxford University Press
%C Oxford
%@ false
%U https://doi.org/10.1093/bioinformatics/btae327
2023
3. Fischer J, Schulz MH: Efficiently quantifying DNA methylation for bulk- and single-cell bisulfite data. Bioinformatics 2023, 39.
Export
BibTeX
@article{Fischer23,
TITLE = {Efficiently quantifying {DNA} methylation for bulk- and single-cell bisulfite data},
AUTHOR = {Fischer, Jonas and Schulz, Marcel Holger},
LANGUAGE = {eng},
ISSN = {1367-4803},
DOI = {10.1093/bioinformatics/btad386},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford},
YEAR = {2023},
MARGINALMARK = {$\bullet$},
JOURNAL = {Bioinformatics},
VOLUME = {39},
NUMBER = {6},
EID = {btad386},
}
Endnote
%0 Journal Article
%A Fischer, Jonas
%A Schulz, Marcel Holger
%+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
%T Efficiently quantifying DNA methylation for bulk- and single-cell bisulfite data :
%G eng
%U http://hdl.handle.net/21.11116/0000-000D-6C74-8
%R 10.1093/bioinformatics/btad386
%2 PMC10310462
%7 2023
%D 2023
%J Bioinformatics
%V 39
%N 6
%Z sequence number: btad386
%I Oxford University Press
%C Oxford
%@ false
4. Grau J, Schmidt F, Schulz MH: Widespread effects of DNA methylation and intra-motif dependencies revealed by novel transcription factor binding models. Nucleic Acids Research 2023, 51.
Export
BibTeX
@article{Grau23,
TITLE = {Widespread effects of {DNA} methylation and intra-motif dependencies revealed by novel transcription factor binding models},
AUTHOR = {Grau, Jan and Schmidt, Florian and Schulz, Marcel Holger},
LANGUAGE = {eng},
ISSN = {0305-1048},
DOI = {10.1093/nar/gkad693},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford},
YEAR = {2023},
MARGINALMARK = {$\bullet$},
JOURNAL = {Nucleic Acids Research},
VOLUME = {51},
NUMBER = {18},
EID = {e95},
}
Endnote
%0 Journal Article
%A Grau, Jan
%A Schmidt, Florian
%A Schulz, Marcel Holger
%+ 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 Widespread effects of DNA methylation and intra-motif dependencies revealed by novel transcription factor binding models :
%G eng
%U http://hdl.handle.net/21.11116/0000-000D-E9B5-0
%R 10.1093/nar/gkad693
%2 PMC10570048
%7 2023
%D 2023
%J Nucleic Acids Research
%O Nucleic Acids Res
%V 51
%N 18
%Z sequence number: e95
%I Oxford University Press
%C Oxford
%@ false
5. Hake A: Predicting and Analyzing HIV-1 Adaptation to Broadly Neutralizing Antibodies and the Host Immune System Using Machine Learning. Universität des Saarlandes; 2023.
Export
BibTeX
@phdthesis{Hake_PhD2023,
TITLE = {Predicting and Analyzing {HIV}-1 Adaptation to Broadly Neutralizing Antibodies and the Host Immune System Using Machine Learning},
AUTHOR = {Hake, Anna},
LANGUAGE = {eng},
URL = {urn:nbn:de:bsz:291--ds-395323},
DOI = {10.22028/D291-39532},
SCHOOL = {Universit{\"a}t des Saarlandes},
ADDRESS = {Saarbr{\"u}cken},
YEAR = {2023},
MARGINALMARK = {$\bullet$},
}
Endnote
%0 Thesis
%A Hake, Anna
%Y Pfeifer, Nico
%A referee: Kalinina, Olga V.
%+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
International Max Planck Research School, MPI for Informatics, Max Planck Society
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
%T Predicting and Analyzing HIV-1 Adaptation to Broadly Neutralizing Antibodies and the Host Immune System Using Machine Learning :
%G eng
%U http://hdl.handle.net/21.11116/0000-000D-10E8-B
%R 10.22028/D291-39532
%U urn:nbn:de:bsz:291--ds-395323
%F OTHER: hdl:20.500.11880/35743
%I Universität des Saarlandes
%C Saarbrücken
%D 2023
%P xv; 210 p
%V phd
%9 phd
%U https://scidok.sulb.uni-saarland.de/handle/20.500.11880/35743
6. Hake A, Germann A, de Beer C, Thielen A, Däumer M, Preiser W, von Briesen H, Pfeifer N: Insights to HIV-1 coreceptor usage by estimating HLA adaptation with Bayesian generalized linear mixed models. PLOS Computational Biology 2023, 19.
Export
BibTeX
@article{hake23,
TITLE = {Insights to {HIV}-1 coreceptor usage by estimating {HLA} adaptation with {B}ayesian generalized linear mixed models},
AUTHOR = {Hake, Anna and Germann, Anja and de Beer, Corena and Thielen, Alexander and D{\"a}umer, Martin and Preiser, Wolfgang and von Briesen, Hagen and Pfeifer, Nico},
LANGUAGE = {eng},
ISSN = {1553-734X},
DOI = {10.1371/journal.pcbi.1010355},
PUBLISHER = {Public Library of Science},
ADDRESS = {San Francisco, CA},
YEAR = {2023},
MARGINALMARK = {$\bullet$},
DATE = {2023},
JOURNAL = {PLOS Computational Biology},
VOLUME = {19},
NUMBER = {12},
EID = {e1010355},
}
Endnote
%0 Journal Article
%A Hake, Anna
%A Germann, Anja
%A de Beer, Corena
%A Thielen, Alexander
%A Däumer, Martin
%A Preiser, Wolfgang
%A von Briesen, Hagen
%A Pfeifer, Nico
%+ 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 Insights to HIV-1 coreceptor usage by estimating HLA adaptation with Bayesian generalized linear mixed models :
%G eng
%U http://hdl.handle.net/21.11116/0000-000E-5B0F-D
%R 10.1371/journal.pcbi.1010355
%2 PMC10769057
%7 2023
%D 2023
%J PLOS Computational Biology
%O PLOS Comput Biol
%V 19
%N 12
%Z sequence number: e1010355
%I Public Library of Science
%C San Francisco, CA
%@ false
7. Maji RK, Czepukojc B, Scherer M, Tierling S, Cadenas C, Gianmoena K, Gasparoni N, Nordström K, Gasparoni G, Laggai S, Yang X, Sinha A, Ebert P, Falk-Paulsen M, Kinkley S, Hoppstädter J, Chung H-R, Rosenstiel P, Hengstler JG, Walter J, Schulz MH, Kessler SM, Kiemer AK: Alterations in the Hepatocyte Epigenetic Landscape in Steatosis. Epigenetics & Chromatin 2023, 16.
Export
BibTeX
@article{Maji23,
TITLE = {Alterations in the Hepatocyte Epigenetic Landscape in Steatosis},
AUTHOR = {Maji, Ranjan Kumar and Czepukojc, Beate and Scherer, Michael and Tierling, Sascha and Cadenas, Cristina and Gianmoena, Kathrin and Gasparoni, Nina and Nordstr{\"o}m, Karl and Gasparoni, Gilles and Laggai, Stephan and Yang, Xinyi and Sinha, Anupam and Ebert, Peter and Falk-Paulsen, Maren and Kinkley, Sarah and Hoppst{\"a}dter, Jessica and Chung, Ho-Ryun and Rosenstiel, Philip and Hengstler, Jan G. and Walter, J{\"o}rn and Schulz, Marcel Holger and Kessler, Sonja M. and Kiemer, Alexandra K.},
LANGUAGE = {eng},
DOI = {10.1186/s13072-023-00504-8},
PUBLISHER = {BioMed Central},
ADDRESS = {London},
YEAR = {2023},
MARGINALMARK = {$\bullet$},
JOURNAL = {Epigenetics \& Chromatin},
VOLUME = {16},
EID = {30},
}
Endnote
%0 Journal Article
%A Maji, Ranjan Kumar
%A Czepukojc, Beate
%A Scherer, Michael
%A Tierling, Sascha
%A Cadenas, Cristina
%A Gianmoena, Kathrin
%A Gasparoni, Nina
%A Nordström, Karl
%A Gasparoni, Gilles
%A Laggai, Stephan
%A Yang, Xinyi
%A Sinha, Anupam
%A Ebert, Peter
%A Falk-Paulsen, Maren
%A Kinkley, Sarah
%A Hoppstädter, Jessica
%A Chung, Ho-Ryun
%A Rosenstiel, Philip
%A Hengstler, Jan G.
%A Walter, Jörn
%A Schulz, Marcel Holger
%A Kessler, Sonja M.
%A Kiemer, Alexandra 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
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
External Organizations
%T Alterations in the Hepatocyte Epigenetic Landscape in Steatosis :
%G eng
%U http://hdl.handle.net/21.11116/0000-000D-943A-B
%R 10.1186/s13072-023-00504-8
%2 PMC10324225
%7 2023
%D 2023
%J Epigenetics & Chromatin
%V 16
%Z sequence number: 30
%I BioMed Central
%C London
8. Schommers P, Kim DS, Schlotz M, Kreer C, Eggeling R, Hake A, Stecher M, Park J, Radford CE, Dingens AS, Ercanoglu MS, Gruell H, Odidika S, Dahlhaus M, Gieselmann L, Ahmadov E, Lawong RY, Heger E, Knops E, Wyen C, Kümmerle T, Römer K, Scholten S, Wolf T, Stephan C, Suárez I, Raju N, Adhikari A, Esser S, Streeck H, et al.: Dynamics and Durability of HIV-1 Neutralization are Determined by Viral Replication. Nature Medicine 2023, 29.
Export
BibTeX
@article{Schommers2023,
TITLE = {Dynamics and Durability of {HIV}-1 Neutralization are Determined by Viral Replication},
AUTHOR = {Schommers, Philipp and Kim, Dae Sung and Schlotz, Maike and Kreer, Christoph and Eggeling, Ralf and Hake, Anna and Stecher, Melanie and Park, Juyeon and Radford, Caelan E. and Dingens, Adam S. and Ercanoglu, Meryem S. and Gruell, Henning and Odidika, Stanley and Dahlhaus, Marten and Gieselmann, Lutz and Ahmadov, Elvin and Lawong, Rene Y. and Heger, Eva and Knops, Elena and Wyen, Christoph and K{\"u}mmerle, Tim and R{\"o}mer, Katja and Scholten, Stefan and Wolf, Timo and Stephan, Christoph and Su{\'a}rez, Isabelle and Raju, Nagarajan and Adhikari, Anurag and Esser, Stefan and Streeck, Hendrik and Duerr, Ralf and Nanfack, Aubin J. and Zolla-Pazner, Susan and Geldmacher, Christof and Geisenberger, Otto and Kroidl, Arne and William, Wiston and Maganga, Lucas and Ntinginya, Nyanda Elias and Georgiev, Ivelin S. and Vehreschild, J{\"o}rg J. and Hoelscher, Michael and F{\"a}tkenheuer, Gerd and Lavinder, Jason J. and Bloom, Jesse D. and Seaman, Michael S. and Lehmann, Clara and Pfeifer, Nico and Georgiou, George and Klein, Florian},
LANGUAGE = {eng},
ISSN = {1078-8956},
DOI = {10.1038/s41591-023-02582-3},
PUBLISHER = {Nature Pub. Co.},
ADDRESS = {New York, NY},
YEAR = {2023},
MARGINALMARK = {$\bullet$},
DATE = {2023},
JOURNAL = {Nature Medicine},
VOLUME = {29},
NUMBER = {11},
PAGES = {2763--2774},
}
Endnote
%0 Journal Article
%A Schommers, Philipp
%A Kim, Dae Sung
%A Schlotz, Maike
%A Kreer, Christoph
%A Eggeling, Ralf
%A Hake, Anna
%A Stecher, Melanie
%A Park, Juyeon
%A Radford, Caelan E.
%A Dingens, Adam S.
%A Ercanoglu, Meryem S.
%A Gruell, Henning
%A Odidika, Stanley
%A Dahlhaus, Marten
%A Gieselmann, Lutz
%A Ahmadov, Elvin
%A Lawong, Rene Y.
%A Heger, Eva
%A Knops, Elena
%A Wyen, Christoph
%A Kümmerle, Tim
%A Römer, Katja
%A Scholten, Stefan
%A Wolf, Timo
%A Stephan, Christoph
%A Suárez, Isabelle
%A Raju, Nagarajan
%A Adhikari, Anurag
%A Esser, Stefan
%A Streeck, Hendrik
%A Duerr, Ralf
%A Nanfack, Aubin J.
%A Zolla-Pazner, Susan
%A Geldmacher, Christof
%A Geisenberger, Otto
%A Kroidl, Arne
%A William, Wiston
%A Maganga, Lucas
%A Ntinginya, Nyanda Elias
%A Georgiev, Ivelin S.
%A Vehreschild, Jörg J.
%A Hoelscher, Michael
%A Fätkenheuer, Gerd
%A Lavinder, Jason J.
%A Bloom, Jesse D.
%A Seaman, Michael S.
%A Lehmann, Clara
%A Pfeifer, Nico
%A Georgiou, George
%A Klein, Florian
%+ 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
External Organizations
External Organizations
%T Dynamics and Durability of HIV-1 Neutralization are Determined by Viral Replication :
%G eng
%U http://hdl.handle.net/21.11116/0000-000E-03E7-A
%R 10.1038/s41591-023-02582-3
%2 PMC10667105
%7 2023
%D 2023
%J Nature Medicine
%O Nat. Med.
%V 29
%N 11
%& 2763
%P 2763 - 2774
%I Nature Pub. Co.
%C New York, NY
%@ false
2022
9. Agkün M, Pfeifer N, Kohlbacher O: Efficient Privacy-preserving Whole-Genome Variant Queries. Bioinformatics 2022, 38.
Export
BibTeX
@article{Agkuen2022,
TITLE = {Efficient Privacy-preserving Whole-Genome Variant Queries},
AUTHOR = {Agk{\"u}n, Mete and Pfeifer, Nico and Kohlbacher, Oliver},
LANGUAGE = {eng},
ISSN = {1367-4803},
DOI = {10.1093/bioinformatics/btac070},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford},
YEAR = {2022},
DATE = {2022},
JOURNAL = {Bioinformatics},
VOLUME = {38},
NUMBER = {8},
PAGES = {2202--2210},
EID = {btac070},
}
Endnote
%0 Journal Article
%A Agkün, Mete
%A Pfeifer, Nico
%A Kohlbacher, Oliver
%+ External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
%T Efficient Privacy-preserving Whole-Genome Variant Queries :
%G eng
%U http://hdl.handle.net/21.11116/0000-000A-170E-E
%R 10.1093/bioinformatics/btac070
%7 2022
%D 2022
%J Bioinformatics
%V 38
%N 8
%& 2202
%P 2202 - 2210
%Z sequence number: btac070
%I Oxford University Press
%C Oxford
%@ false
10. Arend L, Bernett J, Manz Q, Klug M, Lazareva O, Baumbach J, Bongiovanni D, List M: A Systematic Comparison of Novel and Existing Differential Analysis Methods for CyTOF Data. Briefings in Bioinformatics 2022, 23.
Export
BibTeX
@article{Arend2022,
TITLE = {A Systematic Comparison of Novel and Existing Differential Analysis Methods for {CyTOF} Data},
AUTHOR = {Arend, Lis and Bernett, Judith and Manz, Quirin and Klug, Melissa and Lazareva, Olga and Baumbach, Jan and Bongiovanni, Dario and List, Markus},
LANGUAGE = {eng},
ISSN = {1467-5463},
DOI = {10.1093/bib/bbab471},
PUBLISHER = {H. Stewart Publications},
ADDRESS = {London},
YEAR = {2022},
JOURNAL = {Briefings in Bioinformatics},
VOLUME = {23},
NUMBER = {1},
EID = {bbab471},
}
Endnote
%0 Journal Article
%A Arend, Lis
%A Bernett, Judith
%A Manz, Quirin
%A Klug, Melissa
%A Lazareva, Olga
%A Baumbach, Jan
%A Bongiovanni, Dario
%A List, Markus
%+ 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 A Systematic Comparison of Novel and Existing Differential Analysis Methods for CyTOF Data :
%G eng
%U http://hdl.handle.net/21.11116/0000-000A-5D88-5
%R 10.1093/bib/bbab471
%7 2022
%D 2022
%J Briefings in Bioinformatics
%V 23
%N 1
%Z sequence number: bbab471
%I H. Stewart Publications
%C London
%@ false
11. Gress A, Srikakulam SK, Keller S, Ramensky V, Kalinina OV: d-StructMAn: Containerized Structural Annotation on the Scale from Genetic Variants to whole Proteomes. GigaScience 2022, 11.
Export
BibTeX
@article{,
TITLE = {d-{StructMAn}: {C}ontainerized structural annotation on the scale from genetic variants to whole proteomes},
AUTHOR = {Gress, Alexander and Srikakulam, Sanjay K. and Keller, Sebastian and Ramensky, Vasily and Kalinina, Olga V.},
LANGUAGE = {eng},
ISSN = {2047-217X},
DOI = {10.1093/gigascience/giac086},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford},
YEAR = {2022},
JOURNAL = {GigaScience},
VOLUME = {11},
PAGES = {1--11},
EID = {giac086},
}
Endnote
%0 Journal Article
%A Gress, Alexander
%A Srikakulam, Sanjay K.
%A Keller, Sebastian
%A Ramensky, Vasily
%A Kalinina, Olga V.
%+ External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
External Organizations
%T d-StructMAn: Containerized Structural Annotation on the Scale from Genetic Variants to whole Proteomes :
%G eng
%U http://hdl.handle.net/21.11116/0000-000B-4789-B
%R 10.1093/gigascience/giac086
%2 PMC9487898
%7 2022
%D 2022
%J GigaScience
%V 11
%& 1
%P 1 - 11
%Z sequence number: giac086
%I Oxford University Press
%C Oxford
%@ false
12. Horemheb-Rubio G, Eggeling R, Schmeiβer N, Pfeifer N, Lengauer T, Gärtner BC, Prifert C, Kochanek M, Scheid C, Adams O, Kaiser R, Kaiser R, Gärtner B, Weissbrich B, Adams O, Berger A, Palupsky K, Huzly D, Tiemann C, Borena W, Lindauer A, Liebert UG, Siemens H-J, Hofmann J, Eis-Hübinger A-M, Grundmann H, Kehlen A, Oehme A, Schnitzler P, Kühn J, et al.: Respiratory Viruses Dynamics and Interactions: Ten Years of Surveillance in Central Europe. BMC Public Health 2022, 22.
Export
BibTeX
@article{Rubio22,
TITLE = {Respiratory Viruses Dynamics and Interactions: {T}en Years of Surveillance in Central Europe},
AUTHOR = {Horemheb-Rubio, Gibran and Eggeling, Ralf and Schmei$\beta$er, Norbert and Pfeifer, Nico and Lengauer, Thomas and G{\"a}rtner, Barbara C. and Prifert, Christiane and Kochanek, Matthias and Scheid, Christoph and Adams, Ortwin and Kaiser, Rolf and Kaiser, Rolf and G{\"a}rtner, Barbara and Weissbrich, Benedikt and Adams, Ortwin and Berger, Annemarie and Palupsky, Katrin and Huzly, Daniela and Tiemann, Carsten and Borena, Wegene and Lindauer, Andreas and Liebert, Uwe Gerd and Siemens, Hans-Joachim and Hofmann, J{\"o}rg and Eis-H{\"u}binger, Anna-Maria and Grundmann, Hajo and Kehlen, Astrid and Oehme, Albrecht and Schnitzler, Paul and K{\"u}hn, Joachim and Heim, Albert and Sauerbrei, Andreas and Schmidt, Barbara and Beck, Robert and Hoffmann, Dieter and Michel, Detlef and Nitschko, Hans and Aepinus, Christian and Dreier, Jens and Puchhammer-Stoeckl, Elisabeth and Kaup, Theresa Popow and Redlberger, Monika and Kessler, Harald and Obermeier, Martin and Weise, Kerstin and Bartsch, Patricia and Devide, Annette and Niesters, Bert and Kleines, Michael and Krumbholz, Andi and Meyer, Thomas and Gohl, Peter and Sch{\"u}ttler, Christian G. and Gorgievski, Meri and Pagarolas, Andres Anton and Gulich, Wolfgang and Ziegler, Thomas and Wintsche, Babett and Griego, Marcena and Bossart, Walter and {Respiratory Virus Network}},
LANGUAGE = {eng},
ISSN = {1471-2458},
DOI = {10.1186/s12889-022-13555-5},
PUBLISHER = {BioMed Central},
ADDRESS = {London, United Kingdom},
YEAR = {2022},
JOURNAL = {BMC Public Health},
VOLUME = {22},
NUMBER = {1},
EID = {1167},
}
Endnote
%0 Journal Article
%A Horemheb-Rubio, Gibran
%A Eggeling, Ralf
%A Schmeiβer, Norbert
%A Pfeifer, Nico
%A Lengauer, Thomas
%A Gärtner, Barbara C.
%A Prifert, Christiane
%A Kochanek, Matthias
%A Scheid, Christoph
%A Adams, Ortwin
%A Kaiser, Rolf
%A Kaiser, Rolf
%A Gärtner, Barbara
%A Weissbrich, Benedikt
%A Adams, Ortwin
%A Berger, Annemarie
%A Palupsky, Katrin
%A Huzly, Daniela
%A Tiemann, Carsten
%A Borena, Wegene
%A Lindauer, Andreas
%A Liebert, Uwe Gerd
%A Siemens, Hans-Joachim
%A Hofmann, Jörg
%A Eis-Hübinger, Anna-Maria
%A Grundmann, Hajo
%A Kehlen, Astrid
%A Oehme, Albrecht
%A Schnitzler, Paul
%A Kühn, Joachim
%A Heim, Albert
%A Sauerbrei, Andreas
%A Schmidt, Barbara
%A Beck, Robert
%A Hoffmann, Dieter
%A Michel, Detlef
%A Nitschko, Hans
%A Aepinus, Christian
%A Dreier, Jens
%A Puchhammer-Stoeckl, Elisabeth
%A Kaup, Theresa Popow
%A Redlberger, Monika
%A Kessler, Harald
%A Obermeier, Martin
%A Weise, Kerstin
%A Bartsch, Patricia
%A Devide, Annette
%A Niesters, Bert
%A Kleines, Michael
%A Krumbholz, Andi
%A Meyer, Thomas
%A Gohl, Peter
%A Schüttler, Christian G.
%A Gorgievski, Meri
%A Pagarolas, Andres Anton
%A Gulich, Wolfgang
%A Ziegler, Thomas
%A Wintsche, Babett
%A Griego, Marcena
%A Bossart, Walter
%A Respiratory Virus Network,
%+ External Organizations
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
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 Respiratory Viruses Dynamics and Interactions: Ten Years of Surveillance in Central Europe :
%G eng
%U http://hdl.handle.net/21.11116/0000-000A-CD01-E
%R 10.1186/s12889-022-13555-5
%7 2022
%D 2022
%J BMC Public Health
%V 22
%N 1
%Z sequence number: 1167
%I BioMed Central
%C London, United Kingdom
%@ false
13. Jeong H, Grimes K, Rauwolf KK, Bruch P-M, Rausch T, Hasenfeld P, Benito E, Roider T, Sabarinathan R, Porubsky D, Herbst SA, Erarslan-Uysal B, Jann J-C, Marschall T, Nowak D, Bourquin J-P, Kulozik AE, Dietrich S, Bornhauser B, Sanders AD, Korbel JO: Functional Analysis of Structural Variants in Single Cells using Strand-seq. Nature Biotechnology 2022.
Export
BibTeX
@article{Jeong22,
TITLE = {Functional analysis of structural variants in single cells using {S}trand-seq},
AUTHOR = {Jeong, Hyobin and Grimes, Karen and Rauwolf, Kerstin K. and Bruch, Peter-Martin and Rausch, Tobias and Hasenfeld, Patrick and Benito, Eva and Roider, Tobias and Sabarinathan, Radhakrishnan and Porubsky, David and Herbst, Sophie A. and Erarslan-Uysal, Busra and Jann, Johann-Christoph and Marschall, Tobias and Nowak, Daniel and Bourquin, Jean-Pierre and Kulozik, Andreas E. and Dietrich, Sascha and Bornhauser, Beat and Sanders, Ashley D. and Korbel, Jan O.},
LANGUAGE = {eng},
ISSN = {1087-0156},
DOI = {10.1038/s41587-022-01551-4},
PUBLISHER = {Nature},
ADDRESS = {New York, NY},
YEAR = {2022},
JOURNAL = {Nature Biotechnology},
}
Endnote
%0 Journal Article
%A Jeong, Hyobin
%A Grimes, Karen
%A Rauwolf, Kerstin K.
%A Bruch, Peter-Martin
%A Rausch, Tobias
%A Hasenfeld, Patrick
%A Benito, Eva
%A Roider, Tobias
%A Sabarinathan, Radhakrishnan
%A Porubsky, David
%A Herbst, Sophie A.
%A Erarslan-Uysal, Busra
%A Jann, Johann-Christoph
%A Marschall, Tobias
%A Nowak, Daniel
%A Bourquin, Jean-Pierre
%A Kulozik, Andreas E.
%A Dietrich, Sascha
%A Bornhauser, Beat
%A Sanders, Ashley D.
%A Korbel, Jan O.
%+ External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
%T Functional Analysis of Structural Variants in Single Cells using Strand-seq :
%G eng
%U http://hdl.handle.net/21.11116/0000-000C-0012-F
%R 10.1038/s41587-022-01551-4
%7 2022
%D 2022
%J Nature Biotechnology
%O Nat. Biotechnol.
%I Nature
%C New York, NY
%@ false
2021
14. Berzow D, Descamps D, Obermeier M, Charpentier C, Kaiser R, Guertler L, Eberle J, Wensing A, Sierra S, Ruelle J, Gomes P, Mansinho K, Taylor N, Jensen B, Döring M, Stürmer M, Rockstroh J, Camacho R: Human Immunodeficiency Virus-2 (HIV-2): A Summary of the Present Standard of Care and Treatment Options for Individuals Living with HIV-2 in Western Europe. Clinical Infectious Diseases 2021, 72.
Export
BibTeX
@article{Berzow2021,
TITLE = {Human Immunodeficiency Virus-2 ({HIV-2}): A Summary of the Present Standard of Care and Treatment Options for Individuals Living with {HIV}-2 in {Western Europe}},
AUTHOR = {Berzow, Dirk and Descamps, Diane and Obermeier, Martin and Charpentier, Charlotte and Kaiser, Rolf and Guertler, Lutz and Eberle, Josef and Wensing, Annemarie and Sierra, Saleta and Ruelle, Jean and Gomes, Perpetua and Mansinho, Kamal and Taylor, Ninon and Jensen, Bj{\"o}rn and D{\"o}ring, Matthias and St{\"u}rmer, Martin and Rockstroh, J{\"u}rgen and Camacho, Ricardo},
LANGUAGE = {eng},
ISSN = {1058-4838},
DOI = {10.1093/cid/ciaa275},
PUBLISHER = {The University of Chicago Press},
ADDRESS = {Chicago, IL},
YEAR = {2021},
DATE = {2021},
JOURNAL = {Clinical Infectious Diseases},
VOLUME = {72},
NUMBER = {3},
PAGES = {503--509},
}
Endnote
%0 Journal Article
%A Berzow, Dirk
%A Descamps, Diane
%A Obermeier, Martin
%A Charpentier, Charlotte
%A Kaiser, Rolf
%A Guertler, Lutz
%A Eberle, Josef
%A Wensing, Annemarie
%A Sierra, Saleta
%A Ruelle, Jean
%A Gomes, Perpetua
%A Mansinho, Kamal
%A Taylor, Ninon
%A Jensen, Björn
%A Döring, Matthias
%A Stürmer, Martin
%A Rockstroh, Jürgen
%A Camacho, Ricardo
%+ External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
External Organizations
External Organizations
%T Human Immunodeficiency Virus-2 (HIV-2): A Summary of the Present Standard of Care and Treatment Options for Individuals Living with HIV-2 in Western Europe :
%G eng
%U http://hdl.handle.net/21.11116/0000-0008-8DEF-D
%R 10.1093/cid/ciaa275
%7 2021
%D 2021
%J Clinical Infectious Diseases
%V 72
%N 3
%& 503
%P 503 - 509
%I The University of Chicago Press
%C Chicago, IL
%@ false
15. Drews F, Karunanithi S, Gätz U, Marker S, deWijn R, Pirritano M, Rodrigues-Viana AM, Jung M, Gasparoni G, Schulz MH, Simon M: Two Piwis with Ago-like Functions Silence Somatic Genes at the Chromatin Level. RNA Biology 2021, 18.
Export
BibTeX
@article{Drews2021,
TITLE = {Two {P}iwis with {A}go-like Functions Silence Somatic Genes at the Chromatin Level},
AUTHOR = {Drews, Franziska and Karunanithi, Sivarajan and G{\"a}tz, Ulrike and Marker, Simone and deWijn, Raphael and Pirritano, Marcello and Rodrigues-Viana, Angela M. and Jung, Martin and Gasparoni, Gilles and Schulz, Marcel Holger and Simon, Martin},
LANGUAGE = {eng},
ISSN = {1547-6286},
DOI = {10.1080/15476286.2021.1991114},
PUBLISHER = {Taylor \& Francis},
YEAR = {2021},
JOURNAL = {RNA Biology},
VOLUME = {18},
NUMBER = {sup2},
PAGES = {757--769},
}
Endnote
%0 Journal Article
%A Drews, Franziska
%A Karunanithi, Sivarajan
%A Gätz, Ulrike
%A Marker, Simone
%A deWijn, Raphael
%A Pirritano, Marcello
%A Rodrigues-Viana, Angela M.
%A Jung, Martin
%A Gasparoni, Gilles
%A Schulz, Marcel Holger
%A Simon, Martin
%+ External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
%T Two Piwis with Ago-like Functions Silence Somatic Genes at the Chromatin Level :
%G eng
%U http://hdl.handle.net/21.11116/0000-0009-70B4-D
%R 10.1080/15476286.2021.1991114
%7 2021
%D 2021
%J RNA Biology
%V 18
%N sup2
%& 757
%P 757 - 769
%I Taylor & Francis
%@ false
16. Durai DA: Novel graph based algorithms fortranscriptome sequence analysis. Universität des Saarlandes; 2021.
Export
BibTeX
@phdthesis{Duraiphd2020,
TITLE = {Novel graph based algorithms fortranscriptome sequence analysis},
AUTHOR = {Durai, Dilip Ariyur},
LANGUAGE = {eng},
URL = {urn:nbn:de:bsz:291--ds-341585},
DOI = {10.22028/D291-34158},
SCHOOL = {Universit{\"a}t des Saarlandes},
ADDRESS = {Saarbr{\"u}cken},
YEAR = {2021},
DATE = {2021},
}
Endnote
%0 Thesis
%A Durai, Dilip Ariyur
%Y Schulz, Marcel
%A referee: Helms, Volker
%+ 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 Novel graph based algorithms fortranscriptome sequence analysis :
%G eng
%U http://hdl.handle.net/21.11116/0000-0008-E4D6-5
%R 10.22028/D291-34158
%U urn:nbn:de:bsz:291--ds-341585
%F OTHER: hdl:20.500.11880/31478
%I Universität des Saarlandes
%C Saarbrücken
%D 2021
%P 143 p.
%V phd
%9 phd
%U https://publikationen.sulb.uni-saarland.de/handle/20.500.11880/31478
17. Ebert P, Schulz MH: Fast Detection of Differential Chromatin Domains with SCIDDO. Bioinformatics 2021, 37.
Export
BibTeX
@article{Ebert2021b,
TITLE = {Fast detection of differential chromatin domains with {SCIDDO}},
AUTHOR = {Ebert, Peter and Schulz, Marcel Holger},
LANGUAGE = {eng},
ISSN = {1367-4803},
DOI = {10.1093/bioinformatics/btaa960},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford},
YEAR = {2021},
DATE = {2021},
JOURNAL = {Bioinformatics},
VOLUME = {37},
NUMBER = {9},
PAGES = {1198--1205},
}
Endnote
%0 Journal Article
%A Ebert, Peter
%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 Fast Detection of Differential Chromatin Domains with SCIDDO :
%G eng
%U http://hdl.handle.net/21.11116/0000-0008-D98D-5
%R 10.1093/bioinformatics/btaa960
%2 PMC818969
%7 2021
%D 2021
%J Bioinformatics
%V 37
%N 9
%& 1198
%P 1198 - 1205
%I Oxford University Press
%C Oxford
%@ false
18. Ebert P, Audano PA, Zhu Q, Rodriguez-Martin B, Porubsky D, Bonder MJ, Sulovari A, Ebler J, Zhou W, Serra Mari R, Yilmaz F, Zhao X, Hsieh P, Lee J, Kumar S, Lin J, Rausch T, Chen Y, Ren J, Santamarina M, Höps W, Ashraf H, Chuang NT, Yang X, Munson KM, Lewis AP, Fairley S, Tallon LJ, Clarke WE, Basile AO, et al.: Haplotype-resolved Diverse Human Genomes and Integrated Analysis of Structural Variation. Science 2021, 372.
Export
BibTeX
@article{Ebert2021,
TITLE = {Haplotype-resolved Diverse Human Genomes and Integrated Analysis of Structural Variation},
AUTHOR = {Ebert, Peter and Audano, Peter A. and Zhu, Qihui and Rodriguez-Martin, Bernardo and Porubsky, David and Bonder, Marc Jan and Sulovari, Arvis and Ebler, Jana and Zhou, Weichen and Serra Mari, Rebecca and Yilmaz, Feyza and Zhao, Xuefang and Hsieh, PingHsun and Lee, Joyce and Kumar, Sushant and Lin, Jiadong and Rausch, Tobias and Chen, Yu and Ren, Jingwen and Santamarina, Martin and H{\"o}ps, Wolfram and Ashraf, Hufsah and Chuang, Nelson T. and Yang, Xiaofei and Munson, Katherine M. and Lewis, Alexandra P. and Fairley, Susan and Tallon, Luke J. and Clarke, Wayne E. and Basile, Anna O. and Byrska-Bishop, Marta and Corvelo, Andr{\'e} and Evani, Uday S. and Lu, Tsung-Yu and Chaisson, Mark J. P. and Chen, Junjie and Li, Chong and Brand, Harrison and Wenger, Aaron M. and Ghareghani, Maryam and Harvey, William T. and Raeder, Benjamin and Hasenfeld, Patrick and Regier, Allison A. and Abel, Haley J. and Hall, Ira M. and Flicek, Paul and Stegle, Oliver and Gerstein, Mark B. and Tubio, Jose M. C. and Mu, Zepeng and Li, Yang I. and Shi, Xinghua and Hastie, Alex R. and Ye, Kai and Chong, Zechen and Sanders, Ashley D. and Zody, Michael C. and Talkowski, Michael E. and Mills, Ryan E. and Devine, Scott E. and Lee, Charles and Korbel, Jan O. and Marschall, Tobias and Eichler, Evan E.},
LANGUAGE = {eng},
ISSN = {0036-8075},
DOI = {10.1126/science.abf7117},
PUBLISHER = {AAAS},
ADDRESS = {Washington, D.C.},
YEAR = {2021},
DATE = {2021},
JOURNAL = {Science},
VOLUME = {372},
NUMBER = {6537},
EID = {eabf7117},
}
Endnote
%0 Journal Article
%A Ebert, Peter
%A Audano, Peter A.
%A Zhu, Qihui
%A Rodriguez-Martin, Bernardo
%A Porubsky, David
%A Bonder, Marc Jan
%A Sulovari, Arvis
%A Ebler, Jana
%A Zhou, Weichen
%A Serra Mari, Rebecca
%A Yilmaz, Feyza
%A Zhao, Xuefang
%A Hsieh, PingHsun
%A Lee, Joyce
%A Kumar, Sushant
%A Lin, Jiadong
%A Rausch, Tobias
%A Chen, Yu
%A Ren, Jingwen
%A Santamarina, Martin
%A Höps, Wolfram
%A Ashraf, Hufsah
%A Chuang, Nelson T.
%A Yang, Xiaofei
%A Munson, Katherine M.
%A Lewis, Alexandra P.
%A Fairley, Susan
%A Tallon, Luke J.
%A Clarke, Wayne E.
%A Basile, Anna O.
%A Byrska-Bishop, Marta
%A Corvelo, André
%A Evani, Uday S.
%A Lu, Tsung-Yu
%A Chaisson, Mark J. P.
%A Chen, Junjie
%A Li, Chong
%A Brand, Harrison
%A Wenger, Aaron M.
%A Ghareghani, Maryam
%A Harvey, William T.
%A Raeder, Benjamin
%A Hasenfeld, Patrick
%A Regier, Allison A.
%A Abel, Haley J.
%A Hall, Ira M.
%A Flicek, Paul
%A Stegle, Oliver
%A Gerstein, Mark B.
%A Tubio, Jose M. C.
%A Mu, Zepeng
%A Li, Yang I.
%A Shi, Xinghua
%A Hastie, Alex R.
%A Ye, Kai
%A Chong, Zechen
%A Sanders, Ashley D.
%A Zody, Michael C.
%A Talkowski, Michael E.
%A Mills, Ryan E.
%A Devine, Scott E.
%A Lee, Charles
%A Korbel, Jan O.
%A Marschall, Tobias
%A Eichler, Evan E.
%+ External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
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
External Organizations
External Organizations
External Organizations
%T Haplotype-resolved Diverse Human Genomes and Integrated Analysis of Structural Variation :
%G eng
%U http://hdl.handle.net/21.11116/0000-0008-BFCA-E
%R 10.1126/science.abf7117
%7 2021
%D 2021
%J Science
%O Science
%V 372
%N 6537
%Z sequence number: eabf7117
%I AAAS
%C Washington, D.C.
%@ false
19. Fischer J, Ardakani FB, Kattler K, Walter J, Schulz MH: CpG Content-dependent Associations between Transcription Factors and Histone Modifications. PLoS One 2021, 16.
Export
BibTeX
@article{fischer:21:cpgtfhm,
TITLE = {{CpG} content-dependent associations between transcription factors and histone modifications},
AUTHOR = {Fischer, Jonas and Ardakani, Fatemeh Behjati and Kattler, Kathrin and Walter, J{\"o}rn and Schulz, Marcel Holger},
LANGUAGE = {eng},
ISSN = {1932-6203},
DOI = {10.1371/journal.pone.0249985},
PUBLISHER = {Public Library of Science},
ADDRESS = {San Francisco, CA},
YEAR = {2021},
JOURNAL = {PLoS One},
VOLUME = {16},
NUMBER = {4},
EID = {0249985},
}
Endnote
%0 Journal Article
%A Fischer, Jonas
%A Ardakani, Fatemeh Behjati
%A Kattler, Kathrin
%A Walter, Jörn
%A Schulz, Marcel Holger
%+ Databases and Information Systems, 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
%T CpG Content-dependent Associations between Transcription Factors and Histone Modifications :
%G eng
%U http://hdl.handle.net/21.11116/0000-0008-5602-5
%R 10.1371/journal.pone.0249985
%7 2021
%D 2021
%J PLoS One
%V 16
%N 4
%Z sequence number: 0249985
%I Public Library of Science
%C San Francisco, CA
%@ false
20. Garg S, Fungtammasan A, Carroll A, Chou M, Schmitt A, Zhou X, Mac S, Peluso P, Hatas E, Ghurye J, Maguire J, Mahmoud M, Cheng H, Heller D, Zook JM, Moemke T, Marschall T, Sedlazeck FJ, Aach J, Chin C, Church GM, Li H: Chromosome-scale, Haplotype-resolved Assembly of Human Genomes. Nature Biotechnology 2021, 39.
Export
BibTeX
@article{Garg2020,
TITLE = {Chromosome-scale, Haplotype-resolved Assembly of Human Genomes},
AUTHOR = {Garg, Shilpa and Fungtammasan, Arkarachai and Carroll, Andrew and Chou, Mike and Schmitt, Anthony and Zhou, Xiang and Mac, Stephen and Peluso, Paul and Hatas, Emily and Ghurye, Jay and Maguire, Jared and Mahmoud, Medhat and Cheng, Haoyu and Heller, David and Zook, Justin M. and Moemke, Tobias and Marschall, Tobias and Sedlazeck, Fritz J. and Aach, John and Chin, ChenShan and Church, George M. and Li, Heng},
LANGUAGE = {eng},
ISSN = {1087-0156},
DOI = {10.1038/s41587-020-0711-0},
PUBLISHER = {Gale Group Inc.},
ADDRESS = {New York, NY},
YEAR = {2021},
DATE = {2021},
JOURNAL = {Nature Biotechnology},
VOLUME = {39},
PAGES = {309--312},
}
Endnote
%0 Journal Article
%A Garg, Shilpa
%A Fungtammasan, Arkarachai
%A Carroll, Andrew
%A Chou, Mike
%A Schmitt, Anthony
%A Zhou, Xiang
%A Mac, Stephen
%A Peluso, Paul
%A Hatas, Emily
%A Ghurye, Jay
%A Maguire, Jared
%A Mahmoud, Medhat
%A Cheng, Haoyu
%A Heller, David
%A Zook, Justin M.
%A Moemke, Tobias
%A Marschall, Tobias
%A Sedlazeck, Fritz J.
%A Aach, John
%A Chin, ChenShan
%A Church, George M.
%A Li, Heng
%+ External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
%T Chromosome-scale, Haplotype-resolved Assembly of Human Genomes :
%G eng
%U http://hdl.handle.net/21.11116/0000-0007-A6AD-B
%R 10.1038/s41587-020-0711-0
%7 2020
%D 2021
%J Nature Biotechnology
%O Nat. Biotechnol.
%V 39
%& 309
%P 309 - 312
%I Gale Group Inc.
%C New York, NY
%@ false
21. Kitanovski S, Horemheb-Rubio G, Adams O, Gärtner B, Lengauer T, Hoffmann D, Kaiser R: Rhinovirus Prevalence as Indicator for Efficacy of Measures against SARS-CoV-2. BMC Public Health 2021, 21.
Export
BibTeX
@article{Kitaovski2021,
TITLE = {Rhinovirus Prevalence as Indicator for Efficacy of Measures against {SARS}-{CoV}-2},
AUTHOR = {Kitanovski, Simo and Horemheb-Rubio, Gibran and Adams, Ortwin and G{\"a}rtner, Barbara and Lengauer, Thomas and Hoffmann, Daniel and Kaiser, Rolf and {Respiratory Virus Network}},
LANGUAGE = {eng},
ISSN = {1471-2458},
DOI = {10.1186/s12889-021-11178-w},
PUBLISHER = {BioMed Central},
ADDRESS = {London, United Kingdom},
YEAR = {2021},
JOURNAL = {BMC Public Health},
VOLUME = {21},
EID = {1178},
}
Endnote
%0 Journal Article
%A Kitanovski, Simo
%A Horemheb-Rubio, Gibran
%A Adams, Ortwin
%A Gärtner, Barbara
%A Lengauer, Thomas
%A Hoffmann, Daniel
%A Kaiser, Rolf
%A Respiratory Virus Network,
%+ External Organizations
External Organizations
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
External Organizations
%T Rhinovirus Prevalence as Indicator for Efficacy of Measures against SARS-CoV-2 :
%G eng
%U http://hdl.handle.net/21.11116/0000-0008-D984-E
%R 10.1186/s12889-021-11178-w
%2 PMC8215636
%7 2021
%D 2021
%J BMC Public Health
%V 21
%Z sequence number: 1178
%I BioMed Central
%C London, United Kingdom
%@ false
22. Lazareva O, Baumbach J, List M, Blumenthal DB: On the Limits of Active Module Identification. Briefings in Bioinformatics 2021, 22.
Export
BibTeX
@article{10.1093/bib/bbab066,
TITLE = {On the Limits of Active Module Identification},
AUTHOR = {Lazareva, Olga and Baumbach, Jan and List, Markus and Blumenthal, David B.},
LANGUAGE = {eng},
ISSN = {1467-5463},
PUBLISHER = {H. Stewart Publications},
ADDRESS = {London},
YEAR = {2021},
JOURNAL = {Briefings in Bioinformatics},
VOLUME = {22},
NUMBER = {5},
EID = {bbab066},
}
Endnote
%0 Journal Article
%A Lazareva, Olga
%A Baumbach, Jan
%A List, Markus
%A Blumenthal, David B.
%+ External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
%T On the Limits of Active Module Identification :
%G eng
%U http://hdl.handle.net/21.11116/0000-0009-7E65-9
%7 2021
%D 2021
%J Briefings in Bioinformatics
%V 22
%N 5
%Z sequence number: bbab066
%I H. Stewart Publications
%C London
%@ false
23. Llamas B, Narzisi G, Schneider V, Audano PA, Biederstedt E, Blauvelt L, Bradbury P, Chang X, Chin CS, Fungtammasan A, Clarke WE, Cleary A, Ebler J, Eizenga J, Sibbesen JA, Markello CJ, Garrison E, Garg S, Hickey G, Lazo GR, Lin MF, Mahmoud M, Marschall T, Minkin I, Monlong J, Musunuri RL, Sagayaradj S, Novak AM, Rautiainen M, Regier A, et al.: A Strategy for Building and Using a Human Reference Pangenome [Version 2; Peer Review: 2 approved]. F1000Research 2021, 8.
Export
BibTeX
@article{Llamas2021,
TITLE = {A Strategy for Building and Using a Human Reference Pangenome [Version 2; Peer Review: 2 approved]},
AUTHOR = {Llamas, B. and Narzisi, G. and Schneider, V. and Audano, P. A. and Biederstedt, E. and Blauvelt, L. and Bradbury, P. and Chang, X. and Chin, C. S. and Fungtammasan, A. and Clarke, W. E. and Cleary, A. and Ebler, Jana and Eizenga, J. and Sibbesen, J. A. and Markello, C. J. and Garrison, E. and Garg, S. and Hickey, G. and Lazo, G. R. and Lin, M. F. and Mahmoud, M. and Marschall, T. and Minkin, I. and Monlong, J. and Musunuri, R. L. and Sagayaradj, S. and Novak, A. M. and Rautiainen, M. and Regier, A. and Sedlazeck, F. J. and Siren, J. and Souilmi, Y. and Wagner, J. and Wrightsman, T. and Yokoyama, T. T. and Zeng, Q. and Zook, J. M. and Paten, B. and Busby, B.},
LANGUAGE = {eng},
ISSN = {2046-1402},
DOI = {10.12688/f1000research.19630.2},
PUBLISHER = {BioMed Central},
ADDRESS = {London},
YEAR = {2021},
JOURNAL = {F1000Research},
VOLUME = {8},
EID = {1751},
}
Endnote
%0 Journal Article
%A Llamas, B.
%A Narzisi, G.
%A Schneider, V.
%A Audano, P. A.
%A Biederstedt, E.
%A Blauvelt, L.
%A Bradbury, P.
%A Chang, X.
%A Chin, C. S.
%A Fungtammasan, A.
%A Clarke, W. E.
%A Cleary, A.
%A Ebler, Jana
%A Eizenga, J.
%A Sibbesen, J. A.
%A Markello, C. J.
%A Garrison, E.
%A Garg, S.
%A Hickey, G.
%A Lazo, G. R.
%A Lin, M. F.
%A Mahmoud, M.
%A Marschall, T.
%A Minkin, I.
%A Monlong, J.
%A Musunuri, R. L.
%A Sagayaradj, S.
%A Novak, A. M.
%A Rautiainen, M.
%A Regier, A.
%A Sedlazeck, F. J.
%A Siren, J.
%A Souilmi, Y.
%A Wagner, J.
%A Wrightsman, T.
%A Yokoyama, T. T.
%A Zeng, Q.
%A Zook, J. M.
%A Paten, B.
%A Busby, B.
%+ 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
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
%T A Strategy for Building and Using a Human Reference Pangenome [Version 2; Peer Review: 2 approved] :
%G eng
%U http://hdl.handle.net/21.11116/0000-0009-2A58-6
%R 10.12688/f1000research.19630.2
%7 2021
%D 2021
%J F1000Research
%O F1000Research
%V 8
%Z sequence number: 1751
%I BioMed Central
%C London
%@ false
24. Marty N, Saeng-Aroon S, Heger E, Thielen A, Obermeier M, Pfeifer N, Kaiser R, Klimkait T: Adapting the Geno2pheno[coreceptor] Tool to HIV-1 Subtype CRF01_AE by Phenotypic Validation Using Clinical Isolates from South-East Asia. Journal of Clinical Virology 2021, 136.
Export
BibTeX
@article{Marty_2021,
TITLE = {Adapting the geno2pheno[coreceptor] tool to {HIV}-1 subtype {CRF01_AE} by phenotypic validation using clinical isolates from {South-East Asia}},
AUTHOR = {Marty, Nina and Saeng-Aroon, Siriphan and Heger, Eva and Thielen, Alexander and Obermeier, Martin and Pfeifer, Nico and Kaiser, Rolf and Klimkait, Thomas},
LANGUAGE = {eng},
ISSN = {1386-6532},
DOI = {10.1016/j.jcv.2021.104755},
PUBLISHER = {Elsevier},
ADDRESS = {Amsterdam},
YEAR = {2021},
DATE = {2021},
JOURNAL = {Journal of Clinical Virology},
VOLUME = {136},
EID = {104755},
}
Endnote
%0 Journal Article
%A Marty, Nina
%A Saeng-Aroon, Siriphan
%A Heger, Eva
%A Thielen, Alexander
%A Obermeier, Martin
%A Pfeifer, Nico
%A Kaiser, Rolf
%A Klimkait, Thomas
%+ External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
External Organizations
%T Adapting the Geno2pheno[coreceptor] Tool to HIV-1 Subtype CRF01_AE by Phenotypic Validation Using Clinical Isolates from South-East Asia :
%G eng
%U http://hdl.handle.net/21.11116/0000-0008-62DD-1
%R 10.1016/j.jcv.2021.104755
%7 2021
%D 2021
%J Journal of Clinical Virology
%V 136
%Z sequence number: 104755
%I Elsevier
%C Amsterdam
%@ false
25. Matschinske J, Alcaraz N, Benis A, Golebiewski M, Grimm DG, Heumos L, Kacprowski T, Lazareva O, List M, Louadi Z, Pauling JK, Pfeifer N, Roettger R, Schwaemmle V, Sturm G, Traverso A, Van Steen K, de Freitas MV, Villalba Silva GC, Wee L, Wenke NK, Zanin M, Zolotareva O, Baumbach J, Blumenthal DB: The AIMe Registry for Artificial Intelligence in Biomedical Research. Nature Methods 2021, 18.
Export
BibTeX
@article{Matschinske2021,
TITLE = {The {AIMe} Registry for Artificial Intelligence in Biomedical Research},
AUTHOR = {Matschinske, Julian and Alcaraz, Nicolas and Benis, Arriel and Golebiewski, Martin and Grimm, Dominik G. and Heumos, Lukas and Kacprowski, Tim and Lazareva, Olga and List, Markus and Louadi, Zakaria and Pauling, Josch K. and Pfeifer, Nico and Roettger, Richard and Schwaemmle, Veit and Sturm, Gregor and Traverso, Alberto and Van Steen, Kristel and de Freitas, Martiela Vaz and Villalba Silva, Gerda Cristal and Wee, Leonard and Wenke, Nina K. and Zanin, Massimiliano and Zolotareva, Olga and Baumbach, Jan and Blumenthal, David B.},
LANGUAGE = {eng},
ISSN = {1548-7091},
DOI = {10.1038/s41592-021-01241-0},
PUBLISHER = {Nature Pub. Group},
ADDRESS = {New York, NY},
YEAR = {2021},
DATE = {2021},
JOURNAL = {Nature Methods},
VOLUME = {18},
PAGES = {1128--1131},
}
Endnote
%0 Journal Article
%A Matschinske, Julian
%A Alcaraz, Nicolas
%A Benis, Arriel
%A Golebiewski, Martin
%A Grimm, Dominik G.
%A Heumos, Lukas
%A Kacprowski, Tim
%A Lazareva, Olga
%A List, Markus
%A Louadi, Zakaria
%A Pauling, Josch K.
%A Pfeifer, Nico
%A Roettger, Richard
%A Schwaemmle, Veit
%A Sturm, Gregor
%A Traverso, Alberto
%A Van Steen, Kristel
%A de Freitas, Martiela Vaz
%A Villalba Silva, Gerda Cristal
%A Wee, Leonard
%A Wenke, Nina K.
%A Zanin, Massimiliano
%A Zolotareva, Olga
%A Baumbach, Jan
%A Blumenthal, David B.
%+ 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
%T The AIMe Registry for Artificial Intelligence in Biomedical Research :
%G eng
%U http://hdl.handle.net/21.11116/0000-0009-259D-D
%R 10.1038/s41592-021-01241-0
%7 2021
%D 2021
%J Nature Methods
%O Nature Methods
%V 18
%& 1128
%P 1128 - 1131
%I Nature Pub. Group
%C New York, NY
%@ false
26. Mattonet K, Nowack-Weyers N, Vogel V, Moser D, Tierling S, Kasper-Sonnenberg M, Wilhelm M, Scherer M, Walter J, Hengstler JG, Schölmerich A, Kumsta R: Prenatal Exposure to Endocrine Disrupting Chemicals is Associated with Altered DNA Methylation in Cord Blood. Epigenetics 2021, 17.
Export
BibTeX
@article{Mattonet2021,
TITLE = {Prenatal exposure to endocrine disrupting chemicals is associated with altered {DNA} methylation in cord blood},
AUTHOR = {Mattonet, Katharina and Nowack-Weyers, Nikola and Vogel, Vanessa and Moser, Dirk and Tierling, Sascha and Kasper-Sonnenberg, Monika and Wilhelm, Michael and Scherer, Michael and Walter, J{\"o}rn and Hengstler, Jan G. and Sch{\"o}lmerich, Axel and Kumsta, Robert},
LANGUAGE = {eng},
ISSN = {1559-2294},
DOI = {10.1080/15592294.2021.1975917},
PUBLISHER = {Taylor \& Francis},
YEAR = {2021},
JOURNAL = {Epigenetics},
VOLUME = {17},
NUMBER = {9},
PAGES = {935--952},
}
Endnote
%0 Journal Article
%A Mattonet, Katharina
%A Nowack-Weyers, Nikola
%A Vogel, Vanessa
%A Moser, Dirk
%A Tierling, Sascha
%A Kasper-Sonnenberg, Monika
%A Wilhelm, Michael
%A Scherer, Michael
%A Walter, Jörn
%A Hengstler, Jan G.
%A Schölmerich, Axel
%A Kumsta, Robert
%+ External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
External Organizations
External Organizations
External Organizations
%T Prenatal Exposure to Endocrine Disrupting Chemicals is Associated with Altered DNA Methylation in Cord Blood :
%G eng
%U http://hdl.handle.net/21.11116/0000-0009-49E8-0
%R 10.1080/15592294.2021.1975917
%7 2021
%D 2021
%J Epigenetics
%V 17
%N 9
%& 935
%P 935 - 952
%I Taylor & Francis
%@ false
27. Metzler S: Structural Building Blocks in Graph Data. Universität des Saarlandes; 2021.
Abstract
Graph data nowadays easily become so large that it is infeasible to study the underlying structures manually. Thus, computational methods are needed to uncover large-scale structural information. In this thesis, we present methods to understand and summarise large networks.<br>We propose the hyperbolic community model to describe groups of more densely connected nodes within networks using very intuitive parameters. The model accounts for a <br>frequent connectivity pattern in real data: a few community members are highly interconnected; most members mainly have ties to this core. Our model fits real data much better than previously-proposed models. Our corresponding random graph generator, HyGen, creates graphs with realistic intra-community structure.<br>Using the hyperbolic model, we conduct a large-scale study of the temporal evolution of communities on online question–answer sites. We observe that the user activity within a community is constant with respect to its size throughout its lifetime, and a small group of users is responsible for the majority of the social interactions. <br>We propose an approach for Boolean tensor clustering. This special tensor factorisation is restricted to binary data and assumes that one of the tensor directions has only non-overlapping factors. These assumptions – valid for many real-world data, in particular time-evolving networks – enable the use of bitwise operators and lift much of the computational complexity from the task.
Export
BibTeX
@phdthesis{SaskiaDiss21,
TITLE = {Structural Building Blocks in Graph Data},
AUTHOR = {Metzler, Saskia},
LANGUAGE = {eng},
URL = {urn:nbn:de:bsz:291--ds-335366},
DOI = {10.22028/D291-33536},
SCHOOL = {Universit{\"a}t des Saarlandes},
ADDRESS = {Saarbr{\"u}cken},
YEAR = {2021},
DATE = {2021},
ABSTRACT = {Graph data nowadays easily become so large that it is infeasible to study the underlying structures manually. Thus, computational methods are needed to uncover large-scale structural information. In this thesis, we present methods to understand and summarise large networks.<br>We propose the hyperbolic community model to describe groups of more densely connected nodes within networks using very intuitive parameters. The model accounts for a <br>frequent connectivity pattern in real data: a few community members are highly interconnected; most members mainly have ties to this core. Our model fits real data much better than previously-proposed models. Our corresponding random graph generator, HyGen, creates graphs with realistic intra-community structure.<br>Using the hyperbolic model, we conduct a large-scale study of the temporal evolution of communities on online question--answer sites. We observe that the user activity within a community is constant with respect to its size throughout its lifetime, and a small group of users is responsible for the majority of the social interactions. <br>We propose an approach for Boolean tensor clustering. This special tensor factorisation is restricted to binary data and assumes that one of the tensor directions has only non-overlapping factors. These assumptions -- valid for many real-world data, in particular time-evolving networks -- enable the use of bitwise operators and lift much of the computational complexity from the task.},
}
Endnote
%0 Thesis
%A Metzler, Saskia
%Y Miettinen, Pauli
%Y Weikum, Gerhard
%Y Günnemann, Stephan
%+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
International Max Planck Research School, MPI for Informatics, Max Planck Society
Databases and Information Systems, MPI for Informatics, Max Planck Society
Databases and Information Systems, MPI for Informatics, Max Planck Society
External Organizations
%T Structural Building Blocks in Graph Data : Characterised by Hyperbolic Communities and Uncovered by Boolean Tensor Clustering
%G eng
%U http://hdl.handle.net/21.11116/0000-0008-0BC1-2
%R 10.22028/D291-33536
%U urn:nbn:de:bsz:291--ds-335366
%F OTHER: hdl:20.500.11880/30904
%I Universität des Saarlandes
%C Saarbrücken
%D 2021
%P 196 p.
%V phd
%9 phd
%X Graph data nowadays easily become so large that it is infeasible to study the underlying structures manually. Thus, computational methods are needed to uncover large-scale structural information. In this thesis, we present methods to understand and summarise large networks.<br>We propose the hyperbolic community model to describe groups of more densely connected nodes within networks using very intuitive parameters. The model accounts for a <br>frequent connectivity pattern in real data: a few community members are highly interconnected; most members mainly have ties to this core. Our model fits real data much better than previously-proposed models. Our corresponding random graph generator, HyGen, creates graphs with realistic intra-community structure.<br>Using the hyperbolic model, we conduct a large-scale study of the temporal evolution of communities on online question–answer sites. We observe that the user activity within a community is constant with respect to its size throughout its lifetime, and a small group of users is responsible for the majority of the social interactions. <br>We propose an approach for Boolean tensor clustering. This special tensor factorisation is restricted to binary data and assumes that one of the tensor directions has only non-overlapping factors. These assumptions – valid for many real-world data, in particular time-evolving networks – enable the use of bitwise operators and lift much of the computational complexity from the task.
%U https://publikationen.sulb.uni-saarland.de/handle/20.500.11880/30904
28. Porubsky D, Ebert P, Audano PA, Vollger MR, Harvey WT, Marijon P, Ebler J, Munson KM, Sorensen M, Sulovari A, Haukness M, Ghareghani M, Lansdorp PM, Paten B, Devine SE, Sanders AD, Lee C, Chaisson MJP, Korbel JO, Eichler EE, Marschall T: Fully Phased Human Genome Assembly without Parental Data using Single-Cell Strand Sequencing and Long Reads. Nature Biotechnology 2021, 39.
Export
BibTeX
@article{Porubsky2020,
TITLE = {Fully Phased Human Genome Assembly without Parental Data using Single-Cell Strand Sequencing and Long Reads},
AUTHOR = {Porubsky, David and Ebert, Peter and Audano, Peter A. and Vollger, Mitchell R. and Harvey, William T. and Marijon, Pierre and Ebler, Jana and Munson, Katherine M. and Sorensen, Melanie and Sulovari, Arvis and Haukness, Marina and Ghareghani, Maryam and Lansdorp, Peter M. and Paten, Benedict and Devine, Scott E. and Sanders, Ashley D. and Lee, Charles and Chaisson, Mark J. P. and Korbel, Jan O. and Eichler, Evan E. and Marschall, Tobias and {Human Genome Structural Variation Consortium}},
LANGUAGE = {eng},
ISSN = {1087-0156},
DOI = {10.1038/s41587-020-0719-5},
PUBLISHER = {Gale Group Inc.},
ADDRESS = {New York, NY},
YEAR = {2021},
DATE = {2021},
JOURNAL = {Nature Biotechnology},
VOLUME = {39},
PAGES = {302--308},
}
Endnote
%0 Journal Article
%A Porubsky, David
%A Ebert, Peter
%A Audano, Peter A.
%A Vollger, Mitchell R.
%A Harvey, William T.
%A Marijon, Pierre
%A Ebler, Jana
%A Munson, Katherine M.
%A Sorensen, Melanie
%A Sulovari, Arvis
%A Haukness, Marina
%A Ghareghani, Maryam
%A Lansdorp, Peter M.
%A Paten, Benedict
%A Devine, Scott E.
%A Sanders, Ashley D.
%A Lee, Charles
%A Chaisson, Mark J. P.
%A Korbel, Jan O.
%A Eichler, Evan E.
%A Marschall, Tobias
%A Human Genome Structural Variation Consortium,
%+ External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
%T Fully Phased Human Genome Assembly without Parental Data using Single-Cell Strand Sequencing and Long Reads :
%G eng
%U http://hdl.handle.net/21.11116/0000-0007-A6D4-E
%R 10.1038/s41587-020-0719-5
%7 2020
%D 2021
%J Nature Biotechnology
%O Nat. Biotechnol.
%V 39
%& 302
%P 302 - 308
%I Gale Group Inc.
%C New York, NY
%@ false
29. Rautiainen M, Marschall T: MBG: Minimizer-based Sparse de Bruijn Graph Construction. Bioinformatics 2021, 37.
Export
BibTeX
@article{Rautiainen2021,
TITLE = {{MBG}: {M}inimizer-based sparse de {B}ruijn {G}raph construction},
AUTHOR = {Rautiainen, Mikko and Marschall, Tobias},
LANGUAGE = {eng},
ISSN = {1367-4803},
DOI = {10.1093/bioinformatics/btab004},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford},
YEAR = {2021},
DATE = {2021},
JOURNAL = {Bioinformatics},
VOLUME = {37},
NUMBER = {16},
PAGES = {2476--2478},
}
Endnote
%0 Journal Article
%A Rautiainen, Mikko
%A Marschall, Tobias
%+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
%T MBG: Minimizer-based Sparse de Bruijn Graph Construction :
%G eng
%U http://hdl.handle.net/21.11116/0000-0009-617C-F
%R 10.1093/bioinformatics/btab004
%7 2021
%D 2021
%J Bioinformatics
%V 37
%N 16
%& 2476
%P 2476 - 2478
%I Oxford University Press
%C Oxford
%@ false
30. Scherer M, Schmidt F, Lazareva O, Walter J, Baumbach J, Schulz MH, List M: Machine Learning for Deciphering Cell Heterogeneity and Gene Regulation. Nature Computational Science 2021, 1.
Export
BibTeX
@article{Scherer2021,
TITLE = {Machine Learning for Deciphering Cell Heterogeneity and Gene Regulation},
AUTHOR = {Scherer, Michael and Schmidt, Florian and Lazareva, Olga and Walter, J{\"o}rn and Baumbach, Jan and Schulz, Marcel Holger and List, Markus},
LANGUAGE = {eng},
ISSN = {2662-8457},
DOI = {10.1038/s43588-021-00038-7},
PUBLISHER = {Nature Research},
ADDRESS = {London},
YEAR = {2021},
JOURNAL = {Nature Computational Science},
VOLUME = {1},
}
Endnote
%0 Journal Article
%A Scherer, Michael
%A Schmidt, Florian
%A Lazareva, Olga
%A Walter, Jörn
%A Baumbach, Jan
%A Schulz, Marcel Holger
%A List, Markus
%+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
External Organizations
External Organizations
%T Machine Learning for Deciphering Cell Heterogeneity and Gene Regulation :
%G eng
%U http://hdl.handle.net/21.11116/0000-0008-2A4A-7
%R 10.1038/s43588-021-00038-7
%7 2021
%D 2021
%J Nature Computational Science
%V 1
%I Nature Research
%C London
%@ false
31. Scherer M: Computational solutions for addressing heterogeneity in DNA methylation data. Universität des Saarlandes; 2021.
Export
BibTeX
@phdthesis{Schererphd2020,
TITLE = {Computational solutions for addressing heterogeneity in {DNA} methylation data},
AUTHOR = {Scherer, Michael},
LANGUAGE = {eng},
URL = {urn:nbn:de:bsz:291--ds-338080},
DOI = {10.22028/D291-33808},
SCHOOL = {Universit{\"a}t des Saarlandes},
ADDRESS = {Saarbr{\"u}cken},
YEAR = {2021},
DATE = {2021},
}
Endnote
%0 Thesis
%A Scherer, Michael
%Y Lengauer, Thomas
%A referee: Walther, Jörn
%A referee: Marschall, Tobias
%+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
International Max Planck Research School, MPI for Informatics, Max Planck Society
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
%T Computational solutions for addressing heterogeneity in DNA methylation data :
%G eng
%U http://hdl.handle.net/21.11116/0000-0008-BA18-C
%R 10.22028/D291-33808
%U urn:nbn:de:bsz:291--ds-338080
%F OTHER: hdl:20.500.11880/31186
%I Universität des Saarlandes
%C Saarbrücken
%D 2021
%P 147 p.
%V phd
%9 phd
%U https://publikationen.sulb.uni-saarland.de/handle/20.500.11880/31186
32. Scherer M, Gasparoni G, Rahmouni S, Shashkova T, Arnoux M, Louis E, Nostaeva A, Avalos D, Dermitzakis ET, Aulchenko YS, Lengauer T, Lyons PA, Georges M, Walter J: Identification of Tissue-specific and Common Methylation Quantitative Trait Loci in Healthy Individuals using MAGAR. Epigenetics & Chromatin 2021, 14.
Export
BibTeX
@article{Scherer2021b,
TITLE = {Identification of tissue-specific and common methylation quantitative trait loci in healthy individuals using {MAGAR}},
AUTHOR = {Scherer, Michael and Gasparoni, Gilles and Rahmouni, Souad and Shashkova, Tatiana and Arnoux, Marion and Louis, Edouard and Nostaeva, Arina and Avalos, Diana and Dermitzakis, Emmanouil T. and Aulchenko, Yurii S. and Lengauer, Thomas and Lyons, Paul A. and Georges, Michel and Walter, J{\"o}rn},
LANGUAGE = {eng},
DOI = {10.1186/s13072-021-00415-6},
PUBLISHER = {BioMed Central},
ADDRESS = {London},
YEAR = {2021},
JOURNAL = {Epigenetics \& Chromatin},
VOLUME = {14},
NUMBER = {1},
EID = {44},
}
Endnote
%0 Journal Article
%A Scherer, Michael
%A Gasparoni, Gilles
%A Rahmouni, Souad
%A Shashkova, Tatiana
%A Arnoux, Marion
%A Louis, Edouard
%A Nostaeva, Arina
%A Avalos, Diana
%A Dermitzakis, Emmanouil T.
%A Aulchenko, Yurii S.
%A Lengauer, Thomas
%A Lyons, Paul A.
%A Georges, Michel
%A Walter, Jörn
%+ 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
External Organizations
External Organizations
%T Identification of Tissue-specific and Common Methylation Quantitative Trait Loci in Healthy Individuals using MAGAR :
%G eng
%U http://hdl.handle.net/21.11116/0000-0009-49EA-E
%R 10.1186/s13072-021-00415-6
%7 2021
%D 2021
%J Epigenetics & Chromatin
%V 14
%N 1
%Z sequence number: 44
%I BioMed Central
%C London
33. Schmidt F, Marx A, Baumgarten N, Hebel M, Wegner M, Kaulich M, Leisegang MS, Brandes RP, Göke J, Vreeken J, Schulz MH: Integrative Analysis of Epigenetics Data Identifies Gene-specific Regulatory Elements. Nucleic Acids Research (London) 2021, 49.
Export
BibTeX
@article{Schmidt_NAR21,
TITLE = {Integrative Analysis of Epigenetics Data Identifies Gene-specific Regulatory Elements},
AUTHOR = {Schmidt, Florian and Marx, Alexander and Baumgarten, Nina and Hebel, Marie and Wegner, Martin and Kaulich, Manuel and Leisegang, Matthias S. and Brandes, Ralf P and G{\"o}ke, Jonathan and Vreeken, Jilles and Schulz, Marcel Holger},
LANGUAGE = {eng},
ISSN = {0305-1048},
DOI = {10.1093/nar/gkab798},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford},
YEAR = {2021},
DATE = {2021},
JOURNAL = {Nucleic Acids Research (London)},
VOLUME = {49},
NUMBER = {18},
PAGES = {10397--10418},
}
Endnote
%0 Journal Article
%A Schmidt, Florian
%A Marx, Alexander
%A Baumgarten, Nina
%A Hebel, Marie
%A Wegner, Martin
%A Kaulich, Manuel
%A Leisegang, Matthias S.
%A Brandes, Ralf P
%A Göke, Jonathan
%A Vreeken, Jilles
%A Schulz, Marcel Holger
%+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
Databases and Information Systems, MPI for Informatics, Max Planck Society
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
Databases and Information Systems, MPI for Informatics, Max Planck Society
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
%T Integrative Analysis of Epigenetics Data Identifies Gene-specific Regulatory Elements :
%G eng
%U http://hdl.handle.net/21.11116/0000-0009-6D54-F
%R 10.1093/nar/gkab798
%2 PMC8501997
%7 2021
%D 2021
%J Nucleic Acids Research (London)
%O Nucleic Acids Res
%V 49
%N 18
%& 10397
%P 10397 - 10418
%I Oxford University Press
%C Oxford
%@ false
34. Ünal AB, Akgün M, Pfeifer N: ESCAPED: Efficient Secure and Private Dot Product Framework for Kernel-based Machine Learning Algorithms with Applications in Healthcare. In AAAI Technical Track on Machine Learning IV. AAAI; 2021.
Export
BibTeX
@inproceedings{Uenal_AAAI21,
TITLE = {ESCAPED: {E}fficient Secure and Private Dot Product Framework for Kernel-based Machine Learning Algorithms with Applications in Healthcare},
AUTHOR = {{\"U}nal, Ali Burak and Akg{\"u}n, Mete and Pfeifer, Nico},
LANGUAGE = {eng},
ISBN = {978-1-57735-866-4},
URL = {https://ojs.aaai.org/index.php/AAAI/article/view/17199},
PUBLISHER = {AAAI},
YEAR = {2021},
BOOKTITLE = {AAAI Technical Track on Machine Learning IV},
PAGES = {9988--9996},
ADDRESS = {Virtual Conference},
}
Endnote
%0 Conference Proceedings
%A Ünal, Ali Burak
%A Akgün, Mete
%A Pfeifer, Nico
%+ External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
%T ESCAPED: Efficient Secure and Private Dot Product Framework for Kernel-based Machine Learning Algorithms with Applications in Healthcare :
%G eng
%U http://hdl.handle.net/21.11116/0000-0009-3FAC-0
%U https://ojs.aaai.org/index.php/AAAI/article/view/17199
%D 2021
%B Thirty-Fifth AAAI Conference on Artificial Intelligence
%Z date of event: 2021-02-02 - 2021-02-09
%C Virtual Conference
%B AAAI Technical Track on Machine Learning IV
%P 9988 - 9996
%I AAAI
%@ 978-1-57735-866-4
%U https://ojs.aaai.org/index.php/AAAI/article/view/17199/17006
2020
35. Akgün M, Ünal AB, Ergüner B, Pfeifer N, Kohlbacher O: Identifying Disease-causing Mutations with Privacy Protection. Bioinformatics 2020, 36.
Export
BibTeX
@article{Akguen2020,
TITLE = {Identifying Disease-causing Mutations with Privacy Protection},
AUTHOR = {Akg{\"u}n, Mete and {\"U}nal, Ali Burak and Erg{\"u}ner, Bekir and Pfeifer, Nico and Kohlbacher, Oliver},
LANGUAGE = {eng},
ISSN = {1367-4803},
DOI = {10.1093/bioinformatics/btaa641},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford},
YEAR = {2020},
DATE = {2020},
JOURNAL = {Bioinformatics},
VOLUME = {36},
NUMBER = {21},
PAGES = {5205--5213},
}
Endnote
%0 Journal Article
%A Akgün, Mete
%A Ünal, Ali Burak
%A Ergüner, Bekir
%A Pfeifer, Nico
%A Kohlbacher, Oliver
%+ External Organizations
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
%T Identifying Disease-causing Mutations with Privacy Protection :
%G eng
%U http://hdl.handle.net/21.11116/0000-0008-2C56-7
%R 10.1093/bioinformatics/btaa641
%7 2020
%D 2020
%J Bioinformatics
%V 36
%N 21
%& 5205
%P 5205 - 5213
%I Oxford University Press
%C Oxford
%@ false
36. Ardakani FB, Kattler K, Heinen T, Schmidt F, Feuerborn D, Gasparoni G, Lepikhov K, Nell P, Hengstler J, Walter J, Schulz MH: Prediction of Single-cell Gene Expression for Transcription Factor Analysis. GigaScience 2020, 9.
Export
BibTeX
@article{Ardakani2020,
TITLE = {Prediction of Single-cell Gene Expression for Transcription Factor Analysis},
AUTHOR = {Ardakani, Fatemeh Behjati and Kattler, Kathrin and Heinen, Tobias and Schmidt, Florian and Feuerborn, David and Gasparoni, Gilles and Lepikhov, Konstantin and Nell, Patrick and Hengstler, Jan and Walter, Jorn and Schulz, Marcel H.},
LANGUAGE = {eng},
ISSN = {2047-217X},
DOI = {10.1093/gigascience/giaa113},
PUBLISHER = {BioMed Central},
ADDRESS = {London},
YEAR = {2020},
JOURNAL = {GigaScience},
VOLUME = {9},
PAGES = {1--14},
EID = {113},
}
Endnote
%0 Journal Article
%A Ardakani, Fatemeh Behjati
%A Kattler, Kathrin
%A Heinen, Tobias
%A Schmidt, Florian
%A Feuerborn, David
%A Gasparoni, Gilles
%A Lepikhov, Konstantin
%A Nell, Patrick
%A Hengstler, Jan
%A Walter, Jorn
%A Schulz, Marcel H.
%+ External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
%T Prediction of Single-cell Gene Expression for Transcription Factor Analysis :
%G eng
%U http://hdl.handle.net/21.11116/0000-0007-E45F-E
%R 10.1093/gigascience/giaa113
%7 2020
%D 2020
%J GigaScience
%V 9
%& 1
%P 1 - 14
%Z sequence number: 113
%I BioMed Central
%C London
%@ false
37. Bastys T, Gapsys V, Walter H, Heger E, Doncheva NT, Kaiser R, de Groot BL, Kalinina OV: Non-active Site Mutants of HIV-1 Protease Influence Resistance and Sensitisation towards Protease Inhibitors. Retrovirology 2020.
Export
BibTeX
@article{Bastys2020,
TITLE = {Non-active site mutants of {HIV-1} protease influence resistance and sensitisation towards protease inhibitors},
AUTHOR = {Bastys, Tomas and Gapsys, Vytautas and Walter, Hauke and Heger, Eva and Doncheva, Nadezhda Tsankova and Kaiser, Rolf and de Groot, Bert L. and Kalinina, Olga V.},
LANGUAGE = {eng},
ISSN = {1742-4690},
DOI = {10.1186/s12977-020-00520-6},
PUBLISHER = {BioMed Central},
ADDRESS = {London},
YEAR = {2020},
JOURNAL = {Retrovirology},
EID = {13},
}
Endnote
%0 Journal Article
%A Bastys, Tomas
%A Gapsys, Vytautas
%A Walter, Hauke
%A Heger, Eva
%A Doncheva, Nadezhda Tsankova
%A Kaiser, Rolf
%A de Groot, Bert L.
%A Kalinina, Olga V.
%+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
%T Non-active Site Mutants of HIV-1 Protease Influence Resistance and Sensitisation towards Protease Inhibitors :
%G eng
%U http://hdl.handle.net/21.11116/0000-0006-A274-0
%R 10.1186/s12977-020-00520-6
%2 PMC7236880
%7 2020
%D 2020
%J Retrovirology
%Z sequence number: 13
%I BioMed Central
%C London
%@ false
38. Baumgarten N, Schmidt F, Schulz MH: Improved Linking of Motifs to their TFs Using Domain Information. Bioinformatics 2020, 36.
Export
BibTeX
@article{Baumgarten2020,
TITLE = {Improved linking of motifs to their {TFs} using domain information},
AUTHOR = {Baumgarten, Nina and Schmidt, Florian and Schulz, Marcel Holger},
LANGUAGE = {eng},
ISSN = {1367-4803},
DOI = {10.1093/bioinformatics/btz855},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford},
YEAR = {2020},
DATE = {2020},
JOURNAL = {Bioinformatics},
VOLUME = {36},
NUMBER = {6},
PAGES = {1655--1662},
}
Endnote
%0 Journal Article
%A Baumgarten, Nina
%A Schmidt, Florian
%A Schulz, Marcel Holger
%+ 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 Improved Linking of Motifs to their TFs Using Domain Information :
%G eng
%U http://hdl.handle.net/21.11116/0000-0006-A2A9-4
%R 10.1093/bioinformatics/btz855
%7 2019
%D 2020
%J Bioinformatics
%V 36
%N 6
%& 1655
%P 1655 - 1662
%I Oxford University Press
%C Oxford
%@ false
39. Behjati Ardakani F: Computational models of gene expression regulation. Universität des Saarlandes; 2020.
Export
BibTeX
@phdthesis{Ardadiss_2019,
TITLE = {Computational models of gene expression regulation},
AUTHOR = {Behjati Ardakani, Fatemeh},
LANGUAGE = {eng},
URL = {urn:nbn:de:bsz:291--ds-321489},
DOI = {http://dx.doi.org/10.22028/D291-30206},
SCHOOL = {Universit{\"a}t des Saarlandes},
ADDRESS = {Saarbr{\"u}cken},
YEAR = {2020},
DATE = {2020},
}
Endnote
%0 Thesis
%A Behjati Ardakani, Fatemeh
%Y Schulz, Marcel
%A referee: Marschall, Tobias
%+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
International Max Planck Research School, MPI for Informatics, Max Planck Society
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
%T Computational models of gene expression regulation :
%G eng
%U http://hdl.handle.net/21.11116/0000-0007-7163-A
%R http://dx.doi.org/10.22028/D291-30206
%U urn:nbn:de:bsz:291--ds-321489
%F OTHER: hdl:20.500.11880/29766
%I Universität des Saarlandes
%C Saarbrücken
%D 2020
%P 170 p.
%V phd
%9 phd
%U https://publikationen.sulb.uni-saarland.de/handle/20.500.11880/29766
40. Berzow D, Descamps D, Obermeier M, Charpentier C, Kaiser R, Guertler L, Eberle J, Wensing A, Sierra S, Ruelle J, Gomes P, Mansinho K, Taylor N, Jensen B, Döring M, Stürmer M, Rockstroh J, Camacho R: HIV-2: A Summary of Present Standard of Care and Treatment Options for HIV-2 Infected Individuals Living in Western Europe. Clinical Infectious Diseases 2020.
Export
BibTeX
@article{Berzow2020,
TITLE = {{HIV}-2: {A} summary of present standard of care and treatment options for {HIV}-2 infected individuals living in {Western Europe}},
AUTHOR = {Berzow, Dirk and Descamps, Diane and Obermeier, Martin and Charpentier, Charlotte and Kaiser, Rolf and Guertler, Lutz and Eberle, Josef and Wensing, Annemarie and Sierra, Saleta and Ruelle, Jean and Gomes, Perpetua and Mansinho, Kamal and Taylor, Ninon and Jensen, Bj{\"o}rn and D{\"o}ring, Matthias and St{\"u}rmer, Martin and Rockstroh, J{\"u}rgen and Camacho, Ricardo},
LANGUAGE = {eng},
ISSN = {1058-4838},
DOI = {10.1093/cid/ciaa275},
PUBLISHER = {The University of Chicago Press},
ADDRESS = {Chicago, IL},
YEAR = {2020},
JOURNAL = {Clinical Infectious Diseases},
EID = {ciaa275},
}
Endnote
%0 Journal Article
%A Berzow, Dirk
%A Descamps, Diane
%A Obermeier, Martin
%A Charpentier, Charlotte
%A Kaiser, Rolf
%A Guertler, Lutz
%A Eberle, Josef
%A Wensing, Annemarie
%A Sierra, Saleta
%A Ruelle, Jean
%A Gomes, Perpetua
%A Mansinho, Kamal
%A Taylor, Ninon
%A Jensen, Björn
%A Döring, Matthias
%A Stürmer, Martin
%A Rockstroh, Jürgen
%A Camacho, Ricardo
%+ External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
External Organizations
External Organizations
%T HIV-2: A Summary of Present Standard of Care and Treatment Options for HIV-2 Infected Individuals Living in Western Europe :
%G eng
%U http://hdl.handle.net/21.11116/0000-0006-5A74-3
%R 10.1093/cid/ciaa275
%7 2020
%D 2020
%J Clinical Infectious Diseases
%Z sequence number: ciaa275
%I The University of Chicago Press
%C Chicago, IL
%@ false
41. Chakraborty S, Canzar S, Marschall T, Schulz MH: Chromatyping: Reconstructing Nucleosome Profiles from NOMe Sequencing Data. Journal of Computational Biology 2020, 27.
Export
BibTeX
@article{Chakraborty_2020,
TITLE = {Chromatyping: {R}econstructing Nucleosome Profiles from {NOMe} Sequencing Data},
AUTHOR = {Chakraborty, Shounak and Canzar, Stefan and Marschall, Tobias and Schulz, Marcel H.},
LANGUAGE = {eng},
ISSN = {1066-5277},
DOI = {10.1089/cmb.2019.0457},
PUBLISHER = {Mary Ann Liebert},
ADDRESS = {New York, NY},
YEAR = {2020},
DATE = {2020},
JOURNAL = {Journal of Computational Biology},
VOLUME = {27},
NUMBER = {3},
PAGES = {330--341},
}
Endnote
%0 Journal Article
%A Chakraborty, Shounak
%A Canzar, Stefan
%A Marschall, Tobias
%A Schulz, Marcel H.
%+ External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
%T Chromatyping: Reconstructing Nucleosome Profiles from NOMe Sequencing Data :
%G eng
%U http://hdl.handle.net/21.11116/0000-0006-97D4-0
%R 10.1089/cmb.2019.0457
%7 2020
%D 2020
%J Journal of Computational Biology
%V 27
%N 3
%& 330
%P 330 - 341
%I Mary Ann Liebert
%C New York, NY
%@ false
42. Chin C-S, Wagner J, Zeng Q, Garrison E, Garg S, Fungtammasan A, Rautiainen M, Aganezov S, Kirsche M, Zarate S, Schatz MC, Xiao C, Rowell WJ, Markello C, Farek J, Sedlazeck FJ, Bansal V, Yoo B, Miller N, Zhou X, Carroll A, Barrio AM, Salit M, Marschall T, Dilthey AT, Zook JM: A Diploid Assembly-based Benchmark for Variants in the Major Histocompatibility Complex. Nature Communications 2020, 11.
Export
BibTeX
@article{Chin2020,
TITLE = {A Diploid Assembly-based Benchmark for Variants in the Major Histocompatibility Complex},
AUTHOR = {Chin, Chen-Shan and Wagner, Justin and Zeng, Qiandong and Garrison, Erik and Garg, Shilpa and Fungtammasan, Arkarachai and Rautiainen, Mikko and Aganezov, Sergey and Kirsche, Melanie and Zarate, Samantha and Schatz, Michael C. and Xiao, Chunlin and Rowell, William J. and Markello, Charles and Farek, Jesse and Sedlazeck, Fritz J. and Bansal, Vikas and Yoo, Byunggil and Miller, Neil and Zhou, Xin and Carroll, Andrew and Barrio, Alvaro Martinez and Salit, Marc and Marschall, Tobias and Dilthey, Alexander T. and Zook, Justin M.},
LANGUAGE = {eng},
ISSN = {2041-1723},
DOI = {10.1038/s41467-020-18564-9},
PUBLISHER = {Nature Publishing Group},
ADDRESS = {London},
YEAR = {2020},
DATE = {2020},
JOURNAL = {Nature Communications},
VOLUME = {11},
NUMBER = {1},
EID = {4794},
}
Endnote
%0 Journal Article
%A Chin, Chen-Shan
%A Wagner, Justin
%A Zeng, Qiandong
%A Garrison, Erik
%A Garg, Shilpa
%A Fungtammasan, Arkarachai
%A Rautiainen, Mikko
%A Aganezov, Sergey
%A Kirsche, Melanie
%A Zarate, Samantha
%A Schatz, Michael C.
%A Xiao, Chunlin
%A Rowell, William J.
%A Markello, Charles
%A Farek, Jesse
%A Sedlazeck, Fritz J.
%A Bansal, Vikas
%A Yoo, Byunggil
%A Miller, Neil
%A Zhou, Xin
%A Carroll, Andrew
%A Barrio, Alvaro Martinez
%A Salit, Marc
%A Marschall, Tobias
%A Dilthey, Alexander T.
%A Zook, Justin M.
%+ External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
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 Diploid Assembly-based Benchmark for Variants in the Major Histocompatibility Complex :
%G eng
%U http://hdl.handle.net/21.11116/0000-0007-360E-E
%R 10.1038/s41467-020-18564-9
%7 2020
%D 2020
%J Nature Communications
%O Nat. Commun.
%V 11
%N 1
%Z sequence number: 4794
%I Nature Publishing Group
%C London
%@ false
43. Delacher M, Imbusch CD, Hotz-Wagenblatt A, Mallm J-P, Bauer K, Simon M, Riegel D, Rendeiro AF, Bittner S, Sanderink L, Pant A, Schmidleithner L, Braband KL, Echtenachter B, Fischer A, Giunchiglia V, Hoffmann P, Edinger M, Bock C, Rehli M, Brors B, Schmidl C, Feuerer M: Precursors for Nonlymphoid-Tissue Treg Cells Reside in Secondary Lymphoid Organs and Are Programmed by the Transcription Factor BATF. Immunity 2020, 52.
Export
BibTeX
@article{Delacher2020,
TITLE = {Precursors for Nonlymphoid-Tissue Treg Cells Reside in Secondary Lymphoid Organs and Are Programmed by the Transcription Factor {BATF}},
AUTHOR = {Delacher, Michael and Imbusch, Charles D. and Hotz-Wagenblatt, Agnes and Mallm, Jan-Philipp and Bauer, Katharina and Simon, Malte and Riegel, Dania and Rendeiro, Andr{\'e} F. and Bittner, Sebastian and Sanderink, Lieke and Pant, Asmita and Schmidleithner, Lisa and Braband, Kathrin L. and Echtenachter, Bernd and Fischer, Alexander and Giunchiglia, Valentina and Hoffmann, Petra and Edinger, Matthias and Bock, Christoph and Rehli, Michael and Brors, Benedikt and Schmidl, Christian and Feuerer, Markus},
LANGUAGE = {eng},
ISSN = {1074-7613},
DOI = {10.1016/j.immuni.2019.12.002},
PUBLISHER = {Cell Press},
ADDRESS = {Cambridge, Mass.},
YEAR = {2020},
JOURNAL = {Immunity},
VOLUME = {52},
NUMBER = {2},
PAGES = {295--312},
EID = {e11},
}
Endnote
%0 Journal Article
%A Delacher, Michael
%A Imbusch, Charles D.
%A Hotz-Wagenblatt, Agnes
%A Mallm, Jan-Philipp
%A Bauer, Katharina
%A Simon, Malte
%A Riegel, Dania
%A Rendeiro, André F.
%A Bittner, Sebastian
%A Sanderink, Lieke
%A Pant, Asmita
%A Schmidleithner, Lisa
%A Braband, Kathrin L.
%A Echtenachter, Bernd
%A Fischer, Alexander
%A Giunchiglia, Valentina
%A Hoffmann, Petra
%A Edinger, Matthias
%A Bock, Christoph
%A Rehli, Michael
%A Brors, Benedikt
%A Schmidl, Christian
%A Feuerer, Markus
%+ External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
External Organizations
External Organizations
External Organizations
%T Precursors for Nonlymphoid-Tissue Treg Cells Reside in Secondary Lymphoid Organs and Are Programmed by the Transcription Factor BATF :
%G eng
%U http://hdl.handle.net/21.11116/0000-0006-8E56-A
%R 10.1016/j.immuni.2019.12.002
%2 PMC7026712
%7 2020
%D 2020
%J Immunity
%V 52
%N 2
%& 295
%P 295 - 312
%Z sequence number: e11
%I Cell Press
%C Cambridge, Mass.
%@ false
44. Eizenga JM, Novak AM, Sibbesen JA, Heumos S, Ghaffaari A, Hickey G, Chang X, Seaman JD, Rounthwaite R, Ebler J, Rautiainen M, Garg S, Paten B, Marschall T, Sirén J, Garrison E: Pangenome Graphs. Annual Review of Genomics and Human Genetics 2020, 21.
Export
BibTeX
@article{Eizenga2020,
TITLE = {Pangenome Graphs},
AUTHOR = {Eizenga, Jordan M. and Novak, Adam M. and Sibbesen, Jonas A. and Heumos, Simon and Ghaffaari, Ali and Hickey, Glenn and Chang, Xian and Seaman, Josiah D. and Rounthwaite, Robin and Ebler, Jana and Rautiainen, Mikko and Garg, Shilpa and Paten, Benedict and Marschall, Tobias and Sir{\'e}n, Jouni and Garrison, Erik},
LANGUAGE = {eng},
ISSN = {1527-8204},
DOI = {10.1146/annurev-genom-120219-080406},
PUBLISHER = {Annual Reviews},
ADDRESS = {Palo Alto, CA},
YEAR = {2020},
JOURNAL = {Annual Review of Genomics and Human Genetics},
VOLUME = {21},
PAGES = {139--162},
}
Endnote
%0 Journal Article
%A Eizenga, Jordan M.
%A Novak, Adam M.
%A Sibbesen, Jonas A.
%A Heumos, Simon
%A Ghaffaari, Ali
%A Hickey, Glenn
%A Chang, Xian
%A Seaman, Josiah D.
%A Rounthwaite, Robin
%A Ebler, Jana
%A Rautiainen, Mikko
%A Garg, Shilpa
%A Paten, Benedict
%A Marschall, Tobias
%A Sirén, Jouni
%A Garrison, Erik
%+ External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
External Organizations
%T Pangenome Graphs :
%G eng
%U http://hdl.handle.net/21.11116/0000-0008-070D-3
%R 10.1146/annurev-genom-120219-080406
%2 PMC8006571
%7 2020
%D 2020
%J Annual Review of Genomics and Human Genetics
%V 21
%& 139
%P 139 - 162
%I Annual Reviews
%C Palo Alto, CA
%@ false
45. Gier S, Simon M, Gasparoni G, Khalifa S, Schulz MH, Schmitt MJ, Breinig F: Yeast Viral Killer Toxin K1 Induces Specific Host Cell Adaptions via Intrinsic Selection Pressure. Applied and Environmental Microbiology 2020, 86.
Export
BibTeX
@article{Gier2020,
TITLE = {Yeast Viral Killer Toxin {K1} Induces Specific Host Cell Adaptions via Intrinsic Selection Pressure},
AUTHOR = {Gier, Stefanie and Simon, Martin and Gasparoni, Gilles and Khalifa, Salem and Schulz, Marcel Holger and Schmitt, Manfred J. and Breinig, Frank},
LANGUAGE = {eng},
ISSN = {0099-2240},
DOI = {10.1128/AEM.02446-19},
PUBLISHER = {American Society for Microbiology (ASM)},
YEAR = {2020},
JOURNAL = {Applied and Environmental Microbiology},
VOLUME = {86},
NUMBER = {4},
EID = {e02446-19},
}
Endnote
%0 Journal Article
%A Gier, Stefanie
%A Simon, Martin
%A Gasparoni, Gilles
%A Khalifa, Salem
%A Schulz, Marcel Holger
%A Schmitt, Manfred J.
%A Breinig, Frank
%+ External Organizations
External Organizations
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
External Organizations
%T Yeast Viral Killer Toxin K1 Induces Specific Host Cell Adaptions via Intrinsic Selection Pressure :
%G eng
%U http://hdl.handle.net/21.11116/0000-0006-9771-0
%R 10.1128/AEM.02446-19
%7 2020
%D 2020
%J Applied and Environmental Microbiology
%O Appl. Environ. Microbiol.
%V 86
%N 4
%Z sequence number: e02446-19
%I American Society for Microbiology (ASM)
%@ false
46. Karunanithi S, Oruganti V, de Wijn R, Drews F, Cheaib M, Nordström K, Simon M, Schulz MH: Feeding Exogenous dsRNA Interferes with Endogenous sRNA Accumulation in Paramecium. DNA Research 2020, 27.
Export
BibTeX
@article{Karunanithi2020,
TITLE = {Feeding exogenous {dsRNA} interferes with endogenous {sRNA} accumulation in {Paramecium}},
AUTHOR = {Karunanithi, Sivarajan and Oruganti, Vidya and de Wijn, Raphael and Drews, Franziska and Cheaib, Miriam and Nordstr{\"o}m, Karl and Simon, Martin and Schulz, Marcel Holger},
LANGUAGE = {eng},
DOI = {10.1093/dnares/dsaa005},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford, UK},
YEAR = {2020},
JOURNAL = {DNA Research},
VOLUME = {27},
NUMBER = {1},
EID = {dsaa005},
}
Endnote
%0 Journal Article
%A Karunanithi, Sivarajan
%A Oruganti, Vidya
%A de Wijn, Raphael
%A Drews, Franziska
%A Cheaib, Miriam
%A Nordström, Karl
%A Simon, Martin
%A Schulz, Marcel Holger
%+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
%T Feeding Exogenous dsRNA Interferes with Endogenous sRNA Accumulation in Paramecium :
%G eng
%U http://hdl.handle.net/21.11116/0000-0006-D2FC-1
%R 10.1093/dnares/dsaa005
%2 PMC7315353
%7 2020
%D 2020
%J DNA Research
%V 27
%N 1
%Z sequence number: dsaa005
%I Oxford University Press
%C Oxford, UK
47. Kreer C, Döring M, Lehnen N, Ercanoglu MS, Gieselmann L, Luca D, Jain K, Schommers P, Pfeifer N, Klein F: openPrimeR for Multiplex Amplification of Highly Diverse Templates. Journal of Immunological Methods 2020, 420.
Export
BibTeX
@article{Kreer2020,
TITLE = {{openPrimeR} for multiplex amplification of highly diverse templates},
AUTHOR = {Kreer, Christoph and D{\"o}ring, Matthias and Lehnen, Nathalie and Ercanoglu, Meryem S. and Gieselmann, Lutz and Luca, Domnica and Jain, Kanika and Schommers, Philipp and Pfeifer, Nico and Klein, Florian},
LANGUAGE = {eng},
ISSN = {0022-1759},
DOI = {10.1016/j.jim.2020.112752},
PUBLISHER = {Elsevier},
ADDRESS = {Amsterdam},
YEAR = {2020},
DATE = {2020},
JOURNAL = {Journal of Immunological Methods},
VOLUME = {420},
EID = {112752},
}
Endnote
%0 Journal Article
%A Kreer, Christoph
%A Döring, Matthias
%A Lehnen, Nathalie
%A Ercanoglu, Meryem S.
%A Gieselmann, Lutz
%A Luca, Domnica
%A Jain, Kanika
%A Schommers, Philipp
%A Pfeifer, Nico
%A Klein, Florian
%+ 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
%T openPrimeR for Multiplex Amplification of Highly Diverse Templates :
%G eng
%U http://hdl.handle.net/21.11116/0000-0006-5A7E-9
%R 10.1016/j.jim.2020.112752
%7 2020
%D 2020
%J Journal of Immunological Methods
%V 420
%Z sequence number: 112752
%I Elsevier
%C Amsterdam
%@ false
48. Lähnemann D, Köster J, Szczurek E, McCarthy DJ, Hicks SC, Robinson MD, Vallejos CA, Campbell KR, Beerenwinkel N, Mahfouz A, Pinello L, Skums P, Stamatakis A, Attolini CS-O, Aparicio S, Baaijens J, Balvert M, de Barbanson B, Cappuccio A, Corleone G, Dutilh BE, Florescu M, Guryev V, Holmer R, Jahn K, Lobo TJ, Keizer EM, Khatri I, Kielbasa SM, Korbel JO, et al.: Eleven Grand Challenges in Single-Cell Data Science. Genome Biology 2020, 21.
Export
BibTeX
@article{Laehnemann2020,
TITLE = {Eleven Grand Challenges in Single-Cell Data Science},
AUTHOR = {L{\"a}hnemann, David and K{\"o}ster, Johannes and Szczurek, Ewa and McCarthy, Davis J. and Hicks, Stephanie C. and Robinson, Mark D. and Vallejos, Catalina A. and Campbell, Kieran R. and Beerenwinkel, Niko and Mahfouz, Ahmed and Pinello, Luca and Skums, Pavel and Stamatakis, Alexandros and Attolini, Camille Stephan-Otto and Aparicio, Samuel and Baaijens, Jasmijn and Balvert, Marleen and de Barbanson, Buys and Cappuccio, Antonio and Corleone, Giacomo and Dutilh, Bas E. and Florescu, Maria and Guryev, Victor and Holmer, Rens and Jahn, Katharina and Lobo, Thamar Jessurun and Keizer, Emma M. and Khatri, Indu and Kielbasa, Szymon M. and Korbel, Jan O. and Kozlov, Alexey M. and Kuo, Tzu-Hao and Lelieveldt, Boudewijn P. F. and Mandoiu, Ion I. and Marioni, John C. and Marschall, Tobias and Moelder, Felix and Niknejad, Amir and Raczkowski, Lukasz and Reinders, Marcel and de Ridder, Jeroen and Saliba, Antoine-Emmanuel and Somarakis, Antonios and Stegle, Oliver and Theis, Fabian J. and Yang, Huan and Zelikovsky, Alex and MacHardy, Alice C. and Raphael, Benjamin J. and Shah, Sohrab P. and Sch{\"o}nhuth, Alexander},
LANGUAGE = {eng},
ISSN = {1465-6906},
DOI = {10.1186/s13059-020-1926-6},
PUBLISHER = {BioMed Central Ltd.},
ADDRESS = {London},
YEAR = {2020},
JOURNAL = {Genome Biology},
VOLUME = {21},
NUMBER = {1},
EID = {31},
}
Endnote
%0 Journal Article
%A Lähnemann, David
%A Köster, Johannes
%A Szczurek, Ewa
%A McCarthy, Davis J.
%A Hicks, Stephanie C.
%A Robinson, Mark D.
%A Vallejos, Catalina A.
%A Campbell, Kieran R.
%A Beerenwinkel, Niko
%A Mahfouz, Ahmed
%A Pinello, Luca
%A Skums, Pavel
%A Stamatakis, Alexandros
%A Attolini, Camille Stephan-Otto
%A Aparicio, Samuel
%A Baaijens, Jasmijn
%A Balvert, Marleen
%A de Barbanson, Buys
%A Cappuccio, Antonio
%A Corleone, Giacomo
%A Dutilh, Bas E.
%A Florescu, Maria
%A Guryev, Victor
%A Holmer, Rens
%A Jahn, Katharina
%A Lobo, Thamar Jessurun
%A Keizer, Emma M.
%A Khatri, Indu
%A Kielbasa, Szymon M.
%A Korbel, Jan O.
%A Kozlov, Alexey M.
%A Kuo, Tzu-Hao
%A Lelieveldt, Boudewijn P. F.
%A Mandoiu, Ion I.
%A Marioni, John C.
%A Marschall, Tobias
%A Moelder, Felix
%A Niknejad, Amir
%A Raczkowski, Lukasz
%A Reinders, Marcel
%A de Ridder, Jeroen
%A Saliba, Antoine-Emmanuel
%A Somarakis, Antonios
%A Stegle, Oliver
%A Theis, Fabian J.
%A Yang, Huan
%A Zelikovsky, Alex
%A MacHardy, Alice C.
%A Raphael, Benjamin J.
%A Shah, Sohrab P.
%A Schönhuth, Alexander
%+ External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
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
%T Eleven Grand Challenges in Single-Cell Data Science :
%G eng
%U http://hdl.handle.net/21.11116/0000-0006-8E39-B
%R 10.1186/s13059-020-1926-6
%7 2020
%D 2020
%J Genome Biology
%V 21
%N 1
%Z sequence number: 31
%I BioMed Central Ltd.
%C London
%@ false
49. Lengauer T: Statistical Data Analysis in the Era of Big Data. Chemie-Ingenieur-Technik 2020, 92.
Export
BibTeX
@article{LengauerStatData2020,
TITLE = {Statistical Data Analysis in the Era of Big Data},
AUTHOR = {Lengauer, Thomas},
LANGUAGE = {eng},
ISSN = {0009-286X},
DOI = {10.1002/cite.202000024},
PUBLISHER = {Wiley-VCH},
ADDRESS = {Weinheim, Germany},
YEAR = {2020},
JOURNAL = {Chemie-Ingenieur-Technik},
VOLUME = {92},
NUMBER = {7},
PAGES = {831--841},
}
Endnote
%0 Journal Article
%A Lengauer, Thomas
%+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
%T Statistical Data Analysis in the Era of Big Data :
%G eng
%U http://hdl.handle.net/21.11116/0000-0006-9A1B-F
%R 10.1002/cite.202000024
%7 2020
%D 2020
%J Chemie-Ingenieur-Technik
%O Chem. Ing. Tech.
%V 92
%N 7
%& 831
%P 831 - 841
%I Wiley-VCH
%C Weinheim, Germany
%@ false
50. Porubsky D, Sanders AD, Höps W, Hsieh P, Sulovari A, Li R, Mercuri L, Sorensen M, Murali SC, Gordon D, Cantsilieris S, Pollen AA, Ventura M, Antonacci F, Marschall T, Korbel JO, Eichler EE: Recurrent Inversion Toggling and Great Ape Genome Evolution. Nature Genetics 2020, 52.
Export
BibTeX
@article{Porubsky2020a,
TITLE = {Recurrent Inversion Toggling and Great Ape Genome Evolution},
AUTHOR = {Porubsky, David and Sanders, Ashley D. and H{\"o}ps, Wolfram and Hsieh, PingHsun and Sulovari, Arvis and Li, Ruiyang and Mercuri, Ludovica and Sorensen, Melanie and Murali, Shwetha C. and Gordon, David and Cantsilieris, Stuart and Pollen, Alex A. and Ventura, Mario and Antonacci, Francesca and Marschall, Tobias and Korbel, Jan O. and Eichler, Evan E.},
LANGUAGE = {eng},
ISSN = {1061-4036},
DOI = {10.1038/s41588-020-0646-x},
PUBLISHER = {Nature America, Inc.},
ADDRESS = {New York, NY},
YEAR = {2020},
DATE = {2020},
JOURNAL = {Nature Genetics},
VOLUME = {52},
NUMBER = {8},
PAGES = {849--852},
}
Endnote
%0 Journal Article
%A Porubsky, David
%A Sanders, Ashley D.
%A Höps, Wolfram
%A Hsieh, PingHsun
%A Sulovari, Arvis
%A Li, Ruiyang
%A Mercuri, Ludovica
%A Sorensen, Melanie
%A Murali, Shwetha C.
%A Gordon, David
%A Cantsilieris, Stuart
%A Pollen, Alex A.
%A Ventura, Mario
%A Antonacci, Francesca
%A Marschall, Tobias
%A Korbel, Jan O.
%A Eichler, Evan E.
%+ 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
%T Recurrent Inversion Toggling and Great Ape Genome Evolution :
%G eng
%U http://hdl.handle.net/21.11116/0000-0006-A2BE-D
%R 10.1038/s41588-020-0646-x
%7 2020
%D 2020
%J Nature Genetics
%O Nature Genet.
%V 52
%N 8
%& 849
%P 849 - 852
%I Nature America, Inc.
%C New York, NY
%@ false
51. Rautiainen M, Marschall T: GraphAligner: Rapid and Versatile Sequence-to-Graphalignment. Genome Biology 2020, 21.
Export
BibTeX
@article{Rautiainen2020,
TITLE = {{GraphAligner}: {R}apid and Versatile Sequence-to-Graphalignment},
AUTHOR = {Rautiainen, Mikko and Marschall, Tobias},
LANGUAGE = {eng},
ISSN = {1465-6906},
DOI = {10.1186/s13059-020-02157-2},
PUBLISHER = {BioMed Central Ltd.},
ADDRESS = {London},
YEAR = {2020},
JOURNAL = {Genome Biology},
VOLUME = {21},
NUMBER = {1},
EID = {253},
}
Endnote
%0 Journal Article
%A Rautiainen, Mikko
%A Marschall, Tobias
%+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
%T GraphAligner: Rapid and Versatile Sequence-to-Graphalignment :
%G eng
%U http://hdl.handle.net/21.11116/0000-0007-48FA-F
%R 10.1186/s13059-020-02157-2
%7 2020
%D 2020
%J Genome Biology
%V 21
%N 1
%Z sequence number: 253
%I BioMed Central Ltd.
%C London
%@ false
52. Rosser EC, Piper CJM, Matei DE, Blair PA, Rendeiro AF, Orford M, Alber DG, Krausgruber T, Catalan D, Klein N, Manson JJ, Drozdov I, Bock C, Wedderburn LR, Eaton S, Mauri C: Microbiota-Derived Metabolites Suppress Arthritis by Amplifying Aryl-Hydrocarbon Receptor Activation in Regulatory B Cells. Cell Metabolism 2020, 31.
Export
BibTeX
@article{Rosser2020,
TITLE = {Microbiota-Derived Metabolites Suppress Arthritis by Amplifying Aryl-Hydrocarbon Receptor Activation in Regulatory {B} Cells},
AUTHOR = {Rosser, Elizabeth C. and Piper, Christopher J. M. and Matei, Diana E. and Blair, Paul A. and Rendeiro, Andr{\'e} F. and Orford, Michael and Alber, Dagmar G. and Krausgruber, Thomas and Catalan, Diego and Klein, Nigel and Manson, Jessica J. and Drozdov, Ignat and Bock, Christoph and Wedderburn, Lucy R. and Eaton, Simon and Mauri, Claudia},
LANGUAGE = {eng},
ISSN = {1550-4131},
DOI = {10.1016/j.cmet.2020.03.003},
PUBLISHER = {Cell Press},
ADDRESS = {Cambridge, MA},
YEAR = {2020},
DATE = {2020},
JOURNAL = {Cell Metabolism},
VOLUME = {31},
NUMBER = {4},
PAGES = {837--851},
EID = {e10},
}
Endnote
%0 Journal Article
%A Rosser, Elizabeth C.
%A Piper, Christopher J. M.
%A Matei, Diana E.
%A Blair, Paul A.
%A Rendeiro, André F.
%A Orford, Michael
%A Alber, Dagmar G.
%A Krausgruber, Thomas
%A Catalan, Diego
%A Klein, Nigel
%A Manson, Jessica J.
%A Drozdov, Ignat
%A Bock, Christoph
%A Wedderburn, Lucy R.
%A Eaton, Simon
%A Mauri, Claudia
%+ External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
External Organizations
External Organizations
%T Microbiota-Derived Metabolites Suppress Arthritis by Amplifying Aryl-Hydrocarbon Receptor Activation in Regulatory B Cells :
%G eng
%U http://hdl.handle.net/21.11116/0000-0006-97CD-9
%R 10.1016/j.cmet.2020.03.003
%7 2020
%D 2020
%J Cell Metabolism
%O Cell Metabolism
%V 31
%N 4
%& 837
%P 837 - 851
%Z sequence number: e10
%I Cell Press
%C Cambridge, MA
%@ false
53. Scherer M, Nazarov PV, Toth R, Sahay S, Kaoma T, Maurer V, Vedeneev N, Plass C, Lengauer T, Walter J, Lutsik P: Reference-free Deconvolution, Visualization and Interpretation of Complex DNA Methylation Data Using DecompPipeline, MeDeCom and FactorViz. Nature Protocols 2020, 15.
Export
BibTeX
@article{Scherer2020,
TITLE = {Reference-free deconvolution, visualization and interpretation of complex {DNA} methylation data using {DecompPipeline}, {MeDeCom} and {FactorViz}},
AUTHOR = {Scherer, Michael and Nazarov, Petr V. and Toth, Reka and Sahay, Shashwat and Kaoma, Tony and Maurer, Valentin and Vedeneev, Nikita and Plass, Christoph and Lengauer, Thomas and Walter, J{\"o}rn and Lutsik, Pavlo},
LANGUAGE = {eng},
ISSN = {1750-2799},
DOI = {10.1038/s41596-020-0369-6},
PUBLISHER = {Nature Publishing Group},
ADDRESS = {London, UK},
YEAR = {2020},
DATE = {2020},
JOURNAL = {Nature Protocols},
VOLUME = {15},
PAGES = {3240--3263},
}
Endnote
%0 Journal Article
%A Scherer, Michael
%A Nazarov, Petr V.
%A Toth, Reka
%A Sahay, Shashwat
%A Kaoma, Tony
%A Maurer, Valentin
%A Vedeneev, Nikita
%A Plass, Christoph
%A Lengauer, Thomas
%A Walter, Jörn
%A Lutsik, Pavlo
%+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
External Organizations
%T Reference-free Deconvolution, Visualization and Interpretation of Complex DNA Methylation Data Using DecompPipeline, MeDeCom and FactorViz :
%G eng
%U http://hdl.handle.net/21.11116/0000-0007-2C58-6
%R 10.1038/s41596-020-0369-6
%7 2020
%D 2020
%J Nature Protocols
%O Nat. Protoc.
%V 15
%& 3240
%P 3240 - 3263
%I Nature Publishing Group
%C London, UK
%@ false
54. Scherer M, Nebel A, Franke A, Walter J, Lengauer T, Bock C, Müller F, List M: Quantitative Comparison of Within-Sample Heterogeneity Scores for DNA Methylation Data. Nucleic Acids Research (London) 2020, 48.
Export
BibTeX
@article{Scherer2020b,
TITLE = {Quantitative comparison of within-sample heterogeneity scores for {DNA} methylation data},
AUTHOR = {Scherer, Michael and Nebel, Almut and Franke, Andre and Walter, J{\"o}rn and Lengauer, Thomas and Bock, Christoph and M{\"u}ller, Fabian and List, Markus},
LANGUAGE = {eng},
ISSN = {0305-1048},
DOI = {10.1093/nar/gkaa120},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford},
YEAR = {2020},
DATE = {2020},
JOURNAL = {Nucleic Acids Research (London)},
VOLUME = {48},
NUMBER = {8},
EID = {e46},
}
Endnote
%0 Journal Article
%A Scherer, Michael
%A Nebel, Almut
%A Franke, Andre
%A Walter, Jörn
%A Lengauer, Thomas
%A Bock, Christoph
%A Müller, Fabian
%A List, Markus
%+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
External Organizations
%T Quantitative Comparison of Within-Sample Heterogeneity Scores for DNA Methylation Data :
%G eng
%U http://hdl.handle.net/21.11116/0000-0006-95B9-1
%R 10.1093/nar/gkaa120
%2 PMC7192612
%7 2020
%D 2020
%J Nucleic Acids Research (London)
%O Nucleic Acids Res
%V 48
%N 8
%Z sequence number: e46
%I Oxford University Press
%C Oxford
%@ false
55. Schmidt F, Kern F, Schulz MH: Integrative Prediction of Gene Expression with Chromatin Accessibility and Conformation Data. Epigenetics & Chromatin 2020, 13.
Export
BibTeX
@article{Schmidt_Kern_Schulz2020,
TITLE = {Integrative Prediction of Gene Expression with Chromatin Accessibility and Conformation Data},
AUTHOR = {Schmidt, Florian and Kern, Fabian and Schulz, Marcel Holger},
LANGUAGE = {eng},
DOI = {10.1186/s13072-020-0327-0},
PUBLISHER = {BioMed Central},
ADDRESS = {London},
YEAR = {2020},
JOURNAL = {Epigenetics \& Chromatin},
VOLUME = {13},
EID = {4},
}
Endnote
%0 Journal Article
%A Schmidt, Florian
%A Kern, Fabian
%A Schulz, Marcel Holger
%+ External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
%T Integrative Prediction of Gene Expression with Chromatin Accessibility and Conformation Data :
%G eng
%U http://hdl.handle.net/21.11116/0000-0006-8E63-B
%R 10.1186/s13072-020-0327-0
%2 PMC7003490
%7 2020
%D 2020
%J Epigenetics & Chromatin
%V 13
%Z sequence number: 4
%I BioMed Central
%C London
56. Schrinner SD, Mari RS, Ebler J, Rautiainen M, Seillier L, Reimer JJ, Usadel B, Marschall T, Klau GW: Haplotype Threading: Accurate Polyploid Phasing from Long Reads. Genome Biology 2020, 21.
Export
BibTeX
@article{Schrinner2020,
TITLE = {Haplotype threading: {A}ccurate polyploid phasing from long reads},
AUTHOR = {Schrinner, Sven D. and Mari, Rebecca Serra and Ebler, Jana and Rautiainen, Mikko and Seillier, Lancelot and Reimer, Julia J. and Usadel, Bjoern and Marschall, Tobias and Klau, Gunnar W.},
LANGUAGE = {eng},
ISSN = {1465-6906},
DOI = {10.1186/s13059-020-02158-1},
PUBLISHER = {BioMed Central Ltd.},
ADDRESS = {London},
YEAR = {2020},
JOURNAL = {Genome Biology},
VOLUME = {21},
NUMBER = {1},
EID = {252},
}
Endnote
%0 Journal Article
%A Schrinner, Sven D.
%A Mari, Rebecca Serra
%A Ebler, Jana
%A Rautiainen, Mikko
%A Seillier, Lancelot
%A Reimer, Julia J.
%A Usadel, Bjoern
%A Marschall, Tobias
%A Klau, Gunnar W.
%+ 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 Haplotype Threading: Accurate Polyploid Phasing from Long Reads :
%G eng
%U http://hdl.handle.net/21.11116/0000-0007-3619-1
%R 10.1186/s13059-020-02158-1
%7 2020
%D 2020
%J Genome Biology
%V 21
%N 1
%Z sequence number: 252
%I BioMed Central Ltd.
%C London
%@ false
57. Shafin K, Pesout T, Lorig-Roach R, Haukness M, Olsen HE, Bosworth C, Armstrong J, Tigyi K, Maurer N, Koren S, Sedlazeck FJ, Marschall T, Mayes S, Costa V, Zook JM, Liu KJ, Kilburn D, Sorensen M, Munson KM, Vollger MR, Monlong J, Garrison E, Eichler EE, Salama S, Haussler D, Green RE, Akeson M, Phillippy A, Miga KH, Carnevali P, et al.: Nanopore Sequencing and the Shasta Toolkit Enable Efficient de novo Assembly of Eleven Human Genomes. Nature Biotechnology 2020, 38.
Export
BibTeX
@article{Shafin2020,
TITLE = {Nanopore sequencing and the {Shasta} toolkit enable efficient de novo assembly of eleven human genomes},
AUTHOR = {Shafin, Kishwar and Pesout, Trevor and Lorig-Roach, Ryan and Haukness, Marina and Olsen, Hugh E. and Bosworth, Colleen and Armstrong, Joel and Tigyi, Kristof and Maurer, Nicholas and Koren, Sergey and Sedlazeck, Fritz J. and Marschall, Tobias and Mayes, Simon and Costa, Vania and Zook, Justin M. and Liu, Kelvin J. and Kilburn, Duncan and Sorensen, Melanie and Munson, Katy M. and Vollger, Mitchell R. and Monlong, Jean and Garrison, Erik and Eichler, Evan E. and Salama, Sofie and Haussler, David and Green, Richard E. and Akeson, Mark and Phillippy, Adam and Miga, Karen H. and Carnevali, Paolo and Jain, Miten and Paten, Benedict},
LANGUAGE = {eng},
ISSN = {1087-0156},
DOI = {10.1038/s41587-020-0503-6},
PUBLISHER = {Gale Group Inc.},
ADDRESS = {New York},
YEAR = {2020},
JOURNAL = {Nature Biotechnology},
VOLUME = {38},
PAGES = {1044--1053},
}
Endnote
%0 Journal Article
%A Shafin, Kishwar
%A Pesout, Trevor
%A Lorig-Roach, Ryan
%A Haukness, Marina
%A Olsen, Hugh E.
%A Bosworth, Colleen
%A Armstrong, Joel
%A Tigyi, Kristof
%A Maurer, Nicholas
%A Koren, Sergey
%A Sedlazeck, Fritz J.
%A Marschall, Tobias
%A Mayes, Simon
%A Costa, Vania
%A Zook, Justin M.
%A Liu, Kelvin J.
%A Kilburn, Duncan
%A Sorensen, Melanie
%A Munson, Katy M.
%A Vollger, Mitchell R.
%A Monlong, Jean
%A Garrison, Erik
%A Eichler, Evan E.
%A Salama, Sofie
%A Haussler, David
%A Green, Richard E.
%A Akeson, Mark
%A Phillippy, Adam
%A Miga, Karen H.
%A Carnevali, Paolo
%A Jain, Miten
%A Paten, Benedict
%+ 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
%T Nanopore Sequencing and the Shasta Toolkit Enable Efficient de novo Assembly of Eleven Human Genomes :
%G eng
%U http://hdl.handle.net/21.11116/0000-0006-8DD2-E
%R 10.1038/s41587-020-0503-6
%7 2020
%D 2020
%J Nature Biotechnology
%V 38
%& 1044
%P 1044 - 1053
%I Gale Group Inc.
%C New York
%@ false
58. Shanta O, Noor A, Sebat J, Chaisson MJP, Sanders AD, Zhao X, Malhotra A, Porubsky D, Rausch T, Gardner EJ, Rodriguez OL, Guo L, Collins RL, Fan X, Wen J, Handsaker RE, Fairley S, Kronenberg ZN, Kong X, Hormozdiari F, Lee D, Wenger AM, Hastie AR, Antaki D, Anantharaman T, Audano PA, Brand H, Cantsilieris S, Cao H, Cerveira E, et al.: The Effects of Common Structural Variants on 3D Chromatin Structure. BMC Genomics 2020, 21.
Export
BibTeX
@article{Shanta2020,
TITLE = {The Effects of Common Structural Variants on {3D} Chromatin Structure},
AUTHOR = {Shanta, Omar and Noor, Amina and Sebat, Jonathan and Chaisson, Mark J. P. and Sanders, Ashley D. and Zhao, Xuefang and Malhotra, Ankit and Porubsky, David and Rausch, Tobias and Gardner, Eugene J. and Rodriguez, Oscar L. and Guo, Li and Collins, Ryan L. and Fan, Xian and Wen, Jia and Handsaker, Robert E. and Fairley, Susan and Kronenberg, Zev N. and Kong, Xiangmeng and Hormozdiari, Fereydoun and Lee, Dillon and Wenger, Aaron M. and Hastie, Alex R. and Antaki, Danny and Anantharaman, Thomas and Audano, Peter A. and Brand, Harrison and Cantsilieris, Stuart and Cao, Han and Cerveira, Eliza and Chen, Chong and Chen, Xintong and Chin, Chen-Shan and Chong, Zechen and Chuang, Nelson T. and Lambert, Christine C. and Church, Deanna M. and Clarke, Laura and Farrell, Andrew and Flores, Joey and Galeey, Timur and Gujral, Madhusudan and Guryev, Victor and Heaton, William Haynes and Korlach, Jonas and Kumar, Sushant and Kwon, Jee Young and Lam, Ernest T. and Lee, Jong Eun and Lee, Joyce and Lee, Wan-Ping and Lee, Sau Peng and Li, Shantao and Marks, Patrick and Viaud-Martinez, Karine and Meiers, Sascha and Munson, Katherine M. and Navarro, Fabio C. P. and Nelson, Bradley J. and Nodzak, Conor and Kyriazopoulou-Panagiotopoulou, Sofia and Pang, Andy W. C. and Rosanio, Gabriel and Ryan, Mallory and Stuetz, Adrian and Spierings, Diana C. J. and Ward, Alistair and Welch, Anne Marie E. and Xiao, Ming and Xu, Wei and Zhang, Chengsheng and Zhu, Qihui and Zheng-Bradley, Xiangqun and Lowy, Ernesto and Yakneen, Sergei and McCarroll, Steven and Jun, Goo and Ding, Li and Koh, Chong Lek and Flicek, Paul and Chen, Ken and Gerstein, Mark B. and Kwok, Pui-Yan and Lansdorp, Peter M. and Marth, Gabor T. and Shi, Xinghua and Bashir, Ali and Ye, Kai and Devine, Scott E. and Talkowski, Michael E. and Mills, Ryan E. and Marschall, Tobias and Korbel, Jan O. and Eichler, Evan E. and Lee, Charles and {HGSVC}},
LANGUAGE = {eng},
ISSN = {1471-2164},
DOI = {10.1186/s12864-020-6516-1},
PUBLISHER = {BioMed Central},
YEAR = {2020},
JOURNAL = {BMC Genomics},
VOLUME = {21},
NUMBER = {1},
EID = {95},
}
Endnote
%0 Journal Article
%A Shanta, Omar
%A Noor, Amina
%A Sebat, Jonathan
%A Chaisson, Mark J. P.
%A Sanders, Ashley D.
%A Zhao, Xuefang
%A Malhotra, Ankit
%A Porubsky, David
%A Rausch, Tobias
%A Gardner, Eugene J.
%A Rodriguez, Oscar L.
%A Guo, Li
%A Collins, Ryan L.
%A Fan, Xian
%A Wen, Jia
%A Handsaker, Robert E.
%A Fairley, Susan
%A Kronenberg, Zev N.
%A Kong, Xiangmeng
%A Hormozdiari, Fereydoun
%A Lee, Dillon
%A Wenger, Aaron M.
%A Hastie, Alex R.
%A Antaki, Danny
%A Anantharaman, Thomas
%A Audano, Peter A.
%A Brand, Harrison
%A Cantsilieris, Stuart
%A Cao, Han
%A Cerveira, Eliza
%A Chen, Chong
%A Chen, Xintong
%A Chin, Chen-Shan
%A Chong, Zechen
%A Chuang, Nelson T.
%A Lambert, Christine C.
%A Church, Deanna M.
%A Clarke, Laura
%A Farrell, Andrew
%A Flores, Joey
%A Galeey, Timur
%A Gujral, Madhusudan
%A Guryev, Victor
%A Heaton, William Haynes
%A Korlach, Jonas
%A Kumar, Sushant
%A Kwon, Jee Young
%A Lam, Ernest T.
%A Lee, Jong Eun
%A Lee, Joyce
%A Lee, Wan-Ping
%A Lee, Sau Peng
%A Li, Shantao
%A Marks, Patrick
%A Viaud-Martinez, Karine
%A Meiers, Sascha
%A Munson, Katherine M.
%A Navarro, Fabio C. P.
%A Nelson, Bradley J.
%A Nodzak, Conor
%A Kyriazopoulou-Panagiotopoulou, Sofia
%A Pang, Andy W. C.
%A Rosanio, Gabriel
%A Ryan, Mallory
%A Stuetz, Adrian
%A Spierings, Diana C. J.
%A Ward, Alistair
%A Welch, Anne Marie E.
%A Xiao, Ming
%A Xu, Wei
%A Zhang, Chengsheng
%A Zhu, Qihui
%A Zheng-Bradley, Xiangqun
%A Lowy, Ernesto
%A Yakneen, Sergei
%A McCarroll, Steven
%A Jun, Goo
%A Ding, Li
%A Koh, Chong Lek
%A Flicek, Paul
%A Chen, Ken
%A Gerstein, Mark B.
%A Kwok, Pui-Yan
%A Lansdorp, Peter M.
%A Marth, Gabor T.
%A Shi, Xinghua
%A Bashir, Ali
%A Ye, Kai
%A Devine, Scott E.
%A Talkowski, Michael E.
%A Mills, Ryan E.
%A Marschall, Tobias
%A Korbel, Jan O.
%A Eichler, Evan E.
%A Lee, Charles
%A HGSVC,
%+ External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
External Organizations
External Organizations
%T The Effects of Common Structural Variants on 3D Chromatin Structure :
%G eng
%U http://hdl.handle.net/21.11116/0000-0006-8E73-9
%R 10.1186/s12864-020-6516-1
%7 2020
%D 2020
%J BMC Genomics
%V 21
%N 1
%Z sequence number: 95
%I BioMed Central
%@ false
59. Srikakulam SK, Bastys T, Kalinina OV: A Shift of Dynamic Equilibrium between the KIT Active and Inactive States Causes Drug Resistance. Proteins: Structure, Function, and Bioinformatics 2020, 88.
Export
BibTeX
@article{Srikakulam2020,
TITLE = {A shift of dynamic equilibrium between the {KIT} active and inactive states causes drug resistance},
AUTHOR = {Srikakulam, Sanjay K. and Bastys, Tomas and Kalinina, Olga V.},
LANGUAGE = {eng},
ISSN = {0887-3585},
DOI = {10.1002/prot.25963},
PUBLISHER = {John Wiley \& Sons},
ADDRESS = {New York, NY},
YEAR = {2020},
JOURNAL = {Proteins: Structure, Function, and Bioinformatics},
VOLUME = {88},
NUMBER = {11},
PAGES = {1434--1446},
}
Endnote
%0 Journal Article
%A Srikakulam, Sanjay K.
%A Bastys, Tomas
%A Kalinina, Olga V.
%+ External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
%T A Shift of Dynamic Equilibrium between the KIT Active and Inactive States Causes Drug Resistance :
%G eng
%U http://hdl.handle.net/21.11116/0000-0006-B96C-1
%R 10.1002/prot.25963
%7 2020
%D 2020
%J Proteins: Structure, Function, and Bioinformatics
%V 88
%N 11
%& 1434
%P 1434 - 1446
%I John Wiley & Sons
%C New York, NY
%@ false
60. Swoboda A, Soukup R, Eckel O, Kinslechner K, Wingelhofer B, Schoerghofer D, Sternberg C, Pham HTT, Vallianou M, Horvath J, Stoiber D, Kenner L, Larue L, Poli V, Beermann F, Yokota T, Kubicek S, Krausgruber T, Rendeiro AF, Bock C, Zenz R, Kovacic B, Aberger F, Hengstschlaeger M, Petzelbauer P, Mikula M, Moriggl R: STAT3 Promotes Melanoma Metastasis by CEBP-induced Repression of the MITF Pathway. Oncogene 2020.
Export
BibTeX
@article{Swoboda2020,
TITLE = {{STAT3} promotes melanoma metastasis by {CEBP}-induced repression of the {MITF} pathway},
AUTHOR = {Swoboda, Alexander and Soukup, Robert and Eckel, Oliver and Kinslechner, Katharina and Wingelhofer, Bettina and Schoerghofer, David and Sternberg, Christina and Pham, Ha T. T. and Vallianou, Maria and Horvath, Jaqueline and Stoiber, Dagmar and Kenner, Lukas and Larue, Lionel and Poli, Valeria and Beermann, Friedrich and Yokota, Takashi and Kubicek, Stefan and Krausgruber, Thomas and Rendeiro, Andre F. and Bock, Christoph and Zenz, Rainer and Kovacic, Boris and Aberger, Fritz and Hengstschlaeger, Markus and Petzelbauer, Peter and Mikula, Mario and Moriggl, Richard},
LANGUAGE = {eng},
ISSN = {1476-5594},
DOI = {10.1038/s41388-020-01584-6},
PUBLISHER = {NPG},
ADDRESS = {New York, NY},
YEAR = {2020},
JOURNAL = {Oncogene},
}
Endnote
%0 Journal Article
%A Swoboda, Alexander
%A Soukup, Robert
%A Eckel, Oliver
%A Kinslechner, Katharina
%A Wingelhofer, Bettina
%A Schoerghofer, David
%A Sternberg, Christina
%A Pham, Ha T. T.
%A Vallianou, Maria
%A Horvath, Jaqueline
%A Stoiber, Dagmar
%A Kenner, Lukas
%A Larue, Lionel
%A Poli, Valeria
%A Beermann, Friedrich
%A Yokota, Takashi
%A Kubicek, Stefan
%A Krausgruber, Thomas
%A Rendeiro, Andre F.
%A Bock, Christoph
%A Zenz, Rainer
%A Kovacic, Boris
%A Aberger, Fritz
%A Hengstschlaeger, Markus
%A Petzelbauer, Peter
%A Mikula, Mario
%A Moriggl, Richard
%+ External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
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 STAT3 Promotes Melanoma Metastasis by CEBP-induced Repression of the MITF Pathway :
%G eng
%U http://hdl.handle.net/21.11116/0000-0007-A6A2-6
%R 10.1038/s41388-020-01584-6
%7 2020
%D 2020
%J Oncogene
%I NPG
%C New York, NY
%@ false
61. Szymczak S, Dose J, Torres GG, Heinsen F-A, Venkatesh G, Datlinger P, Nygaard M, Mengel-From J, Flachsbart F, Klapper W, Christensen K, Lieb W, Schreiber S, Häsler R, Bock C, Franke A, Nebel A: DNA Methylation QTL Analysis Identifies New Regulators of Human Longevity. Human Molecular Genetics 2020, 29.
Export
BibTeX
@article{Szymczak2020,
TITLE = {{DNA} methylation {QTL} analysis identifies new regulators of human longevity},
AUTHOR = {Szymczak, Silke and Dose, Janina and Torres, Guillermo G. and Heinsen, Femke-Anouska and Venkatesh, Geetha and Datlinger, Paul and Nygaard, Marianne and Mengel-From, Jonas and Flachsbart, Friederike and Klapper, Wolfram and Christensen, Kaare and Lieb, Wolfgang and Schreiber, Stefan and H{\"a}sler, Robert and Bock, Christoph and Franke, Andre and Nebel, Almut},
LANGUAGE = {eng},
ISSN = {0964-6906},
DOI = {10.1093/hmg/ddaa033},
PUBLISHER = {IRL Press},
ADDRESS = {Oxford, England},
YEAR = {2020},
DATE = {2020},
JOURNAL = {Human Molecular Genetics},
VOLUME = {29},
NUMBER = {7},
PAGES = {1154--1167},
}
Endnote
%0 Journal Article
%A Szymczak, Silke
%A Dose, Janina
%A Torres, Guillermo G.
%A Heinsen, Femke-Anouska
%A Venkatesh, Geetha
%A Datlinger, Paul
%A Nygaard, Marianne
%A Mengel-From, Jonas
%A Flachsbart, Friederike
%A Klapper, Wolfram
%A Christensen, Kaare
%A Lieb, Wolfgang
%A Schreiber, Stefan
%A Häsler, Robert
%A Bock, Christoph
%A Franke, Andre
%A Nebel, Almut
%+ External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
External Organizations
%T DNA Methylation QTL Analysis Identifies New Regulators of Human Longevity :
%G eng
%U http://hdl.handle.net/21.11116/0000-0006-A277-D
%R 10.1093/hmg/ddaa033
%2 PMC7206852
%7 2020
%D 2020
%J Human Molecular Genetics
%V 29
%N 7
%& 1154
%P 1154 - 1167
%I IRL Press
%C Oxford, England
%@ false
62. Ulz P, Perakis S, Zhou Q, Moser T, Belic J, Lazzeri I, Woelfler A, Zebisch A, Gerger A, Pristauz G, Petru E, White B, Roberts CES, St Johns J, Schimek MG, Geigl JB, Bauernhofer T, Sill H, Bock C, Heitzer E, Speicher MR: Publisher Correction: Inference of Transcription Factor Binding from Cell-free DNA Enables Tumor Subtype Prediction and Early Detection. Nature Communications 2020, 11.
Export
BibTeX
@article{Ulz_2020,
TITLE = {Publisher Correction: {Inference} of Transcription Factor Binding from Cell-free {DNA} Enables Tumor Subtype Prediction and Early Detection},
AUTHOR = {Ulz, Peter and Perakis, Samantha and Zhou, Qing and Moser, Tina and Belic, Jelena and Lazzeri, Isaac and Woelfler, Albert and Zebisch, Armin and Gerger, Armin and Pristauz, Gunda and Petru, Edgar and White, Brandon and Roberts, Charles E. S. and St Johns, John and Schimek, Michael G. and Geigl, Jochen B. and Bauernhofer, Thomas and Sill, Heinz and Bock, Christoph and Heitzer, Ellen and Speicher, Michael R.},
LANGUAGE = {eng},
ISSN = {2041-1723},
DOI = {10.1038/s41467-020-15799-4},
PUBLISHER = {Nature Publishing Group},
ADDRESS = {London},
YEAR = {2020},
DATE = {2020},
JOURNAL = {Nature Communications},
VOLUME = {11},
EID = {1965},
}
Endnote
%0 Journal Article
%A Ulz, Peter
%A Perakis, Samantha
%A Zhou, Qing
%A Moser, Tina
%A Belic, Jelena
%A Lazzeri, Isaac
%A Woelfler, Albert
%A Zebisch, Armin
%A Gerger, Armin
%A Pristauz, Gunda
%A Petru, Edgar
%A White, Brandon
%A Roberts, Charles E. S.
%A St Johns, John
%A Schimek, Michael G.
%A Geigl, Jochen B.
%A Bauernhofer, Thomas
%A Sill, Heinz
%A Bock, Christoph
%A Heitzer, Ellen
%A Speicher, Michael R.
%+ External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
External Organizations
%T Publisher Correction: Inference of Transcription Factor Binding from Cell-free DNA Enables Tumor Subtype Prediction and Early Detection :
%G eng
%U http://hdl.handle.net/21.11116/0000-0006-99C3-1
%R 10.1038/s41467-020-15799-4
%2 PMC7170910
%7 2020
%D 2020
%J Nature Communications
%O Nat. Commun.
%V 11
%Z sequence number: 1965
%I Nature Publishing Group
%C London
%@ false
2019
63. Ahmad M, Helms V, Kalinina OV, Lengauer T: Relative Principal Components Analysis: Application to Analyzing Biomolecular Conformational Changes. Journal of Chemical Theory and Computation 2019, 15.
Export
BibTeX
@article{Ahmad2019,
TITLE = {Relative Principal Components Analysis: {A}pplication to Analyzing Biomolecular Conformational Changes},
AUTHOR = {Ahmad, Mazen and Helms, Volkhard and Kalinina, Olga V. and Lengauer, Thomas},
LANGUAGE = {eng},
ISSN = {1549-9618},
DOI = {10.1021/acs.jctc.8b01074},
PUBLISHER = {ACM},
ADDRESS = {Washington, D.C.},
YEAR = {2019},
DATE = {2019},
JOURNAL = {Journal of Chemical Theory and Computation},
VOLUME = {15},
NUMBER = {4},
PAGES = {2166--2178},
}
Endnote
%0 Journal Article
%A Ahmad, Mazen
%A Helms, Volkhard
%A Kalinina, Olga V.
%A Lengauer, Thomas
%+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
%T Relative Principal Components Analysis: Application to Analyzing Biomolecular Conformational Changes :
%G eng
%U http://hdl.handle.net/21.11116/0000-0003-8671-6
%R 10.1021/acs.jctc.8b01074
%2 PMC6728065
%7 2019
%D 2019
%J Journal of Chemical Theory and Computation
%O J. Chem. Theory Comput.
%V 15
%N 4
%& 2166
%P 2166 - 2178
%I ACM
%C Washington, D.C.
%@ false
64. Albrecht F: Analyzing Epigenomic Data in a Large-Scale Context. Universität des Saarlandes; 2019.
Export
BibTeX
@phdthesis{Albrechtdiss2019,
TITLE = {Analyzing Epigenomic Data in a Large-Scale Context},
AUTHOR = {Albrecht, Felipe},
LANGUAGE = {eng},
URL = {urn:nbn:de:bsz:291--ds-300644},
DOI = {10.22028/D291-30064},
SCHOOL = {Universit{\"a}t des Saarlandes},
ADDRESS = {Saarbr{\"u}cken},
YEAR = {2019},
DATE = {2019},
}
Endnote
%0 Thesis
%A Albrecht, Felipe
%Y Lengauer, Thomas
%A referee: Helms, Volkhard
%+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
International Max Planck Research School, MPI for Informatics, Max Planck Society
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
%T Analyzing Epigenomic Data in a Large-Scale Context :
%G eng
%U http://hdl.handle.net/21.11116/0000-0007-714A-7
%R 10.22028/D291-30064
%U urn:nbn:de:bsz:291--ds-300644
%F OTHER: hdl:20.500.11880/28473
%I Universität des Saarlandes
%C Saarbrücken
%D 2019
%P 240 p.
%V phd
%9 phd
%U https://publikationen.sulb.uni-saarland.de/handle/20.500.11880/28473
65. Behjati Ardakani F, Schmidt F, Schulz MH: Predicting Transcription Factor Binding Using Ensemble Random Forest Models. Faculty of 1000 Research 2019, 7.
Export
BibTeX
@article{Behjati2019,
TITLE = {Predicting Transcription Factor Binding Using Ensemble Random Forest Models},
AUTHOR = {Behjati Ardakani, Fatemeh and Schmidt, Florian and Schulz, Marcel Holger},
LANGUAGE = {eng},
ISSN = {2046-1402},
DOI = {10.12688/f1000research.16200.2},
PUBLISHER = {BioMed Central},
ADDRESS = {London},
YEAR = {2019},
JOURNAL = {Faculty of 1000 Research},
VOLUME = {7},
EID = {1603},
}
Endnote
%0 Journal Article
%A Behjati Ardakani, Fatemeh
%A Schmidt, Florian
%A Schulz, Marcel Holger
%+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
%T Predicting Transcription Factor Binding Using Ensemble Random Forest Models :
%G eng
%U http://hdl.handle.net/21.11116/0000-0005-69DC-E
%R 10.12688/f1000research.16200.2
%7 2019
%D 2019
%J Faculty of 1000 Research
%O F1000Research
%V 7
%Z sequence number: 1603
%I BioMed Central
%C London
%@ false
66. Blum A, Khalifa S, Nordstroem K, Simon M, Schulz MH, Schmitt MJ: Transcriptomics of a KDELR1 Knockout Cell Line Reveals Modulated Cell Adhesion Properties. Scientific Reports 2019, 9.
Export
BibTeX
@article{Blum2019,
TITLE = {Transcriptomics of a {KDELR1} Knockout Cell Line Reveals Modulated Cell Adhesion Properties},
AUTHOR = {Blum, Andrea and Khalifa, Saleem and Nordstroem, Karl and Simon, Martin and Schulz, Marcel Holger and Schmitt, Manfred J.},
LANGUAGE = {eng},
ISSN = {2045-2322},
DOI = {10.1038/s41598-019-47027-5},
PUBLISHER = {Nature Publishing Group},
ADDRESS = {London, UK},
YEAR = {2019},
JOURNAL = {Scientific Reports},
VOLUME = {9},
EID = {10611},
}
Endnote
%0 Journal Article
%A Blum, Andrea
%A Khalifa, Saleem
%A Nordstroem, Karl
%A Simon, Martin
%A Schulz, Marcel Holger
%A Schmitt, Manfred J.
%+ External Organizations
External Organizations
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
%T Transcriptomics of a KDELR1 Knockout Cell Line Reveals Modulated Cell Adhesion Properties :
%G eng
%U http://hdl.handle.net/21.11116/0000-0004-8320-3
%R 10.1038/s41598-019-47027-5
%7 2019
%D 2019
%J Scientific Reports
%O Sci. Rep.
%V 9
%Z sequence number: 10611
%I Nature Publishing Group
%C London, UK
%@ false
67. Chaisson MJP, Sanders AD, Zhao X, Malhotra A, Porubsky D, Rausch T, Gardner EJ, Rodriguez OL, Guo L, Collins RL, Fan X, Wen J, Handsaker RE, Fairley S, Kronenberg ZN, Kong X, Hormozdiari F, Lee D, Wenger AM, Hastie AR, Antaki D, Anantharaman T, Audano PA, Brand H, Cantsilieris S, Cao H, Cerveira E, Chen C, Chen X, Chin C-S, et al.: Multi-platform Discovery of Haplotype-resolved Structural Variation in Human Genomes. Nature Communications 2019, 10.
Export
BibTeX
@article{Chaisson2019,
TITLE = {Multi-platform Discovery of Haplotype-resolved Structural Variation in Human Genomes},
AUTHOR = {Chaisson, Mark J. P. and Sanders, Ashley D. and Zhao, Xuefang and Malhotra, Ankit and Porubsky, David and Rausch, Tobias and Gardner, Eugene J. and Rodriguez, Oscar L. and Guo, Li and Collins, Ryan L. and Fan, Xian and Wen, Jia and Handsaker, Robert E. and Fairley, Susan and Kronenberg, Zev N. and Kong, Xiangmeng and Hormozdiari, Fereydoun and Lee, Dillon and Wenger, Aaron M. and Hastie, Alex R. and Antaki, Danny and Anantharaman, Thomas and Audano, Peter A. and Brand, Harrison and Cantsilieris, Stuart and Cao, Han and Cerveira, Eliza and Chen, Chong and Chen, Xintong and Chin, Chen-Shan and Chong, Zechen and Chuang, Nelson T. and Lambert, Christine C. and Church, Deanna M. and Clarke, Laura and Farrell, Andrew and Flores, Joey and Galeev, Timur and Gorkin, David U. and Gujral, Madhusudan and Guryev, Victor and Heaton, William Haynes and Korlach, Jonas and Kumar, Sushant and Kwon, Jee Young and Lam, Ernest T. and Lee, Jong Eun and Lee, Joyce and Lee, Wan-Ping and Lee, Sau Peng and Li, Shantao and Marks, Patrick and Viaud-Martinez, Karine and Meiers, Sascha and Munson, Katherine M. and Navarro, Fabio C. P. and Nelson, Bradley J. and Nodzak, Conor and Noor, Amina and Kyriazopoulou-Panagiotopoulou, Sofia and Pang, Andy W. C. and Qiu, Yunjiang and Rosanio, Gabriel and Ryan, Mallory and Stuetz, Adrian and Spierings, Diana C. J. and Ward, Alistair and Welch, AnneMarie E. and Xiao, Ming and Xu, Wei and Zhang, Chengsheng and Zhu, Qihui and Zheng-Bradley, Xiangqun and Lowy, Ernesto and Yakneen, Sergei and McCarroll, Steven and Jun, Goo and Ding, Li and Koh, Chong Lek and Ren, Bing and Flicek, Paul and Chen, Ken and Gerstein, Mark B. and Kwok, Pui-Yan and Lansdorp, Peter M. and Marth, Gabor T. and Sebat, Jonathan and Shi, Xinghua and Bashir, Ali and Ye, Kai and Devine, Scott E. and Talkowski, Michael E. and Mills, Ryan E. and Marschall, Tobias and Korbel, Jan O. and Eichler, Evan E. and Lee, Charles},
LANGUAGE = {eng},
ISSN = {2041-1723},
DOI = {10.1038/s41467-018-08148-z},
PUBLISHER = {Nature Publishing Group},
ADDRESS = {London},
YEAR = {2019},
JOURNAL = {Nature Communications},
VOLUME = {10},
EID = {1784},
}
Endnote
%0 Journal Article
%A Chaisson, Mark J. P.
%A Sanders, Ashley D.
%A Zhao, Xuefang
%A Malhotra, Ankit
%A Porubsky, David
%A Rausch, Tobias
%A Gardner, Eugene J.
%A Rodriguez, Oscar L.
%A Guo, Li
%A Collins, Ryan L.
%A Fan, Xian
%A Wen, Jia
%A Handsaker, Robert E.
%A Fairley, Susan
%A Kronenberg, Zev N.
%A Kong, Xiangmeng
%A Hormozdiari, Fereydoun
%A Lee, Dillon
%A Wenger, Aaron M.
%A Hastie, Alex R.
%A Antaki, Danny
%A Anantharaman, Thomas
%A Audano, Peter A.
%A Brand, Harrison
%A Cantsilieris, Stuart
%A Cao, Han
%A Cerveira, Eliza
%A Chen, Chong
%A Chen, Xintong
%A Chin, Chen-Shan
%A Chong, Zechen
%A Chuang, Nelson T.
%A Lambert, Christine C.
%A Church, Deanna M.
%A Clarke, Laura
%A Farrell, Andrew
%A Flores, Joey
%A Galeev, Timur
%A Gorkin, David U.
%A Gujral, Madhusudan
%A Guryev, Victor
%A Heaton, William Haynes
%A Korlach, Jonas
%A Kumar, Sushant
%A Kwon, Jee Young
%A Lam, Ernest T.
%A Lee, Jong Eun
%A Lee, Joyce
%A Lee, Wan-Ping
%A Lee, Sau Peng
%A Li, Shantao
%A Marks, Patrick
%A Viaud-Martinez, Karine
%A Meiers, Sascha
%A Munson, Katherine M.
%A Navarro, Fabio C. P.
%A Nelson, Bradley J.
%A Nodzak, Conor
%A Noor, Amina
%A Kyriazopoulou-Panagiotopoulou, Sofia
%A Pang, Andy W. C.
%A Qiu, Yunjiang
%A Rosanio, Gabriel
%A Ryan, Mallory
%A Stuetz, Adrian
%A Spierings, Diana C. J.
%A Ward, Alistair
%A Welch, AnneMarie E.
%A Xiao, Ming
%A Xu, Wei
%A Zhang, Chengsheng
%A Zhu, Qihui
%A Zheng-Bradley, Xiangqun
%A Lowy, Ernesto
%A Yakneen, Sergei
%A McCarroll, Steven
%A Jun, Goo
%A Ding, Li
%A Koh, Chong Lek
%A Ren, Bing
%A Flicek, Paul
%A Chen, Ken
%A Gerstein, Mark B.
%A Kwok, Pui-Yan
%A Lansdorp, Peter M.
%A Marth, Gabor T.
%A Sebat, Jonathan
%A Shi, Xinghua
%A Bashir, Ali
%A Ye, Kai
%A Devine, Scott E.
%A Talkowski, Michael E.
%A Mills, Ryan E.
%A Marschall, Tobias
%A Korbel, Jan O.
%A Eichler, Evan E.
%A Lee, Charles
%+ External Organizations
External Organizations
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
External Organizations
External Organizations
%T Multi-platform Discovery of Haplotype-resolved Structural Variation in Human Genomes :
%G eng
%U http://hdl.handle.net/21.11116/0000-0003-865E-D
%R 10.1038/s41467-018-08148-z
%7 2019
%D 2019
%J Nature Communications
%O Nat. Commun.
%V 10
%Z sequence number: 1784
%I Nature Publishing Group
%C London
%@ false
68. De Luca A, Pezzotti P, Boucher C, Döring M, Incardona F, Kaiser R, Lengauer T, Pfeifer N, Schülter E, Vandamme A-M, Zazzi M, Geretti AM: Clinical Use, Efficacy, and Durability of Maraviroc for Antiretroviral Therapy in Routine Care: A European Survey. PLoS One 2019, 11.
Export
BibTeX
@article{DeLuca_2019,
TITLE = {Clinical Use, Efficacy, and Durability of Maraviroc for Antiretroviral Therapy in Routine Care: {A} European Survey},
AUTHOR = {De Luca, Andrea and Pezzotti, Patrizio and Boucher, Charles and D{\"o}ring, Matthias and Incardona, Francesca and Kaiser, Rolf and Lengauer, Thomas and Pfeifer, Nico and Sch{\"u}lter, Eugen and Vandamme, Anne-Mieke and Zazzi, Maurizio and Geretti, Anna Maria and {EucoHIV Study Group}},
LANGUAGE = {eng},
ISSN = {1932-6203},
DOI = {10.1371/journal.pone.0225381},
PUBLISHER = {Public Library of Science},
ADDRESS = {San Francisco, CA},
YEAR = {2019},
JOURNAL = {PLoS One},
VOLUME = {11},
NUMBER = {14},
EID = {e0225381},
}
Endnote
%0 Journal Article
%A De Luca, Andrea
%A Pezzotti, Patrizio
%A Boucher, Charles
%A Döring, Matthias
%A Incardona, Francesca
%A Kaiser, Rolf
%A Lengauer, Thomas
%A Pfeifer, Nico
%A Schülter, Eugen
%A Vandamme, Anne-Mieke
%A Zazzi, Maurizio
%A Geretti, Anna Maria
%A EucoHIV Study Group,
%+ External Organizations
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
External Organizations
External Organizations
External Organizations
%T Clinical Use, Efficacy, and Durability of Maraviroc for Antiretroviral Therapy in Routine Care: A European Survey :
%G eng
%U http://hdl.handle.net/21.11116/0000-0005-4921-4
%R 10.1371/journal.pone.0225381
%2 PMC6874206
%7 2019
%D 2019
%J PLoS One
%V 11
%N 14
%Z sequence number: e0225381
%I Public Library of Science
%C San Francisco, CA
%@ false
69. Dheghani Amirabad A: From genes to transcripts : integrative modeling and analysis of regulatory networks. Universität des Saarlandes; 2019.
Abstract
Although all the cells in an organism posses the same genome, the regulatory mechanisms lead to highly specific cell types. Elucidating these regulatory mechanisms is a great challenge in systems biology research. Nonetheless, it is known that a large fraction of our genome is comprised of regulatory elements, the precise mechanisms by which different combinations of regulatory elements are involved in controlling gene expression and cell identity are poorly understood. This thesis describes algorithms and approaches for modeling and analysis of different modes of gene regulation. We present POSTIT a novel algorithm for modeling and inferring transcript isoform regulation from transcriptomics and epigenomics data. POSTIT uses multi-task learning with structured-sparsity inducing regularizer to share the regulatory information between isoforms of a gene, which is shown to lead to accurate isoform expression prediction and inference of regulators. Furthermore, it can use isoform expression level and annotation as informative priors for gene expression prediction. Hence, it constitute a novel accurate approach applicable to gene or transcript isoform centric analysis using expression data. In an application to microRNA (miRNA) target prioritization, we demonstrate that it out-competes classical gene centric methods. Moreover, pinpoints important transcription factors and miRNAs that regulate differentially expressed isoforms in any biological system. Competing endogenous RNA (ceRNA) interactions mediated by miRNAs were postulated as an important cellular regulatory network, in which cross-talk between different transcripts involves competition for joint regulators. We developed a novel statistical method, called SPONGE, for large-scale inference of ceRNA networks. In this framework, we designed an efficient empirical p-value computation approach, by sampling from derived null models, which addresses important confounding factors such as sample size, number of involved regulators and strength of correlation. In an application to a large pan-cancer dataset with 31 cancers we discovered protein-coding and non-coding RNAs that are generic ceRNAs in cancer. Finally, we present an integrative analysis of miRNA and protein-based posttranscriptional regulation. We postulate a competitive regulation of the RNAbinding protein IMP2 with miRNAs binding the same RNAs using expression and RNA binding data. This function of IMP2 is relevant in the contribution to disease in the context of adult cellular metabolism. As a summary, in this thesis we have presented a number of different novel approaches for inference and the integrative analysis of regulatory networks that we believe will find wide applicability in the biological sciences.
Export
BibTeX
@phdthesis{Dehghaniphd2019,
TITLE = {From genes to transcripts : integrative modeling and analysis of regulatory networks},
AUTHOR = {Dheghani Amirabad, Azim},
LANGUAGE = {eng},
URL = {urn:nbn:de:bsz:291--ds-286598},
DOI = {10.22028/D291-28659},
SCHOOL = {Universit{\"a}t des Saarlandes},
ADDRESS = {Saarbr{\"u}cken},
YEAR = {2019},
DATE = {2019},
ABSTRACT = {Although all the cells in an organism posses the same genome, the regulatory mechanisms lead to highly specific cell types. Elucidating these regulatory mechanisms is a great challenge in systems biology research. Nonetheless, it is known that a large fraction of our genome is comprised of regulatory elements, the precise mechanisms by which different combinations of regulatory elements are involved in controlling gene expression and cell identity are poorly understood. This thesis describes algorithms and approaches for modeling and analysis of different modes of gene regulation. We present POSTIT a novel algorithm for modeling and inferring transcript isoform regulation from transcriptomics and epigenomics data. POSTIT uses multi-task learning with structured-sparsity inducing regularizer to share the regulatory information between isoforms of a gene, which is shown to lead to accurate isoform expression prediction and inference of regulators. Furthermore, it can use isoform expression level and annotation as informative priors for gene expression prediction. Hence, it constitute a novel accurate approach applicable to gene or transcript isoform centric analysis using expression data. In an application to microRNA (miRNA) target prioritization, we demonstrate that it out-competes classical gene centric methods. Moreover, pinpoints important transcription factors and miRNAs that regulate differentially expressed isoforms in any biological system. Competing endogenous RNA (ceRNA) interactions mediated by miRNAs were postulated as an important cellular regulatory network, in which cross-talk between different transcripts involves competition for joint regulators. We developed a novel statistical method, called SPONGE, for large-scale inference of ceRNA networks. In this framework, we designed an efficient empirical p-value computation approach, by sampling from derived null models, which addresses important confounding factors such as sample size, number of involved regulators and strength of correlation. In an application to a large pan-cancer dataset with 31 cancers we discovered protein-coding and non-coding RNAs that are generic ceRNAs in cancer. Finally, we present an integrative analysis of miRNA and protein-based posttranscriptional regulation. We postulate a competitive regulation of the RNAbinding protein IMP2 with miRNAs binding the same RNAs using expression and RNA binding data. This function of IMP2 is relevant in the contribution to disease in the context of adult cellular metabolism. As a summary, in this thesis we have presented a number of different novel approaches for inference and the integrative analysis of regulatory networks that we believe will find wide applicability in the biological sciences.},
}
Endnote
%0 Thesis
%A Dheghani Amirabad, Azim
%Y Schulz, Marcel
%A referee: Keller, Andreas
%+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
International Max Planck Research School, MPI for Informatics, Max Planck Society
External Organizations
External Organizations
%T From genes to transcripts : integrative modeling and analysis of regulatory networks :
%G eng
%U http://hdl.handle.net/21.11116/0000-0005-438D-1
%R 10.22028/D291-28659
%U urn:nbn:de:bsz:291--ds-286598
%F OTHER: hdl:20.500.11880/27669
%I Universität des Saarlandes
%C Saarbrücken
%D 2019
%P 139 p.
%V phd
%9 phd
%X Although all the cells in an organism posses the same genome, the regulatory mechanisms lead to highly specific cell types. Elucidating these regulatory mechanisms is a great challenge in systems biology research. Nonetheless, it is known that a large fraction of our genome is comprised of regulatory elements, the precise mechanisms by which different combinations of regulatory elements are involved in controlling gene expression and cell identity are poorly understood. This thesis describes algorithms and approaches for modeling and analysis of different modes of gene regulation. We present POSTIT a novel algorithm for modeling and inferring transcript isoform regulation from transcriptomics and epigenomics data. POSTIT uses multi-task learning with structured-sparsity inducing regularizer to share the regulatory information between isoforms of a gene, which is shown to lead to accurate isoform expression prediction and inference of regulators. Furthermore, it can use isoform expression level and annotation as informative priors for gene expression prediction. Hence, it constitute a novel accurate approach applicable to gene or transcript isoform centric analysis using expression data. In an application to microRNA (miRNA) target prioritization, we demonstrate that it out-competes classical gene centric methods. Moreover, pinpoints important transcription factors and miRNAs that regulate differentially expressed isoforms in any biological system. Competing endogenous RNA (ceRNA) interactions mediated by miRNAs were postulated as an important cellular regulatory network, in which cross-talk between different transcripts involves competition for joint regulators. We developed a novel statistical method, called SPONGE, for large-scale inference of ceRNA networks. In this framework, we designed an efficient empirical p-value computation approach, by sampling from derived null models, which addresses important confounding factors such as sample size, number of involved regulators and strength of correlation. In an application to a large pan-cancer dataset with 31 cancers we discovered protein-coding and non-coding RNAs that are generic ceRNAs in cancer. Finally, we present an integrative analysis of miRNA and protein-based posttranscriptional regulation. We postulate a competitive regulation of the RNAbinding protein IMP2 with miRNAs binding the same RNAs using expression and RNA binding data. This function of IMP2 is relevant in the contribution to disease in the context of adult cellular metabolism. As a summary, in this thesis we have presented a number of different novel approaches for inference and the integrative analysis of regulatory networks that we believe will find wide applicability in the biological sciences.
%U https://publikationen.sulb.uni-saarland.de/handle/20.500.11880/27669
70. Di Giacomo AM, Covre A, Finotello F, Rieder D, Danielli R, Sigalotti L, Giannarelli D, Petitprez F, Lacroix L, Valente M, Cutaia O, Fazio C, Amato G, Lazzeri A, Monterisi S, Miracco C, Coral S, Anichini A, Bock C, Nemc A, Oganesian A, Lowder J, Azab M, Fridman WH, Sautes-Fridman C, Trajanoski Z, Maio M: Guadecitabine Plus Ipilimumab in Unresectable Melanoma: The NIBIT-M4 Clinical Trial. Clinical Cancer Research 2019, 25.
Export
BibTeX
@article{Giacomo2019,
TITLE = {Guadecitabine Plus Ipilimumab in Unresectable Melanoma: {T}he {NIBIT-M4} Clinical Trial},
AUTHOR = {Di Giacomo, Anna Maria and Covre, Alessia and Finotello, Francesca and Rieder, Dietmar and Danielli, Riccardo and Sigalotti, Luca and Giannarelli, Diana and Petitprez, Florent and Lacroix, Laetitia and Valente, Monica and Cutaia, Ornella and Fazio, Carolina and Amato, Giovanni and Lazzeri, Andrea and Monterisi, Santa and Miracco, Clelia and Coral, Sandra and Anichini, Andrea and Bock, Christoph and Nemc, Amelie and Oganesian, Aram and Lowder, James and Azab, Mohammad and Fridman, Wolf H. and Sautes-Fridman, Catherine and Trajanoski, Zlatko and Maio, Michele},
LANGUAGE = {eng},
ISSN = {1078-0432},
DOI = {10.1158/1078-0432.CCR-19-1335},
PUBLISHER = {Association for Cancer Research},
ADDRESS = {Denville, NJ},
YEAR = {2019},
DATE = {2019},
JOURNAL = {Clinical Cancer Research},
VOLUME = {25},
NUMBER = {24},
PAGES = {7351--7362},
}
Endnote
%0 Journal Article
%A Di Giacomo, Anna Maria
%A Covre, Alessia
%A Finotello, Francesca
%A Rieder, Dietmar
%A Danielli, Riccardo
%A Sigalotti, Luca
%A Giannarelli, Diana
%A Petitprez, Florent
%A Lacroix, Laetitia
%A Valente, Monica
%A Cutaia, Ornella
%A Fazio, Carolina
%A Amato, Giovanni
%A Lazzeri, Andrea
%A Monterisi, Santa
%A Miracco, Clelia
%A Coral, Sandra
%A Anichini, Andrea
%A Bock, Christoph
%A Nemc, Amelie
%A Oganesian, Aram
%A Lowder, James
%A Azab, Mohammad
%A Fridman, Wolf H.
%A Sautes-Fridman, Catherine
%A Trajanoski, Zlatko
%A Maio, Michele
%+ External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
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
%T Guadecitabine Plus Ipilimumab in Unresectable Melanoma: The NIBIT-M4 Clinical Trial :
%G eng
%U http://hdl.handle.net/21.11116/0000-0006-8E4C-6
%R 10.1158/1078-0432.CCR-19-1335
%7 2019
%D 2019
%J Clinical Cancer Research
%O Clin. Cancer Res.
%V 25
%N 24
%& 7351
%P 7351 - 7362
%I Association for Cancer Research
%C Denville, NJ
%@ false
71. Doncheva NT, Domingues FS, McGivern DR, Shimakami T, Zeuzem S, Lengauer T, Lange CM, Albrecht M, Welsch C: Near-Neighbor Interactions in the NS3-4A Protease of HCV Impact Replicative Fitness of Drug-Resistant Viral Variants. Journal of Molecular Biology 2019, 431.
Export
BibTeX
@article{Doncheva2019,
TITLE = {Near-Neighbor Interactions in the {NS3}-{4A} Protease of {HCV} Impact Replicative Fitness of Drug-Resistant Viral Variants},
AUTHOR = {Doncheva, Nadezhda Tsankova and Domingues, Francisco S. and McGivern, David R. and Shimakami, Tetsuro and Zeuzem, Stefan and Lengauer, Thomas and Lange, Christian M. and Albrecht, Mario and Welsch, Christoph},
LANGUAGE = {eng},
ISSN = {0022-2836},
DOI = {10.1016/j.jmb.2019.04.034},
PUBLISHER = {Elsevier},
ADDRESS = {Amsterdam},
YEAR = {2019},
DATE = {2019},
JOURNAL = {Journal of Molecular Biology},
VOLUME = {431},
NUMBER = {12},
PAGES = {2354--2368},
}
Endnote
%0 Journal Article
%A Doncheva, Nadezhda Tsankova
%A Domingues, Francisco S.
%A McGivern, David R.
%A Shimakami, Tetsuro
%A Zeuzem, Stefan
%A Lengauer, Thomas
%A Lange, Christian M.
%A Albrecht, Mario
%A Welsch, Christoph
%+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
External Organizations
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
%T Near-Neighbor Interactions in the NS3-4A Protease of HCV Impact Replicative Fitness of Drug-Resistant Viral Variants :
%G eng
%U http://hdl.handle.net/21.11116/0000-0004-3FC9-4
%R 10.1016/j.jmb.2019.04.034
%7 2019
%D 2019
%J Journal of Molecular Biology
%O J Mol Biol
%V 431
%N 12
%& 2354
%P 2354 - 2368
%I Elsevier
%C Amsterdam
%@ false
72. Döring M: Computational Approaches for Improving Treatment and Prevention of Viral Infections. Universität des Saarlandes; 2019.
Abstract
The treatment of infections with HIV or HCV is challenging. Thus,<br>novel drugs and new computational approaches that support the<br>selection of therapies are required. This work presents methods that<br>support therapy selection as well as methods that advance novel<br>antiviral treatments.<br>geno2pheno[ngs-freq] identifies drug resistance from HIV-1<br>or HCV samples that were subjected to next-generation sequencing<br>by interpreting their sequences either via support vector machines<br>or a rules-based approach. geno2pheno[coreceptor-hiv2] determines the coreceptor that is used for viral cell entry by analyzing a<br>segment of the HIV-2 surface protein with a support vector machine.<br>openPrimeR is capable of finding optimal combinations of primers<br>for multiplex polymerase chain reaction by solving a set cover problem and accessing a new logistic regression model for determining<br>amplification events arising from polymerase chain reaction.<br>geno2pheno[ngs-freq] and geno2pheno[coreceptorhiv2] enable the personalization of antiviral treatments and support<br>clinical decision making. The application of openPrimeR on human<br>immunoglobulin sequences has resulted in novel primer sets that<br>improve the isolation of broadly neutralizing antibodies against<br>HIV-1. The methods that were developed in this work thus constitute<br>important contributions towards improving the prevention and<br>treatment of viral infectious diseases.
Export
BibTeX
@phdthesis{Doringphd2013,
TITLE = {Computational Approaches for Improving Treatment and Prevention of Viral Infections},
AUTHOR = {D{\"o}ring, Matthias},
LANGUAGE = {eng},
URL = {urn:nbn:de:bsz:291--ds-279468},
DOI = {10.22028/D291-27946},
SCHOOL = {Universit{\"a}t des Saarlandes},
ADDRESS = {Saarbr{\"u}cken},
YEAR = {2019},
DATE = {2019},
ABSTRACT = {The treatment of infections with HIV or HCV is challenging. Thus,<br>novel drugs and new computational approaches that support the<br>selection of therapies are required. This work presents methods that<br>support therapy selection as well as methods that advance novel<br>antiviral treatments.<br>geno2pheno[ngs-freq] identifies drug resistance from HIV-1<br>or HCV samples that were subjected to next-generation sequencing<br>by interpreting their sequences either via support vector machines<br>or a rules-based approach. geno2pheno[coreceptor-hiv2] determines the coreceptor that is used for viral cell entry by analyzing a<br>segment of the HIV-2 surface protein with a support vector machine.<br>openPrimeR is capable of finding optimal combinations of primers<br>for multiplex polymerase chain reaction by solving a set cover problem and accessing a new logistic regression model for determining<br>amplification events arising from polymerase chain reaction.<br>geno2pheno[ngs-freq] and geno2pheno[coreceptorhiv2] enable the personalization of antiviral treatments and support<br>clinical decision making. The application of openPrimeR on human<br>immunoglobulin sequences has resulted in novel primer sets that<br>improve the isolation of broadly neutralizing antibodies against<br>HIV-1. The methods that were developed in this work thus constitute<br>important contributions towards improving the prevention and<br>treatment of viral infectious diseases.},
}
Endnote
%0 Thesis
%A Döring, Matthias
%Y Pfeifer, Nico
%A referee: Lengauer, Thomas
%A referee: Kalinina, Olga V.
%+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
International Max Planck Research School, MPI for Informatics, Max Planck Society
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
%T Computational Approaches for Improving Treatment and Prevention of Viral Infections :
%G eng
%U http://hdl.handle.net/21.11116/0000-0003-AEBA-8
%R 10.22028/D291-27946
%U urn:nbn:de:bsz:291--ds-279468
%F OTHER: hdl:20.500.11880/27443
%I Universität des Saarlandes
%C Saarbrücken
%D 2019
%P 337 p.
%V phd
%9 phd
%X The treatment of infections with HIV or HCV is challenging. Thus,<br>novel drugs and new computational approaches that support the<br>selection of therapies are required. This work presents methods that<br>support therapy selection as well as methods that advance novel<br>antiviral treatments.<br>geno2pheno[ngs-freq] identifies drug resistance from HIV-1<br>or HCV samples that were subjected to next-generation sequencing<br>by interpreting their sequences either via support vector machines<br>or a rules-based approach. geno2pheno[coreceptor-hiv2] determines the coreceptor that is used for viral cell entry by analyzing a<br>segment of the HIV-2 surface protein with a support vector machine.<br>openPrimeR is capable of finding optimal combinations of primers<br>for multiplex polymerase chain reaction by solving a set cover problem and accessing a new logistic regression model for determining<br>amplification events arising from polymerase chain reaction.<br>geno2pheno[ngs-freq] and geno2pheno[coreceptorhiv2] enable the personalization of antiviral treatments and support<br>clinical decision making. The application of openPrimeR on human<br>immunoglobulin sequences has resulted in novel primer sets that<br>improve the isolation of broadly neutralizing antibodies against<br>HIV-1. The methods that were developed in this work thus constitute<br>important contributions towards improving the prevention and<br>treatment of viral infectious diseases.
%U https://publikationen.sulb.uni-saarland.de/handle/20.500.11880/27443
73. Döring M, Kreer C, Lehnen N, Klein F, Pfeifer N: Modeling the Amplification of Immunoglobulins through Machine Learning on Sequence-Specific Features. Scientific Reports 2019, 9.
Abstract
Successful primer design for polymerase chain reaction (PCR) hinges on the ability to identify primers<br>that efciently amplify template sequences. Here, we generated a novel Taq PCR data set that reports<br>the amplifcation status for pairs of primers and templates from a reference set of 47 immunoglobulin<br>heavy chain variable sequences and 20 primers. Using logistic regression, we developed TMM, a model<br>for predicting whether a primer amplifes a template given their nucleotide sequences. The model<br>suggests that the free energy of annealing, ΔG, is the key driver of amplifcation (p=7.35e-12) and that<br>3′ mismatches should be considered in dependence on ΔG and the mismatch closest to the 3′ terminus<br>(p=1.67e-05). We validated TMM by comparing its estimates with those from the thermodynamic<br>model of DECIPHER (DE) and a model based solely on the free energy of annealing (FE). TMM<br>outperformed the other approaches in terms of the area under the receiver operating characteristic<br>curve (TMM: 0.953, FE: 0.941, DE: 0.896). TMM can improve primer design and is freely available via<br>openPrimeR (http://openPrimeR.mpi-inf.mpg.de).
Export
BibTeX
@article{DoringPfeiferModel,
TITLE = {Modeling the Amplification of Immunoglobulins through Machine Learning on Sequence-Specific Features},
AUTHOR = {D{\"o}ring, Matthias and Kreer, Christoph and Lehnen, Nathalie and Klein, Florian and Pfeifer, Nico},
LANGUAGE = {eng},
ISSN = {2045-2322},
DOI = {10.1038/s41598-019-47173-w},
PUBLISHER = {Nature Publishing Group},
ADDRESS = {London, UK},
YEAR = {2019},
ABSTRACT = {Successful primer design for polymerase chain reaction (PCR) hinges on the ability to identify primers<br>that efciently amplify template sequences. Here, we generated a novel Taq PCR data set that reports<br>the amplifcation status for pairs of primers and templates from a reference set of 47 immunoglobulin<br>heavy chain variable sequences and 20 primers. Using logistic regression, we developed TMM, a model<br>for predicting whether a primer amplifes a template given their nucleotide sequences. The model<br>suggests that the free energy of annealing, $\Delta$G, is the key driver of amplifcation (p=7.35e-12) and that<br>3′ mismatches should be considered in dependence on $\Delta$G and the mismatch closest to the 3′ terminus<br>(p=1.67e-05). We validated TMM by comparing its estimates with those from the thermodynamic<br>model of DECIPHER (DE) and a model based solely on the free energy of annealing (FE). TMM<br>outperformed the other approaches in terms of the area under the receiver operating characteristic<br>curve (TMM: 0.953, FE: 0.941, DE: 0.896). TMM can improve primer design and is freely available via<br>openPrimeR (http://openPrimeR.mpi-inf.mpg.de).},
JOURNAL = {Scientific Reports},
VOLUME = {9},
EID = {10748},
}
Endnote
%0 Journal Article
%A Döring, Matthias
%A Kreer, Christoph
%A Lehnen, Nathalie
%A Klein, Florian
%A Pfeifer, Nico
%+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
%T Modeling the Amplification of Immunoglobulins through Machine
Learning on Sequence-Specific Features :
%G eng
%U http://hdl.handle.net/21.11116/0000-0004-5F56-2
%R 10.1038/s41598-019-47173-w
%7 2019-07-24
%D 2019
%8 24.07.2019
%X Successful primer design for polymerase chain reaction (PCR) hinges on the ability to identify primers<br>that efciently amplify template sequences. Here, we generated a novel Taq PCR data set that reports<br>the amplifcation status for pairs of primers and templates from a reference set of 47 immunoglobulin<br>heavy chain variable sequences and 20 primers. Using logistic regression, we developed TMM, a model<br>for predicting whether a primer amplifes a template given their nucleotide sequences. The model<br>suggests that the free energy of annealing, ΔG, is the key driver of amplifcation (p=7.35e-12) and that<br>3′ mismatches should be considered in dependence on ΔG and the mismatch closest to the 3′ terminus<br>(p=1.67e-05). We validated TMM by comparing its estimates with those from the thermodynamic<br>model of DECIPHER (DE) and a model based solely on the free energy of annealing (FE). TMM<br>outperformed the other approaches in terms of the area under the receiver operating characteristic<br>curve (TMM: 0.953, FE: 0.941, DE: 0.896). TMM can improve primer design and is freely available via<br>openPrimeR (http://openPrimeR.mpi-inf.mpg.de).
%J Scientific Reports
%O Sci. Rep.
%V 9
%Z sequence number: 10748
%I Nature Publishing Group
%C London, UK
%@ false
74. Durai DA, Schulz MH: Improving in-silico Normalization using Read Weights. Scientific Reports 2019, 9.
Export
BibTeX
@article{Durai2019,
TITLE = {Improving in-silico Normalization using Read Weights},
AUTHOR = {Durai, Dilip Ariyur and Schulz, Marcel Holger},
LANGUAGE = {eng},
ISSN = {2045-2322},
DOI = {10.1038/s41598-019-41502-9},
PUBLISHER = {Nature Publishing Group},
ADDRESS = {London, UK},
YEAR = {2019},
JOURNAL = {Scientific Reports},
VOLUME = {9},
EID = {5133},
}
Endnote
%0 Journal Article
%A Durai, Dilip Ariyur
%A Schulz, Marcel Holger
%+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
%T Improving in-silico Normalization using Read Weights :
%G eng
%U http://hdl.handle.net/21.11116/0000-0003-5F5F-A
%R 10.1038/s41598-019-41502-9
%7 2019
%D 2019
%J Scientific Reports
%O Sci. Rep.
%V 9
%Z sequence number: 5133
%I Nature Publishing Group
%C London, UK
%@ false
%U https://doi.org/10.1038/s41598-019-41502-9
75. Ebert P: What We Leave Behind : Reproducibility in Chromatin Analysis within and Across Species. Universität des Saarlandes; 2019.
Abstract
Epigenetics is the field of biology that investigates heritable factors regulating gene expression without being directly encoded in the genome of an organism. The human genome is densely packed inside a cell's nucleus in the form of chromatin. Certain constituents of chromatin play a vital role as epigenetic factors in the dynamic regulation of gene expression. Epigenetic changes on the chromatin level are thus an integral part of the mechanisms governing the development of the functionally diverse cell types in multicellular species such as human. Studying these mechanisms is not only important to understand the biology of healthy cells, but also necessary to comprehend the epigenetic component in the formation of many complex diseases. Modern wet lab technology enables scientists to probe the epigenome with high throughput and in extensive detail. The fast generation of epigenetic datasets burdens computational researchers with the challenge of rapidly performing elaborate analyses without compromising on the scientific reproducibility of the reported findings. To facilitate reproducible computational research in epigenomics, this thesis proposes a task-oriented metadata model, relying on web technology and supported by database engineering, that aims at consistent and human-readable documentation of standardized computational workflows. The suggested approach features, e.g., computational validation of metadata records, automatic error detection, and progress monitoring of multi-step analyses, and was successfully field-tested as part of a large epigenome research consortium. This work leaves aside theoretical considerations, and intentionally emphasizes the realistic need of providing scientists with tools that assist them in performing reproducible research. Irrespective of the technological progress, the dynamic and cell-type specific nature of the epigenome commonly requires restricting the number of analyzed samples due to resource limitations. The second project of this thesis introduces the software tool SCIDDO, which has been developed for the differential chromatin analysis of cellular samples with potentially limited availability. By combining statistics, algorithmics, and best practices for robust software development, SCIDDO can quickly identify biologically meaningful regions of differential chromatin marking between cell types. We demonstrate SCIDDO's usefulness in an exemplary study in which we identify regions that establish a link between chromatin and gene expression changes. SCIDDO's quantitative approach to differential chromatin analysis is user-customizable, providing the necessary flexibility to adapt SCIDDO to specific research tasks. Given the functional diversity of cell types and the dynamics of the epigenome in response to environmental changes, it is hardly realistic to map the complete epigenome even for a single organism like human or mouse. For non-model organisms, e.g., cow, pig, or dog, epigenome data is particularly scarce. The third project of this thesis investigates to what extent bioinformatics methods can compensate for the comparatively little effort that is invested in charting the epigenome of non-model species. This study implements a large integrative analysis pipeline, including state-of-the-art machine learning, to transfer chromatin data for predictive modeling between 13 species. The evidence presented here indicates that a partial regulatory epigenetic signal is stably retained even over millions of years of evolutionary distance between the considered species. This finding suggests complementary and cost-effective ways for bioinformatics to contribute to comparative epigenome analysis across species boundaries.
Export
BibTeX
@phdthesis{Ebertphd2019,
TITLE = {What We Leave Behind : Reproducibility in Chromatin Analysis within and Across Species},
AUTHOR = {Ebert, Peter},
LANGUAGE = {eng},
URL = {urn:nbn:de:bsz:291--ds-278311},
DOI = {10.22028/D291-27831},
SCHOOL = {Universit{\"a}t des Saarlandes},
ADDRESS = {Saarbr{\"u}cken},
YEAR = {2019},
DATE = {2019},
ABSTRACT = {Epigenetics is the field of biology that investigates heritable factors regulating gene expression without being directly encoded in the genome of an organism. The human genome is densely packed inside a cell's nucleus in the form of chromatin. Certain constituents of chromatin play a vital role as epigenetic factors in the dynamic regulation of gene expression. Epigenetic changes on the chromatin level are thus an integral part of the mechanisms governing the development of the functionally diverse cell types in multicellular species such as human. Studying these mechanisms is not only important to understand the biology of healthy cells, but also necessary to comprehend the epigenetic component in the formation of many complex diseases. Modern wet lab technology enables scientists to probe the epigenome with high throughput and in extensive detail. The fast generation of epigenetic datasets burdens computational researchers with the challenge of rapidly performing elaborate analyses without compromising on the scientific reproducibility of the reported findings. To facilitate reproducible computational research in epigenomics, this thesis proposes a task-oriented metadata model, relying on web technology and supported by database engineering, that aims at consistent and human-readable documentation of standardized computational workflows. The suggested approach features, e.g., computational validation of metadata records, automatic error detection, and progress monitoring of multi-step analyses, and was successfully field-tested as part of a large epigenome research consortium. This work leaves aside theoretical considerations, and intentionally emphasizes the realistic need of providing scientists with tools that assist them in performing reproducible research. Irrespective of the technological progress, the dynamic and cell-type specific nature of the epigenome commonly requires restricting the number of analyzed samples due to resource limitations. The second project of this thesis introduces the software tool SCIDDO, which has been developed for the differential chromatin analysis of cellular samples with potentially limited availability. By combining statistics, algorithmics, and best practices for robust software development, SCIDDO can quickly identify biologically meaningful regions of differential chromatin marking between cell types. We demonstrate SCIDDO's usefulness in an exemplary study in which we identify regions that establish a link between chromatin and gene expression changes. SCIDDO's quantitative approach to differential chromatin analysis is user-customizable, providing the necessary flexibility to adapt SCIDDO to specific research tasks. Given the functional diversity of cell types and the dynamics of the epigenome in response to environmental changes, it is hardly realistic to map the complete epigenome even for a single organism like human or mouse. For non-model organisms, e.g., cow, pig, or dog, epigenome data is particularly scarce. The third project of this thesis investigates to what extent bioinformatics methods can compensate for the comparatively little effort that is invested in charting the epigenome of non-model species. This study implements a large integrative analysis pipeline, including state-of-the-art machine learning, to transfer chromatin data for predictive modeling between 13 species. The evidence presented here indicates that a partial regulatory epigenetic signal is stably retained even over millions of years of evolutionary distance between the considered species. This finding suggests complementary and cost-effective ways for bioinformatics to contribute to comparative epigenome analysis across species boundaries.},
}
Endnote
%0 Thesis
%A Ebert, Peter
%Y Lengauer, Thomas
%A referee: Lenhof, Hans-Peter
%A referee: Weikum, Gerhard
%+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
International Max Planck Research School, MPI for Informatics, Max Planck Society
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
Algorithms and Complexity, MPI for Informatics, Max Planck Society
Databases and Information Systems, MPI for Informatics, Max Planck Society
%T What We Leave Behind : Reproducibility in Chromatin Analysis within and Across Species :
%G eng
%U http://hdl.handle.net/21.11116/0000-0003-9ADF-5
%R 10.22028/D291-27831
%U urn:nbn:de:bsz:291--ds-278311
%F OTHER: hdl:20.500.11880/27387
%I Universität des Saarlandes
%C Saarbrücken
%D 2019
%P 152 p.
%V phd
%9 phd
%X Epigenetics is the field of biology that investigates heritable factors regulating gene expression without being directly encoded in the genome of an organism. The human genome is densely packed inside a cell's nucleus in the form of chromatin. Certain constituents of chromatin play a vital role as epigenetic factors in the dynamic regulation of gene expression. Epigenetic changes on the chromatin level are thus an integral part of the mechanisms governing the development of the functionally diverse cell types in multicellular species such as human. Studying these mechanisms is not only important to understand the biology of healthy cells, but also necessary to comprehend the epigenetic component in the formation of many complex diseases. Modern wet lab technology enables scientists to probe the epigenome with high throughput and in extensive detail. The fast generation of epigenetic datasets burdens computational researchers with the challenge of rapidly performing elaborate analyses without compromising on the scientific reproducibility of the reported findings. To facilitate reproducible computational research in epigenomics, this thesis proposes a task-oriented metadata model, relying on web technology and supported by database engineering, that aims at consistent and human-readable documentation of standardized computational workflows. The suggested approach features, e.g., computational validation of metadata records, automatic error detection, and progress monitoring of multi-step analyses, and was successfully field-tested as part of a large epigenome research consortium. This work leaves aside theoretical considerations, and intentionally emphasizes the realistic need of providing scientists with tools that assist them in performing reproducible research. Irrespective of the technological progress, the dynamic and cell-type specific nature of the epigenome commonly requires restricting the number of analyzed samples due to resource limitations. The second project of this thesis introduces the software tool SCIDDO, which has been developed for the differential chromatin analysis of cellular samples with potentially limited availability. By combining statistics, algorithmics, and best practices for robust software development, SCIDDO can quickly identify biologically meaningful regions of differential chromatin marking between cell types. We demonstrate SCIDDO's usefulness in an exemplary study in which we identify regions that establish a link between chromatin and gene expression changes. SCIDDO's quantitative approach to differential chromatin analysis is user-customizable, providing the necessary flexibility to adapt SCIDDO to specific research tasks. Given the functional diversity of cell types and the dynamics of the epigenome in response to environmental changes, it is hardly realistic to map the complete epigenome even for a single organism like human or mouse. For non-model organisms, e.g., cow, pig, or dog, epigenome data is particularly scarce. The third project of this thesis investigates to what extent bioinformatics methods can compensate for the comparatively little effort that is invested in charting the epigenome of non-model species. This study implements a large integrative analysis pipeline, including state-of-the-art machine learning, to transfer chromatin data for predictive modeling between 13 species. The evidence presented here indicates that a partial regulatory epigenetic signal is stably retained even over millions of years of evolutionary distance between the considered species. This finding suggests complementary and cost-effective ways for bioinformatics to contribute to comparative epigenome analysis across species boundaries.
%U https://publikationen.sulb.uni-saarland.de/handle/20.500.11880/27387
76. Ebler J, Haukness M, Pesout T, Marschall T, Paten B: Haplotype-aware Diplotyping from Noisy Long Reads. Genome Biology 2019, 20.
Export
BibTeX
@article{Ebler2019,
TITLE = {Haplotype-aware Diplotyping from Noisy Long Reads},
AUTHOR = {Ebler, Jana and Haukness, Marina and Pesout, Trevor and Marschall, Tobias and Paten, Benedict},
LANGUAGE = {eng},
ISSN = {1465-6906},
DOI = {10.1186/s13059-019-1709-0},
PUBLISHER = {BioMed Central Ltd.},
ADDRESS = {London},
YEAR = {2019},
JOURNAL = {Genome Biology},
VOLUME = {20},
EID = {116},
}
Endnote
%0 Journal Article
%A Ebler, Jana
%A Haukness, Marina
%A Pesout, Trevor
%A Marschall, Tobias
%A Paten, Benedict
%+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
%T Haplotype-aware Diplotyping from Noisy Long Reads :
%G eng
%U http://hdl.handle.net/21.11116/0000-0003-D417-4
%R 10.1186/s13059-019-1709-0
%2 PMC6547545
%7 2019
%D 2019
%J Genome Biology
%V 20
%Z sequence number: 116
%I BioMed Central Ltd.
%C London
%@ false
77. Gérard D, Schmidt F, Ginolhac A, Schmitz M, Halder R, Ebert P, Schulz MH, Sauter T, Sinkkonen L: Temporal Enhancer Profiling of Parallel Lineages Identifies AHR and GLIS1 as Regulators of Mesenchymal Multipotency. Nucleic Acids Research 2019, 47.
Export
BibTeX
@article{Gerard2019,
TITLE = {Temporal enhancer profiling of parallel lineages identifies {AHR} and {GLIS1} as regulators of mesenchymal multipotency},
AUTHOR = {G{\'e}rard, Deborah and Schmidt, Florian and Ginolhac, Aur{\'e}lien and Schmitz, Martine and Halder, Rashi and Ebert, Peter and Schulz, Marcel Holger and Sauter, Thomas and Sinkkonen, Lasse},
LANGUAGE = {eng},
ISSN = {0305-1048},
DOI = {10.1093/nar/gky1240},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford},
YEAR = {2019},
DATE = {2019},
JOURNAL = {Nucleic Acids Research},
VOLUME = {47},
NUMBER = {3},
PAGES = {1141--1163},
}
Endnote
%0 Journal Article
%A Gérard, Deborah
%A Schmidt, Florian
%A Ginolhac, Aurélien
%A Schmitz, Martine
%A Halder, Rashi
%A Ebert, Peter
%A Schulz, Marcel Holger
%A Sauter, Thomas
%A Sinkkonen, Lasse
%+ External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
External Organizations
%T Temporal Enhancer Profiling of Parallel Lineages Identifies AHR and GLIS1 as Regulators of Mesenchymal Multipotency :
%G eng
%U http://hdl.handle.net/21.11116/0000-0003-1AFD-4
%R 10.1093/nar/gky1240
%7 2018
%D 2019
%J Nucleic Acids Research
%O Nucleic Acids Res
%V 47
%N 3
%& 1141
%P 1141 - 1163
%I Oxford University Press
%C Oxford
%@ false
78. Ghaffaari A, Marschall T: Fully-sensitive Seed Finding in Sequence Graphs Using a Hybrid Index. Bioinformatics (Proc ISMB/ECCB 2019) 2019, 35.
Export
BibTeX
@article{Ghaffaari2019,
TITLE = {Fully-sensitive Seed Finding in Sequence Graphs Using a Hybrid Index},
AUTHOR = {Ghaffaari, Ali and Marschall, Tobias},
LANGUAGE = {eng},
ISSN = {1367-4803},
DOI = {10.1093/bioinformatics/btz341},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford},
YEAR = {2019},
DATE = {2019},
JOURNAL = {Bioinformatics (Proc. ISMB/ECCB)},
VOLUME = {35},
NUMBER = {14},
PAGES = {i81--i89},
BOOKTITLE = {ISMB/ECCB 2019 Proceedings},
}
Endnote
%0 Journal Article
%A Ghaffaari, Ali
%A Marschall, Tobias
%+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
%T Fully-sensitive Seed Finding in Sequence Graphs Using a Hybrid Index :
%G eng
%U http://hdl.handle.net/21.11116/0000-0004-7BC8-1
%R 10.1093/bioinformatics/btz341
%7 2019
%D 2019
%J Bioinformatics
%V 35
%N 14
%& i81
%P i81 - i89
%I Oxford University Press
%C Oxford
%@ false
%B ISMB/ECCB 2019 Proceedings
%O ISMB/ECCB 2019 The biennial joint meeting of ISMB (27th Annual Conference on Intelligent Systems for Molecular Biology) and ECCB (18th
European Conference on Computational Biology) ; Basel, Switzerland, July 21–25, 2019
79. Gier S, Simon M, Nordstroem K, Khalifa S, Schulz MH, Schmitt MJ, Breinig F: Transcriptome Kinetics of Saccharomyces cerevisiae in Response to Viral Killer Toxin K1. Frontiers in Microbiology 2019, 10.
Export
BibTeX
@article{Gier2019,
TITLE = {Transcriptome Kinetics of Saccharomyces cerevisiae in Response to Viral Killer Toxin {K1}},
AUTHOR = {Gier, Stefanie and Simon, Martin and Nordstroem, Karl and Khalifa, Salem and Schulz, Marcel Holger and Schmitt, Manfred J. and Breinig, Frank},
LANGUAGE = {eng},
ISSN = {1664-302X},
DOI = {10.3389/fmicb.2019.01102},
PUBLISHER = {Frontiers Media},
ADDRESS = {Lausanne},
YEAR = {2019},
JOURNAL = {Frontiers in Microbiology},
VOLUME = {10},
EID = {1102},
}
Endnote
%0 Journal Article
%A Gier, Stefanie
%A Simon, Martin
%A Nordstroem, Karl
%A Khalifa, Salem
%A Schulz, Marcel Holger
%A Schmitt, Manfred J.
%A Breinig, Frank
%+ External Organizations
External Organizations
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
External Organizations
%T Transcriptome Kinetics of Saccharomyces cerevisiae in Response to Viral Killer Toxin K1 :
%G eng
%U http://hdl.handle.net/21.11116/0000-0003-B2F8-C
%R 10.3389/fmicb.2019.01102
%7 2019
%D 2019
%J Frontiers in Microbiology
%V 10
%Z sequence number: 1102
%I Frontiers Media
%C Lausanne
%@ false
80. Halbritter F, Farlik M, Schwentner R, Jug G, Fortelny N, Schnoeller T, Pisa H, Schuster LC, Reinprecht A, Czech T, Gojo J, Holter W, Minkov M, Bauer WM, Simonitsch-Klupp I, Bock C, Hutter C: Epigenomics and Singe-Cell Sequencing Define a Developmental Hierarchy in Langerhans Cell Histiocytosis. Cancer Discovery 2019, 9.
Export
BibTeX
@article{Halbritter_2019,
TITLE = {Epigenomics and Singe-Cell Sequencing Define a Developmental Hierarchy in Langerhans Cell Histiocytosis},
AUTHOR = {Halbritter, Florian and Farlik, Matthias and Schwentner, Raphaela and Jug, Gunhild and Fortelny, Nikolaus and Schnoeller, Thomas and Pisa, Hanja and Schuster, Linda C. and Reinprecht, Andrea and Czech, Thomas and Gojo, Johannes and Holter, Wolfgang and Minkov, Milen and Bauer, Wolfgang M. and Simonitsch-Klupp, Ingrid and Bock, Christoph and Hutter, Caroline},
LANGUAGE = {eng},
DOI = {10.1158/2159-8290.CD-19-0138},
PUBLISHER = {AACR},
YEAR = {2019},
JOURNAL = {Cancer Discovery},
VOLUME = {9},
NUMBER = {10},
}
Endnote
%0 Journal Article
%A Halbritter, Florian
%A Farlik, Matthias
%A Schwentner, Raphaela
%A Jug, Gunhild
%A Fortelny, Nikolaus
%A Schnoeller, Thomas
%A Pisa, Hanja
%A Schuster, Linda C.
%A Reinprecht, Andrea
%A Czech, Thomas
%A Gojo, Johannes
%A Holter, Wolfgang
%A Minkov, Milen
%A Bauer, Wolfgang M.
%A Simonitsch-Klupp, Ingrid
%A Bock, Christoph
%A Hutter, Caroline
%+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
%T Epigenomics and Singe-Cell Sequencing Define a Developmental Hierarchy in Langerhans Cell Histiocytosis :
%G eng
%U http://hdl.handle.net/21.11116/0000-0004-EA55-5
%R 10.1158/2159-8290.CD-19-0138
%7 2019
%D 2019
%J Cancer Discovery
%V 9
%N 10
%I AACR
81. Hamdane N, Juhling F, Crouchet E, El Saghire H, Thumann C, Oudot MA, Bandiera S, Saviano A, Ponsolles C, Suarez AAR, Li S, Fujiwara N, Ono A, Davidson I, Bardeesy N, Schmidl C, Bock C, Schuster C, Lupberger J, Habersetzer F, Doffoel M, Piardi T, Sommacale D, Imamura M, Uchida T, Ohdan H, Aikata H, Chayama K, Boldanova T, Pessaux P, et al.: HCV-Induced Epigenetic Changes Associated With Liver Cancer Risk Persist After Sustained Virologic Response. Gastroenterology 2019, 156.
Export
BibTeX
@article{Hamdane2019,
TITLE = {{HCV}-Induced Epigenetic Changes Associated With Liver Cancer Risk Persist After Sustained Virologic Response},
AUTHOR = {Hamdane, Nourdine and Juhling, Frank and Crouchet, Emilie and El Saghire, Houssein and Thumann, Christine and Oudot, Marine A. and Bandiera, Simonetta and Saviano, Antonio and Ponsolles, Clara and Suarez, Armando Andres Roca and Li, Shen and Fujiwara, Naoto and Ono, Atsushi and Davidson, Irwin and Bardeesy, Nabeel and Schmidl, Christian and Bock, Christoph and Schuster, Catherine and Lupberger, Joachim and Habersetzer, Francois and Doffoel, Michel and Piardi, Tullio and Sommacale, Daniele and Imamura, Michio and Uchida, Takuro and Ohdan, Hideki and Aikata, Hiroshi and Chayama, Kazuaki and Boldanova, Tujana and Pessaux, Patrick and Fuchs, Bryan C. and Hoshida, Yujin and Zeisel, Mirjam B. and Duong, Francois H. T. and Baumert, Thomas F.},
LANGUAGE = {eng},
ISSN = {0016-5085},
DOI = {10.1053/j.gastro.2019.02.038},
PUBLISHER = {W.B. Saunders},
ADDRESS = {Philadelphia, Pa},
YEAR = {2019},
DATE = {2019},
JOURNAL = {Gastroenterology},
VOLUME = {156},
NUMBER = {8},
PAGES = {2313--2329},
EID = {e7},
}
Endnote
%0 Journal Article
%A Hamdane, Nourdine
%A Juhling, Frank
%A Crouchet, Emilie
%A El Saghire, Houssein
%A Thumann, Christine
%A Oudot, Marine A.
%A Bandiera, Simonetta
%A Saviano, Antonio
%A Ponsolles, Clara
%A Suarez, Armando Andres Roca
%A Li, Shen
%A Fujiwara, Naoto
%A Ono, Atsushi
%A Davidson, Irwin
%A Bardeesy, Nabeel
%A Schmidl, Christian
%A Bock, Christoph
%A Schuster, Catherine
%A Lupberger, Joachim
%A Habersetzer, Francois
%A Doffoel, Michel
%A Piardi, Tullio
%A Sommacale, Daniele
%A Imamura, Michio
%A Uchida, Takuro
%A Ohdan, Hideki
%A Aikata, Hiroshi
%A Chayama, Kazuaki
%A Boldanova, Tujana
%A Pessaux, Patrick
%A Fuchs, Bryan C.
%A Hoshida, Yujin
%A Zeisel, Mirjam B.
%A Duong, Francois H. T.
%A Baumert, Thomas F.
%+ External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
%T HCV-Induced Epigenetic Changes Associated With Liver Cancer Risk Persist After Sustained Virologic Response :
%G eng
%U http://hdl.handle.net/21.11116/0000-0003-C353-3
%R 10.1053/j.gastro.2019.02.038
%7 2019
%D 2019
%J Gastroenterology
%O Gastroenterology
%V 156
%N 8
%& 2313
%P 2313 - 2329
%Z sequence number: e7
%I W.B. Saunders
%C Philadelphia, Pa
%@ false
82. Handl L, Jalali A, Scherer M, Eggeling R, Pfeifer N: Weighted Elastic Net for Unsupervised Domain Adaptation with Application to Age Prediction from DNA Methylation Data. Bioinformatics (Proc ISMB/ECCB 2019) 2019, 35.
Export
BibTeX
@article{Handl2019,
TITLE = {Weighted Elastic Net for Unsupervised Domain Adaptation with Application to Age Prediction from {DNA} Methylation Data},
AUTHOR = {Handl, Lisa and Jalali, Adrin and Scherer, Michael and Eggeling, Ralf and Pfeifer, Nico},
LANGUAGE = {eng},
ISSN = {1367-4803},
DOI = {10.1093/bioinformatics/btz338},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford},
YEAR = {2019},
DATE = {2019},
JOURNAL = {Bioinformatics (Proc. ISMB/ECCB)},
VOLUME = {35},
NUMBER = {14},
PAGES = {i154--i163},
BOOKTITLE = {ISMB/ECCB 2019 Proceedings},
}
Endnote
%0 Journal Article
%A Handl, Lisa
%A Jalali, Adrin
%A Scherer, Michael
%A Eggeling, Ralf
%A Pfeifer, Nico
%+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
%T Weighted Elastic Net for Unsupervised Domain Adaptation with Application to Age Prediction from DNA Methylation Data :
%G eng
%U http://hdl.handle.net/21.11116/0000-0004-7BC6-3
%R 10.1093/bioinformatics/btz338
%7 2019
%D 2019
%J Bioinformatics
%V 35
%N 14
%& i154
%P i154 - i163
%I Oxford University Press
%C Oxford
%@ false
%B ISMB/ECCB 2019 Proceedings
%O ISMB/ECCB 2019 The biennial joint meeting of ISMB (27th Annual Conference on Intelligent Systems for Molecular Biology) and ECCB (18th
European Conference on Computational Biology) ; Basel, Switzerland, July 21–25, 2019.
83. Kanduri C, Bock C, Gundersen S, Hovig E, Sandve GK: Colocalization Analyses of Genomic Elements: Approaches, Recommendations and Challenges. Bioinformatics 2019, 35.
Export
BibTeX
@article{Kanduri2019,
TITLE = {Colocalization Analyses of Genomic Elements: Approaches, Recommendations and Challenges},
AUTHOR = {Kanduri, Chakravarthi and Bock, Christoph and Gundersen, Sveinung and Hovig, Eivind and Sandve, Geir Kjetil},
LANGUAGE = {eng},
ISSN = {1367-4803},
DOI = {10.1093/bioinformatics/bty835},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford, UK},
YEAR = {2019},
JOURNAL = {Bioinformatics},
VOLUME = {35},
NUMBER = {9},
PAGES = {1615--1624},
}
Endnote
%0 Journal Article
%A Kanduri, Chakravarthi
%A Bock, Christoph
%A Gundersen, Sveinung
%A Hovig, Eivind
%A Sandve, Geir Kjetil
%+ External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
External Organizations
External Organizations
%T Colocalization Analyses of Genomic Elements: Approaches, Recommendations and Challenges :
%G eng
%U http://hdl.handle.net/21.11116/0000-0003-C2A6-6
%R 10.1093/bioinformatics/bty835
%2 PMC6499241
%7 2019
%D 2019
%J Bioinformatics
%V 35
%N 9
%& 1615
%P 1615 - 1624
%I Oxford University Press
%C Oxford, UK
%@ false
84. Karunanithi S, Oruganti V, Marker S, Rodriguez-Viana AM, Drews F, Pirritano M, Nordström K, Simon M, Schulz MH: Exogenous RNAi Mechanisms Contribute to Transcriptome Adaptation by Phased siRNA Clusters in Paramecium. Nucleic Acids Research (London) 2019.
Export
BibTeX
@article{Karunanithi2019,
TITLE = {Exogenous {RNAi} mechanisms contribute to transcriptome adaptation by phased {siRNA} clusters in {Paramecium}},
AUTHOR = {Karunanithi, Sivarajan and Oruganti, Vidya and Marker, Simone and Rodriguez-Viana, Angela M. and Drews, Franziska and Pirritano, Marcello and Nordstr{\"o}m, Karl and Simon, Martin and Schulz, Marcel Holger},
LANGUAGE = {eng},
ISSN = {0305-1048},
DOI = {10.1093/nar/gkz553},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford},
YEAR = {2019},
JOURNAL = {Nucleic Acids Research (London)},
EID = {gkz553},
}
Endnote
%0 Journal Article
%A Karunanithi, Sivarajan
%A Oruganti, Vidya
%A Marker, Simone
%A Rodriguez-Viana, Angela M.
%A Drews, Franziska
%A Pirritano, Marcello
%A Nordström, Karl
%A Simon, Martin
%A Schulz, Marcel Holger
%+ External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
%T Exogenous RNAi Mechanisms Contribute to Transcriptome Adaptation by Phased siRNA Clusters in Paramecium :
%G eng
%U http://hdl.handle.net/21.11116/0000-0003-E818-D
%R 10.1093/nar/gkz553
%2 PMC6735861
%7 2019
%D 2019
%J Nucleic Acids Research (London)
%O Nucleic Acids Res
%Z sequence number: gkz553
%I Oxford University Press
%C Oxford
%@ false
85. Karunanithi S, Simon M, Schulz MH: Automated Analysis of Small RNA Datasets with RAPID. PeerJ 2019, 7.
Export
BibTeX
@article{Karunanithi2019b,
TITLE = {Automated analysis of small {RNA} datasets with {RAPID}},
AUTHOR = {Karunanithi, Sivarajan and Simon, Martin and Schulz, Marcel Holger},
LANGUAGE = {eng},
ISSN = {2167-8359},
DOI = {10.7717/peerj.6710},
PUBLISHER = {PeerJ Inc.},
ADDRESS = {San Francisco, USA},
YEAR = {2019},
JOURNAL = {PeerJ},
VOLUME = {7},
EID = {e6710},
}
Endnote
%0 Journal Article
%A Karunanithi, Sivarajan
%A Simon, Martin
%A Schulz, Marcel Holger
%+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
%T Automated Analysis of Small RNA Datasets with RAPID :
%G eng
%U http://hdl.handle.net/21.11116/0000-0003-7D5F-8
%R 10.7717/peerj.6710
%7 2019
%D 2019
%J PeerJ
%O PeerJ
%V 7
%Z sequence number: e6710
%I PeerJ Inc.
%C San Francisco, USA
%@ false
86. Kosack L, Wingelhofer B, Popa A, Orlova A, Agerer B, Vilagos B, Majek P, Parapatics K, Lercher A, Ringler A, Klughammer J, Smyth M, Khamina K, Baazim H, de Araujo ED, Rosa DA, Park J, Tin G, Ahmar S, Gunning PT, Bock C, Siddle HV, Woods GM, Kubicek S, Murchison EP, Bennett KL, Moriggl R, Bergthaler A: The ERBB-STAT3 Axis Drives Tasmanian Devil Facial Tumor Disease. Cancer Cell 2019, 35.
Export
BibTeX
@article{Kosack2019,
TITLE = {The {ERBB}-{STAT3} Axis Drives {T}asmanian Devil Facial Tumor Disease},
AUTHOR = {Kosack, Lindsay and Wingelhofer, Bettina and Popa, Alexandra and Orlova, Anna and Agerer, Benedikt and Vilagos, Bojan and Majek, Peter and Parapatics, Katja and Lercher, Alexander and Ringler, Anna and Klughammer, Johanna and Smyth, Mark and Khamina, Kseniya and Baazim, Hatoon and de Araujo, Elvin D. and Rosa, David A. and Park, Jisung and Tin, Gary and Ahmar, Siawash and Gunning, Patrick T. and Bock, Christoph and Siddle, Hannah V. and Woods, Gregory M. and Kubicek, Stefan and Murchison, Elizabeth P. and Bennett, Keiryn L. and Moriggl, Richard and Bergthaler, Andreas},
LANGUAGE = {eng},
ISSN = {1535-6108},
DOI = {10.1016/j.ccell.2018.11.018},
PUBLISHER = {Cell Press},
ADDRESS = {Cambridge, Mass.},
YEAR = {2019},
JOURNAL = {Cancer Cell},
VOLUME = {35},
NUMBER = {1},
PAGES = {125--139},
EID = {e9},
}
Endnote
%0 Journal Article
%A Kosack, Lindsay
%A Wingelhofer, Bettina
%A Popa, Alexandra
%A Orlova, Anna
%A Agerer, Benedikt
%A Vilagos, Bojan
%A Majek, Peter
%A Parapatics, Katja
%A Lercher, Alexander
%A Ringler, Anna
%A Klughammer, Johanna
%A Smyth, Mark
%A Khamina, Kseniya
%A Baazim, Hatoon
%A de Araujo, Elvin D.
%A Rosa, David A.
%A Park, Jisung
%A Tin, Gary
%A Ahmar, Siawash
%A Gunning, Patrick T.
%A Bock, Christoph
%A Siddle, Hannah V.
%A Woods, Gregory M.
%A Kubicek, Stefan
%A Murchison, Elizabeth P.
%A Bennett, Keiryn L.
%A Moriggl, Richard
%A Bergthaler, Andreas
%+ External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
%T The ERBB-STAT3 Axis Drives Tasmanian Devil Facial Tumor Disease :
%G eng
%U http://hdl.handle.net/21.11116/0000-0002-F715-0
%R 10.1016/j.ccell.2018.11.018
%7 2019
%D 2019
%J Cancer Cell
%O Cancer Cell
%V 35
%N 1
%& 125
%P 125 - 139
%Z sequence number: e9
%I Cell Press
%C Cambridge, Mass.
%@ false
87. Kröhler T, Kessler SM, Hosseini K, List M, Barghash A, Patial S, Laggai S, Gemperlein K, Haybaeck J, Müller R, Helms V, Schulz MH, Hoppstädter J, Blackshear PJ, Kiemer AK: The mRNA-binding Protein TTP/ZFP36 in Hepatocarcinogenesis and Hepatocellular Carcinoma. Cancers 2019, 11.
Export
BibTeX
@article{Kroehler_2019,
TITLE = {The {mRNA}-binding Protein {TTP}/{ZFP}36 in Hepatocarcinogenesis and Hepatocellular Carcinoma},
AUTHOR = {Kr{\"o}hler, Tarek and Kessler, Sonja M. and Hosseini, Kevan and List, Markus and Barghash, Ahmad and Patial, Sonika and Laggai, Stephan and Gemperlein, Katja and Haybaeck, Johannes and M{\"u}ller, Rolf and Helms, Volkhard and Schulz, Marcel Holger and Hoppst{\"a}dter, Jessica and Blackshear, Perry J. and Kiemer, Alexandra K.},
LANGUAGE = {eng},
ISSN = {2072-6694},
DOI = {10.3390/cancers11111754},
PUBLISHER = {MDPI},
YEAR = {2019},
JOURNAL = {Cancers},
VOLUME = {11},
NUMBER = {11},
EID = {1754},
}
Endnote
%0 Journal Article
%A Kröhler, Tarek
%A Kessler, Sonja M.
%A Hosseini, Kevan
%A List, Markus
%A Barghash, Ahmad
%A Patial, Sonika
%A Laggai, Stephan
%A Gemperlein, Katja
%A Haybaeck, Johannes
%A Müller, Rolf
%A Helms, Volkhard
%A Schulz, Marcel Holger
%A Hoppstädter, Jessica
%A Blackshear, Perry J.
%A Kiemer, Alexandra K.
%+ 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
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
External Organizations
External Organizations
%T The mRNA-binding Protein TTP/ZFP36 in Hepatocarcinogenesis and Hepatocellular Carcinoma :
%G eng
%U http://hdl.handle.net/21.11116/0000-0005-6EB0-9
%R 10.3390/cancers11111754
%7 2019
%D 2019
%J Cancers
%V 11
%N 11
%Z sequence number: 1754
%I MDPI
%@ false
88. List M, Dheghani Amirabad A, Kostka D, Schulz MH: Large-scale Inference of Competing Endogenous RNA Networks with Sparse Partial Correlation. Bioinformatics (Proc ISMB/ECCB 2019) 2019, 35.
Export
BibTeX
@article{List2019,
TITLE = {Large-scale Inference of Competing Endogenous {RNA} Networks with Sparse Partial Correlation},
AUTHOR = {List, Markus and Dheghani Amirabad, Azim and Kostka, Dennis and Schulz, Marcel Holger},
LANGUAGE = {eng},
ISSN = {1367-4803},
DOI = {10.1093/bioinformatics/btz314},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford},
YEAR = {2019},
DATE = {2019},
JOURNAL = {Bioinformatics (Proc. ISMB/ECCB)},
VOLUME = {35},
NUMBER = {14},
PAGES = {i596--i604},
BOOKTITLE = {ISMB/ECCB 2019 Proceedings},
}
Endnote
%0 Journal Article
%A List, Markus
%A Dheghani Amirabad, Azim
%A Kostka, Dennis
%A Schulz, Marcel Holger
%+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
%T Large-scale Inference of Competing Endogenous RNA Networks with Sparse Partial Correlation :
%G eng
%U http://hdl.handle.net/21.11116/0000-0004-7CC2-6
%R 10.1093/bioinformatics/btz314
%7 2019
%D 2019
%J Bioinformatics
%V 35
%N 14
%& i596
%P i596 - i604
%I Oxford University Press
%C Oxford
%@ false
%B ISMB/ECCB 2019 Proceedings
%O ISMB/ECCB 2019 The biennial joint meeting of ISMB (27th Annual Conference on Intelligent Systems for Molecular Biology) and ECCB (18th
European Conference on Computational Biology) ; Basel, Switzerland, July 21–25, 2019
89. Li Z, Schulz MH, Look T, Begemann M, Zenke M, Costa IG: Identification of Transcription Factor Binding Sites using ATAC-seq. Genome Research 2019, 20.
Export
BibTeX
@article{Li2019,
TITLE = {Identification of transcription factor binding sites using {ATAC}-seq},
AUTHOR = {Li, Zhijian and Schulz, Marcel Holger and Look, Thomas and Begemann, Matthias and Zenke, Martin and Costa, Ivan G.},
LANGUAGE = {eng},
ISSN = {1088-9051},
DOI = {10.1186/s13059-019-1642-2},
PUBLISHER = {Cold Spring Harbor Laboratory Press},
ADDRESS = {Cold Spring Harbor, N.Y.},
YEAR = {2019},
JOURNAL = {Genome Research},
VOLUME = {20},
EID = {45},
}
Endnote
%0 Journal Article
%A Li, Zhijian
%A Schulz, Marcel Holger
%A Look, Thomas
%A Begemann, Matthias
%A Zenke, Martin
%A Costa, Ivan G.
%+ External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
External Organizations
External Organizations
External Organizations
%T Identification of Transcription Factor Binding Sites using ATAC-seq :
%G eng
%U http://hdl.handle.net/21.11116/0000-0003-2AF1-E
%R 10.1186/s13059-019-1642-2
%7 2019
%D 2019
%J Genome Research
%V 20
%Z sequence number: 45
%I Cold Spring Harbor Laboratory Press
%C Cold Spring Harbor, N.Y.
%@ false
90. Luebke N, Jensen B, Huettig F, Feldt T, Walker A, Thielen A, Daeumer M, Obermeier M, Kaiser R, Knops E, Heger E, Sierra S, Oette M, Lengauer T, Timm J, Haeussinger D: Failure of Dolutegravir First-Line ART with Selection of Virus Carrying R263K and G118R. The New England Journal of Medicine : NEJM / Publ by the Massachusetts Medical Society 2019, 381.
Export
BibTeX
@article{Luebke2019,
TITLE = {Failure of Dolutegravir First-Line {ART} with Selection of Virus Carrying {R263K} and {G118R}},
AUTHOR = {Luebke, Nadine and Jensen, Bjoern and Huettig, Falk and Feldt, Torsten and Walker, Andreas and Thielen, Alexander and Daeumer, Martin and Obermeier, Martin and Kaiser, Rolf and Knops, Elena and Heger, Eva and Sierra, Saleta and Oette, Mark and Lengauer, Thomas and Timm, Joerg and Haeussinger, Dieter},
LANGUAGE = {eng},
ISSN = {0028-4793},
DOI = {10.1056/NEJMc1806554},
PUBLISHER = {New England Journal of Medicine},
ADDRESS = {Boston},
YEAR = {2019},
DATE = {2019},
JOURNAL = {The New England Journal of Medicine : NEJM / Publ. by the Massachusetts Medical Society},
VOLUME = {381},
NUMBER = {9},
PAGES = {887--889},
}
Endnote
%0 Journal Article
%A Luebke, Nadine
%A Jensen, Bjoern
%A Huettig, Falk
%A Feldt, Torsten
%A Walker, Andreas
%A Thielen, Alexander
%A Daeumer, Martin
%A Obermeier, Martin
%A Kaiser, Rolf
%A Knops, Elena
%A Heger, Eva
%A Sierra, Saleta
%A Oette, Mark
%A Lengauer, Thomas
%A Timm, Joerg
%A Haeussinger, Dieter
%+ External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
External Organizations
%T Failure of Dolutegravir First-Line ART with Selection of Virus Carrying R263K and G118R :
%G eng
%U http://hdl.handle.net/21.11116/0000-0004-B780-C
%R 10.1056/NEJMc1806554
%7 2019
%D 2019
%J The New England Journal of Medicine : NEJM / Publ. by the Massachusetts Medical Society
%O N. Engl. J. Med.
%V 381
%N 9
%& 887
%P 887 - 889
%I New England Journal of Medicine
%C Boston
%@ false
91. Müller F, Scherer M, Assenov Y, Lutsik P, Walter J, Lengauer T, Bock C: RnBeads 2.0: Comprehensive Analysis of DNA Methylation Data. Genome Biology 2019, 20.
Export
BibTeX
@article{Mueller_GenomeBiology2019,
TITLE = {{RnBeads} 2.0: {C}omprehensive analysis of {DNA} methylation data},
AUTHOR = {M{\"u}ller, Fabian and Scherer, Michael and Assenov, Yassen and Lutsik, Pavlo and Walter, J{\"o}rn and Lengauer, Thomas and Bock, Christoph},
LANGUAGE = {eng},
ISSN = {1465-6906},
DOI = {10.1186/s13059-019-1664-9},
PUBLISHER = {BioMed Central Ltd.},
ADDRESS = {London},
YEAR = {2019},
JOURNAL = {Genome Biology},
VOLUME = {20},
EID = {55},
}
Endnote
%0 Journal Article
%A Müller, Fabian
%A Scherer, Michael
%A Assenov, Yassen
%A Lutsik, Pavlo
%A Walter, Jörn
%A Lengauer, Thomas
%A Bock, Christoph
%+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
%T RnBeads 2.0: Comprehensive Analysis of DNA Methylation Data :
%G eng
%U http://hdl.handle.net/21.11116/0000-0003-2DF3-9
%R 10.1186/s13059-019-1664-9
%7 2019
%D 2019
%J Genome Biology
%V 20
%Z sequence number: 55
%I BioMed Central Ltd.
%C London
%@ false
92. Neininger K, Marschall T, Helms V: SNP and Indel Frequencies at Transcription Start Sites and at Canonical and Alternative Translation Initiation Sites in the Human Genome. PLoS One 2019, 14.
Export
BibTeX
@article{Neininger2019,
TITLE = {{SNP} and indel frequencies at transcription start sites and at canonical and alternative translation initiation sites in the human genome},
AUTHOR = {Neininger, Kerstin and Marschall, Tobias and Helms, Volkhard},
LANGUAGE = {eng},
ISSN = {1932-6203},
DOI = {10.1371/journal.pone.0214816},
PUBLISHER = {Public Library of Science},
ADDRESS = {San Francisco, CA},
YEAR = {2019},
JOURNAL = {PLoS One},
VOLUME = {14},
NUMBER = {4},
EID = {e0214816},
}
Endnote
%0 Journal Article
%A Neininger, Kerstin
%A Marschall, Tobias
%A Helms, Volkhard
%+ External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
%T SNP and Indel Frequencies at Transcription Start Sites and at Canonical and Alternative Translation Initiation Sites in the Human Genome :
%G eng
%U http://hdl.handle.net/21.11116/0000-0003-866B-E
%R 10.1371/journal.pone.0214816
%7 2019-04-12
%D 2019
%8 12.04.2019
%J PLoS One
%V 14
%N 4
%Z sequence number: e0214816
%I Public Library of Science
%C San Francisco, CA
%@ false
93. Nikumbh S: Interpretable Machine Learning Methods for Prediction and Analysis of Genome Regulation in 3D. Universität des Saarlandes; 2019.
Abstract
With the development of chromosome conformation capture-based techniques, we now know that chromatin is packed in three-dimensional (3D) space inside the cell nucleus. Changes in the 3D chromatin architecture have already been implicated in diseases such as cancer. Thus, a better understanding of this 3D conformation is of interest to help enhance our comprehension of the complex, multipronged regulatory mechanisms of the genome. The work described in this dissertation largely focuses on development and application of interpretable machine learning methods for prediction and analysis of long-range genomic interactions output from chromatin interaction experiments. In the first part, we demonstrate that the genetic sequence information at the ge- nomic loci is predictive of the long-range interactions of a particular locus of interest (LoI). For example, the genetic sequence information at and around enhancers can help predict whether it interacts with a promoter region of interest. This is achieved by building string kernel-based support vector classifiers together with two novel, in- tuitive visualization methods. These models suggest a potential general role of short tandem repeat motifs in the 3D genome organization. But, the insights gained out of these models are still coarse-grained. To this end, we devised a machine learning method, called CoMIK for Conformal Multi-Instance Kernels, capable of providing more fine-grained insights. When comparing sequences of variable length in the su- pervised learning setting, CoMIK can not only identify the features important for classification but also locate them within the sequence. Such precise identification of important segments of the whole sequence can help in gaining de novo insights into any role played by the intervening chromatin towards long-range interactions. Although CoMIK primarily uses only genetic sequence information, it can also si- multaneously utilize other information modalities such as the numerous functional genomics data if available. The second part describes our pipeline, pHDee, for easy manipulation of large amounts of 3D genomics data. We used the pipeline for analyzing HiChIP experimen- tal data for studying the 3D architectural changes in Ewing sarcoma (EWS) which is a rare cancer affecting adolescents. In particular, HiChIP data for two experimen- tal conditions, doxycycline-treated and untreated, and for primary tumor samples is analyzed. We demonstrate that pHDee facilitates processing and easy integration of large amounts of 3D genomics data analysis together with other data-intensive bioinformatics analyses.
Export
BibTeX
@phdthesis{Nikumbhphd2019,
TITLE = {Interpretable Machine Learning Methods for Prediction and Analysis of Genome Regulation in {3D}},
AUTHOR = {Nikumbh, Sarvesh},
LANGUAGE = {eng},
URL = {urn:nbn:de:bsz:291--ds-281533},
DOI = {10.22028/D291-28153},
SCHOOL = {Universit{\"a}t des Saarlandes},
ADDRESS = {Saarbr{\"u}cken},
YEAR = {2019},
DATE = {2019},
ABSTRACT = {With the development of chromosome conformation capture-based techniques, we now know that chromatin is packed in three-dimensional (3D) space inside the cell nucleus. Changes in the 3D chromatin architecture have already been implicated in diseases such as cancer. Thus, a better understanding of this 3D conformation is of interest to help enhance our comprehension of the complex, multipronged regulatory mechanisms of the genome. The work described in this dissertation largely focuses on development and application of interpretable machine learning methods for prediction and analysis of long-range genomic interactions output from chromatin interaction experiments. In the first part, we demonstrate that the genetic sequence information at the ge- nomic loci is predictive of the long-range interactions of a particular locus of interest (LoI). For example, the genetic sequence information at and around enhancers can help predict whether it interacts with a promoter region of interest. This is achieved by building string kernel-based support vector classifiers together with two novel, in- tuitive visualization methods. These models suggest a potential general role of short tandem repeat motifs in the 3D genome organization. But, the insights gained out of these models are still coarse-grained. To this end, we devised a machine learning method, called CoMIK for Conformal Multi-Instance Kernels, capable of providing more fine-grained insights. When comparing sequences of variable length in the su- pervised learning setting, CoMIK can not only identify the features important for classification but also locate them within the sequence. Such precise identification of important segments of the whole sequence can help in gaining de novo insights into any role played by the intervening chromatin towards long-range interactions. Although CoMIK primarily uses only genetic sequence information, it can also si- multaneously utilize other information modalities such as the numerous functional genomics data if available. The second part describes our pipeline, pHDee, for easy manipulation of large amounts of 3D genomics data. We used the pipeline for analyzing HiChIP experimen- tal data for studying the 3D architectural changes in Ewing sarcoma (EWS) which is a rare cancer affecting adolescents. In particular, HiChIP data for two experimen- tal conditions, doxycycline-treated and untreated, and for primary tumor samples is analyzed. We demonstrate that pHDee facilitates processing and easy integration of large amounts of 3D genomics data analysis together with other data-intensive bioinformatics analyses.},
}
Endnote
%0 Thesis
%A Nikumbh, Sarvesh
%Y Pfeifer, Nico
%A referee: Marschall, Tobias
%A referee: Ebert, Peter
%+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
International Max Planck Research School, MPI for Informatics, Max Planck Society
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
%T Interpretable Machine Learning Methods for Prediction and Analysis of Genome Regulation in 3D :
%G eng
%U http://hdl.handle.net/21.11116/0000-0004-A5CE-A
%R 10.22028/D291-28153
%U urn:nbn:de:bsz:291--ds-281533
%F OTHER: hdl:20.500.11880/27471
%I Universität des Saarlandes
%C Saarbrücken
%D 2019
%P 150 p.
%V phd
%9 phd
%X With the development of chromosome conformation capture-based techniques, we now know that chromatin is packed in three-dimensional (3D) space inside the cell nucleus. Changes in the 3D chromatin architecture have already been implicated in diseases such as cancer. Thus, a better understanding of this 3D conformation is of interest to help enhance our comprehension of the complex, multipronged regulatory mechanisms of the genome. The work described in this dissertation largely focuses on development and application of interpretable machine learning methods for prediction and analysis of long-range genomic interactions output from chromatin interaction experiments. In the first part, we demonstrate that the genetic sequence information at the ge- nomic loci is predictive of the long-range interactions of a particular locus of interest (LoI). For example, the genetic sequence information at and around enhancers can help predict whether it interacts with a promoter region of interest. This is achieved by building string kernel-based support vector classifiers together with two novel, in- tuitive visualization methods. These models suggest a potential general role of short tandem repeat motifs in the 3D genome organization. But, the insights gained out of these models are still coarse-grained. To this end, we devised a machine learning method, called CoMIK for Conformal Multi-Instance Kernels, capable of providing more fine-grained insights. When comparing sequences of variable length in the su- pervised learning setting, CoMIK can not only identify the features important for classification but also locate them within the sequence. Such precise identification of important segments of the whole sequence can help in gaining de novo insights into any role played by the intervening chromatin towards long-range interactions. Although CoMIK primarily uses only genetic sequence information, it can also si- multaneously utilize other information modalities such as the numerous functional genomics data if available. The second part describes our pipeline, pHDee, for easy manipulation of large amounts of 3D genomics data. We used the pipeline for analyzing HiChIP experimen- tal data for studying the 3D architectural changes in Ewing sarcoma (EWS) which is a rare cancer affecting adolescents. In particular, HiChIP data for two experimen- tal conditions, doxycycline-treated and untreated, and for primary tumor samples is analyzed. We demonstrate that pHDee facilitates processing and easy integration of large amounts of 3D genomics data analysis together with other data-intensive bioinformatics analyses.
%U https://publikationen.sulb.uni-saarland.de/handle/20.500.11880/27471
94. Nordström KJV, Schmidt F, Gasparoni N, Salhab A, Gasparoni G, Kattler K, Müller F, Ebert P, Costa IG, Pfeifer N, Lengauer T, Schulz MH, Walter J: Unique and Essay Specific Features of NOMe-, ATAC- and DNase I-seq Data. Nucleic Acids Research (London) 2019, 47.
Export
BibTeX
@article{Norstroem_2019,
TITLE = {Unique and assay specific features of {NOMe}-, {ATAC}- and {DNase} {I}-seq data},
AUTHOR = {Nordstr{\"o}m, Karl J. V. and Schmidt, Florian and Gasparoni, Nina and Salhab, Abdulrahman and Gasparoni, Gilles and Kattler, Kathrin and M{\"u}ller, Fabian and Ebert, Peter and Costa, Ivan G. and {DEEP Consortium} and Pfeifer, Nico and Lengauer, Thomas and Schulz, Marcel Holger and Walter, J{\"o}rn},
LANGUAGE = {eng},
ISSN = {0305-1048},
DOI = {10.1093/nar/gkz799},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford},
YEAR = {2019},
DATE = {2019},
JOURNAL = {Nucleic Acids Research (London)},
VOLUME = {47},
NUMBER = {20},
PAGES = {10580--10596},
}
Endnote
%0 Journal Article
%A Nordström, Karl J. V.
%A Schmidt, Florian
%A Gasparoni, Nina
%A Salhab, Abdulrahman
%A Gasparoni, Gilles
%A Kattler, Kathrin
%A Müller, Fabian
%A Ebert, Peter
%A Costa, Ivan G.
%A DEEP Consortium,
%A Pfeifer, Nico
%A Lengauer, Thomas
%A Schulz, Marcel Holger
%A Walter, Jörn
%+ External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
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 Unique and Essay Specific Features of NOMe-, ATAC- and DNase I-seq Data :
%G eng
%U http://hdl.handle.net/21.11116/0000-0005-69B2-C
%R 10.1093/nar/gkz799
%2 PMC6847574
%7 2019
%D 2019
%J Nucleic Acids Research (London)
%O Nucleic Acids Res
%V 47
%N 20
%& 10580
%P 10580 - 10596
%I Oxford University Press
%C Oxford
%@ false
95. Pfitzer L, Moser C, Gegenfurtner F, Arner A, Foerster F, Atzberger C, Zisis T, Kubisch-Dohmen R, Busse J, Smith R, Timinszky G, Kalinina OV, Müller R, Wagner E, Vollmar AM, Zahler S: Targeting Actin Inhibits Repair of Doxorubicin-induced DNA Damage: A Novel Therapeutic Approach for Combination Therapy. Cell Death and Disease 2019, 10.
Export
BibTeX
@article{Pfitzer2019,
TITLE = {Targeting actin inhibits repair of doxorubicin-induced {DNA} damage: {A} novel therapeutic approach for combination therapy},
AUTHOR = {Pfitzer, Lisa and Moser, Christina and Gegenfurtner, Florian and Arner, Anja and Foerster, Florian and Atzberger, Carina and Zisis, Themistoklis and Kubisch-Dohmen, Rebekka and Busse, Johanna and Smith, Rebecca and Timinszky, Gyula and Kalinina, Olga V. and M{\"u}ller, Rolf and Wagner, Ernst and Vollmar, Angelika M. and Zahler, Stefan},
LANGUAGE = {eng},
DOI = {10.1038/s41419-019-1546-9},
PUBLISHER = {Nature Publishing Group},
ADDRESS = {London},
YEAR = {2019},
JOURNAL = {Cell Death and Disease},
VOLUME = {10},
EID = {302},
}
Endnote
%0 Journal Article
%A Pfitzer, Lisa
%A Moser, Christina
%A Gegenfurtner, Florian
%A Arner, Anja
%A Foerster, Florian
%A Atzberger, Carina
%A Zisis, Themistoklis
%A Kubisch-Dohmen, Rebekka
%A Busse, Johanna
%A Smith, Rebecca
%A Timinszky, Gyula
%A Kalinina, Olga V.
%A Müller, Rolf
%A Wagner, Ernst
%A Vollmar, Angelika M.
%A Zahler, Stefan
%+ External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
External Organizations
External Organizations
External Organizations
%T Targeting Actin Inhibits Repair of Doxorubicin-induced DNA Damage: A Novel Therapeutic Approach for Combination Therapy :
%G eng
%U http://hdl.handle.net/21.11116/0000-0003-8A7E-5
%R 10.1038/s41419-019-1546-9
%7 2019
%D 2019
%J Cell Death and Disease
%O Cell Death Dis
%V 10
%Z sequence number: 302
%I Nature Publishing Group
%C London
96. Piper CJM, Rosser EC, Oleinika K, Nistala K, Krausgruber T, Rendeiro AF, Banos A, Drozdov I, Villa M, Thomson S, Xanthou G, Bock C, Stockinger B, Mauri C: Aryl Hydrocarbon Receptor Contributes to the Transcriptional Program of IL-10-Producing Regulatory B Cells. Cell Reports 2019, 29.
Export
BibTeX
@article{Piper2019,
TITLE = {Aryl Hydrocarbon Receptor Contributes to the Transcriptional Program of {IL}-10-Producing Regulatory {B} Cells},
AUTHOR = {Piper, Christopher J.M. and Rosser, Elizabeth C. and Oleinika, Kristine and Nistala, Kiran and Krausgruber, Thomas and Rendeiro, Andr{\'e} F. and Banos, Aggelos and Drozdov, Ignat and Villa, Matteo and Thomson, Scott and Xanthou, Georgina and Bock, Christoph and Stockinger, Brigitta and Mauri, Claudia},
LANGUAGE = {eng},
ISSN = {2211-1247},
DOI = {10.1016/j.celrep.2019.10.018},
PUBLISHER = {Cell Press},
ADDRESS = {Maryland Heights, MO},
YEAR = {2019},
JOURNAL = {Cell Reports},
VOLUME = {29},
NUMBER = {7},
PAGES = {1878--1892},
EID = {e7},
}
Endnote
%0 Journal Article
%A Piper, Christopher J.M.
%A Rosser, Elizabeth C.
%A Oleinika, Kristine
%A Nistala, Kiran
%A Krausgruber, Thomas
%A Rendeiro, André F.
%A Banos, Aggelos
%A Drozdov, Ignat
%A Villa, Matteo
%A Thomson, Scott
%A Xanthou, Georgina
%A Bock, Christoph
%A Stockinger, Brigitta
%A Mauri, Claudia
%+ External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
External Organizations
%T Aryl Hydrocarbon Receptor Contributes to the Transcriptional Program of IL-10-Producing Regulatory B Cells :
%G eng
%U http://hdl.handle.net/21.11116/0000-0005-5CAA-5
%R 10.1016/j.celrep.2019.10.018
%7 2019
%D 2019
%J Cell Reports
%V 29
%N 7
%& 1878
%P 1878 - 1892
%Z sequence number: e7
%I Cell Press
%C Maryland Heights, MO
%@ false
97. Rautiainen M, Mäkinen V, Marschall T: Bit-parallel Sequence-to-Graph Alignment. Bioinformatics 2019, 35.
Export
BibTeX
@article{Rautiainen_2019,
TITLE = {Bit-parallel Sequence-to-Graph Alignment},
AUTHOR = {Rautiainen, Mikko and M{\"a}kinen, Veli and Marschall, Tobias},
LANGUAGE = {eng},
ISSN = {1367-4803},
DOI = {10.1093/bioinformatics/btz162},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford},
YEAR = {2019},
DATE = {2019},
JOURNAL = {Bioinformatics},
VOLUME = {35},
NUMBER = {19},
PAGES = {3599--3607},
}
Endnote
%0 Journal Article
%A Rautiainen, Mikko
%A Mäkinen, Veli
%A Marschall, Tobias
%+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
%T Bit-parallel Sequence-to-Graph Alignment :
%G eng
%U http://hdl.handle.net/21.11116/0000-0004-E4CA-7
%R 10.1093/bioinformatics/btz162
%2 PMC6761980
%7 2019
%D 2019
%J Bioinformatics
%V 35
%N 19
%& 3599
%P 3599 - 3607
%I Oxford University Press
%C Oxford
%@ false
98. Roeder B, Kersten N, Herr M, Speicher NK, Pfeifer N: web-rMKL: A Web Server for Dimensionality Reduction and Sample Clustering of Multi-view Data Based on Unsupervised Multiple Kernel Learning. Nucleic Acids Research (London) 2019, 47.
Export
BibTeX
@article{Roeder2019,
TITLE = {{web-rMKL}: {A} Web Server for Dimensionality Reduction and Sample Clustering of Multi-view Data Based on Unsupervised Multiple Kernel Learning},
AUTHOR = {Roeder, Benedict and Kersten, Nicolas and Herr, Marius and Speicher, Nora K. and Pfeifer, Nico},
LANGUAGE = {eng},
ISSN = {0305-1048},
DOI = {10.1093/nar/gkz422},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford},
YEAR = {2019},
DATE = {2019},
JOURNAL = {Nucleic Acids Research (London)},
VOLUME = {47},
NUMBER = {W1},
PAGES = {W605--W609},
}
Endnote
%0 Journal Article
%A Roeder, Benedict
%A Kersten, Nicolas
%A Herr, Marius
%A Speicher, Nora K.
%A Pfeifer, Nico
%+ External Organizations
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
%T web-rMKL: A Web Server for Dimensionality Reduction and Sample Clustering of Multi-view Data Based on Unsupervised Multiple Kernel Learning :
%G eng
%U http://hdl.handle.net/21.11116/0000-0004-7AE0-6
%R 10.1093/nar/gkz422
%7 2019
%D 2019
%J Nucleic Acids Research (London)
%O Nucleic Acids Res
%V 47
%N W1
%& W605
%P W605 - W609
%I Oxford University Press
%C Oxford
%@ false
99. Sanders AD, Meiers S, Ghareghani M, Porubsky D, Jeong H, van Vliet MACC, Rausch T, Richter-Pechanska P, Kunz JB, Jenni S, Bolognini D, Longo GMC, Raeder B, Kinanen V, Zimmermann J, Benes V, Schrappe M, Mardin BR, Kulozik AE, Bornhauser B, Bourquin J-P, Marschall T, Korbel JO: Single-Cell Analysis of Structural Variations and Complex Rearrangements with Tri-Channel Processing. Nature Biotechnology 2019, 38.
Export
BibTeX
@article{Sanders2019,
TITLE = {Single-Cell Analysis of Structural Variations and Complex Rearrangements with Tri-Channel Processing},
AUTHOR = {Sanders, Ashley D. and Meiers, Sascha and Ghareghani, Maryam and Porubsky, David and Jeong, Hyobin and van Vliet, M. Alexandra C. C. and Rausch, Tobias and Richter-Pechanska, Paulina and Kunz, Joachim B. and Jenni, Silvia and Bolognini, Davide and Longo, Gabriel M. C. and Raeder, Benjamin and Kinanen, Venla and Zimmermann, Juergen and Benes, Vladimir and Schrappe, Martin and Mardin, Balca R. and Kulozik, Andreas E. and Bornhauser, Beat and Bourquin, Jean-Pierre and Marschall, Tobias and Korbel, Jan O.},
LANGUAGE = {eng},
ISSN = {1087-0156},
DOI = {10.1038/s41587-019-0366-x},
PUBLISHER = {Gale Group Inc.},
ADDRESS = {New York},
YEAR = {2019},
JOURNAL = {Nature Biotechnology},
VOLUME = {38},
PAGES = {343--354},
}
Endnote
%0 Journal Article
%A Sanders, Ashley D.
%A Meiers, Sascha
%A Ghareghani, Maryam
%A Porubsky, David
%A Jeong, Hyobin
%A van Vliet, M. Alexandra C. C.
%A Rausch, Tobias
%A Richter-Pechanska, Paulina
%A Kunz, Joachim B.
%A Jenni, Silvia
%A Bolognini, Davide
%A Longo, Gabriel M. C.
%A Raeder, Benjamin
%A Kinanen, Venla
%A Zimmermann, Juergen
%A Benes, Vladimir
%A Schrappe, Martin
%A Mardin, Balca R.
%A Kulozik, Andreas E.
%A Bornhauser, Beat
%A Bourquin, Jean-Pierre
%A Marschall, Tobias
%A Korbel, Jan O.
%+ 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
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
%T Single-Cell Analysis of Structural Variations and Complex Rearrangements with Tri-Channel Processing :
%G eng
%U http://hdl.handle.net/21.11116/0000-0005-9E8C-C
%R 10.1038/s41587-019-0366-x
%7 2019
%D 2019
%J Nature Biotechnology
%V 38
%& 343
%P 343 - 354
%I Gale Group Inc.
%C New York
%@ false
100. Schick S, Rendeiro AF, Runggatscher K, Ringler A, Boidol B, Hinkel M, Majek P, Vulliard L, Penz T, Parapatics K, Schmidl C, Menche J, Boehmelt G, Petronczki M, Mueller AC, Bock C, Kubicek S: Systematic Characterization of BAF Mutations Provides Insights into Intracomplex Synthetic Lethalities in Human Cancers. Nature Genetics 2019, 51.
Export
BibTeX
@article{Schick2019,
TITLE = {Systematic characterization of {BAF} mutations provides insights into intracomplex synthetic lethalities in human cancers},
AUTHOR = {Schick, Sandra and Rendeiro, Andre F. and Runggatscher, Kathrin and Ringler, Anna and Boidol, Bernd and Hinkel, Melanie and Majek, Peter and Vulliard, Loan and Penz, Thomas and Parapatics, Katja and Schmidl, Christian and Menche, Joerg and Boehmelt, Guido and Petronczki, Mark and Mueller, Andre C. and Bock, Christoph and Kubicek, Stefan},
LANGUAGE = {eng},
ISSN = {1061-4036},
DOI = {10.1038/s41588-019-0477-9},
PUBLISHER = {Nature America, Inc.},
ADDRESS = {New York, NY},
YEAR = {2019},
DATE = {2019},
JOURNAL = {Nature Genetics},
VOLUME = {51},
NUMBER = {9},
PAGES = {1399--1410},
}
Endnote
%0 Journal Article
%A Schick, Sandra
%A Rendeiro, Andre F.
%A Runggatscher, Kathrin
%A Ringler, Anna
%A Boidol, Bernd
%A Hinkel, Melanie
%A Majek, Peter
%A Vulliard, Loan
%A Penz, Thomas
%A Parapatics, Katja
%A Schmidl, Christian
%A Menche, Joerg
%A Boehmelt, Guido
%A Petronczki, Mark
%A Mueller, Andre C.
%A Bock, Christoph
%A Kubicek, Stefan
%+ External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
%T Systematic Characterization of BAF Mutations Provides Insights into Intracomplex Synthetic Lethalities in Human Cancers :
%G eng
%U http://hdl.handle.net/21.11116/0000-0004-B774-B
%R 10.1038/s41588-019-0477-9
%7 2019
%D 2019
%J Nature Genetics
%O Nature Genet.
%V 51
%N 9
%& 1399
%P 1399 - 1410
%I Nature America, Inc.
%C New York, NY
%@ false
101. Schmidl C, Vladimer GI, Rendeiro AF, Schnabl S, Krausgruber T, Taubert C, Krall N, Pemovska T, Araghi M, Snijder B, Hubmann R, Ringler A, Runggatscher K, Demirtas D, Lopez de la Fuente O, Hilgarth M, Skrabs C, Porpaczy E, Gruber M, Hoermann G, Kubicek S, Staber PB, Shehata M, Superti-Furga G, Jaeger U, Bock C: Combined Chemosensitivity and Chromatin Profiling Prioritizes Drug Combinations in CLL. Nature Chemical Biology 2019, 15.
Export
BibTeX
@article{Schmidl2019,
TITLE = {Combined Chemosensitivity and Chromatin Profiling Prioritizes Drug Combinations in {CLL}},
AUTHOR = {Schmidl, Christian and Vladimer, Gregory I. and Rendeiro, Andre F. and Schnabl, Susanne and Krausgruber, Thomas and Taubert, Christina and Krall, Nikolaus and Pemovska, Tea and Araghi, Mohammad and Snijder, Berend and Hubmann, Rainer and Ringler, Anna and Runggatscher, Kathrin and Demirtas, Dita and Lopez de la Fuente, Oscar and Hilgarth, Martin and Skrabs, Cathrin and Porpaczy, Edit and Gruber, Michaela and Hoermann, Gregor and Kubicek, Stefan and Staber, Philipp B. and Shehata, Medhat and Superti-Furga, Giulio and Jaeger, Ulrich and Bock, Christoph},
LANGUAGE = {eng},
ISSN = {1552-4450},
DOI = {10.1038/s41589-018-0205-2},
PUBLISHER = {Nature Pub. Group},
ADDRESS = {New York, NY},
YEAR = {2019},
DATE = {2019},
JOURNAL = {Nature Chemical Biology},
VOLUME = {15},
NUMBER = {3},
PAGES = {232--240},
}
Endnote
%0 Journal Article
%A Schmidl, Christian
%A Vladimer, Gregory I.
%A Rendeiro, Andre F.
%A Schnabl, Susanne
%A Krausgruber, Thomas
%A Taubert, Christina
%A Krall, Nikolaus
%A Pemovska, Tea
%A Araghi, Mohammad
%A Snijder, Berend
%A Hubmann, Rainer
%A Ringler, Anna
%A Runggatscher, Kathrin
%A Demirtas, Dita
%A Lopez de la Fuente, Oscar
%A Hilgarth, Martin
%A Skrabs, Cathrin
%A Porpaczy, Edit
%A Gruber, Michaela
%A Hoermann, Gregor
%A Kubicek, Stefan
%A Staber, Philipp B.
%A Shehata, Medhat
%A Superti-Furga, Giulio
%A Jaeger, Ulrich
%A Bock, Christoph
%+ External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
%T Combined Chemosensitivity and Chromatin Profiling Prioritizes Drug Combinations in CLL :
%G eng
%U http://hdl.handle.net/21.11116/0000-0003-1434-C
%R 10.1038/s41589-018-0205-2
%2 PMC6746620
%7 2019
%D 2019
%J Nature Chemical Biology
%O Nat. Chem. Biol.
%V 15
%N 3
%& 232
%P 232 - 240
%I Nature Pub. Group
%C New York, NY
%@ false
102. Schmidt F, Kern F, Ebert P, Baumgarten N, Schulz MH: TEPIC 2 - an Extended Framework for Transcription Factor Binding Prediction and Integrative Epigenomic Analysis. Bioinformatics 2019, 35.
Export
BibTeX
@article{Schmidt2019Tepic,
TITLE = {{TEPIC} 2 -- an Extended Framework for Transcription Factor Binding Prediction and Integrative Epigenomic Analysis},
AUTHOR = {Schmidt, Florian and Kern, Fabian and Ebert, Peter and Baumgarten, Nina and Schulz, Marcel Holger},
LANGUAGE = {eng},
ISSN = {1367-4803},
DOI = {10.1093/bioinformatics/bty856},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford, UK},
YEAR = {2019},
JOURNAL = {Bioinformatics},
VOLUME = {35},
NUMBER = {9},
PAGES = {1608--1609},
}
Endnote
%0 Journal Article
%A Schmidt, Florian
%A Kern, Fabian
%A Ebert, Peter
%A Baumgarten, Nina
%A Schulz, Marcel Holger
%+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
%T TEPIC 2 - an Extended Framework for Transcription Factor Binding Prediction and Integrative Epigenomic Analysis :
%G eng
%U http://hdl.handle.net/21.11116/0000-0003-C333-7
%R 10.1093/bioinformatics/bty856
%2 PMC6499243
%7 2019
%D 2019
%J Bioinformatics
%V 35
%N 9
%& 1608
%P 1608 - 1609
%I Oxford University Press
%C Oxford, UK
%@ false
103. Schmidt F, Schulz MH: On the Problem of Confounders in Modeling Gene Expression. Bioinformatics 2019, 35.
Export
BibTeX
@article{Schmidt2019,
TITLE = {On the Problem of Confounders in Modeling Gene Expression},
AUTHOR = {Schmidt, Florian and Schulz, Marcel Holger},
LANGUAGE = {eng},
ISSN = {1367-4803},
DOI = {10.1093/bioinformatics/bty674},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford},
YEAR = {2019},
DATE = {2019},
JOURNAL = {Bioinformatics},
VOLUME = {35},
NUMBER = {4},
PAGES = {711--719},
}
Endnote
%0 Journal Article
%A Schmidt, Florian
%A Schulz, Marcel Holger
%+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
%T On the Problem of Confounders in Modeling Gene Expression :
%G eng
%U http://hdl.handle.net/21.11116/0000-0003-2094-1
%R 10.1093/bioinformatics/bty674
%2 PMC6530814
%7 2018
%D 2019
%J Bioinformatics
%V 35
%N 4
%& 711
%P 711 - 719
%I Oxford University Press
%C Oxford
%@ false
104. Sdelci S, Rendeiro AF, Rathert P, You W, Lin J-MG, Ringler A, Hofstaetter G, Moll HP, Guertl B, Farlik M, Schick S, Klepsch F, Oldach M, Buphamalai P, Schischlik F, Majek P, Parapatics K, Schmidl C, Schuster M, Penz T, Buckley DL, Hudecz O, Imre R, Wang S-Y, Maric HM, Kralovics R, Bennett KL, Mueller AC, Mechtler K, Menche J, et al.: MTHFD1 Interaction with BRD4 Links Folate Metabolism to Transcriptional Regulation. Nature Genetics 2019, 51.
Export
BibTeX
@article{Sdelci2019,
TITLE = {{MTHFD1} interaction with {BRD4} links folate metabolism to transcriptional regulation},
AUTHOR = {Sdelci, Sara and Rendeiro, Andre F. and Rathert, Philipp and You, Wanhui and Lin, Jung-Ming G. and Ringler, Anna and Hofstaetter, Gerald and Moll, Herwig P. and Guertl, Bettina and Farlik, Matthias and Schick, Sandra and Klepsch, Freya and Oldach, Matthew and Buphamalai, Pisanu and Schischlik, Fiorella and Majek, Peter and Parapatics, Katja and Schmidl, Christian and Schuster, Michael and Penz, Thomas and Buckley, Dennis L. and Hudecz, Otto and Imre, Richard and Wang, Shuang-Yan and Maric, Hans Michael and Kralovics, Robert and Bennett, Keiryn L. and Mueller, Andre C. and Mechtler, Karl and Menche, Joerg and Bradner, James E. and Winter, Georg E. and Klavins, Kristaps and Casanova, Emilio and Bock, Christoph and Zuber, Johannes and Kubicek, Stefan},
LANGUAGE = {eng},
ISSN = {1061-4036},
DOI = {10.1038/s41588-019-0413-z},
PUBLISHER = {Nature America, Inc.},
ADDRESS = {New York, NY},
YEAR = {2019},
DATE = {2019},
JOURNAL = {Nature Genetics},
VOLUME = {51},
NUMBER = {6},
PAGES = {990--998},
}
Endnote
%0 Journal Article
%A Sdelci, Sara
%A Rendeiro, Andre F.
%A Rathert, Philipp
%A You, Wanhui
%A Lin, Jung-Ming G.
%A Ringler, Anna
%A Hofstaetter, Gerald
%A Moll, Herwig P.
%A Guertl, Bettina
%A Farlik, Matthias
%A Schick, Sandra
%A Klepsch, Freya
%A Oldach, Matthew
%A Buphamalai, Pisanu
%A Schischlik, Fiorella
%A Majek, Peter
%A Parapatics, Katja
%A Schmidl, Christian
%A Schuster, Michael
%A Penz, Thomas
%A Buckley, Dennis L.
%A Hudecz, Otto
%A Imre, Richard
%A Wang, Shuang-Yan
%A Maric, Hans Michael
%A Kralovics, Robert
%A Bennett, Keiryn L.
%A Mueller, Andre C.
%A Mechtler, Karl
%A Menche, Joerg
%A Bradner, James E.
%A Winter, Georg E.
%A Klavins, Kristaps
%A Casanova, Emilio
%A Bock, Christoph
%A Zuber, Johannes
%A Kubicek, Stefan
%+ External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
External Organizations
%T MTHFD1 Interaction with BRD4 Links Folate Metabolism to Transcriptional Regulation :
%G eng
%U http://hdl.handle.net/21.11116/0000-0003-D413-8
%R 10.1038/s41588-019-0413-z
%7 2019
%D 2019
%J Nature Genetics
%O Nature Genet.
%V 51
%N 6
%& 990
%P 990 - 998
%I Nature America, Inc.
%C New York, NY
%@ false
105. Sippl C, Ketter R, Braun L, Teping F, Schoeneberger L, Kim YJ, List M, Nakhoda A, Wemmert S, Oertel J, Urbschat S: miRNA-26a Expression Influences the Therapy Response to Carmustine Wafer Implantation in Patients with Glioblastoma Multiforme. Acta Neurochirurgica 2019, 161.
Export
BibTeX
@article{Sippl2019,
TITLE = {{miRNA}-26a Expression Influences the Therapy Response to Carmustine Wafer Implantation in Patients with Glioblastoma Multiforme},
AUTHOR = {Sippl, Christoph and Ketter, Ralf and Braun, Luisa and Teping, Fritz and Schoeneberger, Louisa and Kim, Yoo Jin and List, Markus and Nakhoda, Arjang and Wemmert, Silke and Oertel, Joachim and Urbschat, Steffi},
LANGUAGE = {eng},
ISSN = {0001-6268},
DOI = {10.1007/s00701-019-04051-8},
PUBLISHER = {Springer-Verlag.},
ADDRESS = {Vienna},
YEAR = {2019},
DATE = {2019},
JOURNAL = {Acta Neurochirurgica},
VOLUME = {161},
NUMBER = {11},
PAGES = {2299--2309},
}
Endnote
%0 Journal Article
%A Sippl, Christoph
%A Ketter, Ralf
%A Braun, Luisa
%A Teping, Fritz
%A Schoeneberger, Louisa
%A Kim, Yoo Jin
%A List, Markus
%A Nakhoda, Arjang
%A Wemmert, Silke
%A Oertel, Joachim
%A Urbschat, Steffi
%+ External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
External Organizations
External Organizations
External Organizations
%T miRNA-26a Expression Influences the Therapy Response to Carmustine Wafer Implantation in Patients with Glioblastoma Multiforme :
%G eng
%U http://hdl.handle.net/21.11116/0000-0005-6B6C-B
%R 10.1007/s00701-019-04051-8
%7 2019
%D 2019
%J Acta Neurochirurgica
%O Acta Neurochir.
%V 161
%N 11
%& 2299
%P 2299 - 2309
%I Springer-Verlag.
%C Vienna
%@ false
106. Soldatov R, Kaucka M, Kastriti ME, Petersen J, Chontorotzea T, Englmaier L, Akkuratova N, Yang Y, Haring M, Dyachuk V, Bock C, Farlik M, Piacentino ML, Boismoreau F, Hilscher MM, Yokota C, Qian X, Nilsson M, Bronner ME, Croci L, Hsiao W-Y, Guertin DA, Brunet J-F, Consalez GG, Ernfors P, Fried K, Kharchenko PV, Adameyko I: Spatiotemporal Structure of Cell Fate Decisions in Murine Neural Crest. Science 2019, 364.
Export
BibTeX
@article{Soldatov2019b,
TITLE = {Spatiotemporal Structure of Cell Fate Decisions in Murine Neural Crest},
AUTHOR = {Soldatov, Ruslan and Kaucka, Marketa and Kastriti, Maria Eleni and Petersen, Julian and Chontorotzea, Tatiana and Englmaier, Lukas and Akkuratova, Natalia and Yang, Yunshi and Haring, Martin and Dyachuk, Viacheslav and Bock, Christoph and Farlik, Matthias and Piacentino, Michael L. and Boismoreau, Franck and Hilscher, Markus M. and Yokota, Chika and Qian, Xiaoyan and Nilsson, Mats and Bronner, Marianne E. and Croci, Laura and Hsiao, Wen-Yu and Guertin, David A. and Brunet, Jean-Francois and Consalez, Gian Giacomo and Ernfors, Patrik and Fried, Kaj and Kharchenko, Peter V. and Adameyko, Igor},
LANGUAGE = {eng},
ISSN = {0036-8075},
DOI = {10.1126/science.aas9536},
PUBLISHER = {AAAS},
ADDRESS = {Washington, D.C.},
YEAR = {2019},
DATE = {2019},
JOURNAL = {Science},
VOLUME = {364},
NUMBER = {64444},
EID = {eaas9536},
}
Endnote
%0 Journal Article
%A Soldatov, Ruslan
%A Kaucka, Marketa
%A Kastriti, Maria Eleni
%A Petersen, Julian
%A Chontorotzea, Tatiana
%A Englmaier, Lukas
%A Akkuratova, Natalia
%A Yang, Yunshi
%A Haring, Martin
%A Dyachuk, Viacheslav
%A Bock, Christoph
%A Farlik, Matthias
%A Piacentino, Michael L.
%A Boismoreau, Franck
%A Hilscher, Markus M.
%A Yokota, Chika
%A Qian, Xiaoyan
%A Nilsson, Mats
%A Bronner, Marianne E.
%A Croci, Laura
%A Hsiao, Wen-Yu
%A Guertin, David A.
%A Brunet, Jean-Francois
%A Consalez, Gian Giacomo
%A Ernfors, Patrik
%A Fried, Kaj
%A Kharchenko, Peter V.
%A Adameyko, Igor
%+ External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
%T Spatiotemporal Structure of Cell Fate Decisions in Murine Neural Crest
:
%G eng
%U http://hdl.handle.net/21.11116/0000-0003-E117-5
%R 10.1126/science.aas9536
%7 2019
%D 2019
%J Science
%O Science
%V 364
%N 64444
%Z sequence number: eaas9536
%I AAAS
%C Washington, D.C.
%@ false
107. Ulz P, Perakis S, Zhou Q, Moser T, Belic J, Lazzeri I, Woelfler A, Zebisch A, Gerger A, Pristauz G, Petru E, White B, Roberts CES, St Johns J, Schimek MG, Geigl JB, Bauernhofer T, Sill H, Bock C, Heitzer E, Speicher MR: Inference of Transcription Factor Binding from Cell-free DNA Enables Tumor Subtype Prediction and Early Detection. Nature Communications 2019, 10.
Export
BibTeX
@article{Ulz_2019,
TITLE = {Inference of Transcription Factor Binding from Cell-free {DNA} Enables Tumor Subtype Prediction and Early Detection},
AUTHOR = {Ulz, Peter and Perakis, Samantha and Zhou, Qing and Moser, Tina and Belic, Jelena and Lazzeri, Isaac and Woelfler, Albert and Zebisch, Armin and Gerger, Armin and Pristauz, Gunda and Petru, Edgar and White, Brandon and Roberts, Charles E. S. and St Johns, John and Schimek, Michael G. and Geigl, Jochen B. and Bauernhofer, Thomas and Sill, Heinz and Bock, Christoph and Heitzer, Ellen and Speicher, Michael R.},
LANGUAGE = {eng},
ISSN = {2041-1723},
DOI = {10.1038/s41467-019-12714-4},
PUBLISHER = {Nature Publishing Group},
ADDRESS = {London},
YEAR = {2019},
DATE = {2019},
JOURNAL = {Nature Communications},
VOLUME = {10},
EID = {4666},
}
Endnote
%0 Journal Article
%A Ulz, Peter
%A Perakis, Samantha
%A Zhou, Qing
%A Moser, Tina
%A Belic, Jelena
%A Lazzeri, Isaac
%A Woelfler, Albert
%A Zebisch, Armin
%A Gerger, Armin
%A Pristauz, Gunda
%A Petru, Edgar
%A White, Brandon
%A Roberts, Charles E. S.
%A St Johns, John
%A Schimek, Michael G.
%A Geigl, Jochen B.
%A Bauernhofer, Thomas
%A Sill, Heinz
%A Bock, Christoph
%A Heitzer, Ellen
%A Speicher, Michael R.
%+ External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
External Organizations
%T Inference of Transcription Factor Binding from Cell-free DNA Enables Tumor Subtype Prediction and Early Detection :
%G eng
%U http://hdl.handle.net/21.11116/0000-0004-E6B9-8
%R 10.1038/s41467-019-12714-4
%7 2019
%D 2019
%J Nature Communications
%O Nat. Commun.
%V 10
%Z sequence number: 4666
%I Nature Publishing Group
%C London
%@ false
108. Ünal AB, Akgün M, Pfeifer N: A Framework with Randomized Encoding for a Fast Privacy Preserving Calculation of Non-linear Kernels for Machine Learning Applications in Precision Medicine. In Cryptology and Network Security (CANS 2019). Springer; 2019. [Lecture Notes in Computer Science, vol. 11829]
Export
BibTeX
@inproceedings{Uenal_CANS2019,
TITLE = {A Framework with Randomized Encoding for a Fast Privacy Preserving Calculation of Non-linear Kernels for Machine Learning Applications in Precision Medicine},
AUTHOR = {{\"U}nal, Ali Burak and Akg{\"u}n, Mete and Pfeifer, Nico},
LANGUAGE = {eng},
ISBN = {978-3-030-31577-1},
DOI = {10.1007/978-3-030-31578-8_27},
PUBLISHER = {Springer},
YEAR = {2019},
DATE = {2019},
BOOKTITLE = {Cryptology and Network Security (CANS 2019)},
EDITOR = {Mu, Yi and Deng, Robert H. and Huang, Xinyi},
PAGES = {493--511},
SERIES = {Lecture Notes in Computer Science},
VOLUME = {11829},
ADDRESS = {Fuzhou, China},
}
Endnote
%0 Conference Proceedings
%A Ünal, Ali Burak
%A Akgün, Mete
%A Pfeifer, Nico
%+ External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
%T A Framework with Randomized Encoding for a Fast Privacy Preserving Calculation of Non-linear Kernels for Machine Learning Applications in Precision Medicine :
%G eng
%U http://hdl.handle.net/21.11116/0000-0006-DB9F-1
%R 10.1007/978-3-030-31578-8_27
%D 2019
%B 18th International Conference on Cryptology and Network Security
%Z date of event: 2019-10-25 - 2019-10-27
%C Fuzhou, China
%B Cryptology and Network Security
%E Mu, Yi; Deng, Robert H.; Huang, Xinyi
%P 493 - 511
%I Springer
%@ 978-3-030-31577-1
%B Lecture Notes in Computer Science
%N 11829
109. Wenger AM, Peluso P, Rowell WJ, Chang P-C, Hall RJ, Concepcion GT, Ebler J, Fungtammasan A, Kolesnikov A, Olson ND, Topfer A, Alonge M, Mahmoud M, Qian Y, Chin C-S, Phillippy AM, Schate MC, Myers G, DePristo MA, Ruan J, Marschall T, Sedlazeck FJ, Zook JM, Li H, Koren S, Carroll A, Rank DR, Hunkapiller MW: Accurate Circular Consensus Long-read Sequencing Improves Variant Detection and Assembly of a Human Genome. Nature Biotechnology 2019, 37.
Export
BibTeX
@article{Wenger2019,
TITLE = {Accurate Circular Consensus Long-read Sequencing Improves Variant Detection and Assembly of a Human Genome},
AUTHOR = {Wenger, Aaron M. and Peluso, Paul and Rowell, William J. and Chang, Pi-Chuan and Hall, Richard J. and Concepcion, Gregory T. and Ebler, Jana and Fungtammasan, Arkarachai and Kolesnikov, Alexey and Olson, Nathan D. and Topfer, Armin and Alonge, Michael and Mahmoud, Medhat and Qian, Yufeng and Chin, Chen-Shan and Phillippy, Adam M. and Schate, Michael C. and Myers, Gene and DePristo, Mark A. and Ruan, Jue and Marschall, Tobias and Sedlazeck, Fritz J. and Zook, Justin M. and Li, Heng and Koren, Sergey and Carroll, Andrew and Rank, David R. and Hunkapiller, Michael W.},
LANGUAGE = {eng},
ISSN = {1087-0156},
DOI = {10.1038/s41587-019-0217-9},
PUBLISHER = {Gale Group Inc.},
ADDRESS = {New York},
YEAR = {2019},
DATE = {2019},
JOURNAL = {Nature Biotechnology},
VOLUME = {37},
PAGES = {1155--1162},
}
Endnote
%0 Journal Article
%A Wenger, Aaron M.
%A Peluso, Paul
%A Rowell, William J.
%A Chang, Pi-Chuan
%A Hall, Richard J.
%A Concepcion, Gregory T.
%A Ebler, Jana
%A Fungtammasan, Arkarachai
%A Kolesnikov, Alexey
%A Olson, Nathan D.
%A Topfer, Armin
%A Alonge, Michael
%A Mahmoud, Medhat
%A Qian, Yufeng
%A Chin, Chen-Shan
%A Phillippy, Adam M.
%A Schate, Michael C.
%A Myers, Gene
%A DePristo, Mark A.
%A Ruan, Jue
%A Marschall, Tobias
%A Sedlazeck, Fritz J.
%A Zook, Justin M.
%A Li, Heng
%A Koren, Sergey
%A Carroll, Andrew
%A Rank, David R.
%A Hunkapiller, Michael W.
%+ External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
%T Accurate Circular Consensus Long-read Sequencing Improves Variant Detection and Assembly of a Human Genome :
%G eng
%U http://hdl.handle.net/21.11116/0000-0005-6AF6-F
%R 10.1038/s41587-019-0217-9
%7 2019
%D 2019
%J Nature Biotechnology
%V 37
%& 1155
%P 1155 - 1162
%I Gale Group Inc.
%C New York
%@ false
110. Wiegand SB, Beggel B, Wranke A, Aliabadi E, Jaroszewicz J, Xu C-J, Li Y, Manns MP, Lengauer T, Wedemeyer H, Kraft ARM, Falk CS, Cornberg M: Soluble Immune Markers in the Different Phases of Chronic Hepatitis B Virus Infection. Scientific Reports 2019, 9.
Export
BibTeX
@article{Wiegand_2019,
TITLE = {Soluble immune markers in the different phases of chronic hepatitis {B} virus infection},
AUTHOR = {Wiegand, Steffen B. and Beggel, Bastian and Wranke, Anika and Aliabadi, Elmira and Jaroszewicz, Jerzy and Xu, Cheng-Jian and Li, Yang and Manns, Michael P. and Lengauer, Thomas and Wedemeyer, Heiner and Kraft, Anke R. M. and Falk, Christine S. and Cornberg, Markus},
LANGUAGE = {eng},
ISSN = {2045-2322},
DOI = {10.1038/s41598-019-50729-5},
PUBLISHER = {Nature Publishing Group},
ADDRESS = {London, UK},
YEAR = {2019},
JOURNAL = {Scientific Reports},
VOLUME = {9},
EID = {14118},
}
Endnote
%0 Journal Article
%A Wiegand, Steffen B.
%A Beggel, Bastian
%A Wranke, Anika
%A Aliabadi, Elmira
%A Jaroszewicz, Jerzy
%A Xu, Cheng-Jian
%A Li, Yang
%A Manns, Michael P.
%A Lengauer, Thomas
%A Wedemeyer, Heiner
%A Kraft, Anke R. M.
%A Falk, Christine S.
%A Cornberg, Markus
%+ External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
External Organizations
External Organizations
External Organizations
%T Soluble Immune Markers in the Different Phases of Chronic Hepatitis B Virus Infection :
%G eng
%U http://hdl.handle.net/21.11116/0000-0004-E49F-8
%R 10.1038/s41598-019-50729-5
%2 PMC6773856
%7 2019
%D 2019
%J Scientific Reports
%O Sci. Rep.
%V 9
%Z sequence number: 14118
%I Nature Publishing Group
%C London, UK
%@ false
111. Yi G, Wierenga ATJ, Petraglia F, Narang P, Janssen-Megens EM, Mandoli A, Merkel A, Berentsen K, Kim B, Matarese F, Singh AA, Habibi E, Prange KHM, Mulder AB, Jansen JH, Clarke L, Heath S, van der Reijden BA, Flicek P, Yaspo M-L, Gut I, Bock C, Schuringa JJ, Altucci L, Vellenga E, Stunnenberg HG, Martens J, H. A: Chromatin-Based Classification of Genetically Heterogeneous AMLs into Two Distinct Subtypes with Diverse Stemness Phenotypes. Cell Reports 2019, 26.
Export
BibTeX
@article{Yi2019,
TITLE = {Chromatin-Based Classification of Genetically Heterogeneous {AMLs} into Two Distinct Subtypes with Diverse Stemness Phenotypes},
AUTHOR = {Yi, Guoqiang and Wierenga, Albertus T. J. and Petraglia, Francesca and Narang, Pankaj and Janssen-Megens, Eva M. and Mandoli, Amit and Merkel, Angelika and Berentsen, Kim and Kim, Bowon and Matarese, Filomena and Singh, Abhishek A. and Habibi, Ehsan and Prange, Koen H. M. and Mulder, Andre B. and Jansen, Joop H. and Clarke, Laura and Heath, Simon and van der Reijden, Bert A. and Flicek, Paul and Yaspo, Marie-Laure and Gut, Ivo and Bock, Christoph and Schuringa, Jan Jacob and Altucci, Lucia and Vellenga, Edo and Stunnenberg, Hendrik G. and Martens, Joost and H., A.},
LANGUAGE = {eng},
ISSN = {2211-1247},
DOI = {10.1016/j.celrep.2018.12.098},
PUBLISHER = {Cell Press},
ADDRESS = {Maryland Heights, MO},
YEAR = {2019},
JOURNAL = {Cell Reports},
VOLUME = {26},
NUMBER = {4},
PAGES = {1059--1069},
EID = {e6},
}
Endnote
%0 Journal Article
%A Yi, Guoqiang
%A Wierenga, Albertus T. J.
%A Petraglia, Francesca
%A Narang, Pankaj
%A Janssen-Megens, Eva M.
%A Mandoli, Amit
%A Merkel, Angelika
%A Berentsen, Kim
%A Kim, Bowon
%A Matarese, Filomena
%A Singh, Abhishek A.
%A Habibi, Ehsan
%A Prange, Koen H. M.
%A Mulder, Andre B.
%A Jansen, Joop H.
%A Clarke, Laura
%A Heath, Simon
%A van der Reijden, Bert A.
%A Flicek, Paul
%A Yaspo, Marie-Laure
%A Gut, Ivo
%A Bock, Christoph
%A Schuringa, Jan Jacob
%A Altucci, Lucia
%A Vellenga, Edo
%A Stunnenberg, Hendrik G.
%A Martens, Joost
%A H., A.
%+ External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
%T Chromatin-Based Classification of Genetically Heterogeneous AMLs into Two Distinct Subtypes with Diverse Stemness Phenotypes :
%G eng
%U http://hdl.handle.net/21.11116/0000-0002-F6CB-4
%R 10.1016/j.celrep.2018.12.098
%7 2019
%D 2019
%J Cell Reports
%V 26
%N 4
%& 1059
%P 1059 - 1069
%Z sequence number: e6
%I Cell Press
%C Maryland Heights, MO
%@ false
2018
112. Allison TF, Andrews PW, Avior Y, Barbaric I, Benvenisty N, Bock C, Brehm J, Bruestle O, Damjanov I, Elefanty A, Felkner D, Gokhale PJ, Halbritter F, Healy LE, Hu TX, Knowles BB, Loring JF, Ludwig TE, Mayberry R, Micallef S, Mohamed JS, Mueller F-J, Mummery CL, Nakatsuji N, Ng ES, Oh SKW, O’Shea O, Pera MF, Reubinoff B, Robson P, et al.: Assessment of Established Techniques to Determine Developmental and Malignant Potential of Human Pluripotent Stem Cells. Nature Communications 2018.
Export
BibTeX
@article{Allison2018,
TITLE = {Assessment of Established Techniques to Determine Developmental and Malignant Potential of Human Pluripotent Stem Cells},
AUTHOR = {Allison, Thomas F. and Andrews, Peter W. and Avior, Yishai and Barbaric, Ivana and Benvenisty, Nissim and Bock, Christoph and Brehm, Jennifer and Bruestle, Oliver and Damjanov, Ivan and Elefanty, Andrew and Felkner, Daniel and Gokhale, Paul J. and Halbritter, Florian and Healy, Lyn E. and Hu, Tim X. and Knowles, Barbara B. and Loring, Jeanne F. and Ludwig, Tenneille E. and Mayberry, Robyn and Micallef, Suzanne and Mohamed, Jameelah S. and Mueller, Franz-Josef and Mummery, Christine L. and Nakatsuji, Norio and Ng, Elizabeth S. and Oh, Steve K. W. and O'Shea, Orla and Pera, Martin F. and Reubinoff, Benjamin and Robson, Paul and Rossant, Janet and Schuldt, Bernhard M. and Solter, Davor and Sourris, Koula and Stacey, Glyn and Stanley, Edouard G. and Suemori, Hirofumi and Takahashi, Kazutoshi and Yamanaka, Shinya},
LANGUAGE = {eng},
ISSN = {2041-1723},
DOI = {10.1038/s41467-018-04011-3},
PUBLISHER = {Nature Publishing Group},
ADDRESS = {London},
YEAR = {2018},
JOURNAL = {Nature Communications},
EID = {1925},
}
Endnote
%0 Journal Article
%A Allison, Thomas F.
%A Andrews, Peter W.
%A Avior, Yishai
%A Barbaric, Ivana
%A Benvenisty, Nissim
%A Bock, Christoph
%A Brehm, Jennifer
%A Bruestle, Oliver
%A Damjanov, Ivan
%A Elefanty, Andrew
%A Felkner, Daniel
%A Gokhale, Paul J.
%A Halbritter, Florian
%A Healy, Lyn E.
%A Hu, Tim X.
%A Knowles, Barbara B.
%A Loring, Jeanne F.
%A Ludwig, Tenneille E.
%A Mayberry, Robyn
%A Micallef, Suzanne
%A Mohamed, Jameelah S.
%A Mueller, Franz-Josef
%A Mummery, Christine L.
%A Nakatsuji, Norio
%A Ng, Elizabeth S.
%A Oh, Steve K. W.
%A O'Shea, Orla
%A Pera, Martin F.
%A Reubinoff, Benjamin
%A Robson, Paul
%A Rossant, Janet
%A Schuldt, Bernhard M.
%A Solter, Davor
%A Sourris, Koula
%A Stacey, Glyn
%A Stanley, Edouard G.
%A Suemori, Hirofumi
%A Takahashi, Kazutoshi
%A Yamanaka, Shinya
%+ External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
%T Assessment of Established Techniques to Determine Developmental and Malignant Potential of Human Pluripotent Stem Cells :
%G eng
%U http://hdl.handle.net/21.11116/0000-0001-66DB-6
%R 10.1038/s41467-018-04011-3
%7 2018
%D 2018
%J Nature Communications
%O Nat. Commun.
%Z sequence number: 1925
%I Nature Publishing Group
%C London
%@ false
113. Apweiler R, Beissbarth T, Berthold MR, Bluethgen N, Burmeister Y, Dammann O, Deutsch A, Feuerhake F, Franke A, Hasenauer J, Hoffmann S, Hoefer T, Jansen PLM, Kaderali L, Klingmueller U, Koch I, Kohlbacher O, Kuepfer L, Lammert F, Maier D, Pfeifer N, Radde N, Rehm M, Roeder I, Saez-Rodriguez J, Sax U, Schmeck B, Schuppert A, Seilheimer B, Theis FJ, et al.: Whither systems medicine?Experimental & Molecular Medicine 2018, 50.
Export
BibTeX
@article{Apweiler2018,
TITLE = {Whither systems medicine?},
AUTHOR = {Apweiler, Rolf and Beissbarth, Tim and Berthold, Michael R. and Bluethgen, Nils and Burmeister, Yvonne and Dammann, Olaf and Deutsch, Andreas and Feuerhake, Friedrich and Franke, Andre and Hasenauer, Jan and Hoffmann, Steve and Hoefer, Thomas and Jansen, Peter L. M. and Kaderali, Lars and Klingmueller, Ursula and Koch, Ina and Kohlbacher, Oliver and Kuepfer, Lars and Lammert, Frank and Maier, Dieter and Pfeifer, Nico and Radde, Nicole and Rehm, Markus and Roeder, Ingo and Saez-Rodriguez, Julio and Sax, Ulrich and Schmeck, Bernd and Schuppert, Andreas and Seilheimer, Bernd and Theis, Fabian J. and Vera, Julio and Wolkenhauer, Olaf},
LANGUAGE = {eng},
ISSN = {2092-6413},
DOI = {10.1038/emm.2017.290},
PUBLISHER = {Korean Society of Medical Biochemistry and Molecular Biology},
ADDRESS = {Seoul},
YEAR = {2018},
DATE = {2018},
JOURNAL = {Experimental \& Molecular Medicine},
VOLUME = {50},
EID = {e453},
}
Endnote
%0 Journal Article
%A Apweiler, Rolf
%A Beissbarth, Tim
%A Berthold, Michael R.
%A Bluethgen, Nils
%A Burmeister, Yvonne
%A Dammann, Olaf
%A Deutsch, Andreas
%A Feuerhake, Friedrich
%A Franke, Andre
%A Hasenauer, Jan
%A Hoffmann, Steve
%A Hoefer, Thomas
%A Jansen, Peter L. M.
%A Kaderali, Lars
%A Klingmueller, Ursula
%A Koch, Ina
%A Kohlbacher, Oliver
%A Kuepfer, Lars
%A Lammert, Frank
%A Maier, Dieter
%A Pfeifer, Nico
%A Radde, Nicole
%A Rehm, Markus
%A Roeder, Ingo
%A Saez-Rodriguez, Julio
%A Sax, Ulrich
%A Schmeck, Bernd
%A Schuppert, Andreas
%A Seilheimer, Bernd
%A Theis, Fabian J.
%A Vera, Julio
%A Wolkenhauer, Olaf
%+ External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
%T Whither systems medicine? :
%G eng
%U http://hdl.handle.net/21.11116/0000-0001-2D95-5
%R 10.1038/emm.2017.290
%7 2018
%D 2018
%J Experimental & Molecular Medicine
%O EMM
%V 50
%Z sequence number: e453
%I Korean Society of Medical Biochemistry and Molecular Biology
%C Seoul
%@ false
114. Barakat TS, Halbritter F, Zhang M, Rendeiro AF, Perenthaler E, Bock C, Chambers I: Functional Dissection of the Enhancer Repertoire in Human Embryonic Stem Cells. Cell Stem Cell 2018, 23.
Export
BibTeX
@article{Bakarat2018,
TITLE = {Functional Dissection of the Enhancer Repertoire in Human Embryonic Stem Cells},
AUTHOR = {Barakat, Tahsin Stefan and Halbritter, Florian and Zhang, Man and Rendeiro, Andre F. and Perenthaler, Elena and Bock, Christoph and Chambers, Ian},
LANGUAGE = {eng},
ISSN = {1934-5909; 1875-9777},
DOI = {10.1016/j.stem.2018.06.014},
PUBLISHER = {Elsevier},
ADDRESS = {Amsterdam},
YEAR = {2018},
DATE = {2018},
JOURNAL = {Cell Stem Cell},
VOLUME = {23},
NUMBER = {2},
PAGES = {276--288},
EID = {e8},
}
Endnote
%0 Journal Article
%A Barakat, Tahsin Stefan
%A Halbritter, Florian
%A Zhang, Man
%A Rendeiro, Andre F.
%A Perenthaler, Elena
%A Bock, Christoph
%A Chambers, Ian
%+ External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
%T Functional Dissection of the Enhancer Repertoire in Human Embryonic Stem Cells :
%G eng
%U http://hdl.handle.net/21.11116/0000-0001-EE1A-7
%R 10.1016/j.stem.2018.06.014
%7 2018
%D 2018
%J Cell Stem Cell
%V 23
%N 2
%& 276
%P 276 - 288
%Z sequence number: e8
%I Elsevier
%C Amsterdam
%@ false
115. Bar-On Y, Gruell H, Schoofs T, Pai JA, Nogueira L, Butler AL, Millard K, Lehmann C, Suarez I, Oliveira TY, Karagounis T, Cohen YZ, Wyen C, Scholten S, Handl L, Belblidia S, Dizon JP, Vehreschild JJ, Witmer-Pack M, Shimeliovich I, Jain K, Fiddike K, Seaton KE, Yates NL, Horowitz J, Gulick RM, Pfeifer N, Tomaras GD, Seaman MS, Faetkenheuer G, et al.: Safety and Antiviral Activity of Combination HIV-1 Broadly Neutralizing Antibodies in Viremic Individuals. Nature Medicine 2018, 24.
Export
BibTeX
@article{Bar-On_2018,
TITLE = {Safety and antiviral activity of combination {HIV}-1 broadly neutralizing antibodies in viremic individuals},
AUTHOR = {Bar-On, Yotam and Gruell, Henning and Schoofs, Till and Pai, Joy A. and Nogueira, Lilian and Butler, Allison L. and Millard, Katrina and Lehmann, Clara and Suarez, Isabelle and Oliveira, Thiago Y. and Karagounis, Theodora and Cohen, Yehuda Z. and Wyen, Christoph and Scholten, Stefan and Handl, Lisa and Belblidia, Shiraz and Dizon, Juan P. and Vehreschild, Joerg J. and Witmer-Pack, Maggi and Shimeliovich, Irina and Jain, Kanika and Fiddike, Kerstin and Seaton, Kelly E. and Yates, Nicole L. and Horowitz, Jill and Gulick, Roy M. and Pfeifer, Nico and Tomaras, Georgia D. and Seaman, Michael S. and Faetkenheuer, Gerd and Caskey, Marina and Klein, Florian and Nussenzweig, Michel C.},
LANGUAGE = {eng},
ISSN = {1078-8956},
DOI = {10.1038/s41591-018-0186-4},
PUBLISHER = {Nature Pub. Co.},
ADDRESS = {New York, NY},
YEAR = {2018},
DATE = {2018},
JOURNAL = {Nature Medicine},
VOLUME = {24},
NUMBER = {1},
PAGES = {1701--1707},
}
Endnote
%0 Journal Article
%A Bar-On, Yotam
%A Gruell, Henning
%A Schoofs, Till
%A Pai, Joy A.
%A Nogueira, Lilian
%A Butler, Allison L.
%A Millard, Katrina
%A Lehmann, Clara
%A Suarez, Isabelle
%A Oliveira, Thiago Y.
%A Karagounis, Theodora
%A Cohen, Yehuda Z.
%A Wyen, Christoph
%A Scholten, Stefan
%A Handl, Lisa
%A Belblidia, Shiraz
%A Dizon, Juan P.
%A Vehreschild, Joerg J.
%A Witmer-Pack, Maggi
%A Shimeliovich, Irina
%A Jain, Kanika
%A Fiddike, Kerstin
%A Seaton, Kelly E.
%A Yates, Nicole L.
%A Horowitz, Jill
%A Gulick, Roy M.
%A Pfeifer, Nico
%A Tomaras, Georgia D.
%A Seaman, Michael S.
%A Faetkenheuer, Gerd
%A Caskey, Marina
%A Klein, Florian
%A Nussenzweig, Michel C.
%+ External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
%T Safety and Antiviral Activity of Combination HIV-1 Broadly Neutralizing Antibodies in Viremic Individuals
:
%G eng
%U http://hdl.handle.net/21.11116/0000-0002-8636-A
%R 10.1038/s41591-018-0186-4
%7 2018
%D 2018
%J Nature Medicine
%O Nat. Med.
%V 24
%N 1
%& 1701
%P 1701 - 1707
%I Nature Pub. Co.
%C New York, NY
%@ false
116. Bastys T: Analysis of the protein-Ligand and protein-peptide interactions using a combined sequence- and structure-based approach. Universität des Saarlandes; 2018.
Abstract
Proteins participate in most of the important processes in cells, and their ability to perform their function ultimately depends on their three-dimensional structure. They usually act in these processes through interactions with other molecules. Because of the importance of their role, proteins are also the common target for small molecule drugs that inhibit their activity, which may include targeting protein interactions. Understanding protein interactions and how they are affected by mutations is thus crucial for combating drug resistance and aiding drug design. This dissertation combines bioinformatics studies of protein interactions at both primary sequence and structural level. We analyse protein-protein interactions through linear motifs, as well as protein-small molecule interactions, and study how mutations affect them. This is done in the context of two systems. In the first study of drug resistance mutations in the protease of the human immunodeficiency virus type 1, we successfully apply molecular dynamics simulations to estimate the effects of known resistance-associated mutations on the free binding energy, also revealing molecular mechanisms of resistance. In the second study, we analyse consensus profiles of linear motifs that mediate the recognition by the mitogen-activated protein kinases of their target proteins. We thus gain insights into the cellular processes these proteins are involved in.
Export
BibTeX
@phdthesis{Bastysphd2013,
TITLE = {Analysis of the protein-Ligand and protein-peptide interactions using a combined sequence- and structure-based approach},
AUTHOR = {Bastys, Tomas},
LANGUAGE = {eng},
URL = {urn:nbn:de:bsz:291--ds-279202},
DOI = {10.22028/D291-27920},
SCHOOL = {Universit{\"a}t des Saarlandes},
ADDRESS = {Saarbr{\"u}cken},
YEAR = {2018},
DATE = {2018},
ABSTRACT = {Proteins participate in most of the important processes in cells, and their ability to perform their function ultimately depends on their three-dimensional structure. They usually act in these processes through interactions with other molecules. Because of the importance of their role, proteins are also the common target for small molecule drugs that inhibit their activity, which may include targeting protein interactions. Understanding protein interactions and how they are affected by mutations is thus crucial for combating drug resistance and aiding drug design. This dissertation combines bioinformatics studies of protein interactions at both primary sequence and structural level. We analyse protein-protein interactions through linear motifs, as well as protein-small molecule interactions, and study how mutations affect them. This is done in the context of two systems. In the first study of drug resistance mutations in the protease of the human immunodeficiency virus type 1, we successfully apply molecular dynamics simulations to estimate the effects of known resistance-associated mutations on the free binding energy, also revealing molecular mechanisms of resistance. In the second study, we analyse consensus profiles of linear motifs that mediate the recognition by the mitogen-activated protein kinases of their target proteins. We thus gain insights into the cellular processes these proteins are involved in.},
}
Endnote
%0 Thesis
%A Bastys, Tomas
%Y Kalinina, Olga V.
%A referee: Helms, Volkhard
%+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
International Max Planck Research School, MPI for Informatics, Max Planck Society
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
%T Analysis of the protein-Ligand and protein-peptide interactions using a combined sequence- and structure-based approach :
%G eng
%U http://hdl.handle.net/21.11116/0000-0003-CE47-6
%R 10.22028/D291-27920
%U urn:nbn:de:bsz:291--ds-279202
%F OTHER: hdl:20.500.11880/27455
%I Universität des Saarlandes
%C Saarbrücken
%D 2018
%P 134 p.
%V phd
%9 phd
%X Proteins participate in most of the important processes in cells, and their ability to perform their function ultimately depends on their three-dimensional structure. They usually act in these processes through interactions with other molecules. Because of the importance of their role, proteins are also the common target for small molecule drugs that inhibit their activity, which may include targeting protein interactions. Understanding protein interactions and how they are affected by mutations is thus crucial for combating drug resistance and aiding drug design. This dissertation combines bioinformatics studies of protein interactions at both primary sequence and structural level. We analyse protein-protein interactions through linear motifs, as well as protein-small molecule interactions, and study how mutations affect them. This is done in the context of two systems. In the first study of drug resistance mutations in the protease of the human immunodeficiency virus type 1, we successfully apply molecular dynamics simulations to estimate the effects of known resistance-associated mutations on the free binding energy, also revealing molecular mechanisms of resistance. In the second study, we analyse consensus profiles of linear motifs that mediate the recognition by the mitogen-activated protein kinases of their target proteins. We thus gain insights into the cellular processes these proteins are involved in.
%U https://publikationen.sulb.uni-saarland.de/handle/20.500.11880/27455
117. Bastys T, Gapsys V, Doncheva NT, Kaiser R, de Groot BL, Kalinina OV: Consistent Prediction of Mutation Effect on Drug Binding in HIV-1 Protease Using Alchemical Calculations. Journal of Chemical Theory and Computation 2018, 14.
Abstract
Despite of a large number of antiretroviral drugs targeting HIV-1 protease for inhibition, mutations in this protein during the course of patient treatment can render them inefficient. This emerging resistance inspired numerous computational studies of the HIV-1 protease aimed at predicting the effect of mutations on drug binding in terms of free binding energy $\Delta G$, as well as in mechanistic terms. In this study, we analyse ten different protease-inhibitor complexes carrying major resistance-associated mutations (RAMs) G48V, I50V, and L90M using molecular dynamics simulations. We demonstrate that alchemical free energy calculations can consistently predict the effect of mutations on drug binding. By explicitly probing different protonation states of the catalytic aspartic dyad, we reveal the importance of the correct choice of protonation state for the accuracy of the result. We also provide insight into how different mutations affect drug binding in their specific ways, with the unifying theme of how all of them affect the crucial for drug binding regions of the protease.
Export
BibTeX
@article{Bastys2018,
TITLE = {Consistent Prediction of Mutation Effect on Drug Binding in {HIV}-1 Protease Using Alchemical Calculations},
AUTHOR = {Bastys, Tomas and Gapsys, Vytautas and Doncheva, Nadezhda Tsankova and Kaiser, Rolf and de Groot, Bert L. and Kalinina, Olga V.},
LANGUAGE = {eng},
DOI = {10.1021/acs.jctc.7b01109},
PUBLISHER = {American Chemical Society},
ADDRESS = {Washington, D.C.},
YEAR = {2018},
DATE = {2018},
ABSTRACT = {Despite of a large number of antiretroviral drugs targeting HIV-1 protease for inhibition, mutations in this protein during the course of patient treatment can render them inefficient. This emerging resistance inspired numerous computational studies of the HIV-1 protease aimed at predicting the effect of mutations on drug binding in terms of free binding energy $\Delta G$, as well as in mechanistic terms. In this study, we analyse ten different protease-inhibitor complexes carrying major resistance-associated mutations (RAMs) G48V, I50V, and L90M using molecular dynamics simulations. We demonstrate that alchemical free energy calculations can consistently predict the effect of mutations on drug binding. By explicitly probing different protonation states of the catalytic aspartic dyad, we reveal the importance of the correct choice of protonation state for the accuracy of the result. We also provide insight into how different mutations affect drug binding in their specific ways, with the unifying theme of how all of them affect the crucial for drug binding regions of the protease.},
JOURNAL = {Journal of Chemical Theory and Computation},
VOLUME = {14},
NUMBER = {7},
PAGES = {3397--3408},
}
Endnote
%0 Journal Article
%A Bastys, Tomas
%A Gapsys, Vytautas
%A Doncheva, Nadezhda Tsankova
%A Kaiser, Rolf
%A de Groot, Bert L.
%A Kalinina, Olga V.
%+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
%T Consistent Prediction of Mutation Effect on Drug Binding in HIV-1 Protease Using Alchemical Calculations :
%G eng
%U http://hdl.handle.net/21.11116/0000-0001-E5BA-B
%R 10.1021/acs.jctc.7b01109
%7 2018-05-30
%D 2018
%* Review method: peer-reviewed
%X Despite of a large number of antiretroviral drugs targeting HIV-1 protease for inhibition, mutations in this protein during the course of patient treatment can render them inefficient. This emerging resistance inspired numerous computational studies of the HIV-1 protease aimed at predicting the effect of mutations on drug binding in terms of free binding energy $\Delta G$, as well as in mechanistic terms. In this study, we analyse ten different protease-inhibitor complexes carrying major resistance-associated mutations (RAMs) G48V, I50V, and L90M using molecular dynamics simulations. We demonstrate that alchemical free energy calculations can consistently predict the effect of mutations on drug binding. By explicitly probing different protonation states of the catalytic aspartic dyad, we reveal the importance of the correct choice of protonation state for the accuracy of the result. We also provide insight into how different mutations affect drug binding in their specific ways, with the unifying theme of how all of them affect the crucial for drug binding regions of the protease.
%J Journal of Chemical Theory and Computation
%O J. Chem. Theory Comput.
%V 14
%N 7
%& 3397
%P 3397 - 3408
%I American Chemical Society
%C Washington, D.C.
118. Baumgartner C, Toifl S, Farlik M, Halbritter F, Scheicher R, Fischer I, Sexl V, Bock C, Baccarini M: An ERK-Dependent Feedback Mechanism Prevents Hematopoietic Stem Cell Exhaustion. Cell Stem Cell 2018, 22.
Export
BibTeX
@article{Baumgartner2018,
TITLE = {An {ERK}-Dependent Feedback Mechanism Prevents Hematopoietic Stem Cell Exhaustion},
AUTHOR = {Baumgartner, Christian and Toifl, Stefanie and Farlik, Matthias and Halbritter, Florian and Scheicher, Ruth and Fischer, Irmgard and Sexl, Veronika and Bock, Christoph and Baccarini, Manuela},
LANGUAGE = {eng},
ISSN = {1934-5909},
DOI = {10.1016/j.stem.2018.05.003},
PUBLISHER = {Cell Press},
ADDRESS = {Cambridge, Mass.},
YEAR = {2018},
DATE = {2018},
JOURNAL = {Cell Stem Cell},
VOLUME = {22},
NUMBER = {6},
PAGES = {879--892},
EID = {e6},
}
Endnote
%0 Journal Article
%A Baumgartner, Christian
%A Toifl, Stefanie
%A Farlik, Matthias
%A Halbritter, Florian
%A Scheicher, Ruth
%A Fischer, Irmgard
%A Sexl, Veronika
%A Bock, Christoph
%A Baccarini, Manuela
%+ External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
%T An ERK-Dependent Feedback Mechanism Prevents Hematopoietic Stem Cell Exhaustion :
%G eng
%U http://hdl.handle.net/21.11116/0000-0001-88D5-5
%R 10.1016/j.stem.2018.05.003
%7 2018
%D 2018
%J Cell Stem Cell
%V 22
%N 6
%& 879
%P 879 - 892
%Z sequence number: e6
%I Cell Press
%C Cambridge, Mass.
%@ false
119. Behjati Ardakani F, Kattler K, Nordstroem K, Gasparoni N, Gasparoni G, Fuchs S, Sinha A, Barann M, Ebert P, Fischer J, Hutter B, Zipprich G, Imbusch CD, Felder B, Eils J, Brors B, Lengauer T, Manke T, Rosenstiel P, Walter J, Schulz MH: Integrative Analysis of Single-Cell Expression Data Reveals Distinct Regulatory States in Bidirectional Promoters. Epigenetics & Chromatin 2018, 11.
Export
BibTeX
@article{Ardakani2018,
TITLE = {Integrative Analysis of Single-Cell Expression Data Reveals Distinct Regulatory States in Bidirectional Promoters},
AUTHOR = {Behjati Ardakani, Fatemeh and Kattler, Kathrin and Nordstroem, Karl and Gasparoni, Nina and Gasparoni, Gilles and Fuchs, Sarah and Sinha, Anupam and Barann, Matthias and Ebert, Peter and Fischer, Jonas and Hutter, Barbara and Zipprich, Gideon and Imbusch, Charles D. and Felder, Baerbel and Eils, Juergen and Brors, Benedikt and Lengauer, Thomas and Manke, Thomas and Rosenstiel, Philip and Walter, Joern and Schulz, Marcel Holger},
LANGUAGE = {eng},
DOI = {10.1186/s13072-018-0236-7},
PUBLISHER = {BioMed Central},
ADDRESS = {London},
YEAR = {2018},
JOURNAL = {Epigenetics \& Chromatin},
VOLUME = {11},
EID = {66},
}
Endnote
%0 Journal Article
%A Behjati Ardakani, Fatemeh
%A Kattler, Kathrin
%A Nordstroem, Karl
%A Gasparoni, Nina
%A Gasparoni, Gilles
%A Fuchs, Sarah
%A Sinha, Anupam
%A Barann, Matthias
%A Ebert, Peter
%A Fischer, Jonas
%A Hutter, Barbara
%A Zipprich, Gideon
%A Imbusch, Charles D.
%A Felder, Baerbel
%A Eils, Juergen
%A Brors, Benedikt
%A Lengauer, Thomas
%A Manke, Thomas
%A Rosenstiel, Philip
%A Walter, Joern
%A Schulz, Marcel Holger
%+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
%T Integrative Analysis of Single-Cell Expression Data Reveals Distinct Regulatory States in Bidirectional Promoters :
%G eng
%U http://hdl.handle.net/21.11116/0000-0002-D61C-E
%R 10.1186/s13072-018-0236-7
%7 2018
%D 2018
%J Epigenetics & Chromatin
%V 11
%Z sequence number: 66
%I BioMed Central
%C London
120. Chakraborty S, Canzar S, Marschall T, Schulz MH: Chromatyping: Reconstructing Nucleosome Profiles from NOMe Sequencing Data. In Research in Computational Molecular Biology (RECOMB 2018). Springer; 2018. [Lecture Notes in Bioinformatics, vol. 10812]
Export
BibTeX
@inproceedings{Chakraborty_RECOMB2018,
TITLE = {Chromatyping: {R}econstructing Nucleosome Profiles from {NOMe} Sequencing Data},
AUTHOR = {Chakraborty, Shounak and Canzar, Stefan and Marschall, Tobias and Schulz, Marcel H.},
LANGUAGE = {eng},
ISBN = {978-3-319-89928-2},
DOI = {10.1007/978-3-319-89929-9_2},
PUBLISHER = {Springer},
YEAR = {2018},
DATE = {2018},
BOOKTITLE = {Research in Computational Molecular Biology (RECOMB 2018)},
EDITOR = {Raphael, Benjamin H.},
PAGES = {21--36},
SERIES = {Lecture Notes in Bioinformatics},
VOLUME = {10812},
ADDRESS = {Paris, France},
}
Endnote
%0 Conference Proceedings
%A Chakraborty, Shounak
%A Canzar, Stefan
%A Marschall, Tobias
%A Schulz, Marcel H.
%+ External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
%T Chromatyping: Reconstructing Nucleosome Profiles from NOMe Sequencing Data :
%G eng
%U http://hdl.handle.net/21.11116/0000-0001-404B-3
%R 10.1007/978-3-319-89929-9_2
%D 2018
%B 22nd International Conference on Research in Computational Molecular Biology
%Z date of event: 2018-04-21 - 2018-04-24
%C Paris, France
%B Research in Computational Molecular Biology
%E Raphael, Benjamin H.
%P 21 - 36
%I Springer
%@ 978-3-319-89928-2
%B Lecture Notes in Bioinformatics
%N 10812
121. Dheghani Amirabad A, Ramasamy P, Wierz M, Nordstroem K, Kessler SM, Schulz MH, Simon M: Transgenic Expression of the RNA Binding Protein IMP2 Stabilizes miRNA Targets in Murine Microsteatosis. Biochimica et Biophysica Acta - Molecular Basis of Disease 2018, 1864.
Export
BibTeX
@article{Dheghani_2018,
TITLE = {Transgenic expression of the {RNA} binding protein {IMP2} stabilizes {miRNA} targets in murine microsteatosis},
AUTHOR = {Dheghani Amirabad, Azim and Ramasamy, Pathmanaban and Wierz, Marina and Nordstroem, Karl and Kessler, Sonja M. and Schulz, Marcel H. and Simon, Martin},
LANGUAGE = {eng},
ISSN = {0925-4439},
DOI = {10.1016/j.bbadis.2018.05.024},
PUBLISHER = {Elsevier},
ADDRESS = {New York, NY},
YEAR = {2018},
DATE = {2018},
JOURNAL = {Biochimica et Biophysica Acta -- Molecular Basis of Disease},
VOLUME = {1864},
NUMBER = {10},
PAGES = {3099--3108},
}
Endnote
%0 Journal Article
%A Dheghani Amirabad, Azim
%A Ramasamy, Pathmanaban
%A Wierz, Marina
%A Nordstroem, Karl
%A Kessler, Sonja M.
%A Schulz, Marcel H.
%A Simon, Martin
%+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
External Organizations
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
%T Transgenic Expression of the RNA Binding Protein IMP2 Stabilizes miRNA Targets in Murine Microsteatosis :
%G eng
%U http://hdl.handle.net/21.11116/0000-0002-576D-3
%R 10.1016/j.bbadis.2018.05.024
%7 2018
%D 2018
%J Biochimica et Biophysica Acta - Molecular Basis of Disease
%O Biochim. Biophys. Acta-Mol. Basis Dis.
%V 1864
%N 10
%& 3099
%P 3099 - 3108
%I Elsevier
%C New York, NY
%@ false
122. Döring M, Büch J, Friedrich G, Pironti A, Kalaghatgi P, Knops E, Heger E, Obermeier M, Däumer M, Thielen A, Kaiser R, Lengauer T, Pfeifer N: Geno2pheno[ngs-freq]: a Genotypic Interpretation System for Identifying Viral Drug Resistance using Next-Generation Sequencing Data. Nucleic Acids Research 2018, 46(Web Server issue).
Export
BibTeX
@article{Doering2018,
TITLE = {Geno2pheno[ngs-freq]: a Genotypic Interpretation System for Identifying Viral Drug Resistance using Next-Generation Sequencing Data},
AUTHOR = {D{\"o}ring, Matthias and B{\"u}ch, Joachim and Friedrich, Georg and Pironti, Alejandro and Kalaghatgi, Prabhav and Knops, Elena and Heger, Eva and Obermeier, Martin and D{\"a}umer, Martin and Thielen, Alexander and Kaiser, Rolf and Lengauer, Thomas and Pfeifer, Nico},
LANGUAGE = {eng},
ISSN = {0305-1048},
DOI = {10.1093/nar/gky349},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford},
YEAR = {2018},
DATE = {2018},
JOURNAL = {Nucleic Acids Research},
VOLUME = {46},
NUMBER = {Web Server issue},
PAGES = {W271--W277},
EID = {gky349},
}
Endnote
%0 Journal Article
%A Döring, Matthias
%A Büch, Joachim
%A Friedrich, Georg
%A Pironti, Alejandro
%A Kalaghatgi, Prabhav
%A Knops, Elena
%A Heger, Eva
%A Obermeier, Martin
%A Däumer, Martin
%A Thielen, Alexander
%A Kaiser, Rolf
%A Lengauer, Thomas
%A Pfeifer, Nico
%+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
%T Geno2pheno[ngs-freq]: a Genotypic Interpretation System for Identifying Viral Drug Resistance using Next-Generation Sequencing Data :
%G eng
%U http://hdl.handle.net/21.11116/0000-0001-3F53-C
%R 10.1093/nar/gky349
%2 PMC6031006
%7 2018
%D 2018
%J Nucleic Acids Research
%O Nucleic Acids Res
%V 46
%N Web Server issue
%& W271
%P W271 - W277
%Z sequence number: gky349
%I Oxford University Press
%C Oxford
%@ false
123. Durai DA, Schulz MH: In silico Read Normalization using Set Multi-cover Optimization. Bioinformatics 2018, 34.
Export
BibTeX
@article{Durai2018,
TITLE = {In silico Read Normalization using Set Multi-cover Optimization},
AUTHOR = {Durai, Dilip Ariyur and Schulz, Marcel Holger},
LANGUAGE = {eng},
ISSN = {1367-4803},
DOI = {10.1093/bioinformatics/bty307},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford},
YEAR = {2018},
DATE = {2018},
JOURNAL = {Bioinformatics},
VOLUME = {34},
NUMBER = {19},
PAGES = {3273--3280},
}
Endnote
%0 Journal Article
%A Durai, Dilip Ariyur
%A Schulz, Marcel Holger
%+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
%T In silico Read Normalization using Set Multi-cover Optimization :
%G eng
%U http://hdl.handle.net/21.11116/0000-0002-5C51-C
%R 10.1093/bioinformatics/bty307
%7 2018
%D 2018
%J Bioinformatics
%V 34
%N 19
%& 3273
%P 3273 - 3280
%I Oxford University Press
%C Oxford
%@ false
124. Fröhlich H, Balling R, Beerenwinkel N, Kohlbacher O, Kumar S, Lengauer T, Maathuis MH, Moreau Y, Murphy SA, Przytycka TM, Rebhan M, Röst H, Schuppert A, Schwab M, Spang R, Stekhoven D, Sun J, Weber A, Ziemek D, Zupan B: From Hype to Reality: Data Science Enabling Personalized Medicine. BMC Medicine 2018, 16.
Export
BibTeX
@article{Froehlich2018,
TITLE = {From Hype to Reality: Data Science Enabling Personalized Medicine},
AUTHOR = {Fr{\"o}hlich, Holger and Balling, Rudi and Beerenwinkel, Niko and Kohlbacher, Oliver and Kumar, Santosh and Lengauer, Thomas and Maathuis, Marloes H. and Moreau, Yves and Murphy, Susan A. and Przytycka, Teresa M. and Rebhan, Michael and R{\"o}st, Hannes and Schuppert, Andreas and Schwab, Matthias and Spang, Rainer and Stekhoven, Daniel and Sun, Jimeng and Weber, Andreas and Ziemek, Daniel and Zupan, Blaz},
LANGUAGE = {eng},
ISSN = {1741-7015},
DOI = {10.1186/s12916-018-1122-7},
PUBLISHER = {BioMed Central},
YEAR = {2018},
JOURNAL = {BMC Medicine},
VOLUME = {16},
EID = {150},
}
Endnote
%0 Journal Article
%A Fröhlich, Holger
%A Balling, Rudi
%A Beerenwinkel, Niko
%A Kohlbacher, Oliver
%A Kumar, Santosh
%A Lengauer, Thomas
%A Maathuis, Marloes H.
%A Moreau, Yves
%A Murphy, Susan A.
%A Przytycka, Teresa M.
%A Rebhan, Michael
%A Röst, Hannes
%A Schuppert, Andreas
%A Schwab, Matthias
%A Spang, Rainer
%A Stekhoven, Daniel
%A Sun, Jimeng
%A Weber, Andreas
%A Ziemek, Daniel
%A Zupan, Blaz
%+ External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
%T From Hype to Reality: Data Science Enabling Personalized Medicine :
%G eng
%U http://hdl.handle.net/21.11116/0000-0002-09BD-0
%R 10.1186/s12916-018-1122-7
%7 2018
%D 2018
%J BMC Medicine
%V 16
%Z sequence number: 150
%I BioMed Central
%@ false
125. Fun A, Leitner T, Vandekerckhove L, Däumer M, Thielen A, Buchholz B, Hoepelman AIM, Gisolf EH, Schipper PJ, Wensing AMJ, Nijhuis M: Impact of the HIV-1 Genetic Background and HIV-1 Population Size on the Evolution of Raltegravir Resistance. Retrovirology 2018, 15.
Export
BibTeX
@article{Fun2018,
TITLE = {Impact of the {HIV}-1 Genetic Background and {HIV}-1 Population Size on the Evolution of Raltegravir Resistance},
AUTHOR = {Fun, Axel and Leitner, Thomas and Vandekerckhove, Linos and D{\"a}umer, Martin and Thielen, Alexander and Buchholz, Bernd and Hoepelman, Andy I. M. and Gisolf, Elizabeth H. and Schipper, Pauline J. and Wensing, Annemarie M. J. and Nijhuis, Monique},
LANGUAGE = {eng},
ISSN = {1742-4690},
DOI = {10.1186/s12977-017-0384-z},
PUBLISHER = {BioMed Central},
ADDRESS = {London},
YEAR = {2018},
DATE = {2018},
JOURNAL = {Retrovirology},
VOLUME = {15},
EID = {1},
}
Endnote
%0 Journal Article
%A Fun, Axel
%A Leitner, Thomas
%A Vandekerckhove, Linos
%A Däumer, Martin
%A Thielen, Alexander
%A Buchholz, Bernd
%A Hoepelman, Andy I. M.
%A Gisolf, Elizabeth H.
%A Schipper, Pauline J.
%A Wensing, Annemarie M. J.
%A Nijhuis, Monique
%+ External Organizations
External Organizations
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
%T Impact of the HIV-1 Genetic Background and HIV-1 Population Size on
the Evolution of Raltegravir Resistance :
%G eng
%U http://hdl.handle.net/21.11116/0000-0000-376A-C
%R 10.1186/s12977-017-0384-z
%7 2018
%D 2018
%J Retrovirology
%V 15
%Z sequence number: 1
%I BioMed Central
%C London
%@ false
126. Garg S, Rautiainen M, Novak AM, Garrison E, Durbin R, Marschall T: A Graph-based Approach to Diploid Genome Assembly. Bioinformatics (Proc ISMB 2018) 2018, 34.
Export
BibTeX
@article{Garg_Bioinformatics2018,
TITLE = {A Graph-based Approach to Diploid Genome Assembly},
AUTHOR = {Garg, Shilpa and Rautiainen, Mikko and Novak, Adam M. and Garrison, Erik and Durbin, Richard and Marschall, Tobias},
LANGUAGE = {eng},
ISSN = {1367-4803},
DOI = {10.1093/bioinformatics/bty279},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford},
YEAR = {2018},
DATE = {2018},
JOURNAL = {Bioinformatics (Proc. ISMB)},
VOLUME = {34},
PAGES = {i105--i114},
BOOKTITLE = {ISMB 2018 Proceedings},
}
Endnote
%0 Journal Article
%A Garg, Shilpa
%A Rautiainen, Mikko
%A Novak, Adam M.
%A Garrison, Erik
%A Durbin, Richard
%A Marschall, Tobias
%+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
%T A Graph-based Approach to Diploid Genome Assembly :
%G eng
%U http://hdl.handle.net/21.11116/0000-0001-E5A6-1
%R 10.1093/bioinformatics/bty279
%7 2018
%D 2018
%J Bioinformatics
%V 34
%& i105
%P i105 - i114
%I Oxford University Press
%C Oxford
%@ false
%B ISMB 2018 Proceedings
%O ISMB 2018 July 6 to July 10, 2018, Chicago, IL, United States
127. Garg S: Computational Haplotyping: Theory and Practice. Universität des Saarlandes; 2018.
Abstract
Genomics has paved a new way to comprehend life and its evolution, and also to investigate causes of diseases and their treatment. One of the important problems in genomic analyses is haplotype assembly. Constructing complete and accurate haplotypes plays an essential role in understanding population genetics and how species evolve. In this thesis, we focus on computational approaches to haplotype assembly from third generation sequencing technologies. This involves huge amounts of sequencing data, and such data contain errors due to the single molecule sequencing protocols employed. Taking advantage of combinatorial formulations helps to correct for these errors to solve the haplotyping problem. Various computational techniques such as dynamic programming, parameterized algorithms, and graph algorithms are used to solve this problem. This thesis presents several contributions concerning the area of haplotyping. First, a novel algorithm based on dynamic programming is proposed to provide approximation guarantees for phasing a single individual. Second, an integrative approach is introduced to combining multiple sequencing datasets to generating complete and accurate haplotypes. The effectiveness of this integrative approach is demonstrated on a real human genome. Third, we provide a novel efficient approach to phasing pedigrees and demonstrate its advantages in comparison to phasing a single individual. Fourth, we present a generalized graph-based framework for performing haplotype-aware de novo assembly. Specifically, this generalized framework consists of a hybrid pipeline for generating accurate and complete haplotypes from data stemming from multiple sequencing technologies, one that provides accurate reads and other that provides long reads.
Export
BibTeX
@phdthesis{gargphd2017,
TITLE = {Computational Haplotyping: Theory and Practice},
AUTHOR = {Garg, Shilpa},
LANGUAGE = {eng},
URL = {urn:nbn:de:bsz:291-scidok-ds-272520},
DOI = {10.22028/D291-27252},
SCHOOL = {Universit{\"a}t des Saarlandes},
ADDRESS = {Saarbr{\"u}cken},
YEAR = {2018},
DATE = {2018},
ABSTRACT = {Genomics has paved a new way to comprehend life and its evolution, and also to investigate causes of diseases and their treatment. One of the important problems in genomic analyses is haplotype assembly. Constructing complete and accurate haplotypes plays an essential role in understanding population genetics and how species evolve. In this thesis, we focus on computational approaches to haplotype assembly from third generation sequencing technologies. This involves huge amounts of sequencing data, and such data contain errors due to the single molecule sequencing protocols employed. Taking advantage of combinatorial formulations helps to correct for these errors to solve the haplotyping problem. Various computational techniques such as dynamic programming, parameterized algorithms, and graph algorithms are used to solve this problem. This thesis presents several contributions concerning the area of haplotyping. First, a novel algorithm based on dynamic programming is proposed to provide approximation guarantees for phasing a single individual. Second, an integrative approach is introduced to combining multiple sequencing datasets to generating complete and accurate haplotypes. The effectiveness of this integrative approach is demonstrated on a real human genome. Third, we provide a novel efficient approach to phasing pedigrees and demonstrate its advantages in comparison to phasing a single individual. Fourth, we present a generalized graph-based framework for performing haplotype-aware de novo assembly. Specifically, this generalized framework consists of a hybrid pipeline for generating accurate and complete haplotypes from data stemming from multiple sequencing technologies, one that provides accurate reads and other that provides long reads.},
}
Endnote
%0 Thesis
%A Garg, Shilpa
%Y Marschall, Tobias
%A referee: Helms, Volkhard
%+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
International Max Planck Research School, MPI for Informatics, Max Planck Society
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
%T Computational Haplotyping: Theory and Practice :
%G eng
%U http://hdl.handle.net/21.11116/0000-0001-9D80-D
%R 10.22028/D291-27252
%U urn:nbn:de:bsz:291-scidok-ds-272520
%F OTHER: hdl:20.500.11880/27102
%I Universität des Saarlandes
%C Saarbrücken
%D 2018
%P 119 p.
%V phd
%9 phd
%X Genomics has paved a new way to comprehend life and its evolution, and also to investigate causes of diseases and their treatment. One of the important problems in genomic analyses is haplotype assembly. Constructing complete and accurate haplotypes plays an essential role in understanding population genetics and how species evolve. In this thesis, we focus on computational approaches to haplotype assembly from third generation sequencing technologies. This involves huge amounts of sequencing data, and such data contain errors due to the single molecule sequencing protocols employed. Taking advantage of combinatorial formulations helps to correct for these errors to solve the haplotyping problem. Various computational techniques such as dynamic programming, parameterized algorithms, and graph algorithms are used to solve this problem. This thesis presents several contributions concerning the area of haplotyping. First, a novel algorithm based on dynamic programming is proposed to provide approximation guarantees for phasing a single individual. Second, an integrative approach is introduced to combining multiple sequencing datasets to generating complete and accurate haplotypes. The effectiveness of this integrative approach is demonstrated on a real human genome. Third, we provide a novel efficient approach to phasing pedigrees and demonstrate its advantages in comparison to phasing a single individual. Fourth, we present a generalized graph-based framework for performing haplotype-aware de novo assembly. Specifically, this generalized framework consists of a hybrid pipeline for generating accurate and complete haplotypes from data stemming from multiple sequencing technologies, one that provides accurate reads and other that provides long reads.
%U https://publikationen.sulb.uni-saarland.de/handle/20.500.11880/27102
128. Garrison E, Siren J, Novak AM, Hickey G, Eizenga JM, Dawson ET, Jones W, Garg S, Markello C, Lin MF, Paten B, Durbin R: Variation Graph Toolkit Improves Read Mapping by Representing Genetic Variation in the Reference. Nature Biotechnology 2018, 36.
Export
BibTeX
@article{Garrison_2018,
TITLE = {Variation Graph Toolkit Improves Read Mapping by Representing Genetic Variation in the Reference},
AUTHOR = {Garrison, Erik and Siren, Jouni and Novak, Adam M. and Hickey, Glenn and Eizenga, Jordan M. and Dawson, Eric T. and Jones, William and Garg, Shilpa and Markello, Charles and Lin, Michael F. and Paten, Benedict and Durbin, Richard},
LANGUAGE = {eng},
ISSN = {1087-0156},
DOI = {10.1038/nbt.4227},
PUBLISHER = {NPG},
ADDRESS = {New York},
YEAR = {2018},
DATE = {2018},
JOURNAL = {Nature Biotechnology},
VOLUME = {36},
NUMBER = {9},
PAGES = {875--879},
}
Endnote
%0 Journal Article
%A Garrison, Erik
%A Siren, Jouni
%A Novak, Adam M.
%A Hickey, Glenn
%A Eizenga, Jordan M.
%A Dawson, Eric T.
%A Jones, William
%A Garg, Shilpa
%A Markello, Charles
%A Lin, Michael F.
%A Paten, Benedict
%A Durbin, Richard
%+ External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
External Organizations
External Organizations
External Organizations
%T Variation Graph Toolkit Improves Read Mapping by Representing Genetic Variation in the Reference :
%G eng
%U http://hdl.handle.net/21.11116/0000-0002-5761-F
%R 10.1038/nbt.4227
%7 2018
%D 2018
%J Nature Biotechnology
%V 36
%N 9
%& 875
%P 875 - 879
%I NPG
%C New York
%@ false
129. Ghareghani M, Porubsky D, Sanders AD, Meiers S, Eichler EE, Korbel JO, Marschall T: Strand-seq Enables Reliable Separation of Long Reads by Chromosome via Expectation Maximization. Bioinformatics (Proc ISMB 2018) 2018, 34.
Export
BibTeX
@article{Ghareghani_ISMB2018,
TITLE = {Strand-seq Enables Reliable Separation of Long Reads by Chromosome via Expectation Maximization},
AUTHOR = {Ghareghani, Maryam and Porubsky, David and Sanders, Ashley D. and Meiers, Sascha and Eichler, Evan E. and Korbel, Jan O. and Marschall, Tobias},
LANGUAGE = {eng},
ISSN = {1367-4803},
DOI = {10.1093/bioinformatics/bty290},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford},
YEAR = {2018},
DATE = {2018},
JOURNAL = {Bioinformatics (Proc. ISMB)},
VOLUME = {34},
NUMBER = {13},
PAGES = {i115--I123},
BOOKTITLE = {ISMB 2018 Proceedings},
}
Endnote
%0 Journal Article
%A Ghareghani, Maryam
%A Porubsky, David
%A Sanders, Ashley D.
%A Meiers, Sascha
%A Eichler, Evan E.
%A Korbel, Jan O.
%A Marschall, Tobias
%+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
External Organizations
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
%T Strand-seq Enables Reliable Separation of Long Reads by Chromosome via Expectation Maximization :
%G eng
%U http://hdl.handle.net/21.11116/0000-0001-E5AA-D
%R 10.1093/bioinformatics/bty290
%7 2018
%D 2018
%J Bioinformatics
%V 34
%N 13
%& i115
%P i115 - I123
%I Oxford University Press
%C Oxford
%@ false
%B ISMB 2018 Proceedings
%O July 6 to July 10, 2018, Chicago, IL, United States ISMB 2018
130. Goeschl L, Preglej T, Hamminger P, Bonelli M, Andersen L, Boucheron N, Guelich AF, Mueller L, Saferding V, Mufazalov IA, Hirahara K, Seiser C, Matthias P, Penz T, Schuster M, Bock C, Waisman A, Steiner G, Ellmeier W: A T Cell-specific Deletion of HDAC1 Protects Against Experimental Autoimmune Encephalomyelitis. Journal of Autoimmunity 2018, 86.
Export
BibTeX
@article{Goeschl2018,
TITLE = {A {T} Cell-specific Deletion of {HDAC}1 Protects Against Experimental Autoimmune Encephalomyelitis},
AUTHOR = {Goeschl, Lisa and Preglej, Teresa and Hamminger, Patricia and Bonelli, Michael and Andersen, Liisa and Boucheron, Nicole and Guelich, Alexandra F. and Mueller, Lena and Saferding, Victoria and Mufazalov, Ilgiz A. and Hirahara, Kiyoshi and Seiser, Christian and Matthias, Patrick and Penz, Thomas and Schuster, Michael and Bock, Christoph and Waisman, Ari and Steiner, Guenter and Ellmeier, Wilfried},
LANGUAGE = {eng},
ISSN = {0896-8411},
DOI = {10.1016/j.jaut.2017.09.008},
PUBLISHER = {Academic Press},
ADDRESS = {London},
YEAR = {2018},
DATE = {2018},
JOURNAL = {Journal of Autoimmunity},
VOLUME = {86},
PAGES = {51--61},
}
Endnote
%0 Journal Article
%A Goeschl, Lisa
%A Preglej, Teresa
%A Hamminger, Patricia
%A Bonelli, Michael
%A Andersen, Liisa
%A Boucheron, Nicole
%A Guelich, Alexandra F.
%A Mueller, Lena
%A Saferding, Victoria
%A Mufazalov, Ilgiz A.
%A Hirahara, Kiyoshi
%A Seiser, Christian
%A Matthias, Patrick
%A Penz, Thomas
%A Schuster, Michael
%A Bock, Christoph
%A Waisman, Ari
%A Steiner, Guenter
%A Ellmeier, Wilfried
%+ External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
External Organizations
External Organizations
%T A T Cell-specific Deletion of HDAC1 Protects Against Experimental Autoimmune Encephalomyelitis :
%G eng
%U http://hdl.handle.net/21.11116/0000-0000-8438-C
%R 10.1016/j.jaut.2017.09.008
%7 2018
%D 2018
%J Journal of Autoimmunity
%O J. Autoimmun.
%V 86
%& 51
%P 51 - 61
%I Academic Press
%C London
%@ false
131. Grosser K, Ramasamy P, Dheghani Amirabad A, Schulz MH, Gasparoni G, Simon M, Schrallhammer M: More than the “Killer Trait”: Infection with the Bacterial Endosymbiont Caedibacter taeniospiralis Causes Transcriptomic Modulation in Paramecium Host. Genome Biology and Evolution 2018, 10.
Export
BibTeX
@article{Grosser2018,
TITLE = {More than the “Killer Trait”: {I}nfection with the Bacterial Endosymbiont {C}aedibacter taeniospiralis Causes Transcriptomic Modulation in Paramecium Host},
AUTHOR = {Grosser, Katrin and Ramasamy, Pathmanaban and Dheghani Amirabad, Azim and Schulz, Marcel Holger and Gasparoni, Gilles and Simon, Martin and Schrallhammer, Martina},
LANGUAGE = {eng},
DOI = {10.1093/gbe/evy024},
PUBLISHER = {Oxford Univ. Press},
ADDRESS = {Oxford},
YEAR = {2018},
DATE = {2018},
JOURNAL = {Genome Biology and Evolution},
VOLUME = {10},
NUMBER = {2},
PAGES = {646--656},
}
Endnote
%0 Journal Article
%A Grosser, Katrin
%A Ramasamy, Pathmanaban
%A Dheghani Amirabad, Azim
%A Schulz, Marcel Holger
%A Gasparoni, Gilles
%A Simon, Martin
%A Schrallhammer, Martina
%+ External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
External Organizations
External Organizations
%T More than the “Killer Trait”: Infection with the Bacterial Endosymbiont Caedibacter taeniospiralis Causes Transcriptomic Modulation in Paramecium Host :
%G eng
%U http://hdl.handle.net/21.11116/0000-0000-C023-F
%R 10.1093/gbe/evy024
%7 2018
%D 2018
%J Genome Biology and Evolution
%O GBE Genome Biol Evol
%V 10
%N 2
%& 646
%P 646 - 656
%I Oxford Univ. Press
%C Oxford
132. Ha Thanh Pham T, Maurer B, Prchal-Murphy M, Grausenburger R, Grundschober E, Javaheri T, Nivarthi H, Boersma A, Kolbe T, Elabd M, Halbritter F, Pencik J, Kazemi Z, Grebien F, Hengstschlaeger M, Kenner L, Kubicek S, Farlik M, Bock C, Valent P, Mueller M, Ruelicke T, Sexl V, Moriggl R: STAT5B(N642H) is a Driver Mutation for T Cell Neoplasia. The Journal of Clinical Investigation 2018, 128.
Export
BibTeX
@article{Bock_JCI2018,
TITLE = {{STAT5B}^({N642H)} is a Driver Mutation for {T} Cell Neoplasia},
AUTHOR = {Ha Thanh Pham, Thi and Maurer, Barbara and Prchal-Murphy, Michaela and Grausenburger, Reinhard and Grundschober, Eva and Javaheri, Tahereh and Nivarthi, Harini and Boersma, Auke and Kolbe, Thomas and Elabd, Mohamed and Halbritter, Florian and Pencik, Jan and Kazemi, Zahra and Grebien, Florian and Hengstschlaeger, Markus and Kenner, Lukas and Kubicek, Stefan and Farlik, Matthias and Bock, Christoph and Valent, Peter and Mueller, Mathias and Ruelicke, Thomas and Sexl, Veronika and Moriggl, Richard},
LANGUAGE = {eng},
ISSN = {0021-9738},
DOI = {10.1172/JCI94509},
PUBLISHER = {American Society for Clinical Investigation},
ADDRESS = {New York, NY},
YEAR = {2018},
DATE = {2018},
JOURNAL = {The Journal of Clinical Investigation},
VOLUME = {128},
NUMBER = {1},
PAGES = {387--401},
}
Endnote
%0 Journal Article
%A Ha Thanh Pham, Thi
%A Maurer, Barbara
%A Prchal-Murphy, Michaela
%A Grausenburger, Reinhard
%A Grundschober, Eva
%A Javaheri, Tahereh
%A Nivarthi, Harini
%A Boersma, Auke
%A Kolbe, Thomas
%A Elabd, Mohamed
%A Halbritter, Florian
%A Pencik, Jan
%A Kazemi, Zahra
%A Grebien, Florian
%A Hengstschlaeger, Markus
%A Kenner, Lukas
%A Kubicek, Stefan
%A Farlik, Matthias
%A Bock, Christoph
%A Valent, Peter
%A Mueller, Mathias
%A Ruelicke, Thomas
%A Sexl, Veronika
%A Moriggl, Richard
%+ External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
%T STAT5B(N642H) is a Driver Mutation for T Cell Neoplasia :
%G eng
%U http://hdl.handle.net/21.11116/0000-0000-2DDC-7
%R 10.1172/JCI94509
%7 2018
%D 2018
%J The Journal of Clinical Investigation
%O JCI
%V 128
%N 1
%& 387
%P 387 - 401
%I American Society for Clinical Investigation
%C New York, NY
%@ false
133. Horňáková A, List M, Vreeken J, Schulz MH: JAMI: Fast Computation of Conditional Mutual Information for ceRNA Network Analysis. Bioinformatics 2018, 34.
Export
BibTeX
@article{Hornakova_Bioinformatics2018,
TITLE = {{JAMI}: {F}ast Computation of Conditional Mutual Information for {ceRNA} Network Analysis},
AUTHOR = {Hor{\v n}{\'a}kov{\'a}, Andrea and List, Markus and Vreeken, Jilles and Schulz, Marcel H.},
LANGUAGE = {eng},
ISSN = {1367-4803},
DOI = {10.1093/bioinformatics/bty221},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford},
YEAR = {2018},
DATE = {2018},
JOURNAL = {Bioinformatics},
VOLUME = {34},
NUMBER = {17},
PAGES = {3050--3051},
}
Endnote
%0 Journal Article
%A Horňáková, Andrea
%A List, Markus
%A Vreeken, Jilles
%A Schulz, Marcel H.
%+ Computer Vision and Multimodal Computing, MPI for Informatics, Max Planck Society
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
Databases and Information Systems, MPI for Informatics, Max Planck Society
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
%T JAMI: Fast Computation of Conditional Mutual Information for ceRNA Network Analysis :
%G eng
%U http://hdl.handle.net/21.11116/0000-0002-573A-C
%R 10.1093/bioinformatics/bty221
%7 2018
%D 2018
%J Bioinformatics
%V 34
%N 17
%& 3050
%P 3050 - 3051
%I Oxford University Press
%C Oxford
%@ false
134. Klughammer J, Kiesel B, Roetzer T, Fortelny N, Nemc A, Nenning K-H, Furtner J, Sheffield NC, Datlinger P, Peter N, Nowosielski M, Augustin M, Mischkulnig M, Stroebel T, Alpar D, Erguener B, Senekowitsch M, Moser P, Freyschlag CF, Kerschbaumer J, Thome C, Grams AE, Stockhammer G, Kitzwoegerer M, Oberndorfer S, Marhold F, Weis S, Trenkler J, Buchroithner J, Pichler J, et al.: The DNA Methylation Landscape of Glioblastoma Disease Progression Shows Extensive Heterogeneity in Time and Space. Nature Medicine 2018, 24.
Export
BibTeX
@article{Klughammer_2018,
TITLE = {The {DNA} Methylation Landscape of Glioblastoma Disease Progression Shows Extensive Heterogeneity in Time and Space},
AUTHOR = {Klughammer, Johanna and Kiesel, Barbara and Roetzer, Thomas and Fortelny, Nikolaus and Nemc, Amelie and Nenning, Karl-Heinz and Furtner, Julia and Sheffield, Nathan C. and Datlinger, Paul and Peter, Nadine and Nowosielski, Martha and Augustin, Marco and Mischkulnig, Mario and Stroebel, Thomas and Alpar, Donat and Erguener, Bekir and Senekowitsch, Martin and Moser, Patrizia and Freyschlag, Christian F. and Kerschbaumer, Johannes and Thome, Claudius and Grams, Astrid E. and Stockhammer, Guenther and Kitzwoegerer, Melitta and Oberndorfer, Stefan and Marhold, Franz and Weis, Serge and Trenkler, Johannes and Buchroithner, Johanna and Pichler, Josef and Haybaeck, Johannes and Krassnig, Stefanie and Ali, Kariem Mahdy and von Campe, Gord and Payer, Franz and Sherif, Camillo and Preiser, Julius and Hauser, Thomas and Winkler, Peter A. and Kleindienst, Waltraud and Wuertz, Franz and Brandner-Kokalj, Tanisa and Stultschnig, Martin and Schweiger, Stefan and Dieckmann, Karin and Preusser, Matthias and Langs, Georg and Baumann, Bernhard and Knosp, Engelbert and Widhalm, Georg and Marosi, Christine and Hainfellner, Johannes A. and Woehrer, Adelheid and Bock, Christoph},
LANGUAGE = {eng},
ISSN = {1078-8956},
DOI = {10.1038/s41591-018-0156-x},
PUBLISHER = {Nature Pub. Co.},
ADDRESS = {New York, NY},
YEAR = {2018},
DATE = {2018},
JOURNAL = {Nature Medicine},
VOLUME = {24},
NUMBER = {10},
PAGES = {1611--1624},
}
Endnote
%0 Journal Article
%A Klughammer, Johanna
%A Kiesel, Barbara
%A Roetzer, Thomas
%A Fortelny, Nikolaus
%A Nemc, Amelie
%A Nenning, Karl-Heinz
%A Furtner, Julia
%A Sheffield, Nathan C.
%A Datlinger, Paul
%A Peter, Nadine
%A Nowosielski, Martha
%A Augustin, Marco
%A Mischkulnig, Mario
%A Stroebel, Thomas
%A Alpar, Donat
%A Erguener, Bekir
%A Senekowitsch, Martin
%A Moser, Patrizia
%A Freyschlag, Christian F.
%A Kerschbaumer, Johannes
%A Thome, Claudius
%A Grams, Astrid E.
%A Stockhammer, Guenther
%A Kitzwoegerer, Melitta
%A Oberndorfer, Stefan
%A Marhold, Franz
%A Weis, Serge
%A Trenkler, Johannes
%A Buchroithner, Johanna
%A Pichler, Josef
%A Haybaeck, Johannes
%A Krassnig, Stefanie
%A Ali, Kariem Mahdy
%A von Campe, Gord
%A Payer, Franz
%A Sherif, Camillo
%A Preiser, Julius
%A Hauser, Thomas
%A Winkler, Peter A.
%A Kleindienst, Waltraud
%A Wuertz, Franz
%A Brandner-Kokalj, Tanisa
%A Stultschnig, Martin
%A Schweiger, Stefan
%A Dieckmann, Karin
%A Preusser, Matthias
%A Langs, Georg
%A Baumann, Bernhard
%A Knosp, Engelbert
%A Widhalm, Georg
%A Marosi, Christine
%A Hainfellner, Johannes A.
%A Woehrer, Adelheid
%A Bock, Christoph
%+ External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
%T The DNA Methylation Landscape of Glioblastoma Disease Progression Shows Extensive Heterogeneity in Time and Space :
%G eng
%U http://hdl.handle.net/21.11116/0000-0002-5F1F-3
%R 10.1038/s41591-018-0156-x
%7 2018
%D 2018
%J Nature Medicine
%O Nat. Med.
%V 24
%N 10
%& 1611
%P 1611 - 1624
%I Nature Pub. Co.
%C New York, NY
%@ false
135. Knops E, Sierra S, Kalaghatgi P, Heger E, Kaiser R, Kalinina OV: Epistatic Interactions in NS5A of Hepatitis C Virus Suggest Drug Resistance Mechanisms. Genes 2018, 9.
Export
BibTeX
@article{Knops2018,
TITLE = {Epistatic Interactions in {NS5A} of Hepatitis {C} Virus Suggest Drug Resistance Mechanisms},
AUTHOR = {Knops, Elena and Sierra, Saleta and Kalaghatgi, Prabhav and Heger, Eva and Kaiser, Rolf and Kalinina, Olga V.},
LANGUAGE = {eng},
ISSN = {2073-4425},
DOI = {10.3390/genes9070343},
PUBLISHER = {MDPI},
ADDRESS = {Basel},
YEAR = {2018},
JOURNAL = {Genes},
VOLUME = {9},
NUMBER = {7},
EID = {343},
}
Endnote
%0 Journal Article
%A Knops, Elena
%A Sierra, Saleta
%A Kalaghatgi, Prabhav
%A Heger, Eva
%A Kaiser, Rolf
%A Kalinina, Olga V.
%+ External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
%T Epistatic Interactions in NS5A of Hepatitis C Virus Suggest Drug Resistance Mechanisms :
%G eng
%U http://hdl.handle.net/21.11116/0000-0002-09C6-5
%R 10.3390/genes9070343
%7 2018-07-06
%D 2018
%8 06.07.2018
%J Genes
%V 9
%N 7
%Z sequence number: 343
%I MDPI
%C Basel
%@ false
136. Lowe R, Barton C, Jenkins CA, Ernst C, Forman O, Fernandez-Twinn DS, Bock C, Rossiter SJ, Faulkes CG, Ozanne SE, Walter L, Odom DT, Mellersh C, Rakyan VK: Ageing-associated DNA Methylation Dynamics are a Molecular Readout of Lifespan Variation among Mammalian Species. Genome Biology 2018, 19.
Export
BibTeX
@article{Lowe2018,
TITLE = {Ageing-associated {DNA} Methylation Dynamics are a Molecular Readout of Lifespan Variation among Mammalian Species},
AUTHOR = {Lowe, Robert and Barton, Carl and Jenkins, Christopher A. and Ernst, Christina and Forman, Oliver and Fernandez-Twinn, Denise S. and Bock, Christoph and Rossiter, Stephen J. and Faulkes, Chris G. and Ozanne, Susan E. and Walter, Lutz and Odom, Duncan T. and Mellersh, Cathryn and Rakyan, Vardhman K.},
LANGUAGE = {eng},
ISSN = {1465-6906},
DOI = {10.1186/s13059-018-1397-1},
PUBLISHER = {BioMed Central Ltd.},
ADDRESS = {London},
YEAR = {2018},
JOURNAL = {Genome Biology},
VOLUME = {19},
EID = {22},
}
Endnote
%0 Journal Article
%A Lowe, Robert
%A Barton, Carl
%A Jenkins, Christopher A.
%A Ernst, Christina
%A Forman, Oliver
%A Fernandez-Twinn, Denise S.
%A Bock, Christoph
%A Rossiter, Stephen J.
%A Faulkes, Chris G.
%A Ozanne, Susan E.
%A Walter, Lutz
%A Odom, Duncan T.
%A Mellersh, Cathryn
%A Rakyan, Vardhman K.
%+ External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
%T Ageing-associated DNA Methylation Dynamics are a Molecular Readout of Lifespan Variation among Mammalian Species :
%G eng
%U http://hdl.handle.net/21.11116/0000-0000-C8CF-6
%R 10.1186/s13059-018-1397-1
%7 2018
%D 2018
%J Genome Biology
%V 19
%Z sequence number: 22
%I BioMed Central Ltd.
%C London
%@ false
137. Marschall T, Marz M, Abeel T, Dijkstra L, Dutilh BE, Ghaffaari A, Kersey P, Kloosterman WP, Makinen V, Novak AM, Paten B, Porubsky D, Rivals E, Alkan C, Baaijens JA, De Bakker PIW, Boeva V, Bonnal RJP, Chiaromonte F, Chikhi R, Ciccarelli FD, Cijvat R, Datema E, Van Duijn CM, Eichler EE, Ernst C, Eskin E, Garrison E, El-Kebir M, Klau GW, et al.: Computational Pan-genomics: Status, Promises and Challenges. Briefings in Bioinformatics 2018, 19.
Export
BibTeX
@article{Marschall2016,
TITLE = {Computational Pan-genomics: Status, Promises and Challenges},
AUTHOR = {Marschall, Tobias and Marz, Manja and Abeel, Thomas and Dijkstra, Louis and Dutilh, Bas E. and Ghaffaari, Ali and Kersey, Paul and Kloosterman, Wigard P. and Makinen, Veli and Novak, Adam M. and Paten, Benedict and Porubsky, David and Rivals, Eric and Alkan, Can and Baaijens, Jasmijn A. and De Bakker, Paul I. W. and Boeva, Valentina and Bonnal, Raoul J. P. and Chiaromonte, Francesca and Chikhi, Rayan and Ciccarelli, Francesca D. and Cijvat, Robin and Datema, Erwin and Van Duijn, Cornelia M. and Eichler, Evan E. and Ernst, Corinna and Eskin, Eleazar and Garrison, Erik and El-Kebir, Mohammed and Klau, Gunnar W. and Korbel, Jan O. and Lameijer, Eric-Wubbo and Langmead, Benjamin and Martin, Marcel and Medvedev, Paul and Mu, John C. and Neerincx, Pieter and Ouwens, Klaasjan and Peterlongo, Pierre and Pisanti, Nadia and Rahmann, Sven and Raphael, Ben and Reinert, Knut and de Ridder, Dick and de Ridder, Jeroen and Schlesner, Matthias and Schulz-Trieglaff, Ole and Sanders, Ashley D. and Sheikhizadeh, Siavash and Shneider, Carl and Smit, Sandra and Valenzuela, Daniel and Wang, Jiayin and Wessels, Lodewyk and Zhang, Ying and Guryev, Victor and Vandin, Fabio and Ye, Kai and Schonhuth, Alexander},
LANGUAGE = {eng},
ISSN = {1467-5463},
DOI = {10.1093/bib/bbw089},
PUBLISHER = {Oxford University Press},
ADDRESS = {London},
YEAR = {2018},
DATE = {2018},
JOURNAL = {Briefings in Bioinformatics},
VOLUME = {19},
NUMBER = {1},
PAGES = {118--135},
EID = {bbw089},
}
Endnote
%0 Journal Article
%A Marschall, Tobias
%A Marz, Manja
%A Abeel, Thomas
%A Dijkstra, Louis
%A Dutilh, Bas E.
%A Ghaffaari, Ali
%A Kersey, Paul
%A Kloosterman, Wigard P.
%A Makinen, Veli
%A Novak, Adam M.
%A Paten, Benedict
%A Porubsky, David
%A Rivals, Eric
%A Alkan, Can
%A Baaijens, Jasmijn A.
%A De Bakker, Paul I. W.
%A Boeva, Valentina
%A Bonnal, Raoul J. P.
%A Chiaromonte, Francesca
%A Chikhi, Rayan
%A Ciccarelli, Francesca D.
%A Cijvat, Robin
%A Datema, Erwin
%A Van Duijn, Cornelia M.
%A Eichler, Evan E.
%A Ernst, Corinna
%A Eskin, Eleazar
%A Garrison, Erik
%A El-Kebir, Mohammed
%A Klau, Gunnar W.
%A Korbel, Jan O.
%A Lameijer, Eric-Wubbo
%A Langmead, Benjamin
%A Martin, Marcel
%A Medvedev, Paul
%A Mu, John C.
%A Neerincx, Pieter
%A Ouwens, Klaasjan
%A Peterlongo, Pierre
%A Pisanti, Nadia
%A Rahmann, Sven
%A Raphael, Ben
%A Reinert, Knut
%A de Ridder, Dick
%A de Ridder, Jeroen
%A Schlesner, Matthias
%A Schulz-Trieglaff, Ole
%A Sanders, Ashley D.
%A Sheikhizadeh, Siavash
%A Shneider, Carl
%A Smit, Sandra
%A Valenzuela, Daniel
%A Wang, Jiayin
%A Wessels, Lodewyk
%A Zhang, Ying
%A Guryev, Victor
%A Vandin, Fabio
%A Ye, Kai
%A Schonhuth, Alexander
%+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
%T Computational Pan-genomics: Status, Promises and Challenges :
%G eng
%U http://hdl.handle.net/11858/00-001M-0000-002B-AF03-A
%R 10.1093/bib/bbw089
%7 2016-10-21
%D 2018
%J Briefings in Bioinformatics
%V 19
%N 1
%& 118
%P 118 - 135
%Z sequence number: bbw089
%I Oxford University Press
%C London
%@ false
138. Mendoza P, Gruell H, Nogueira L, Pai JA, Butler AL, Millard K, Lehmann C, Suarez I, Oliveira TY, Lorenzi JCC, Cohen YZ, Wyen C, Kuemmerle T, Karagounis T, Lu C-L, Handl L, Unson-O’Brien C, Patel R, Ruping C, Schlotz M, Witmer-Pack M, Shimeliovich I, Kremer G, Thomas E, Seaton KE, Horowitz J, West Jr. AP, Bjorkman PJ, Tomaras GD, Gulick RM, et al.: Combination Therapy with anti-HIV-1 Antibodies Maintains Viral Suppression. Nature 2018, 561.
Export
BibTeX
@article{Mendoza_2018,
TITLE = {Combination therapy with anti-{HIV}-1 antibodies maintains viral suppression},
AUTHOR = {Mendoza, Pilar and Gruell, Henning and Nogueira, Lilian and Pai, Joy A. and Butler, Allison L. and Millard, Katrina and Lehmann, Clara and Suarez, Isabelle and Oliveira, Thiago Y. and Lorenzi, Julio C. C. and Cohen, Yehuda Z. and Wyen, Christoph and Kuemmerle, Tim and Karagounis, Theodora and Lu, Ching-Lan and Handl, Lisa and Unson-O'Brien, Cecilia and Patel, Roshni and Ruping, Carola and Schlotz, Maike and Witmer-Pack, Maggi and Shimeliovich, Irina and Kremer, Gisela and Thomas, Eleonore and Seaton, Kelly E. and Horowitz, Jill and West Jr., Anthony P. and Bjorkman, Pamela J. and Tomaras, Georgia D. and Gulick, Roy M. and Pfeifer, Nico and Faetkenheuer, Gerd and Seaman, Michael S. and Klein, Florian and Caskey, Marina and Nussenzweig, Michel C.},
LANGUAGE = {eng},
ISSN = {0028-0836},
DOI = {10.1038/s41586-018-0531-2},
PUBLISHER = {Nature Publishing Group},
ADDRESS = {London},
YEAR = {2018},
DATE = {2018},
JOURNAL = {Nature},
VOLUME = {561},
PAGES = {479--484},
}
Endnote
%0 Journal Article
%A Mendoza, Pilar
%A Gruell, Henning
%A Nogueira, Lilian
%A Pai, Joy A.
%A Butler, Allison L.
%A Millard, Katrina
%A Lehmann, Clara
%A Suarez, Isabelle
%A Oliveira, Thiago Y.
%A Lorenzi, Julio C. C.
%A Cohen, Yehuda Z.
%A Wyen, Christoph
%A Kuemmerle, Tim
%A Karagounis, Theodora
%A Lu, Ching-Lan
%A Handl, Lisa
%A Unson-O'Brien, Cecilia
%A Patel, Roshni
%A Ruping, Carola
%A Schlotz, Maike
%A Witmer-Pack, Maggi
%A Shimeliovich, Irina
%A Kremer, Gisela
%A Thomas, Eleonore
%A Seaton, Kelly E.
%A Horowitz, Jill
%A West Jr., Anthony P.
%A Bjorkman, Pamela J.
%A Tomaras, Georgia D.
%A Gulick, Roy M.
%A Pfeifer, Nico
%A Faetkenheuer, Gerd
%A Seaman, Michael S.
%A Klein, Florian
%A Caskey, Marina
%A Nussenzweig, Michel C.
%+ External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
%T Combination Therapy with anti-HIV-1 Antibodies Maintains Viral Suppression :
%G eng
%U http://hdl.handle.net/21.11116/0000-0002-5770-E
%R 10.1038/s41586-018-0531-2
%7 2018
%D 2018
%J Nature
%O Nature
%V 561
%& 479
%P 479 - 484
%I Nature Publishing Group
%C London
%@ false
139. Nazarieh M: Understanding Regulatory Mechanisms Underlying Stem Cells Helps to Identify Cancer Biomarkers. Universität des Saarlandes; 2018.
Abstract
Detection of biomarker genes play a crucial role in disease detection and treatment. Bioinformatics offers a variety of approaches for identification of biomarker genes which play key roles in complex diseases. These computational approaches enhance the insight derived from experiments and reduce the efforts of biologists and experimentalists. This is essentially achieved through prioritizing a set of genes with certain attributes. In this thesis, we show that understanding the regulatory mechanisms underlying stem cells helps to identify cancer biomarkers. We got inspired by the regulatory mechanisms of the pluripotency network in mouse embryonic stem cells and formulated the problem where a set of master regulatory genes in regulatory networks is identified with two combinatorial optimization problems namely as minimum dominating set and minimum connected dominating set in weakly and strongly connected components. Then we applied the developed methods to regulatory cancer networks to identify disease-associated genes and anti-cancer drug targets in breast cancer and hepatocellular carcinoma. As not all the nodes in the solutions are critical, we developed a prioritization method to rank a set of candidate genes which are related to a certain disease based on systematic analysis of the genes that are differentially expressed in tumor and normal conditions. Moreover, we demonstrated that the topological features in regulatory networks surrounding differentially expressed genes are highly consistent in terms of using the output of several analysis tools. We compared two randomization strategies for TF-miRNA co-regulatory networks to infer significant network motifs underlying cellular identity. We showed that the edge-type conserving method surpasses the non-conserving method in terms of biological relevance and centrality overlap. We presented several web servers and software packages that are publicly available at no cost. The Cytoscape plugin of minimum connected dominating set identifies a set of key regulatory genes in a user provided regulatory network based on a heuristic approach. The ILP formulations of minimum dominating set and minimum connected dominating set return the optimal solutions for the aforementioned problems. Our source code is publicly available. The web servers TFmiR and TFmiR2 construct disease-, tissue-, process-specific networks for the sets of deregulated genes and miRNAs provided by a user. They highlight topological hotspots and offer detection of three- and four-node FFL motifs as a separate web service for both organisms mouse and human.
Export
BibTeX
@phdthesis{nazariehphd2017,
TITLE = {Understanding Regulatory Mechanisms Underlying Stem Cells Helps to Identify Cancer Biomarkers},
AUTHOR = {Nazarieh, Maryam},
LANGUAGE = {eng},
URL = {urn:nbn:de:bsz:291-scidok-ds-272650},
DOI = {10.22028/D291-27265},
SCHOOL = {Universit{\"a}t des Saarlandes},
ADDRESS = {Saarbr{\"u}cken},
YEAR = {2018},
DATE = {2018},
ABSTRACT = {Detection of biomarker genes play a crucial role in disease detection and treatment. Bioinformatics offers a variety of approaches for identification of biomarker genes which play key roles in complex diseases. These computational approaches enhance the insight derived from experiments and reduce the efforts of biologists and experimentalists. This is essentially achieved through prioritizing a set of genes with certain attributes. In this thesis, we show that understanding the regulatory mechanisms underlying stem cells helps to identify cancer biomarkers. We got inspired by the regulatory mechanisms of the pluripotency network in mouse embryonic stem cells and formulated the problem where a set of master regulatory genes in regulatory networks is identified with two combinatorial optimization problems namely as minimum dominating set and minimum connected dominating set in weakly and strongly connected components. Then we applied the developed methods to regulatory cancer networks to identify disease-associated genes and anti-cancer drug targets in breast cancer and hepatocellular carcinoma. As not all the nodes in the solutions are critical, we developed a prioritization method to rank a set of candidate genes which are related to a certain disease based on systematic analysis of the genes that are differentially expressed in tumor and normal conditions. Moreover, we demonstrated that the topological features in regulatory networks surrounding differentially expressed genes are highly consistent in terms of using the output of several analysis tools. We compared two randomization strategies for TF-miRNA co-regulatory networks to infer significant network motifs underlying cellular identity. We showed that the edge-type conserving method surpasses the non-conserving method in terms of biological relevance and centrality overlap. We presented several web servers and software packages that are publicly available at no cost. The Cytoscape plugin of minimum connected dominating set identifies a set of key regulatory genes in a user provided regulatory network based on a heuristic approach. The ILP formulations of minimum dominating set and minimum connected dominating set return the optimal solutions for the aforementioned problems. Our source code is publicly available. The web servers TFmiR and TFmiR2 construct disease-, tissue-, process-specific networks for the sets of deregulated genes and miRNAs provided by a user. They highlight topological hotspots and offer detection of three- and four-node FFL motifs as a separate web service for both organisms mouse and human.},
}
Endnote
%0 Thesis
%A Nazarieh, Maryam
%Y Helms, Volker
%A referee: Lengauer, Thomas
%+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
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 Understanding Regulatory Mechanisms Underlying Stem Cells Helps to Identify Cancer Biomarkers :
%G eng
%U http://hdl.handle.net/21.11116/0000-0001-9D69-9
%R 10.22028/D291-27265
%U urn:nbn:de:bsz:291-scidok-ds-272650
%F OTHER: hdl:20.500.11880/27104
%I Universität des Saarlandes
%C Saarbrücken
%D 2018
%P 139 p.
%V phd
%9 phd
%X Detection of biomarker genes play a crucial role in disease detection and treatment. Bioinformatics offers a variety of approaches for identification of biomarker genes which play key roles in complex diseases. These computational approaches enhance the insight derived from experiments and reduce the efforts of biologists and experimentalists. This is essentially achieved through prioritizing a set of genes with certain attributes. In this thesis, we show that understanding the regulatory mechanisms underlying stem cells helps to identify cancer biomarkers. We got inspired by the regulatory mechanisms of the pluripotency network in mouse embryonic stem cells and formulated the problem where a set of master regulatory genes in regulatory networks is identified with two combinatorial optimization problems namely as minimum dominating set and minimum connected dominating set in weakly and strongly connected components. Then we applied the developed methods to regulatory cancer networks to identify disease-associated genes and anti-cancer drug targets in breast cancer and hepatocellular carcinoma. As not all the nodes in the solutions are critical, we developed a prioritization method to rank a set of candidate genes which are related to a certain disease based on systematic analysis of the genes that are differentially expressed in tumor and normal conditions. Moreover, we demonstrated that the topological features in regulatory networks surrounding differentially expressed genes are highly consistent in terms of using the output of several analysis tools. We compared two randomization strategies for TF-miRNA co-regulatory networks to infer significant network motifs underlying cellular identity. We showed that the edge-type conserving method surpasses the non-conserving method in terms of biological relevance and centrality overlap. We presented several web servers and software packages that are publicly available at no cost. The Cytoscape plugin of minimum connected dominating set identifies a set of key regulatory genes in a user provided regulatory network based on a heuristic approach. The ILP formulations of minimum dominating set and minimum connected dominating set return the optimal solutions for the aforementioned problems. Our source code is publicly available. The web servers TFmiR and TFmiR2 construct disease-, tissue-, process-specific networks for the sets of deregulated genes and miRNAs provided by a user. They highlight topological hotspots and offer detection of three- and four-node FFL motifs as a separate web service for both organisms mouse and human.
%U https://publikationen.sulb.uni-saarland.de/handle/20.500.11880/27104
140. Palanisamy N, Kalaghatgi P, Akaberi D, Lundkvist Å, Chen Z, Hu P, Lennerstrand J: Worldwide Prevalence of Baseline Resistance-associated Polymorphisms and Resistance Mutations in HCV against Current Direct-Acting Antivirals. Antiviral Therapy 2018, 23.
Export
BibTeX
@article{Palanisamy2018,
TITLE = {Worldwide prevalence of baseline resistance-associated polymorphisms and resistance mutations in {HCV} against current direct-acting antivirals},
AUTHOR = {Palanisamy, Navaneethan and Kalaghatgi, Prabhav and Akaberi, Dario and Lundkvist, {\AA}ke and Chen, Zhi-wei and Hu, Peng and Lennerstrand, Johan},
LANGUAGE = {eng},
ISSN = {1359-6535},
DOI = {10.3851/IMP3237 2018},
PUBLISHER = {International Medical Press},
ADDRESS = {London},
YEAR = {2018},
JOURNAL = {Antiviral Therapy},
VOLUME = {23},
PAGES = {485--493},
}
Endnote
%0 Journal Article
%A Palanisamy, Navaneethan
%A Kalaghatgi, Prabhav
%A Akaberi, Dario
%A Lundkvist, Åke
%A Chen, Zhi-wei
%A Hu, Peng
%A Lennerstrand, Johan
%+ External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
%T Worldwide Prevalence of Baseline Resistance-associated Polymorphisms and Resistance Mutations in HCV against Current Direct-Acting Antivirals :
%G eng
%U http://hdl.handle.net/21.11116/0000-0002-CB09-0
%R 10.3851/IMP3237 2018
%7 2018
%D 2018
%J Antiviral Therapy
%V 23
%& 485
%P 485 - 493
%I International Medical Press
%C London
%@ false
141. Pan W-H, Sommer F, Falk-Paulsen M, Ulas T, Best P, Fazio A, Kachroo P, Luzius A, Jentzsch M, Rehman A, Müller F, Lengauer T, Walter J, Kuenzel S, Baines JF, Schreiber S, Franke A, Schultze JL, Backhed F, Rosenstiel P: Exposure to the Gut Microbiota Drives Distinct Methylome and Transcriptome Changes in Intestinal Epithelial Cells during Postnatal Development. Genome Medicine 2018, 10.
Export
BibTeX
@article{Pan2018,
TITLE = {Exposure to the Gut Microbiota Drives Distinct Methylome and Transcriptome Changes in Intestinal Epithelial Cells during Postnatal Development},
AUTHOR = {Pan, Wei-Hung and Sommer, Felix and Falk-Paulsen, Maren and Ulas, Thomas and Best, Philipp and Fazio, Antonella and Kachroo, Priyadarshini and Luzius, Anne and Jentzsch, Marlene and Rehman, Ateequr and M{\"u}ller, Fabian and Lengauer, Thomas and Walter, Joern and Kuenzel, Sven and Baines, John F. and Schreiber, Stefan and Franke, Andre and Schultze, Joachim L. and Backhed, Fredrik and Rosenstiel, Philip},
LANGUAGE = {eng},
DOI = {10.1186/s13073-018-0534-5},
PUBLISHER = {BioMed Central},
ADDRESS = {London},
YEAR = {2018},
JOURNAL = {Genome Medicine},
VOLUME = {10},
EID = {27},
}
Endnote
%0 Journal Article
%A Pan, Wei-Hung
%A Sommer, Felix
%A Falk-Paulsen, Maren
%A Ulas, Thomas
%A Best, Philipp
%A Fazio, Antonella
%A Kachroo, Priyadarshini
%A Luzius, Anne
%A Jentzsch, Marlene
%A Rehman, Ateequr
%A Müller, Fabian
%A Lengauer, Thomas
%A Walter, Joern
%A Kuenzel, Sven
%A Baines, John F.
%A Schreiber, Stefan
%A Franke, Andre
%A Schultze, Joachim L.
%A Backhed, Fredrik
%A Rosenstiel, Philip
%+ External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
%T Exposure to the Gut Microbiota Drives Distinct Methylome and Transcriptome Changes in Intestinal Epithelial Cells during Postnatal Development :
%G eng
%U http://hdl.handle.net/21.11116/0000-0001-37F8-A
%R 10.1186/s13073-018-0534-5
%7 2018
%D 2018
%J Genome Medicine
%V 10
%Z sequence number: 27
%I BioMed Central
%C London
142. Pirritano M, Goetz U, Karunanithi S, Nordstroem K, Schulz MH, Simon M: Environmental Temperature Controls Accumulation of Transacting siRNAs Involved in Heterochromatin Formation. Genes 2018, 9.
Export
BibTeX
@article{Pirritano2018,
TITLE = {Environmental Temperature Controls Accumulation of Transacting {siRNAs} Involved in Heterochromatin Formation},
AUTHOR = {Pirritano, Marcello and Goetz, Ulrike and Karunanithi, Sivarajan and Nordstroem, Karl and Schulz, Marcel H. and Simon, Martin},
LANGUAGE = {eng},
ISSN = {2073-4425},
DOI = {10.3390/genes9020117},
PUBLISHER = {MPDI},
ADDRESS = {Basel},
YEAR = {2018},
JOURNAL = {Genes},
VOLUME = {9},
NUMBER = {2},
EID = {117},
}
Endnote
%0 Journal Article
%A Pirritano, Marcello
%A Goetz, Ulrike
%A Karunanithi, Sivarajan
%A Nordstroem, Karl
%A Schulz, Marcel H.
%A Simon, Martin
%+ External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
%T Environmental Temperature Controls Accumulation of Transacting siRNAs Involved in Heterochromatin Formation :
%G eng
%U http://hdl.handle.net/21.11116/0000-0001-1F9E-C
%R 10.3390/genes9020117
%2 PMC5852613
%7 2018
%D 2018
%J Genes
%V 9
%N 2
%Z sequence number: 117
%I MPDI
%C Basel
%@ false
143. Salhab A, Nordstroem K, Gasparoni G, Kattler K, Ebert P, Ramirez F, Arrigoni L, Mueller F, Polansky JK, Cadenas C, Hengstler JG, Lengauer T, Manke T, Walter J: A Comprehensive Analysis of 195 DNA Methylomes Reveals Shared and Cell-specific Features of Partially Methylated Domains. Genome Biology 2018, 19.
Export
BibTeX
@article{Salhab_2018,
TITLE = {A comprehensive analysis of 195 {DNA} methylomes reveals shared and cell-specific features of partially methylated domains},
AUTHOR = {Salhab, Abdulrahman and Nordstroem, Karl and Gasparoni, Gilles and Kattler, Kathrin and Ebert, Peter and Ramirez, Fidel and Arrigoni, Laura and Mueller, Fabian and Polansky, Julia K. and Cadenas, Cristina and Hengstler, Jan G. and Lengauer, Thomas and Manke, Thomas and Walter, Joern},
LANGUAGE = {eng},
ISSN = {1465-6906},
DOI = {10.1186/s13059-018-1510-5},
PUBLISHER = {BioMed Central Ltd.},
ADDRESS = {London},
YEAR = {2018},
JOURNAL = {Genome Biology},
VOLUME = {19},
EID = {150},
}
Endnote
%0 Journal Article
%A Salhab, Abdulrahman
%A Nordstroem, Karl
%A Gasparoni, Gilles
%A Kattler, Kathrin
%A Ebert, Peter
%A Ramirez, Fidel
%A Arrigoni, Laura
%A Mueller, Fabian
%A Polansky, Julia K.
%A Cadenas, Cristina
%A Hengstler, Jan G.
%A Lengauer, Thomas
%A Manke, Thomas
%A Walter, Joern
%+ External Organizations
External Organizations
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
External Organizations
%T A Comprehensive Analysis of 195 DNA Methylomes Reveals Shared and Cell-specific Features of Partially Methylated Domains :
%G eng
%U http://hdl.handle.net/21.11116/0000-0002-5F29-7
%R 10.1186/s13059-018-1510-5
%7 2018
%D 2018
%J Genome Biology
%V 19
%Z sequence number: 150
%I BioMed Central Ltd.
%C London
%@ false
144. Schmidt F, List M, Cukuroglu E, Koehler S, Goke J, Schulz MH: An Ontology-based Method for Assessing Batch Effect Adjustment Approaches in Heterogeneous Datasets. Bioinformatics (Proc ECCB 2018) 2018, 34.
Export
BibTeX
@article{Schmidt_Bioinformatics2018,
TITLE = {An Ontology-based Method for Assessing Batch Effect Adjustment Approaches in Heterogeneous Datasets},
AUTHOR = {Schmidt, Florian and List, Markus and Cukuroglu, Engin and Koehler, Sebastian and Goke, Jonathan and Schulz, Marcel H.},
LANGUAGE = {eng},
ISSN = {1367-4803},
DOI = {10.1093/bioinformatics/bty553},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford},
YEAR = {2018},
DATE = {2018},
JOURNAL = {Bioinformatics (Proc. ECCB)},
VOLUME = {34},
NUMBER = {17},
PAGES = {i908--i916},
BOOKTITLE = {The 17th European Conference on Computational Biology (ECCB 2018)},
}
Endnote
%0 Journal Article
%A Schmidt, Florian
%A List, Markus
%A Cukuroglu, Engin
%A Koehler, Sebastian
%A Goke, Jonathan
%A Schulz, Marcel H.
%+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
%T An Ontology-based Method for Assessing Batch Effect Adjustment Approaches in Heterogeneous Datasets :
%G eng
%U http://hdl.handle.net/21.11116/0000-0002-5732-4
%R 10.1093/bioinformatics/bty553
%7 2018
%D 2018
%J Bioinformatics
%V 34
%N 17
%& i908
%P i908 - i916
%I Oxford University Press
%C Oxford
%@ false
%B The 17th European Conference on Computational Biology
%O ECCB 2018 Athens, Greece, 8 - 12 September 2018
145. Sikandar A, Cirnski K, Testolin G, Volz C, Broenstrup M, Kalinina OV, Müller R, Koehnke J: Adaptation of a Bacterial Multidrug Resistance System Revealed by the Structure and Function of AlbA. Journal of the American Chemical Society 2018, 140.
Export
BibTeX
@article{Sikandar2018,
TITLE = {Adaptation of a Bacterial Multidrug Resistance System Revealed by the Structure and Function of {AlbA}},
AUTHOR = {Sikandar, Asfandyar and Cirnski, Katarina and Testolin, Giambattista and Volz, Carsten and Broenstrup, Mark and Kalinina, Olga V. and M{\"u}ller, Rolf and Koehnke, Jesko},
LANGUAGE = {eng},
ISSN = {0002-7863},
DOI = {10.1021/jacs.8b08895},
PUBLISHER = {American Chemical Society},
ADDRESS = {Washington, DC},
YEAR = {2018},
DATE = {2018},
JOURNAL = {Journal of the American Chemical Society},
VOLUME = {140},
NUMBER = {48},
PAGES = {16641--16649},
}
Endnote
%0 Journal Article
%A Sikandar, Asfandyar
%A Cirnski, Katarina
%A Testolin, Giambattista
%A Volz, Carsten
%A Broenstrup, Mark
%A Kalinina, Olga V.
%A Müller, Rolf
%A Koehnke, Jesko
%+ External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
External Organizations
%T Adaptation of a Bacterial Multidrug Resistance System Revealed by the Structure and Function of AlbA :
%G eng
%U http://hdl.handle.net/21.11116/0000-0002-BA2F-9
%R 10.1021/jacs.8b08895
%7 2018
%D 2018
%J Journal of the American Chemical Society
%O J. Am. Chem. Soc. JACS
%V 140
%N 48
%& 16641
%P 16641 - 16649
%I American Chemical Society
%C Washington, DC
%@ false
146. Simovski B, Kanduri C, Gundersen S, Titov D, Domanska D, Bock C, Bossini-Castillo L, Chikina M, Favorov A, Layer RM, Mironov AA, Quinlan AR, Sheffield NC, Trynka G, Sandve GK: Coloc-stats: A Unified Web Interface to Perform Colocalization Analysis of Genomic Features. Nucleic Acids Research 2018, 46(Web Server issue).
Export
BibTeX
@article{Simovski_2018,
TITLE = {Coloc-stats: A Unified Web Interface to Perform Colocalization Analysis of Genomic Features},
AUTHOR = {Simovski, Boris and Kanduri, Chakravarthi and Gundersen, Sveinung and Titov, Dmytro and Domanska, Diana and Bock, Christoph and Bossini-Castillo, Lara and Chikina, Maria and Favorov, Alexander and Layer, Ryan M. and Mironov, Andrey A. and Quinlan, Aaron R. and Sheffield, Nathan C. and Trynka, Gosia and Sandve, Geir K.},
LANGUAGE = {eng},
ISSN = {0301-5610},
DOI = {10.1093/nar/gky474},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford, UK},
YEAR = {2018},
DATE = {2018},
JOURNAL = {Nucleic Acids Research},
VOLUME = {46},
NUMBER = {Web Server issue},
PAGES = {W186--W193},
}
Endnote
%0 Journal Article
%A Simovski, Boris
%A Kanduri, Chakravarthi
%A Gundersen, Sveinung
%A Titov, Dmytro
%A Domanska, Diana
%A Bock, Christoph
%A Bossini-Castillo, Lara
%A Chikina, Maria
%A Favorov, Alexander
%A Layer, Ryan M.
%A Mironov, Andrey A.
%A Quinlan, Aaron R.
%A Sheffield, Nathan C.
%A Trynka, Gosia
%A Sandve, Geir K.
%+ External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
%T Coloc-stats: A Unified Web Interface to Perform Colocalization Analysis of Genomic Features :
%G eng
%U http://hdl.handle.net/21.11116/0000-0001-E5C6-D
%R 10.1093/nar/gky474
%7 2018
%D 2018
%J Nucleic Acids Research
%O Nucleic Acids Res.
%V 46
%N Web Server issue
%& W186
%P W186 - W193
%I Oxford University Press
%C Oxford, UK
%@ false
2017
147. Ahmad M, Helms V, Kalinina OV, Lengauer T: Elucidating the Energetic Contributions to the Binding Free Energy. The Journal of Chemical Physics 2017, 146.
Export
BibTeX
@article{Ahmad2017,
TITLE = {Elucidating the Energetic Contributions to the Binding Free Energy},
AUTHOR = {Ahmad, Mazen and Helms, Volkhard and Kalinina, Olga V. and Lengauer, Thomas},
LANGUAGE = {eng},
ISSN = {0021-9606},
DOI = {10.1063/1.4973349},
PUBLISHER = {American Institute of Physics},
ADDRESS = {Woodbury, N.Y.},
YEAR = {2017},
DATE = {2017},
JOURNAL = {The Journal of Chemical Physics},
VOLUME = {146},
NUMBER = {1},
EID = {014105},
}
Endnote
%0 Journal Article
%A Ahmad, Mazen
%A Helms, Volkhard
%A Kalinina, Olga V.
%A Lengauer, Thomas
%+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
%T Elucidating the Energetic Contributions to the Binding Free Energy :
%G eng
%U http://hdl.handle.net/11858/00-001M-0000-002C-3A74-2
%R 10.1063/1.4973349
%7 2017
%D 2017
%J The Journal of Chemical Physics
%O J. Chem. Phys.
%V 146
%N 1
%Z sequence number: 014105
%I American Institute of Physics
%C Woodbury, N.Y.
%@ false
148. Albrecht F, List M, Bock C, Lengauer T: DeepBlueR: Large-scale Epigenomic Analysis in R. Bioinformatics 2017, 33.
Export
BibTeX
@article{AlbrechtBioinformatics2017,
TITLE = {{DeepBlueR}: {L}arge-scale Epigenomic Analysis in {R}},
AUTHOR = {Albrecht, Felipe and List, Markus and Bock, Christoph and Lengauer, Thomas},
LANGUAGE = {eng},
ISSN = {1367-4803},
DOI = {10.1093/bioinformatics/btx099},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford},
YEAR = {2017},
DATE = {2017},
JOURNAL = {Bioinformatics},
VOLUME = {33},
NUMBER = {13},
PAGES = {2063--2064},
EID = {btx099},
}
Endnote
%0 Journal Article
%A Albrecht, Felipe
%A List, Markus
%A Bock, Christoph
%A Lengauer, Thomas
%+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
%T DeepBlueR: Large-scale Epigenomic Analysis in R :
%G eng
%U http://hdl.handle.net/11858/00-001M-0000-002C-8AB4-4
%R 10.1093/bioinformatics/btx099
%2 PMC5870546
%7 2017-02-22
%D 2017
%J Bioinformatics
%V 33
%N 13
%& 2063
%P 2063 - 2064
%Z sequence number: btx099
%I Oxford University Press
%C Oxford
%@ false
149. Alcaraz N, List M, Batra R, Vandin F, Ditzel HJ, Baumbach J: De novo Pathway-based Biomarker Identification. Nucleic Acids Research 2017, 45.
Export
BibTeX
@article{Alcaraz2017,
TITLE = {\textit{De novo} pathway-based biomarker identification},
AUTHOR = {Alcaraz, Nicolas and List, Markus and Batra, Richa and Vandin, Fabio and Ditzel, Henrik J. and Baumbach, Jan},
LANGUAGE = {eng},
ISSN = {0305-1048},
DOI = {10.1093/nar/gkx642},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford},
YEAR = {2017},
DATE = {2017},
JOURNAL = {Nucleic Acids Research},
VOLUME = {45},
NUMBER = {16},
EID = {e151},
}
Endnote
%0 Journal Article
%A Alcaraz, Nicolas
%A List, Markus
%A Batra, Richa
%A Vandin, Fabio
%A Ditzel, Henrik J.
%A Baumbach, Jan
%+ External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
%T De novo Pathway-based Biomarker Identification :
%G eng
%U http://hdl.handle.net/11858/00-001M-0000-002D-DDE0-C
%R 10.1093/nar/gkx642
%7 2017
%D 2017
%J Nucleic Acids Research
%O Nucleic Acids Res
%V 45
%N 16
%Z sequence number: e151
%I Oxford University Press
%C Oxford
%@ false
150. Almeida D, Skov I, Silva A, Vandin F, Tan Q, Röttger R, Baumbach J: Efficient Detection of Differentially Methylated Regions using DiMmeR. Bioinformatics 2017, 33.
Export
BibTeX
@article{Almeida2017,
TITLE = {Efficient Detection of Differentially Methylated Regions using {DiMmeR}},
AUTHOR = {Almeida, Diogo and Skov, Ida and Silva, Artur and Vandin, Fabio and Tan, Qihua and R{\"o}ttger, Richard and Baumbach, Jan},
LANGUAGE = {eng},
ISSN = {1367-4803},
DOI = {10.1093/bioinformatics/btw657},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford},
YEAR = {2017},
DATE = {2017},
JOURNAL = {Bioinformatics},
VOLUME = {33},
NUMBER = {4},
PAGES = {549--551},
}
Endnote
%0 Journal Article
%A Almeida, Diogo
%A Skov, Ida
%A Silva, Artur
%A Vandin, Fabio
%A Tan, Qihua
%A Röttger, Richard
%A Baumbach, Jan
%+ External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
%T Efficient Detection of Differentially Methylated Regions using DiMmeR :
%G eng
%U http://hdl.handle.net/11858/00-001M-0000-002C-ECA5-7
%R 10.1093/bioinformatics/btw657
%7 2016
%D 2017
%J Bioinformatics
%V 33
%N 4
%& 549
%P 549 - 551
%I Oxford University Press
%C Oxford
%@ false
151. Bader J, Däumer M, Schöni-Affolter F, Böni J, Gorgievski-Hrisoho M, Martinetti G, Thielen A, Klimkait T: Therapeutic Immune Recovery and Reduction of CXCR4-Tropic HIV-1. Clinical Infectious Diseases 2017, 64.
Export
BibTeX
@article{Bader2017,
TITLE = {Therapeutic Immune Recovery and Reduction of {CXCR4}-Tropic {HIV}-1},
AUTHOR = {Bader, Jo{\"e}lle and D{\"a}umer, Martin and Sch{\"o}ni-Affolter, Franziska and B{\"o}ni, J{\"u}rg and Gorgievski-Hrisoho, Meri and Martinetti, Gladys and Thielen, Alexander and Klimkait, Thomas},
LANGUAGE = {eng},
ISSN = {1058-4838},
DOI = {10.1093/cid/ciw737},
PUBLISHER = {The University of Chicago Press},
ADDRESS = {Chicago, IL},
YEAR = {2017},
DATE = {2017},
JOURNAL = {Clinical Infectious Diseases},
VOLUME = {64},
NUMBER = {3},
PAGES = {295--300},
}
Endnote
%0 Journal Article
%A Bader, Joëlle
%A Däumer, Martin
%A Schöni-Affolter, Franziska
%A Böni, Jürg
%A Gorgievski-Hrisoho, Meri
%A Martinetti, Gladys
%A Thielen, Alexander
%A Klimkait, Thomas
%+ External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
%T Therapeutic Immune Recovery and Reduction of CXCR4-Tropic HIV-1 :
%G eng
%U http://hdl.handle.net/11858/00-001M-0000-002C-ECAE-6
%R 10.1093/cid/ciw737
%7 2016
%D 2017
%J Clinical Infectious Diseases
%V 64
%N 3
%& 295
%P 295 - 300
%I The University of Chicago Press
%C Chicago, IL
%@ false
152. Batra R, Alcaraz N, Gitzhofer K, Pauling J, Ditzel HJ, Hellmuth M, Baumbach J, List M: On the Performance of De Novo Pathway Enrichment. njp Systems Biology and Applications 2017, 3.
Export
BibTeX
@article{Baumbachnjp2016,
TITLE = {On the Performance of De Novo Pathway Enrichment},
AUTHOR = {Batra, Richa and Alcaraz, Nicolas and Gitzhofer, Kevin and Pauling, Josch and Ditzel, Henrik J. and Hellmuth, Marc and Baumbach, Jan and List, Markus},
LANGUAGE = {eng},
DOI = {10.1038/s41540-017-0007-2},
PUBLISHER = {Nature Publishing Group},
ADDRESS = {London},
YEAR = {2017},
JOURNAL = {njp Systems Biology and Applications},
VOLUME = {3},
PAGES = {1--8},
EID = {6},
}
Endnote
%0 Journal Article
%A Batra, Richa
%A Alcaraz, Nicolas
%A Gitzhofer, Kevin
%A Pauling, Josch
%A Ditzel, Henrik J.
%A Hellmuth, Marc
%A Baumbach, Jan
%A List, Markus
%+ External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
%T On the Performance of De Novo Pathway Enrichment :
%G eng
%U http://hdl.handle.net/11858/00-001M-0000-002C-2039-6
%R 10.1038/s41540-017-0007-2
%7 2017
%D 2017
%J njp Systems Biology and Applications
%V 3
%& 1
%P 1 - 8
%Z sequence number: 6
%I Nature Publishing Group
%C London
153. Berger B, Gaasterland T, Lengauer T, Orengo C, Gaeta B, Markel S, Valencia A: ISCB’s Initial Reaction to The New England Journal of Medicine Editorial on Data Sharing. Bioinformatics 2017, 33.
Export
BibTeX
@article{Berger2017,
TITLE = {{ISCB}'s Initial Reaction to {The New England Journal of Medicine} Editorial on Data Sharing},
AUTHOR = {Berger, Bonnie and Gaasterland, Terry and Lengauer, Thomas and Orengo, Christine and Gaeta, Bruno and Markel, Scott and Valencia, Alfonso},
LANGUAGE = {eng},
ISSN = {1367-4803},
DOI = {10.1093/bioinformatics/btw090},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford},
YEAR = {2017},
DATE = {2017},
JOURNAL = {Bioinformatics},
VOLUME = {33},
NUMBER = {18},
PAGES = {2968--2968},
}
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/21.11116/0000-0000-39C4-3
%R 10.1093/bioinformatics/btw090
%7 2017
%D 2017
%J Bioinformatics
%V 33
%N 18
%& 2968
%P 2968 - 2968
%I Oxford University Press
%C Oxford
%@ false
154. Busch CJ-L, Hendrikx T, Weismann D, Jäckel S, Walenbergh SMA, Rendeiro AF, Weißer J, Puhm F, Hladik A, Göderle L, Papac-Milicevic N, Haas G, Millischer V, Subramaniam S, Knapp S, Bennett KL, Bock C, Reinhardt C, Shiri-Sverdlov R, Binder CJ: Malondialdehyde Epitopes Are Sterile Mediators of Hepatic Inflammation in Hypercholesterolemic Mice. Hepatology 2017, 65.
Export
BibTeX
@article{Busch2017,
TITLE = {Malondialdehyde Epitopes Are Sterile Mediators of Hepatic Inflammation in Hypercholesterolemic Mice},
AUTHOR = {Busch, Clara Jana-Lui and Hendrikx, Tim and Weismann, David and J{\"a}ckel, Sven and Walenbergh, Sofie M. A. and Rendeiro, Andr{\'e} F. and Wei{\ss}er, Juliane and Puhm, Florian and Hladik, Anastasiya and G{\"o}derle, Laura and Papac-Milicevic, Nikolina and Haas, Gerald and Millischer, Vincent and Subramaniam, Saravanan and Knapp, Sylvia and Bennett, Keiryn L. and Bock, Christoph and Reinhardt, Christoph and Shiri-Sverdlov, Ronit and Binder, Christoph J.},
LANGUAGE = {eng},
ISSN = {0270-9139},
DOI = {10.1002/hep.28970},
PUBLISHER = {AASLD},
ADDRESS = {Alexandria, VA},
YEAR = {2017},
JOURNAL = {Hepatology},
VOLUME = {65},
NUMBER = {4},
PAGES = {1181--1195},
}
Endnote
%0 Journal Article
%A Busch, Clara Jana-Lui
%A Hendrikx, Tim
%A Weismann, David
%A Jäckel, Sven
%A Walenbergh, Sofie M. A.
%A Rendeiro, André F.
%A Weißer, Juliane
%A Puhm, Florian
%A Hladik, Anastasiya
%A Göderle, Laura
%A Papac-Milicevic, Nikolina
%A Haas, Gerald
%A Millischer, Vincent
%A Subramaniam, Saravanan
%A Knapp, Sylvia
%A Bennett, Keiryn L.
%A Bock, Christoph
%A Reinhardt, Christoph
%A Shiri-Sverdlov, Ronit
%A Binder, Christoph J.
%+ External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
External Organizations
External Organizations
%T Malondialdehyde Epitopes Are Sterile Mediators of Hepatic Inflammation in Hypercholesterolemic Mice :
%G eng
%U http://hdl.handle.net/11858/00-001M-0000-002C-576B-C
%R 10.1002/hep.28970
%2 PMC5892702
%7 2017
%D 2017
%J Hepatology
%V 65
%N 4
%& 1181
%P 1181 - 1195
%I AASLD
%C Alexandria, VA
%@ false
155. Caskey M, Schoofs T, Gruell H, Settler A, Karagounis T, Kreider EF, Murrell B, Pfeifer N, Nogueira L, Oliveira TY, Learn GH, Cohen YZ, Lehmann C, Gillor D, Shimeliovich I, Unson-O’Brien C, Weiland D, Robles A, Kümmerle T, Wyen C, Levin R, Witmer-Pack M, Eren K, Ignacio C, Kiss S, Jr APW, Mouquet H, Zingman BS, Gulick RM, Keler T, et al.: Antibody 10-1074 Suppresses Viremia in HIV-1-infected Individuals. Nature Medicine 2017, 23.
Export
BibTeX
@article{Pfeifernature2017,
TITLE = {Antibody 10-1074 Suppresses Viremia in {HIV}-1-infected Individuals},
AUTHOR = {Caskey, Marina and Schoofs, Till and Gruell, Henning and Settler, Allison and Karagounis, Theodora and Kreider, Edward F and Murrell, Ben and Pfeifer, Nico and Nogueira, Lilian and Oliveira, Thiago Y and Learn, Gerald H and Cohen, Yehuda Z and Lehmann, Clara and Gillor, Daniel and Shimeliovich, Irina and Unson-O{\textquoteright}Brien, Cecilia and Weiland, Daniela and Robles, Alexander and K{\"u}mmerle, Tim and Wyen, Christoph and Levin, Rebeka and Witmer-Pack, Maggi and Eren, Kemal and Ignacio, Caroline and Kiss, Szilard and Jr, Anthony P West and Mouquet, Hugo and Zingman, Barry S and Gulick, Roy M and Keler, Tibor and Bjorkman, Pamela J and Seaman, Michael S and Hahn, Beatrice H and F{\"a}tkenheuer, Gerd and Schlesinger, Sarah J and Nussenzweig, Michel C and Klein, Florian},
LANGUAGE = {eng},
ISSN = {1078-8956},
DOI = {10.1038/nm.4268},
PUBLISHER = {Nature Pub. Co.},
ADDRESS = {New York, NY},
YEAR = {2017},
DATE = {2017},
JOURNAL = {Nature Medicine},
VOLUME = {23},
NUMBER = {2},
PAGES = {185--191},
}
Endnote
%0 Journal Article
%A Caskey, Marina
%A Schoofs, Till
%A Gruell, Henning
%A Settler, Allison
%A Karagounis, Theodora
%A Kreider, Edward F
%A Murrell, Ben
%A Pfeifer, Nico
%A Nogueira, Lilian
%A Oliveira, Thiago Y
%A Learn, Gerald H
%A Cohen, Yehuda Z
%A Lehmann, Clara
%A Gillor, Daniel
%A Shimeliovich, Irina
%A Unson-O’Brien, Cecilia
%A Weiland, Daniela
%A Robles, Alexander
%A Kümmerle, Tim
%A Wyen, Christoph
%A Levin, Rebeka
%A Witmer-Pack, Maggi
%A Eren, Kemal
%A Ignacio, Caroline
%A Kiss, Szilard
%A Jr, Anthony P West
%A Mouquet, Hugo
%A Zingman, Barry S
%A Gulick, Roy M
%A Keler, Tibor
%A Bjorkman, Pamela J
%A Seaman, Michael S
%A Hahn, Beatrice H
%A Fätkenheuer, Gerd
%A Schlesinger, Sarah J
%A Nussenzweig, Michel C
%A Klein, Florian
%+ External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
%T Antibody 10-1074 Suppresses Viremia in HIV-1-infected Individuals :
%G eng
%U http://hdl.handle.net/11858/00-001M-0000-002C-7F0C-8
%R 10.1038/nm.4268
%7 2017-01-16
%D 2017
%J Nature Medicine
%O Nat. Med.
%V 23
%N 2
%& 185
%P 185 - 191
%I Nature Pub. Co.
%C New York, NY
%@ false
156. Datlinger P, Rendeiro AF, Schmidl C, Krausgruber T, Traxler P, Klughammer J, Schuster LC, Kuchler A, Alpar D, Bock C: Pooled CRISPR Screening with Single-cell Transcriptome Readout. Nature Methods 2017, 14.
Export
BibTeX
@article{Bocknature2017,
TITLE = {Pooled {CRISPR} Screening with Single-cell Transcriptome Readout},
AUTHOR = {Datlinger, Paul and Rendeiro, Andr{\'e} F and Schmidl, Christian and Krausgruber, Thomas and Traxler, Peter and Klughammer, Johanna and Schuster, Linda C and Kuchler, Amelie and Alpar, Donat and Bock, Christoph},
LANGUAGE = {eng},
ISSN = {1548-7091},
DOI = {10.1038/nmeth.4177},
PUBLISHER = {Nature Pub. Group},
ADDRESS = {New York, NY},
YEAR = {2017},
DATE = {2017},
JOURNAL = {Nature Methods},
VOLUME = {14},
NUMBER = {3},
PAGES = {297--301},
}
Endnote
%0 Journal Article
%A Datlinger, Paul
%A Rendeiro, André F
%A Schmidl, Christian
%A Krausgruber, Thomas
%A Traxler, Peter
%A Klughammer, Johanna
%A Schuster, Linda C
%A Kuchler, Amelie
%A Alpar, Donat
%A Bock, Christoph
%+ External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
%T Pooled CRISPR Screening with Single-cell Transcriptome Readout :
%G eng
%U http://hdl.handle.net/11858/00-001M-0000-002C-532B-2
%R 10.1038/nmeth.4177
%7 2017
%D 2017
%J Nature Methods
%O Nature methods
%V 14
%N 3
%& 297
%P 297 - 301
%I Nature Pub. Group
%C New York, NY
%@ false
157. Demirci MDS, Baumbach J, Allmer J: On the Performance of pre-microRNA Detection Algorithms. Nature Communications 2017, 8.
Export
BibTeX
@article{Demirci2017,
TITLE = {On the performance of pre-micro{RNA} detection algorithms},
AUTHOR = {Demirci, M{\"u}{\c s}erref Duygu Sa{\c c}ar and Baumbach, Jan and Allmer, Jens},
LANGUAGE = {eng},
ISSN = {2041-1723},
DOI = {10.1038/s41467-017-00403-z},
PUBLISHER = {Nature Publishing Group},
ADDRESS = {London},
YEAR = {2017},
JOURNAL = {Nature Communications},
VOLUME = {8},
EID = {330},
}
Endnote
%0 Journal Article
%A Demirci, Müşerref Duygu Saçar
%A Baumbach, Jan
%A Allmer, Jens
%+ External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
%T On the Performance of pre-microRNA Detection Algorithms :
%G eng
%U http://hdl.handle.net/11858/00-001M-0000-002D-DC7E-1
%R 10.1038/s41467-017-00403-z
%2 PMC5571158
%7 2017-08-24
%D 2017
%8 24.08.2017
%J Nature Communications
%O Nat. Commun.
%V 8
%Z sequence number: 330
%I Nature Publishing Group
%C London
%@ false
158. Ebler J, Schönhuth A, Marschall T: Genotyping of Inversions and Tandem Duplications. Bioinformatics 2017, 33.
Export
BibTeX
@article{Marshallbio17,
TITLE = {Genotyping of Inversions and Tandem Duplications},
AUTHOR = {Ebler, Jana and Sch{\"o}nhuth, Alexander and Marschall, Tobias},
LANGUAGE = {eng},
ISSN = {1367-4803},
DOI = {10.1093/bioinformatics/btx020},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford},
YEAR = {2017},
DATE = {2017},
JOURNAL = {Bioinformatics},
VOLUME = {33},
NUMBER = {24},
PAGES = {4015--4023},
EID = {btx020},
}
Endnote
%0 Journal Article
%A Ebler, Jana
%A Schönhuth, Alexander
%A Marschall, Tobias
%+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
%T Genotyping of Inversions and Tandem Duplications :
%G eng
%U http://hdl.handle.net/11858/00-001M-0000-002C-468F-7
%R 10.1093/bioinformatics/btx020
%7 2017-02-07
%D 2017
%J Bioinformatics
%V 33
%N 24
%& 4015
%P 4015 - 4023
%Z sequence number: btx020
%I Oxford University Press
%C Oxford
%@ false
159. Gress A, Ramensky V, Kalinina OV: Spatial Distribution of Disease-associated Variants in Three-dimensional Structures of Protein Complexes. Oncogenesis 2017, 6.
Export
BibTeX
@article{Gress_2017,
TITLE = {Spatial Distribution of Disease-associated Variants in Three-dimensional Structures of Protein Complexes},
AUTHOR = {Gress, Alexander and Ramensky, V. and Kalinina, Olga V.},
LANGUAGE = {eng},
ISSN = {2157-9024},
DOI = {10.1038/oncsis.2017.79},
PUBLISHER = {Nature Publishing},
YEAR = {2017},
JOURNAL = {Oncogenesis},
VOLUME = {6},
NUMBER = {9},
EID = {e380},
}
Endnote
%0 Journal Article
%A Gress, Alexander
%A Ramensky, V.
%A Kalinina, Olga V.
%+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
%T Spatial Distribution of Disease-associated Variants in Three-dimensional Structures of Protein Complexes :
%G eng
%U http://hdl.handle.net/11858/00-001M-0000-002E-24CF-8
%R 10.1038/oncsis.2017.79
%2 PMC5623905
%7 2017
%D 2017
%J Oncogenesis
%V 6
%N 9
%Z sequence number: e380
%I Nature Publishing
%@ false
160. Hake A, Pfeifer N: Prediction of HIV-1 Sensitivity to Broadly Neutralizing Antibodies Shows a Trend towards Resistance over Time. PLoS Computational Biology 2017, 13.
Export
BibTeX
@article{HakePfeifer2017,
TITLE = {Prediction of {HIV}-1 Sensitivity to Broadly Neutralizing Antibodies Shows a Trend towards Resistance over Time},
AUTHOR = {Hake, Anna and Pfeifer, Nico},
LANGUAGE = {eng},
ISSN = {1553-734X},
DOI = {10.1371/journal.pcbi.1005789},
PUBLISHER = {Public Library of Science},
ADDRESS = {San Francisco, CA},
YEAR = {2017},
JOURNAL = {PLoS Computational Biology},
VOLUME = {13},
NUMBER = {10},
EID = {e1005789},
}
Endnote
%0 Journal Article
%A Hake, Anna
%A Pfeifer, Nico
%+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
%T Prediction of HIV-1 Sensitivity to Broadly Neutralizing Antibodies Shows a Trend towards Resistance over Time :
%G eng
%U http://hdl.handle.net/11858/00-001M-0000-002E-3127-A
%R 10.1371/journal.pcbi.1005789
%2 PMC5669501
%7 2017
%D 2017
%J PLoS Computational Biology
%V 13
%N 10
%Z sequence number: e1005789
%I Public Library of Science
%C San Francisco, CA
%@ false
161. Hashemi S, Dalini AN, Jalali A, Banaei-Moghaddam AM, Razaghi-Moghadam Z: Cancerouspdomains: Comprehensive Analysis of Cancer Type-specific Recurrent Somatic Mutations in Proteins and Domains. BMC Bioinformatics 2017, 18.
Export
BibTeX
@article{Hashemi2017,
TITLE = {Cancerouspdomains: {C}omprehensive analysis of cancer type-specific recurrent somatic mutations in proteins and domains},
AUTHOR = {Hashemi, Seirana and Dalini, Abbas Nowzari and Jalali, Adrin and Banaei-Moghaddam, Ali Mohammad and Razaghi-Moghadam, Zahra},
LANGUAGE = {eng},
ISSN = {1471-2105},
DOI = {10.1186/s12859-017-1779-5},
PUBLISHER = {BioMed Central},
YEAR = {2017},
JOURNAL = {BMC Bioinformatics},
VOLUME = {18},
EID = {370},
}
Endnote
%0 Journal Article
%A Hashemi, Seirana
%A Dalini, Abbas Nowzari
%A Jalali, Adrin
%A Banaei-Moghaddam, Ali Mohammad
%A Razaghi-Moghadam, Zahra
%+ External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
External Organizations
%T Cancerouspdomains: Comprehensive Analysis of Cancer Type-specific Recurrent Somatic Mutations in Proteins and Domains :
%G eng
%U http://hdl.handle.net/11858/00-001M-0000-002D-DDC4-C
%R 10.1186/s12859-017-1779-5
%7 2017
%D 2017
%J BMC Bioinformatics
%V 18
%Z sequence number: 370
%I BioMed Central
%@ false
162. Heger E, Kaiser R, Knops E, Neumann-Fraune M, Pironti A, Lengauer T, Walter H, Sierra S: Results of the First International HIV-1 Coreceptor Proficiency Panel Test. Journal of Clinical Virology 2017, 93.
Export
BibTeX
@article{Heger2017,
TITLE = {Results of the First International {HIV}-1 Coreceptor Proficiency Panel Test},
AUTHOR = {Heger, Eva and Kaiser, Rolf and Knops, Elena and Neumann-Fraune, Maria and Pironti, Alejandro and Lengauer, Thomas and Walter, Hauke and Sierra, Saleta},
LANGUAGE = {eng},
ISSN = {1386-6532},
DOI = {10.1016/j.jcv.2017.06.002},
PUBLISHER = {Elsevier},
ADDRESS = {Amsterdam},
YEAR = {2017},
DATE = {2017},
JOURNAL = {Journal of Clinical Virology},
VOLUME = {93},
PAGES = {53--56},
}
Endnote
%0 Journal Article
%A Heger, Eva
%A Kaiser, Rolf
%A Knops, Elena
%A Neumann-Fraune, Maria
%A Pironti, Alejandro
%A Lengauer, Thomas
%A Walter, Hauke
%A Sierra, Saleta
%+ External Organizations
External Organizations
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
External Organizations
%T Results of the First International HIV-1 Coreceptor Proficiency Panel Test :
%G eng
%U http://hdl.handle.net/11858/00-001M-0000-002E-0189-7
%R 10.1016/j.jcv.2017.06.002
%7 2017
%D 2017
%J Journal of Clinical Virology
%V 93
%& 53
%P 53 - 56
%I Elsevier
%C Amsterdam
%@ false
163. Jühling F, Bandiera S, Hamdane N, Thumann C, Durand SC, Saghire H. E, Davidson I, Habersetzer F, Pessaux P, Bardeesy N, Schmidl C, Bock C, Hoshida Y, Zeisel MB, Baumert TF: Hepatitis C Virus-induced Epigenetic and Transcriptional Changes Persist Post Cure. Journal of Hepatology 2017, 66.
Export
BibTeX
@article{Juehling2017,
TITLE = {Hepatitis {C} Virus-induced Epigenetic and Transcriptional Changes Persist Post Cure},
AUTHOR = {J{\"u}hling, F. and Bandiera, S. and Hamdane, N. and Thumann, C. and Durand, S. C. and Saghire, H .E. and Davidson, I. and Habersetzer, F. and Pessaux, P. and Bardeesy, N. and Schmidl, C. and Bock, Christoph and Hoshida, Y. and Zeisel, M. B. and Baumert, T. F.},
LANGUAGE = {eng},
ISBN = {0168-8278},
URL = {http://dx.doi.org/10.1016/S0168-8278(17)30304-5},
DOI = {10.1016/S0168-8278(17)30304-5},
PUBLISHER = {Elsevier},
ADDRESS = {Amsterdam},
YEAR = {2017},
DATE = {2017},
JOURNAL = {Journal of Hepatology},
VOLUME = {66},
NUMBER = {1},
PAGES = {S21--S21},
}
Endnote
%0 Journal Article
%A Jühling, F.
%A Bandiera, S.
%A Hamdane, N.
%A Thumann, C.
%A Durand, S. C.
%A Saghire, H .E.
%A Davidson, I.
%A Habersetzer, F.
%A Pessaux, P.
%A Bardeesy, N.
%A Schmidl, C.
%A Bock, Christoph
%A Hoshida, Y.
%A Zeisel, M. B.
%A Baumert, T. F.
%+ external
external
external
external
external
external
external
external
external
external
external
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
external
external
external
%T Hepatitis C Virus-induced Epigenetic and Transcriptional Changes Persist Post Cure :
%G eng
%U http://hdl.handle.net/11858/00-001M-0000-002D-7861-8
%U http://dx.doi.org/10.1016/S0168-8278(17)30304-5
%R 10.1016/S0168-8278(17)30304-5
%7 2017
%D 2017
%J Journal of Hepatology
%V 66
%N 1
%& S21
%P S21 - S21
%I Elsevier
%C Amsterdam
%@ 0168-8278
164. Kalaghatgi P, Lengauer T: Computing Phylogenetic Trees Using Topologically Related Minimum Spanning Trees. Journal of Graph Algorithms and Applications 2017, 21.
Export
BibTeX
@article{Kalaghatgi2017a,
TITLE = {Computing Phylogenetic Trees Using Topologically Related Minimum Spanning Trees},
AUTHOR = {Kalaghatgi, Prabhav and Lengauer, Thomas},
LANGUAGE = {eng},
ISSN = {1526-1719},
DOI = {10.7155/jgaa.00447},
PUBLISHER = {Brown University, Dept. of Computer Science},
ADDRESS = {Providence, R.I.},
YEAR = {2017},
JOURNAL = {Journal of Graph Algorithms and Applications},
VOLUME = {21},
NUMBER = {6},
PAGES = {1003--1025},
}
Endnote
%0 Journal Article
%A Kalaghatgi, Prabhav
%A Lengauer, Thomas
%+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
%T Computing Phylogenetic Trees Using Topologically Related Minimum Spanning Trees :
%G eng
%U http://hdl.handle.net/21.11116/0000-0000-39A9-2
%R 10.7155/jgaa.00447
%7 2017
%D 2017
%J Journal of Graph Algorithms and Applications
%V 21
%N 6
%& 1003
%P 1003 - 1025
%I Brown University, Dept. of Computer Science
%C Providence, R.I.
%@ false
165. Selecting Optimal Minimum Spanning Trees that Share a Topological Correspondence with Phylogenetic Trees [http://arxiv.org/abs/1701.02844]
(arXiv: 1701.02844) Abstract
Choi et. al (2011) introduced a minimum spanning tree (MST)-based method
called CLGrouping, for constructing tree-structured probabilistic graphical
models, a statistical framework that is commonly used for inferring
phylogenetic trees. While CLGrouping works correctly if there is a unique MST,
we observe an indeterminacy in the method in the case that there are multiple
MSTs. In this work we remove this indeterminacy by introducing so-called
vertex-ranked MSTs. We note that the effectiveness of CLGrouping is inversely
related to the number of leaves in the MST. This motivates the problem of
finding a vertex-ranked MST with the minimum number of leaves (MLVRMST). We
provide a polynomial time algorithm for the MLVRMST problem, and prove its
correctness for graphs whose edges are weighted with tree-additive distances.
Export
BibTeX
@online{Kalaghatgi2017,
TITLE = {Selecting Optimal Minimum Spanning Trees that Share a Topological Correspondence with Phylogenetic Trees},
AUTHOR = {Kalaghatgi, Prabhav and Lengauer, Thomas},
LANGUAGE = {eng},
URL = {http://arxiv.org/abs/1701.02844},
EPRINT = {1701.02844},
EPRINTTYPE = {arXiv},
YEAR = {2017},
ABSTRACT = {Choi et. al (2011) introduced a minimum spanning tree (MST)-based method called CLGrouping, for constructing tree-structured probabilistic graphical models, a statistical framework that is commonly used for inferring phylogenetic trees. While CLGrouping works correctly if there is a unique MST, we observe an indeterminacy in the method in the case that there are multiple MSTs. In this work we remove this indeterminacy by introducing so-called vertex-ranked MSTs. We note that the effectiveness of CLGrouping is inversely related to the number of leaves in the MST. This motivates the problem of finding a vertex-ranked MST with the minimum number of leaves (MLVRMST). We provide a polynomial time algorithm for the MLVRMST problem, and prove its correctness for graphs whose edges are weighted with tree-additive distances.},
}
Endnote
%0 Report
%A Kalaghatgi, Prabhav
%A Lengauer, Thomas
%+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
%T Selecting Optimal Minimum Spanning Trees that Share a Topological Correspondence with Phylogenetic Trees :
%G eng
%U http://hdl.handle.net/11858/00-001M-0000-002C-3E81-2
%U http://arxiv.org/abs/1701.02844
%D 2017
%X Choi et. al (2011) introduced a minimum spanning tree (MST)-based method
called CLGrouping, for constructing tree-structured probabilistic graphical
models, a statistical framework that is commonly used for inferring
phylogenetic trees. While CLGrouping works correctly if there is a unique MST,
we observe an indeterminacy in the method in the case that there are multiple
MSTs. In this work we remove this indeterminacy by introducing so-called
vertex-ranked MSTs. We note that the effectiveness of CLGrouping is inversely
related to the number of leaves in the MST. This motivates the problem of
finding a vertex-ranked MST with the minimum number of leaves (MLVRMST). We
provide a polynomial time algorithm for the MLVRMST problem, and prove its
correctness for graphs whose edges are weighted with tree-additive distances.
%K Mathematics, Combinatorics, math.CO,Computer Science, Data Structures and Algorithms, cs.DS
166. Kehl T, Schneider L, Schmidt F, Stöckel D, Gerstner N, Backes C, Meese E, Keller A, Schulz MH, Lenhof H-P: RegulatorTrail: A Web Service for the Identification of Key Transcriptional Regulators. Nucleic Acids Research 2017, 45.
Export
BibTeX
@article{Kehl2017,
TITLE = {{RegulatorTrail}: {A} Web Service for the Identification of Key Transcriptional Regulators},
AUTHOR = {Kehl, Tim and Schneider, Lara and Schmidt, Florian and St{\"o}ckel, Daniel and Gerstner, Nico and Backes, Christina and Meese, Eckart and Keller, Andreas and Schulz, Marcel Holger and Lenhof, Hans-Peter},
LANGUAGE = {eng},
ISSN = {0305-1048},
DOI = {10.1093/nar/gkx350},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford},
YEAR = {2017},
DATE = {2017},
JOURNAL = {Nucleic Acids Research},
VOLUME = {45},
NUMBER = {W1},
PAGES = {W146--W153},
}
Endnote
%0 Journal Article
%A Kehl, Tim
%A Schneider, Lara
%A Schmidt, Florian
%A Stöckel, Daniel
%A Gerstner, Nico
%A Backes, Christina
%A Meese, Eckart
%A Keller, Andreas
%A Schulz, Marcel Holger
%A Lenhof, Hans-Peter
%+ External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
%T RegulatorTrail: A Web Service for the Identification of Key Transcriptional Regulators :
%G eng
%U http://hdl.handle.net/11858/00-001M-0000-002D-C393-D
%R 10.1093/nar/gkx350
%2 PMC5570139
%7 2017
%D 2017
%J Nucleic Acids Research
%O Nucleic Acids Res
%V 45
%N W1
%& W146
%P W146 - W153
%I Oxford University Press
%C Oxford
%@ false
167. Klau GW, Marschall T: A Guided Tour to Computational Haplotyping. In Unveiling Dynamics and Complexity (CiE 2017). Springer; 2017. [Lecture Notes in Computer Science, vol. 10307]
Export
BibTeX
@inproceedings{Klau_CiE2017,
TITLE = {A Guided Tour to Computational Haplotyping},
AUTHOR = {Klau, Gunnar W. and Marschall, Tobias},
LANGUAGE = {eng},
ISBN = {978-3-319-58740-0},
DOI = {10.1007/978-3-319-58741-7_6},
PUBLISHER = {Springer},
YEAR = {2017},
DATE = {2017},
BOOKTITLE = {Unveiling Dynamics and Complexity (CiE 2017)},
EDITOR = {Kari, Jarkko and Manea, Florin and Petre, Ion},
PAGES = {50-63},
SERIES = {Lecture Notes in Computer Science},
VOLUME = {10307},
ADDRESS = {Turku, Finland},
}
Endnote
%0 Conference Proceedings
%A Klau, Gunnar W.
%A Marschall, Tobias
%+ External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
%T A Guided Tour to Computational Haplotyping :
%G eng
%U http://hdl.handle.net/21.11116/0000-0001-4053-9
%R 10.1007/978-3-319-58741-7_6
%D 2017
%B 13th Conference on Computability in Europe
%Z date of event: 2017-06-12 - 2017-06-16
%C Turku, Finland
%B Unveiling Dynamics and Complexity
%E Kari, Jarkko; Manea, Florin; Petre, Ion
%P 50-63
%I Springer
%@ 978-3-319-58740-0
%B Lecture Notes in Computer Science
%N 10307
168. Knops E, Schübel N, Heger E, Neumann-Fraune M, Kaiser R, Inden S, Kalaghatgi P, Sierra S: HCV Resistance Profile Evolution in a GT1b, DAA-Naive Patient Before, On, and After Failing Triple DAA Therapy. Clinical Gastroenterology and Hepatology 2017, 15.
Export
BibTeX
@article{Knops2017,
TITLE = {{HCV} Resistance Profile Evolution in a {GT1b}, {DAA}-Naive Patient Before, On, and After Failing Triple {DAA} Therapy},
AUTHOR = {Knops, Elena and Sch{\"u}bel, Niels and Heger, Eva and Neumann-Fraune, Maria and Kaiser, Rolf and Inden, Stephanie and Kalaghatgi, Prabhav and Sierra, Saleta},
LANGUAGE = {eng},
DOI = {10.1016/j.cgh.2016.09.139},
PUBLISHER = {Elsevier},
ADDRESS = {Amsterdam},
YEAR = {2017},
DATE = {2017},
JOURNAL = {Clinical Gastroenterology and Hepatology},
VOLUME = {15},
NUMBER = {2},
PAGES = {307--309},
}
Endnote
%0 Journal Article
%A Knops, Elena
%A Schübel, Niels
%A Heger, Eva
%A Neumann-Fraune, Maria
%A Kaiser, Rolf
%A Inden, Stephanie
%A Kalaghatgi, Prabhav
%A Sierra, Saleta
%+ External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
%T HCV Resistance Profile Evolution in a GT1b, DAA-Naive Patient Before, On, and After Failing Triple DAA Therapy :
%G eng
%U http://hdl.handle.net/11858/00-001M-0000-002C-ECB2-B
%R 10.1016/j.cgh.2016.09.139
%7 2017
%D 2017
%J Clinical Gastroenterology and Hepatology
%V 15
%N 2
%& 307
%P 307 - 309
%I Elsevier
%C Amsterdam
169. Licciardello MP, Ringler A, Markt P, Klepsch F, Lardeau C-H, Sdelci S, Schirghuber E, Müller AC, Caldera M, Wagner A, Herzog R, Penz T, Schuster M, Boidol B, Dürnberger G, Folkvaljon Y, Stattin P, Ivanov V, Colinge J, Bock C, Kratochwill K, Menche J, Bennett KL, Kubicek S: A Combinatorial Screen of the CLOUD Uncovers a Synergy Targeting the Androgen Receptor. Nature Chemical Biology 2017, 13.
Export
BibTeX
@article{Licciardello2017,
TITLE = {A Combinatorial Screen of the {CLOUD} Uncovers a Synergy Targeting the Androgen Receptor},
AUTHOR = {Licciardello, Marco P. and Ringler, Anna and Markt, Patrick and Klepsch, Freya and Lardeau, Charles-Hugues and Sdelci, Sara and Schirghuber, Erika and M{\"u}ller, Andr{\'e} C. and Caldera, Michael and Wagner, Anja and Herzog, Rebecca and Penz, Thomas and Schuster, Michael and Boidol, Bernd and D{\"u}rnberger, Gerhard and Folkvaljon, Yasin and Stattin, P{\"a}r and Ivanov, Vladimir and Colinge, Jacques and Bock, Christoph and Kratochwill, Klaus and Menche, J{\"o}rg and Bennett, Keiryn L. and Kubicek, Stefan},
LANGUAGE = {eng},
ISSN = {1552-4450},
DOI = {10.1038/nchembio.2382},
PUBLISHER = {Nature Pub. Group},
ADDRESS = {New York, NY},
YEAR = {2017},
DATE = {2017},
JOURNAL = {Nature Chemical Biology},
VOLUME = {13},
PAGES = {771--778},
}
Endnote
%0 Journal Article
%A Licciardello, Marco P.
%A Ringler, Anna
%A Markt, Patrick
%A Klepsch, Freya
%A Lardeau, Charles-Hugues
%A Sdelci, Sara
%A Schirghuber, Erika
%A Müller, André C.
%A Caldera, Michael
%A Wagner, Anja
%A Herzog, Rebecca
%A Penz, Thomas
%A Schuster, Michael
%A Boidol, Bernd
%A Dürnberger, Gerhard
%A Folkvaljon, Yasin
%A Stattin, Pär
%A Ivanov, Vladimir
%A Colinge, Jacques
%A Bock, Christoph
%A Kratochwill, Klaus
%A Menche, Jörg
%A Bennett, Keiryn L.
%A Kubicek, Stefan
%+ External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
External Organizations
External Organizations
External Organizations
%T A Combinatorial Screen of the CLOUD Uncovers a Synergy Targeting the Androgen Receptor :
%G eng
%U http://hdl.handle.net/11858/00-001M-0000-002D-8F17-5
%R 10.1038/nchembio.2382
%7 2017-05-22
%D 2017
%J Nature Chemical Biology
%O Nat. Chem. Biol.
%V 13
%& 771
%P 771 - 778
%I Nature Pub. Group
%C New York, NY
%@ false
170. Li J, Casteels T, Frogne T, Ingvorsen C, Honoré C, Courtney M, Huber KVM, Schmitner N, Kimmel RA, Romanov RA, Sturtzel C, Lardeau C-H, Klughammer J, Farlik M, Sdelci S, Vieira A, Avolio F, Briand F, Baburin I, Májek P, Pauler FM, Penz T, Stukalov A, Gridling M, Parapatics K, Barbieux C, Berishvili E, Spittler A, Colinge J, Bennett KL, et al.: Artemisinins Target GABA A Receptor Signaling and Impair α Cell Identity. Cell 2017, 168.
Export
BibTeX
@article{Li2017,
TITLE = {Artemisinins Target {GABA$_{\mathrm A}$} Receptor Signaling and Impair $\alpha$ Cell Identity},
AUTHOR = {Li, Jin and Casteels, Tamara and Frogne, Thomas and Ingvorsen, Camilla and Honor{\'e}, Christian and Courtney, Monica and Huber, Kilian V. M. and Schmitner, Nicole and Kimmel, Robin A. and Romanov, Roman A. and Sturtzel, Caterina and Lardeau, Charles-Hugues and Klughammer, Johanna and Farlik, Matthias and Sdelci, Sara and Vieira, Andhira and Avolio, Fabio and Briand, Fran{\c c}ois and Baburin, Igor and M{\'a}jek, Peter and Pauler, Florian M. and Penz, Thomas and Stukalov, Alexey and Gridling, Manuela and Parapatics, Katja and Barbieux, Charlotte and Berishvili, Ekaterine and Spittler, Andreas and Colinge, Jacques and Bennett, Keiryn L. and Hering, Steffen and Sulpice, Thierry and Bock, Christoph and Distel, Martin and Harkany, Tibor and Meyer, Dirk and Superti-Furga, Giulio and Collombat, Patrick and Hecksher-S{\o}rensen, Jacob and Kubicek, Stefan},
LANGUAGE = {eng},
ISSN = {0092-8674},
DOI = {10.1016/j.cell.2016.11.010},
PUBLISHER = {Elsevier},
ADDRESS = {Amsterdam},
YEAR = {2017},
DATE = {2017},
JOURNAL = {Cell},
VOLUME = {168},
NUMBER = {1-2},
PAGES = {86--100},
EID = {e15},
}
Endnote
%0 Journal Article
%A Li, Jin
%A Casteels, Tamara
%A Frogne, Thomas
%A Ingvorsen, Camilla
%A Honoré, Christian
%A Courtney, Monica
%A Huber, Kilian V. M.
%A Schmitner, Nicole
%A Kimmel, Robin A.
%A Romanov, Roman A.
%A Sturtzel, Caterina
%A Lardeau, Charles-Hugues
%A Klughammer, Johanna
%A Farlik, Matthias
%A Sdelci, Sara
%A Vieira, Andhira
%A Avolio, Fabio
%A Briand, François
%A Baburin, Igor
%A Májek, Peter
%A Pauler, Florian M.
%A Penz, Thomas
%A Stukalov, Alexey
%A Gridling, Manuela
%A Parapatics, Katja
%A Barbieux, Charlotte
%A Berishvili, Ekaterine
%A Spittler, Andreas
%A Colinge, Jacques
%A Bennett, Keiryn L.
%A Hering, Steffen
%A Sulpice, Thierry
%A Bock, Christoph
%A Distel, Martin
%A Harkany, Tibor
%A Meyer, Dirk
%A Superti-Furga, Giulio
%A Collombat, Patrick
%A Hecksher-Sørensen, Jacob
%A Kubicek, Stefan
%+ External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
%T Artemisinins Target GABA A Receptor Signaling and Impair α Cell Identity :
%G eng
%U http://hdl.handle.net/11858/00-001M-0000-002C-5C72-1
%2 PMC5236063
%R 10.1016/j.cell.2016.11.010
%7 2017
%D 2017
%J Cell
%V 168
%N 1-2
%& 86
%P 86 - 100
%Z sequence number: e15
%I Elsevier
%C Amsterdam
%@ false
171. List M, Ebert P, Albrecht F: Ten Simple Rules for Developing Usable Software in Computational Biology. PLoS Computational Biology 2017, 13.
Export
BibTeX
@article{ListPloSCompBiol2016,
TITLE = {Ten Simple Rules for Developing Usable Software in Computational Biology},
AUTHOR = {List, Markus and Ebert, Peter and Albrecht, Felipe},
LANGUAGE = {eng},
ISSN = {1553-734X},
DOI = {10.1371/journal.pcbi.1005265},
PUBLISHER = {Public Library of Science},
ADDRESS = {San Francisco, CA},
YEAR = {2017},
JOURNAL = {PLoS Computational Biology},
VOLUME = {13},
NUMBER = {1},
EID = {e1005265},
}
Endnote
%0 Journal Article
%A List, Markus
%A Ebert, Peter
%A Albrecht, Felipe
%+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
%T Ten Simple Rules for Developing Usable Software in Computational Biology :
%G eng
%U http://hdl.handle.net/11858/00-001M-0000-002C-203B-2
%R 10.1371/journal.pcbi.1005265
%7 2017-01-05
%D 2017
%8 05.01.2017
%J PLoS Computational Biology
%V 13
%N 1
%Z sequence number: e1005265
%I Public Library of Science
%C San Francisco, CA
%@ false
172. List M, Elnegaard MP, Schmidt S, Christiansen H, Tan Q, Mollenhauer J, Baumbach J: Efficient Management of High-Throughput Screening Libraries with SAVANAH. Journal of Biomolecular Screening 2017, 22.
Export
BibTeX
@article{List2016b,
TITLE = {Efficient Management of High-Throughput Screening Libraries with {SAVANAH}},
AUTHOR = {List, Markus and Elnegaard, Marlene Pedersen and Schmidt, Steffen and Christiansen, Helle and Tan, Qihua and Mollenhauer, Jan and Baumbach, Jan},
LANGUAGE = {eng},
ISSN = {1087-0571},
DOI = {10.1177/1087057116673607},
PUBLISHER = {Sage Publications, Inc.},
ADDRESS = {Larchmont, NY},
YEAR = {2017},
DATE = {2017},
JOURNAL = {Journal of Biomolecular Screening},
VOLUME = {22},
NUMBER = {2},
PAGES = {196--202},
}
Endnote
%0 Journal Article
%A List, Markus
%A Elnegaard, Marlene Pedersen
%A Schmidt, Steffen
%A Christiansen, Helle
%A Tan, Qihua
%A Mollenhauer, Jan
%A Baumbach, Jan
%+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
%T Efficient Management of High-Throughput Screening Libraries with SAVANAH :
%G eng
%U http://hdl.handle.net/11858/00-001M-0000-002C-202F-D
%R 10.1177/1087057116673607
%7 2016-10-11
%D 2017
%J Journal of Biomolecular Screening
%V 22
%N 2
%& 196
%P 196 - 202
%I Sage Publications, Inc.
%C Larchmont, NY
%@ false
173. List M: Using Docker Compose for the Simple Deployment of an Integrated Drug Target Screening Platform. Journal of Integrative Bioinformatics 2017, 14.
Export
BibTeX
@article{ListJIB2017,
TITLE = {Using {Docker} Compose for the Simple Deployment of an Integrated Drug Target Screening Platform},
AUTHOR = {List, Markus},
LANGUAGE = {eng},
ISSN = {1613-4516},
DOI = {10.1515/jib-2017-0016},
PUBLISHER = {de Gruyter},
ADDRESS = {Berlin},
YEAR = {2017},
JOURNAL = {Journal of Integrative Bioinformatics},
VOLUME = {14},
NUMBER = {2},
EID = {20170016},
}
Endnote
%0 Journal Article
%A List, Markus
%+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
%T Using Docker Compose for the Simple Deployment of an Integrated Drug Target Screening Platform :
%G eng
%U http://hdl.handle.net/11858/00-001M-0000-002D-DDE3-6
%R 10.1515/jib-2017-0016
%7 2017
%D 2017
%J Journal of Integrative Bioinformatics
%V 14
%N 2
%Z sequence number: 20170016
%I de Gruyter
%C Berlin
%@ false
174. Lund JB, List M, Baumbach J: Interactive Microbial Distribution Analysis using BioAtlas. Nucleic Acids Research 2017, 45.
Export
BibTeX
@article{LundListBaumbach2017,
TITLE = {Interactive microbial distribution analysis using {BioAtlas}},
AUTHOR = {Lund, Jesper Beltoft and List, Markus and Baumbach, Jan},
LANGUAGE = {eng},
ISSN = {0305-1048},
DOI = {10.1093/nar/gkx304},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford},
YEAR = {2017},
DATE = {2017},
JOURNAL = {Nucleic Acids Research},
VOLUME = {45},
NUMBER = {W1},
PAGES = {W509--W513},
}
Endnote
%0 Journal Article
%A Lund, Jesper Beltoft
%A List, Markus
%A Baumbach, Jan
%+ External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
%T Interactive Microbial Distribution Analysis using BioAtlas :
%G eng
%U http://hdl.handle.net/11858/00-001M-0000-002D-C387-9
%R 10.1093/nar/gkx304
%2 PMC5570126
%7 2017
%D 2017
%J Nucleic Acids Research
%O Nucleic Acids Res
%V 45
%N W1
%& W509
%P W509 - W513
%I Oxford University Press
%C Oxford
%@ false
175. Müller F: Analyzing DNA Methylation Signatures of Cell Identity. Universität des Saarlandes; 2017.
Abstract
Although virtually all cells in an organism share the same genome, regulatory mechanisms give rise to hundreds of different, highly specialized cell types. Understanding these mechanisms has been in the limelight of epigenomic research. It is now evident that cellular identity is inscribed in the epigenome of each individual cell. Nonetheless, the precise mechanisms by which different epigenomic marks are involved in regulating gene expression are just beginning to be unraveled. Furthermore, epigenomic patterns are highly dynamic and subject to environmental influences. Any given cell type is defined by cell populations exhibiting epigenetic heterogeneity at different levels. Characterizing this heterogeneity is paramount in understanding the regulatory role of the epigenome. Different epigenomic marks can be profiled using high-throughput sequencing, and global initiatives have started to provide a comprehensive picture of the human epigenome by assaying a multitude of marks across a broad panel of cell types and conditions. In particular, DNA methylation has been extensively studied for its gene-regulatory role in health and disease. This thesis describes computational methods and pipelines for the analysis of DNA methylation data. It provides concepts for addressing bioinformatic challenges such as the processing of large, epigenome-wide datasets and integrating multiple levels of information in an interpretable manner. We developed RnBeads, an R package that facilitates comprehensive, interpretable analysis of large-scale DNA methylation datasets at the level of single CpGs or genomic regions of interest. With the epiRepeatR pipeline, we introduced additional tools for studying global patterns of epigenomic marks in transposons and other repetitive regions of the genome. Blood-cell differentiation represents a useful model for studying trajectories of cellular differentiation. We developed and applied bioinformatic methods to dissect the DNA methylation landscape of the hematopoietic system. Here, we provide a broad outline of cell-type-specific DNA methylation signatures and phenotypic diversity reflected in the epigenomes of human mature blood cells. We also describe the DNA methylation dynamics in the process of immune memory formation in T helper cells. Moreover, we portrayed epigenetic fingerprints of defined progenitor cell types and derived computational models that were capable of accurately inferring cell identity. We used these models in order to characterize heterogeneity in progenitor cell populations, to identify DNA methylation signatures of hematopoietic differentiation and to infer the epigenomic similarities of blood cell types. Finally, by interpreting DNA methylation patterns in leukemia and derived pluripotent cells, we started to discern how epigenomic patterns are altered in disease and explored how reprogramming of these patterns could potentially be used to restore a non-malignant state. In summary, this work showcases novel methods and computational tools for the identification and interpretation of epigenetic signatures of cell identity. It provides a detailed view on the epigenomic landscape spanned by DNA methylation patterns in hematopoietic cells that enhances our understanding of epigenetic regulation in cell differentiation and disease.
Export
BibTeX
@phdthesis{muellerphd17,
TITLE = {Analyzing {DNA} Methylation Signatures of Cell Identity},
AUTHOR = {M{\"u}ller, Fabian},
LANGUAGE = {eng},
URL = {urn:nbn:de:bsz:291-scidok-69432},
DOI = {10.17617/2.2474737},
SCHOOL = {Universit{\"a}t des Saarlandes},
ADDRESS = {Saarbr{\"u}cken},
YEAR = {2017},
DATE = {2017},
ABSTRACT = {Although virtually all cells in an organism share the same genome, regulatory mechanisms give rise to hundreds of different, highly specialized cell types. Understanding these mechanisms has been in the limelight of epigenomic research. It is now evident that cellular identity is inscribed in the epigenome of each individual cell. Nonetheless, the precise mechanisms by which different epigenomic marks are involved in regulating gene expression are just beginning to be unraveled. Furthermore, epigenomic patterns are highly dynamic and subject to environmental influences. Any given cell type is defined by cell populations exhibiting epigenetic heterogeneity at different levels. Characterizing this heterogeneity is paramount in understanding the regulatory role of the epigenome. Different epigenomic marks can be profiled using high-throughput sequencing, and global initiatives have started to provide a comprehensive picture of the human epigenome by assaying a multitude of marks across a broad panel of cell types and conditions. In particular, DNA methylation has been extensively studied for its gene-regulatory role in health and disease. This thesis describes computational methods and pipelines for the analysis of DNA methylation data. It provides concepts for addressing bioinformatic challenges such as the processing of large, epigenome-wide datasets and integrating multiple levels of information in an interpretable manner. We developed RnBeads, an R package that facilitates comprehensive, interpretable analysis of large-scale DNA methylation datasets at the level of single CpGs or genomic regions of interest. With the epiRepeatR pipeline, we introduced additional tools for studying global patterns of epigenomic marks in transposons and other repetitive regions of the genome. Blood-cell differentiation represents a useful model for studying trajectories of cellular differentiation. We developed and applied bioinformatic methods to dissect the DNA methylation landscape of the hematopoietic system. Here, we provide a broad outline of cell-type-specific DNA methylation signatures and phenotypic diversity reflected in the epigenomes of human mature blood cells. We also describe the DNA methylation dynamics in the process of immune memory formation in T helper cells. Moreover, we portrayed epigenetic fingerprints of defined progenitor cell types and derived computational models that were capable of accurately inferring cell identity. We used these models in order to characterize heterogeneity in progenitor cell populations, to identify DNA methylation signatures of hematopoietic differentiation and to infer the epigenomic similarities of blood cell types. Finally, by interpreting DNA methylation patterns in leukemia and derived pluripotent cells, we started to discern how epigenomic patterns are altered in disease and explored how reprogramming of these patterns could potentially be used to restore a non-malignant state. In summary, this work showcases novel methods and computational tools for the identification and interpretation of epigenetic signatures of cell identity. It provides a detailed view on the epigenomic landscape spanned by DNA methylation patterns in hematopoietic cells that enhances our understanding of epigenetic regulation in cell differentiation and disease.},
}
Endnote
%0 Thesis
%A Müller, Fabian
%Y Lengauer, Thomas
%A referee: Bock, Christoph
%A referee: Brors, Benedikt
%+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
International Max Planck Research School, MPI for Informatics, Max Planck Society
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
%T Analyzing DNA Methylation Signatures of Cell Identity :
%G eng
%U http://hdl.handle.net/11858/00-001M-0000-002D-D9AA-6
%U urn:nbn:de:bsz:291-scidok-69432
%R 10.17617/2.2474737
%F OTHER: hdl:20.500.11880/26867
%I Universität des Saarlandes
%C Saarbrücken
%D 2017
%P 177 p.
%V phd
%9 phd
%X Although virtually all cells in an organism share the same genome, regulatory mechanisms give rise to hundreds of different, highly specialized cell types. Understanding these mechanisms has been in the limelight of epigenomic research. It is now evident that cellular identity is inscribed in the epigenome of each individual cell. Nonetheless, the precise mechanisms by which different epigenomic marks are involved in regulating gene expression are just beginning to be unraveled. Furthermore, epigenomic patterns are highly dynamic and subject to environmental influences. Any given cell type is defined by cell populations exhibiting epigenetic heterogeneity at different levels. Characterizing this heterogeneity is paramount in understanding the regulatory role of the epigenome. Different epigenomic marks can be profiled using high-throughput sequencing, and global initiatives have started to provide a comprehensive picture of the human epigenome by assaying a multitude of marks across a broad panel of cell types and conditions. In particular, DNA methylation has been extensively studied for its gene-regulatory role in health and disease. This thesis describes computational methods and pipelines for the analysis of DNA methylation data. It provides concepts for addressing bioinformatic challenges such as the processing of large, epigenome-wide datasets and integrating multiple levels of information in an interpretable manner. We developed RnBeads, an R package that facilitates comprehensive, interpretable analysis of large-scale DNA methylation datasets at the level of single CpGs or genomic regions of interest. With the epiRepeatR pipeline, we introduced additional tools for studying global patterns of epigenomic marks in transposons and other repetitive regions of the genome. Blood-cell differentiation represents a useful model for studying trajectories of cellular differentiation. We developed and applied bioinformatic methods to dissect the DNA methylation landscape of the hematopoietic system. Here, we provide a broad outline of cell-type-specific DNA methylation signatures and phenotypic diversity reflected in the epigenomes of human mature blood cells. We also describe the DNA methylation dynamics in the process of immune memory formation in T helper cells. Moreover, we portrayed epigenetic fingerprints of defined progenitor cell types and derived computational models that were capable of accurately inferring cell identity. We used these models in order to characterize heterogeneity in progenitor cell populations, to identify DNA methylation signatures of hematopoietic differentiation and to infer the epigenomic similarities of blood cell types. Finally, by interpreting DNA methylation patterns in leukemia and derived pluripotent cells, we started to discern how epigenomic patterns are altered in disease and explored how reprogramming of these patterns could potentially be used to restore a non-malignant state. In summary, this work showcases novel methods and computational tools for the identification and interpretation of epigenetic signatures of cell identity. It provides a detailed view on the epigenomic landscape spanned by DNA methylation patterns in hematopoietic cells that enhances our understanding of epigenetic regulation in cell differentiation and disease.
%U http://scidok.sulb.uni-saarland.de/volltexte/2017/6943/http://scidok.sulb.uni-saarland.de/doku/lic_ohne_pod.php?la=de
176. Müller H, Jimenez-Heredia R, Krolo A, Hirschmugl T, Dmytrus J, Boztug K, Bock C: VCF.Filter: Interactive Prioritization of Disease-linked Genetic Variants from Sequencing Data. Nucleic Acids Research 2017, 45.
Export
BibTeX
@article{BockVCF2017,
TITLE = {{VCF}.{Filter}: {I}nteractive Prioritization of Disease-linked Genetic Variants from Sequencing Data},
AUTHOR = {M{\"u}ller, Heiko and Jimenez-Heredia, Raul and Krolo, Ana and Hirschmugl, Tatjana and Dmytrus, Jasmin and Boztug, Kaan and Bock, Christoph},
LANGUAGE = {eng},
ISSN = {0305-1048},
DOI = {10.1093/nar/gkx425},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford},
YEAR = {2017},
DATE = {2017},
JOURNAL = {Nucleic Acids Research},
VOLUME = {45},
NUMBER = {W1},
PAGES = {W567--W572},
}
Endnote
%0 Journal Article
%A Müller, Heiko
%A Jimenez-Heredia, Raul
%A Krolo, Ana
%A Hirschmugl, Tatjana
%A Dmytrus, Jasmin
%A Boztug, Kaan
%A Bock, Christoph
%+ External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
%T VCF.Filter: Interactive Prioritization of Disease-linked Genetic Variants from Sequencing Data :
%G eng
%U http://hdl.handle.net/11858/00-001M-0000-002D-C37D-1
%R 10.1093/nar/gkx425
%2 PMC5570181
%7 2017
%D 2017
%J Nucleic Acids Research
%O Nucleic Acids Res
%V 45
%N W1
%& W567
%P W567 - W572
%I Oxford University Press
%C Oxford
%@ false
177. Neogi U, Siddik AB, Kalaghatgi P, Gisslén M, Bratt G, Marrone G, Sönnerborg A: Recent Increased Identification and Transmission of HIV-1 unique Recombinant Forms in Sweden. Scientific Reports 2017, 7.
Export
BibTeX
@article{Neogi2017,
TITLE = {Recent Increased Identification and Transmission of {HIV}-1 unique Recombinant Forms in {Sweden}},
AUTHOR = {Neogi, Ujjwal and Siddik, Abu Bakar and Kalaghatgi, Prabhav and Gissl{\'e}n, Magnus and Bratt, G{\"o}ran and Marrone, Gaetano and S{\"o}nnerborg, Anders},
LANGUAGE = {eng},
ISSN = {2045-2322},
DOI = {10.1038/s41598-017-06860-2},
PUBLISHER = {Nature Publishing Group},
ADDRESS = {London, UK},
YEAR = {2017},
JOURNAL = {Scientific Reports},
VOLUME = {7},
EID = {6371},
}
Endnote
%0 Journal Article
%A Neogi, Ujjwal
%A Siddik, Abu Bakar
%A Kalaghatgi, Prabhav
%A Gisslén, Magnus
%A Bratt, Göran
%A Marrone, Gaetano
%A Sönnerborg, Anders
%+ External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
External Organizations
External Organizations
External Organizations
%T Recent Increased Identification and Transmission of HIV-1 unique
Recombinant Forms in Sweden :
%G eng
%U http://hdl.handle.net/11858/00-001M-0000-002D-BC30-F
%2 PMC5527090
%R 10.1038/s41598-017-06860-2
%7 2017
%D 2017
%J Scientific Reports
%O Sci. Rep.
%V 7
%Z sequence number: 6371
%I Nature Publishing Group
%C London, UK
%@ false
178. Nikumbh S, Ebert P, Pfeifer N: All Fingers Are Not the Same: Handling Variable-Length Sequences in a Discriminative Setting Using Conformal Multi-Instance Kernels. In 17th International Workshop on Algorithms in Bioinformatics (WABI 2017). Schloss Dagstuhl; 2017. [Leibniz International Proceedings in Informatics, vol. 88]
Export
BibTeX
@inproceedings{nikumbh_et_al:LIPIcs:2017:7645,
TITLE = {All Fingers Are Not the Same: {H}andling Variable-Length Sequences in a Discriminative Setting Using Conformal Multi-Instance Kernels},
AUTHOR = {Nikumbh, Sarvesh and Ebert, Peter and Pfeifer, Nico},
LANGUAGE = {eng},
ISSN = {1868-8969},
ISBN = {978-3-95977-050-7},
DOI = {10.4230/LIPIcs.WABI.2017.16},
PUBLISHER = {Schloss Dagstuhl},
YEAR = {2017},
BOOKTITLE = {17th International Workshop on Algorithms in Bioinformatics (WABI 2017)},
EDITOR = {Schwartz, Russell and Reinert, Knut},
PAGES = {1--14},
EID = {16},
SERIES = {Leibniz International Proceedings in Informatics},
VOLUME = {88},
ADDRESS = {Boston, MA, USA},
}
Endnote
%0 Conference Proceedings
%A Nikumbh, Sarvesh
%A Ebert, Peter
%A Pfeifer, Nico
%+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
%T All Fingers Are Not the Same: Handling Variable-Length Sequences in a Discriminative Setting Using Conformal Multi-Instance Kernels :
%G eng
%U http://hdl.handle.net/11858/00-001M-0000-002D-BC17-7
%R 10.4230/LIPIcs.WABI.2017.16
%D 2017
%B 17th International Workshop on Algorithms in Bioinformatics
%Z date of event: 2017-08-21 - 2017-08-23
%C Boston, MA, USA
%B 17th International Workshop on Algorithms in Bioinformatics
%E Schwartz, Russell; Reinert, Knut
%P 1 - 14
%Z sequence number: 16
%I Schloss Dagstuhl
%@ 978-3-95977-050-7
%B Leibniz International Proceedings in Informatics
%N 88
%@ false
%U http://drops.dagstuhl.de/opus/volltexte/2017/7645/http://drops.dagstuhl.de/doku/urheberrecht1.html
179. Nikumbh S, Pfeifer N: Genetic Sequence-based Prediction of Long-range Chromatin Interactions Suggests a Potential Role of Short Tandem Repeat Sequences in Genome Organization. BMC Bioinformatics 2017, 18.
Export
BibTeX
@article{Nikumbh2017,
TITLE = {Genetic Sequence-based Prediction of Long-range Chromatin Interactions Suggests a Potential Role of Short Tandem Repeat Sequences in Genome Organization},
AUTHOR = {Nikumbh, Sarvesh and Pfeifer, Nico},
LANGUAGE = {eng},
ISSN = {1471-2105},
DOI = {10.1186/s12859-017-1624-x},
PUBLISHER = {BioMed Central},
ADDRESS = {London},
YEAR = {2017},
JOURNAL = {BMC Bioinformatics},
VOLUME = {18},
PAGES = {1--16},
EID = {218},
}
Endnote
%0 Journal Article
%A Nikumbh, Sarvesh
%A Pfeifer, Nico
%+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
%T Genetic Sequence-based Prediction of Long-range Chromatin Interactions Suggests a Potential Role of Short Tandem Repeat Sequences in Genome Organization :
%G eng
%U http://hdl.handle.net/11858/00-001M-0000-002D-26AD-4
%R 10.1186/s12859-017-1624-x
%7 2017-04-18
%D 2017
%8 18.04.2017
%J BMC Bioinformatics
%V 18
%& 1
%P 1 - 16
%Z sequence number: 218
%I BioMed Central
%C London
%@ false
180. Pironti A, Walter H, Pfeifer N, Knops E, Lübke N, Büch J, Di Giambenedetto S, Kaiser R, Lengauer T: Determination of Phenotypic Resistance Cutoffs from Routine Clinical Data. Journal of Acquired Immune Deficiency Syndromes 2017, 74.
Export
BibTeX
@article{Pironti_Pfeifer_Lengauer2017,
TITLE = {Determination of Phenotypic Resistance Cutoffs from Routine Clinical Data},
AUTHOR = {Pironti, Alejandro and Walter, Hauke and Pfeifer, Nico and Knops, Elena and L{\"u}bke, Nadine and B{\"u}ch, Joachim and Di Giambenedetto, Simona and Kaiser, Rolf and Lengauer, Thomas},
LANGUAGE = {eng},
DOI = {10.1097/QAI.0000000000001198},
PUBLISHER = {Lippincott Williams \& Wilkins},
ADDRESS = {Philadelphia, PA},
YEAR = {2017},
JOURNAL = {Journal of Acquired Immune Deficiency Syndromes},
VOLUME = {74},
NUMBER = {5},
PAGES = {e129--e137},
}
Endnote
%0 Journal Article
%A Pironti, Alejandro
%A Walter, Hauke
%A Pfeifer, Nico
%A Knops, Elena
%A Lübke, Nadine
%A Büch, Joachim
%A Di Giambenedetto, Simona
%A Kaiser, Rolf
%A Lengauer, Thomas
%+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
%T Determination of Phenotypic Resistance Cutoffs from Routine Clinical Data :
%G eng
%U http://hdl.handle.net/11858/00-001M-0000-002C-3F1D-D
%R 10.1097/QAI.0000000000001198
%7 2017
%D 2017
%J Journal of Acquired Immune Deficiency Syndromes
%O JAIDS
%V 74
%N 5
%& e129
%P e129 - e137
%I Lippincott Williams & Wilkins
%C Philadelphia, PA
181. Pironti A, Pfeifer N, Walter H, Jensen B-EO, Zazzi M, Gomes P, Kaiser R, Lengauer T: Using Drug Exposure for Predicting Drug Resistance – A data-driven Genotypic Interpretation Tool. PLoS One 2017, 12.
Export
BibTeX
@article{Pironti_Pfeifer_Lengauer_2017,
TITLE = {Using Drug Exposure for Predicting Drug Resistance -- A data-driven Genotypic Interpretation Tool},
AUTHOR = {Pironti, Alejandro and Pfeifer, Nico and Walter, Hauke and Jensen, Bj{\"o}rn-Erik O. and Zazzi, Maurizio and Gomes, Perp{\'e}tua and Kaiser, Rolf and Lengauer, Thomas},
LANGUAGE = {eng},
ISSN = {1932-6203},
DOI = {10.1371/journal.pone.0174992},
PUBLISHER = {Public Library of Science},
ADDRESS = {San Francisco, CA},
YEAR = {2017},
JOURNAL = {PLoS One},
VOLUME = {12},
NUMBER = {4},
EID = {e0174992},
}
Endnote
%0 Journal Article
%A Pironti, Alejandro
%A Pfeifer, Nico
%A Walter, Hauke
%A Jensen, Björn-Erik O.
%A Zazzi, Maurizio
%A Gomes, Perpétua
%A Kaiser, Rolf
%A Lengauer, Thomas
%+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
%T Using Drug Exposure for Predicting Drug Resistance – A data-driven Genotypic Interpretation Tool :
%G eng
%U http://hdl.handle.net/11858/00-001M-0000-002D-48E5-0
%R 10.1371/journal.pone.0174992
%2 PMC5386274
%7 2017-04-10
%D 2017
%8 10.04.2017
%J PLoS One
%V 12
%N 4
%Z sequence number: e0174992
%I Public Library of Science
%C San Francisco, CA
%@ false
182. Porubsky D, Garg S, Sanders AD, Korbel JO, Guryev V, Lansdorp PM, Marschall T: Dense and Accurate Whole-chromosome Haplotyping of Individual Genomes. Nature Communications 2017, 8.
Export
BibTeX
@article{Porubsky2017,
TITLE = {Dense and Accurate Whole-chromosome Haplotyping of Individual Genomes},
AUTHOR = {Porubsky, David and Garg, Shilpa and Sanders, Ashley D. and Korbel, Jan O. and Guryev, Victor and Lansdorp, Peter M. and Marschall, Tobias},
LANGUAGE = {eng},
ISSN = {2041-1723},
DOI = {10.1038/s41467-017-01389-4},
PUBLISHER = {Nature Publishing Group},
ADDRESS = {London},
YEAR = {2017},
JOURNAL = {Nature Communications},
VOLUME = {8},
EID = {1293},
}
Endnote
%0 Journal Article
%A Porubsky, David
%A Garg, Shilpa
%A Sanders, Ashley D.
%A Korbel, Jan O.
%A Guryev, Victor
%A Lansdorp, Peter M.
%A Marschall, Tobias
%+ External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
External Organizations
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
%T Dense and Accurate Whole-chromosome Haplotyping of Individual Genomes :
%G eng
%U http://hdl.handle.net/11858/00-001M-0000-002E-3109-E
%R 10.1038/s41467-017-01389-4
%2 PMC5670131
%7 2017
%D 2017
%J Nature Communications
%O Nat. Commun.
%V 8
%Z sequence number: 1293
%I Nature Publishing Group
%C London
%@ false
183. Schmidt F, Gasparoni N, Gasparoni G, Gianmoena K, Cadenas C, Polansky JK, Ebert P, Nordström K, Barann M, Sinha A, Fröhler S, Xiong J, Dheghani Amirabad A, Behjati Ardakani F, Hutter B, Zipprich G, Felder B, Eils J, Brors B, Chen W, Hengstler JG, Hamann A, Lengauer T, Rosenstiel P, Walter J, Schulz MH: Combining Transcription Factor Binding Affinities with Open-Chromatin Data for Accurate Gene Expression Prediction. Nucleic Acids Research 2017, 45.
Export
BibTeX
@article{pmid27899623,
TITLE = {Combining Transcription Factor Binding Affinities with Open-Chromatin Data for Accurate Gene Expression Prediction},
AUTHOR = {Schmidt, Florian and Gasparoni, Nina and Gasparoni, Gilles and Gianmoena, Kathrin and Cadenas, Cristina and Polansky, Julia K. and Ebert, Peter and Nordstr{\"o}m, Karl and Barann, Matthias and Sinha, Anupam and Fr{\"o}hler, Sebastian and Xiong, Jieyi and Dheghani Amirabad, Azim and Behjati Ardakani, Fatemeh and Hutter, Barbara and Zipprich, Gideon and Felder, B{\"a}rbel and Eils, J{\"u}rgen and Brors, Benedikt and Chen, Wei and Hengstler, Jan G. and Hamann, Alf and Lengauer, Thomas and Rosenstiel, Philip and Walter, J{\"o}rn and Schulz, Marcel H.},
LANGUAGE = {eng},
ISSN = {0305-1048},
DOI = {10.1093/nar/gkw1061},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford},
YEAR = {2017},
DATE = {2017},
JOURNAL = {Nucleic Acids Research},
VOLUME = {45},
NUMBER = {1},
PAGES = {54--66},
}
Endnote
%0 Journal Article
%A Schmidt, Florian
%A Gasparoni, Nina
%A Gasparoni, Gilles
%A Gianmoena, Kathrin
%A Cadenas, Cristina
%A Polansky, Julia K.
%A Ebert, Peter
%A Nordström, Karl
%A Barann, Matthias
%A Sinha, Anupam
%A Fröhler, Sebastian
%A Xiong, Jieyi
%A Dheghani Amirabad, Azim
%A Behjati Ardakani, Fatemeh
%A Hutter, Barbara
%A Zipprich, Gideon
%A Felder, Bärbel
%A Eils, Jürgen
%A Brors, Benedikt
%A Chen, Wei
%A Hengstler, Jan G.
%A Hamann, Alf
%A Lengauer, Thomas
%A Rosenstiel, Philip
%A Walter, Jörn
%A Schulz, Marcel H.
%+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
%T Combining Transcription Factor Binding Affinities with Open-Chromatin Data for Accurate Gene Expression Prediction :
%G eng
%U http://hdl.handle.net/11858/00-001M-0000-002C-378F-F
%R 10.1093/nar/gkw1061
%7 2016
%D 2017
%J Nucleic Acids Research
%O Nucleic Acids Res
%V 45
%N 1
%& 54
%P 54 - 66
%I Oxford University Press
%C Oxford
%@ false
184. Schultheiss CS, Laggai S, Czepukojc B, Hussein UK, List M, Barghash A, Tierling S, Hosseini K, Golob-Schwarzl N, Pokorny J, Hachenthal N, Schulz MH, Helms V, Walter J, Zimmer V, Lammert F, Bohle RM, Dandolo L, Haybaeck J, Kiemer AK, Kessler SM: The Long Non-coding RNA H19 Suppresses Carcinogenesis and Chemoresistance in Hepatocellular Carcinoma. Cell Stress 2017, 1.
Export
BibTeX
@article{Schultheiss2019,
TITLE = {The long non-coding {RNA} {H19} suppresses carcinogenesis and chemoresistance in hepatocellular carcinoma},
AUTHOR = {Schultheiss, Christina S. and Laggai, Stephan and Czepukojc, Beate and Hussein, Usama K. and List, Markus and Barghash, Ahmad and Tierling, Sascha and Hosseini, Kevan and Golob-Schwarzl, Nicole and Pokorny, Juliane and Hachenthal, Nina and Schulz, Marcel Holger and Helms, Volkhard and Walter, J{\"o}rn and Zimmer, Vincent and Lammert, Frank and Bohle, Rainer M. and Dandolo, Luisa and Haybaeck, Johannes and Kiemer, Alexandra K. and Kessler, Sonja M.},
LANGUAGE = {eng},
ISSN = {2523-0204},
DOI = {10.15698/cst2017.10.105},
PUBLISHER = {Shared Science Publishers},
ADDRESS = {Graz},
YEAR = {2017},
JOURNAL = {Cell Stress},
VOLUME = {1},
NUMBER = {1},
PAGES = {37--54},
}
Endnote
%0 Journal Article
%A Schultheiss, Christina S.
%A Laggai, Stephan
%A Czepukojc, Beate
%A Hussein, Usama K.
%A List, Markus
%A Barghash, Ahmad
%A Tierling, Sascha
%A Hosseini, Kevan
%A Golob-Schwarzl, Nicole
%A Pokorny, Juliane
%A Hachenthal, Nina
%A Schulz, Marcel Holger
%A Helms, Volkhard
%A Walter, Jörn
%A Zimmer, Vincent
%A Lammert, Frank
%A Bohle, Rainer M.
%A Dandolo, Luisa
%A Haybaeck, Johannes
%A Kiemer, Alexandra K.
%A Kessler, Sonja M.
%+ External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
%T The Long Non-coding RNA H19 Suppresses Carcinogenesis and Chemoresistance in Hepatocellular Carcinoma :
%G eng
%U http://hdl.handle.net/21.11116/0000-0003-EBF6-F
%R 10.15698/cst2017.10.105
%2 PMC6551655
%7 2017
%D 2017
%J Cell Stress
%V 1
%N 1
%& 37
%P 37 - 54
%I Shared Science Publishers
%C Graz
%@ false
185. Sheffield NC, Pierron G, Klughammer J, Datlinger P, Schönegger A, Schuster M, Hadler J, Surdez D, Guillemot D, Lapouble E, Freneaux P, Champigneulle J, Bouvier R, Walder D, Ambros IM, Hutter C, Sorz E, Amaral AT, de Álava E, Schallmoser K, Strunk D, Rinner B, Liegl-Atzwanger B, Huppertz B, Leithner A, de Pinieux G, Terrier P, Laurence V, Michon J, Ladenstein R, et al.: DNA Methylation Heterogeneity Defines a Disease Spectrum in Ewing Sarcoma. Nature Medicine 2017, 23.
Export
BibTeX
@article{Sheffield2017,
TITLE = {{DNA} methylation heterogeneity defines a disease spectrum in {Ewing} sarcoma},
AUTHOR = {Sheffield, Nathan C. and Pierron, Gaelle and Klughammer, Johanna and Datlinger, Paul and Sch{\"o}negger, Andreas and Schuster, Michael and Hadler, Johanna and Surdez, Didier and Guillemot, Delphine and Lapouble, Eve and Freneaux, Paul and Champigneulle, Jacqueline and Bouvier, Raymonde and Walder, Diana and Ambros, Ingeborg M. and Hutter, Caroline and Sorz, Eva and Amaral, Ana T. and de {\'A}lava, Enrique and Schallmoser, Katharina and Strunk, Dirk and Rinner, Beate and Liegl-Atzwanger, Bernadette and Huppertz, Berthold and Leithner, Andreas and de Pinieux, Gonzague and Terrier, Philippe and Laurence, Val{\'e}rie and Michon, Jean and Ladenstein, Ruth and Holter, Wolfgang and Windhager, Reinhard and Dirksen, Uta and Ambros, Peter F. and Delattre, Olivier and Kovar, Heinrich and Bock, Christoph and Tomazou, Eleni M.},
LANGUAGE = {eng},
ISSN = {1078-8956},
DOI = {10.1038/nm.4273},
PUBLISHER = {Nature Publishing Group},
ADDRESS = {New York, NY},
YEAR = {2017},
DATE = {2017},
JOURNAL = {Nature Medicine},
VOLUME = {23},
NUMBER = {3},
PAGES = {386--395},
}
Endnote
%0 Journal Article
%A Sheffield, Nathan C.
%A Pierron, Gaelle
%A Klughammer, Johanna
%A Datlinger, Paul
%A Schönegger, Andreas
%A Schuster, Michael
%A Hadler, Johanna
%A Surdez, Didier
%A Guillemot, Delphine
%A Lapouble, Eve
%A Freneaux, Paul
%A Champigneulle, Jacqueline
%A Bouvier, Raymonde
%A Walder, Diana
%A Ambros, Ingeborg M.
%A Hutter, Caroline
%A Sorz, Eva
%A Amaral, Ana T.
%A de Álava, Enrique
%A Schallmoser, Katharina
%A Strunk, Dirk
%A Rinner, Beate
%A Liegl-Atzwanger, Bernadette
%A Huppertz, Berthold
%A Leithner, Andreas
%A de Pinieux, Gonzague
%A Terrier, Philippe
%A Laurence, Valérie
%A Michon, Jean
%A Ladenstein, Ruth
%A Holter, Wolfgang
%A Windhager, Reinhard
%A Dirksen, Uta
%A Ambros, Peter F.
%A Delattre, Olivier
%A Kovar, Heinrich
%A Bock, Christoph
%A Tomazou, Eleni M.
%+ External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
%T DNA Methylation Heterogeneity Defines a Disease Spectrum in Ewing Sarcoma :
%G eng
%U http://hdl.handle.net/11858/00-001M-0000-002C-CBE6-E
%R 10.1038/nm.4273
%7 2017-01-30
%D 2017
%J Nature Medicine
%O Nat. Med.
%V 23
%N 3
%& 386
%P 386 - 395
%I Nature Publishing Group
%C New York, NY
%@ false
186. Siu A: Knowledge-driven Entity Recognition and Disambiguation in Biomedical Text. Universität des Saarlandes; 2017.
Abstract
Entity recognition and disambiguation (ERD) for the biomedical domain are notoriously difficult problems due to the variety of entities and their often long names in many variations. Existing works focus heavily on the molecular level in two ways. First, they target scientific literature as the input text genre. Second, they target single, highly specialized entity types such as chemicals, genes, and proteins. However, a wealth of biomedical information is also buried in the vast universe of Web content. In order to fully utilize all the information available, there is a need to tap into Web content as an additional input. Moreover, there is a need to cater for other entity types such as symptoms and risk factors since Web content focuses on consumer health. The goal of this thesis is to investigate ERD methods that are applicable to all entity types in scientific literature as well as Web content. In addition, we focus on under-explored aspects of the biomedical ERD problems -- scalability, long noun phrases, and out-of-knowledge base (OOKB) entities. This thesis makes four main contributions, all of which leverage knowledge in UMLS (Unified Medical Language System), the largest and most authoritative knowledge base (KB) of the biomedical domain. The first contribution is a fast dictionary lookup method for entity recognition that maximizes throughput while balancing the loss of precision and recall. The second contribution is a semantic type classification method targeting common words in long noun phrases. We develop a custom set of semantic types to capture word usages; besides biomedical usage, these types also cope with non-biomedical usage and the case of generic, non-informative usage. The third contribution is a fast heuristics method for entity disambiguation in MEDLINE abstracts, again maximizing throughput but this time maintaining accuracy. The fourth contribution is a corpus-driven entity disambiguation method that addresses OOKB entities. The method first captures the entities expressed in a corpus as latent representations that comprise in-KB and OOKB entities alike before performing entity disambiguation.
Export
BibTeX
@phdthesis{siuphd17,
TITLE = {Knowledge-driven Entity Recognition and Disambiguation in Biomedical Text},
AUTHOR = {Siu, Amy},
LANGUAGE = {eng},
URL = {urn:nbn:de:bsz:291-scidok-69580},
DOI = {10.22028/D291-26790},
SCHOOL = {Universit{\"a}t des Saarlandes},
ADDRESS = {Saarbr{\"u}cken},
YEAR = {2017},
DATE = {2017},
ABSTRACT = {Entity recognition and disambiguation (ERD) for the biomedical domain are notoriously difficult problems due to the variety of entities and their often long names in many variations. Existing works focus heavily on the molecular level in two ways. First, they target scientific literature as the input text genre. Second, they target single, highly specialized entity types such as chemicals, genes, and proteins. However, a wealth of biomedical information is also buried in the vast universe of Web content. In order to fully utilize all the information available, there is a need to tap into Web content as an additional input. Moreover, there is a need to cater for other entity types such as symptoms and risk factors since Web content focuses on consumer health. The goal of this thesis is to investigate ERD methods that are applicable to all entity types in scientific literature as well as Web content. In addition, we focus on under-explored aspects of the biomedical ERD problems -- scalability, long noun phrases, and out-of-knowledge base (OOKB) entities. This thesis makes four main contributions, all of which leverage knowledge in UMLS (Unified Medical Language System), the largest and most authoritative knowledge base (KB) of the biomedical domain. The first contribution is a fast dictionary lookup method for entity recognition that maximizes throughput while balancing the loss of precision and recall. The second contribution is a semantic type classification method targeting common words in long noun phrases. We develop a custom set of semantic types to capture word usages; besides biomedical usage, these types also cope with non-biomedical usage and the case of generic, non-informative usage. The third contribution is a fast heuristics method for entity disambiguation in MEDLINE abstracts, again maximizing throughput but this time maintaining accuracy. The fourth contribution is a corpus-driven entity disambiguation method that addresses OOKB entities. The method first captures the entities expressed in a corpus as latent representations that comprise in-KB and OOKB entities alike before performing entity disambiguation.},
}
Endnote
%0 Thesis
%A Siu, Amy
%Y Weikum, Gerhard
%A referee: Berberich, Klaus
%A referee: Leser, Ulf
%+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
International Max Planck Research School, MPI for Informatics, Max Planck Society
Databases and Information Systems, MPI for Informatics, Max Planck Society
Databases and Information Systems, MPI for Informatics, Max Planck Society
External Organizations
%T Knowledge-driven Entity Recognition and Disambiguation in Biomedical Text :
%G eng
%U http://hdl.handle.net/11858/00-001M-0000-002D-DD18-E
%R 10.22028/D291-26790
%U urn:nbn:de:bsz:291-scidok-69580
%F OTHER: hdl:20.500.11880/26803
%I Universität des Saarlandes
%C Saarbrücken
%D 2017
%P 169 p.
%V phd
%9 phd
%X Entity recognition and disambiguation (ERD) for the biomedical domain are notoriously difficult problems due to the variety of entities and their often long names in many variations. Existing works focus heavily on the molecular level in two ways. First, they target scientific literature as the input text genre. Second, they target single, highly specialized entity types such as chemicals, genes, and proteins. However, a wealth of biomedical information is also buried in the vast universe of Web content. In order to fully utilize all the information available, there is a need to tap into Web content as an additional input. Moreover, there is a need to cater for other entity types such as symptoms and risk factors since Web content focuses on consumer health. The goal of this thesis is to investigate ERD methods that are applicable to all entity types in scientific literature as well as Web content. In addition, we focus on under-explored aspects of the biomedical ERD problems -- scalability, long noun phrases, and out-of-knowledge base (OOKB) entities. This thesis makes four main contributions, all of which leverage knowledge in UMLS (Unified Medical Language System), the largest and most authoritative knowledge base (KB) of the biomedical domain. The first contribution is a fast dictionary lookup method for entity recognition that maximizes throughput while balancing the loss of precision and recall. The second contribution is a semantic type classification method targeting common words in long noun phrases. We develop a custom set of semantic types to capture word usages; besides biomedical usage, these types also cope with non-biomedical usage and the case of generic, non-informative usage. The third contribution is a fast heuristics method for entity disambiguation in MEDLINE abstracts, again maximizing throughput but this time maintaining accuracy. The fourth contribution is a corpus-driven entity disambiguation method that addresses OOKB entities. The method first captures the entities expressed in a corpus as latent representations that comprise in-KB and OOKB entities alike before performing entity disambiguation.
%U https://publikationen.sulb.uni-saarland.de/handle/20.500.11880/26803
187. Towards Multiple Kernel Principal Component Analysis for Integrative Analysis of Tumor Samples [http://arxiv.org/abs/1701.00422]
(arXiv: 1701.00422) Abstract
Personalized treatment of patients based on tissue-specific cancer subtypes
has strongly increased the efficacy of the chosen therapies. Even though the
amount of data measured for cancer patients has increased over the last years,
most cancer subtypes are still diagnosed based on individual data sources (e.g.
gene expression data). We propose an unsupervised data integration method based
on kernel principal component analysis. Principal component analysis is one of
the most widely used techniques in data analysis. Unfortunately, the
straight-forward multiple-kernel extension of this method leads to the use of
only one of the input matrices, which does not fit the goal of gaining
information from all data sources. Therefore, we present a scoring function to
determine the impact of each input matrix. The approach enables visualizing the
integrated data and subsequent clustering for cancer subtype identification.
Due to the nature of the method, no free parameters have to be set. We apply
the methodology to five different cancer data sets and demonstrate its
advantages in terms of results and usability.
Export
BibTeX
@online{SpeicherarXiv2017,
TITLE = {Towards Multiple Kernel Principal Component Analysis for Integrative Analysis of Tumor Samples},
AUTHOR = {Speicher, Nora K. and Pfeifer, Nico},
LANGUAGE = {eng},
URL = {http://arxiv.org/abs/1701.00422},
EPRINT = {1701.00422},
EPRINTTYPE = {arXiv},
YEAR = {2017},
ABSTRACT = {Personalized treatment of patients based on tissue-specific cancer subtypes has strongly increased the efficacy of the chosen therapies. Even though the amount of data measured for cancer patients has increased over the last years, most cancer subtypes are still diagnosed based on individual data sources (e.g. gene expression data). We propose an unsupervised data integration method based on kernel principal component analysis. Principal component analysis is one of the most widely used techniques in data analysis. Unfortunately, the straight-forward multiple-kernel extension of this method leads to the use of only one of the input matrices, which does not fit the goal of gaining information from all data sources. Therefore, we present a scoring function to determine the impact of each input matrix. The approach enables visualizing the integrated data and subsequent clustering for cancer subtype identification. Due to the nature of the method, no free parameters have to be set. We apply the methodology to five different cancer data sets and demonstrate its advantages in terms of results and usability.},
}
Endnote
%0 Report
%A Speicher, Nora K.
%A Pfeifer, Nico
%+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
%T Towards Multiple Kernel Principal Component Analysis for Integrative Analysis of Tumor Samples :
%G eng
%U http://hdl.handle.net/11858/00-001M-0000-002C-4D68-3
%U http://arxiv.org/abs/1701.00422
%D 2017
%X Personalized treatment of patients based on tissue-specific cancer subtypes
has strongly increased the efficacy of the chosen therapies. Even though the
amount of data measured for cancer patients has increased over the last years,
most cancer subtypes are still diagnosed based on individual data sources (e.g.
gene expression data). We propose an unsupervised data integration method based
on kernel principal component analysis. Principal component analysis is one of
the most widely used techniques in data analysis. Unfortunately, the
straight-forward multiple-kernel extension of this method leads to the use of
only one of the input matrices, which does not fit the goal of gaining
information from all data sources. Therefore, we present a scoring function to
determine the impact of each input matrix. The approach enables visualizing the
integrated data and subsequent clustering for cancer subtype identification.
Due to the nature of the method, no free parameters have to be set. We apply
the methodology to five different cancer data sets and demonstrate its
advantages in terms of results and usability.
%K Statistics, Machine Learning, stat.ML
188. Speicher NK, Pfeifer N: Towards Multiple Kernel Principal Component Analysis for Integrative Analysis of Tumor Samples. Journal of Integrative Bioinformatics 2017, 14.
Export
BibTeX
@article{Speicher2017,
TITLE = {Towards Multiple Kernel Principal Component Analysis for Integrative Analysis of Tumor Samples},
AUTHOR = {Speicher, Nora K. and Pfeifer, Nico},
LANGUAGE = {eng},
ISSN = {1613-4516},
DOI = {10.1515/jib-2017-0019},
PUBLISHER = {Walter de Gruyter GmbH},
ADDRESS = {Berlin},
YEAR = {2017},
JOURNAL = {Journal of Integrative Bioinformatics},
VOLUME = {14},
NUMBER = {2},
EID = {20170019},
}
Endnote
%0 Journal Article
%A Speicher, Nora K.
%A Pfeifer, Nico
%+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
%T Towards Multiple Kernel Principal Component Analysis for Integrative Analysis of Tumor Samples :
%G eng
%U http://hdl.handle.net/21.11116/0000-0002-F720-3
%R 10.1515/jib-2017-0019
%2 PMC6042822
%7 2017
%D 2017
%J Journal of Integrative Bioinformatics
%V 14
%N 2
%Z sequence number: 20170019
%I Walter de Gruyter GmbH
%C Berlin
%@ false
189. Stancu MC, van Roosmalen MJ, Renkens I, Nieboer MM, Middelkamp S, de Ligt J, Pregno G, Giachino D, Mandrile G, Valle-Inclan JE, Korzelius J, de Bruijn E, Cuppen E, Talkowski ME, Marschall T, de Ridder J, Kloosterman WP: Mapping and Phasing of Structural Variation in Patient Genomes Using Nanopore Sequencing. Nature Communications 2017, 8.
Export
BibTeX
@article{Stancu2017,
TITLE = {Mapping and Phasing of Structural Variation in Patient Genomes Using Nanopore Sequencing},
AUTHOR = {Stancu, Mircea Cretu and van Roosmalen, Markus J. and Renkens, Ivo and Nieboer, Marleen M. and Middelkamp, Sjors and de Ligt, Joep and Pregno, Giulia and Giachino, Daniela and Mandrile, Giorgia and Valle-Inclan, Jose Espejo and Korzelius, Jerome and de Bruijn, Ewart and Cuppen, Edwin and Talkowski, Michael E. and Marschall, Tobias and de Ridder, Jeroen and Kloosterman, Wigard P.},
LANGUAGE = {eng},
ISSN = {2041-1723},
DOI = {10.1038/s41467-017-01343-4},
PUBLISHER = {Nature Publishing Group},
ADDRESS = {London},
YEAR = {2017},
JOURNAL = {Nature Communications},
VOLUME = {8},
EID = {1326},
}
Endnote
%0 Journal Article
%A Stancu, Mircea Cretu
%A van Roosmalen, Markus J.
%A Renkens, Ivo
%A Nieboer, Marleen M.
%A Middelkamp, Sjors
%A de Ligt, Joep
%A Pregno, Giulia
%A Giachino, Daniela
%A Mandrile, Giorgia
%A Valle-Inclan, Jose Espejo
%A Korzelius, Jerome
%A de Bruijn, Ewart
%A Cuppen, Edwin
%A Talkowski, Michael E.
%A Marschall, Tobias
%A de Ridder, Jeroen
%A Kloosterman, Wigard P.
%+ External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
External Organizations
%T Mapping and Phasing of Structural Variation in Patient Genomes Using Nanopore Sequencing :
%G eng
%U http://hdl.handle.net/11858/00-001M-0000-002E-55B2-A
%R 10.1038/s41467-017-01343-4
%7 2017
%D 2017
%J Nature Communications
%O Nat. Commun.
%V 8
%Z sequence number: 1326
%I Nature Publishing Group
%C London
%@ false
190. Sun P: Bi-(N-) cluster editing and its biomedical applications. Universität des Saarlandes; 2017.
Abstract
he extremely fast advances in wet-lab techniques lead to an exponential growth of heterogeneous and unstructured biological data, posing a great challenge to data integration in nowadays system biology. The traditional clustering approach, although widely used to divide the data into groups sharing common features, is less powerful in the analysis of heterogeneous data from n different sources (n _ 2). The co-clustering approach has been widely used for combined analyses of multiple networks to address the challenge of heterogeneity. In this thesis, novel methods for the co-clustering of large scale heterogeneous data sets are presented in the software package n-CluE: one exact algorithm and two heuristic algorithms based on the model of bi-/n-cluster editing by modeling the input as n-partite graphs and solving the clustering problem with various strategies. In the first part of the thesis, the complexity and the fixed-parameter tractability of the extended bicluster editing model with relaxed constraints are investigated, namely the ?-bicluster editing model and its NP-hardness is proven. Based on the results of this analysis, three strategies within the n-CluE software package are then established and discussed, together with the evaluations on performances and the systematic comparisons against other algorithms of the same type in solving bi-/n-cluster editing problem. To demonstrate the practical impact, three real-world analyses using n-CluE are performed, including (a) prediction of novel genotype-phenotype associations by clustering the data from Genome-Wide Association Studies; (b) comparison between n-CluE and eight other biclustering tools on GEO Omnibus microarray data sets; (c) drug repositioning predictions by co-clustering on drug, gene and disease networks. The outstanding performance of n-CluE in the real-world applications shows its strength and flexibility in integrating heterogeneous data and extracting biological relevant information in bioinformatic analyses.
Export
BibTeX
@phdthesis{Sunphd17,
TITLE = {Bi-(N-) cluster editing and its biomedical applications},
AUTHOR = {Sun, Peng},
LANGUAGE = {eng},
URL = {urn:nbn:de:bsz:291-scidok-69309},
DOI = {10.22028/D291-26781},
SCHOOL = {Universit{\"a}t des Saarlandes},
ADDRESS = {Saarbr{\"u}cken},
YEAR = {2017},
DATE = {2017},
ABSTRACT = {he extremely fast advances in wet-lab techniques lead to an exponential growth of heterogeneous and unstructured biological data, posing a great challenge to data integration in nowadays system biology. The traditional clustering approach, although widely used to divide the data into groups sharing common features, is less powerful in the analysis of heterogeneous data from n different sources (n _ 2). The co-clustering approach has been widely used for combined analyses of multiple networks to address the challenge of heterogeneity. In this thesis, novel methods for the co-clustering of large scale heterogeneous data sets are presented in the software package n-CluE: one exact algorithm and two heuristic algorithms based on the model of bi-/n-cluster editing by modeling the input as n-partite graphs and solving the clustering problem with various strategies. In the first part of the thesis, the complexity and the fixed-parameter tractability of the extended bicluster editing model with relaxed constraints are investigated, namely the ?-bicluster editing model and its NP-hardness is proven. Based on the results of this analysis, three strategies within the n-CluE software package are then established and discussed, together with the evaluations on performances and the systematic comparisons against other algorithms of the same type in solving bi-/n-cluster editing problem. To demonstrate the practical impact, three real-world analyses using n-CluE are performed, including (a) prediction of novel genotype-phenotype associations by clustering the data from Genome-Wide Association Studies; (b) comparison between n-CluE and eight other biclustering tools on GEO Omnibus microarray data sets; (c) drug repositioning predictions by co-clustering on drug, gene and disease networks. The outstanding performance of n-CluE in the real-world applications shows its strength and flexibility in integrating heterogeneous data and extracting biological relevant information in bioinformatic analyses.},
}
Endnote
%0 Thesis
%A Sun, Peng
%Y Baumbach, Jan
%A referee: Guo, Jiong
%A referee: Lengauer, Thomas
%+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
International Max Planck Research School, MPI for Informatics, Max Planck Society
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
%T Bi-(N-) cluster editing and its biomedical applications :
%G eng
%U http://hdl.handle.net/11858/00-001M-0000-002D-A65E-F
%U urn:nbn:de:bsz:291-scidok-69309
%R 10.22028/D291-26781
%F OTHER: hdl:20.500.11880/26794
%I Universität des Saarlandes
%C Saarbrücken
%D 2017
%P 192 p.
%V phd
%9 phd
%X he extremely fast advances in wet-lab techniques lead to an exponential growth of heterogeneous and unstructured biological data, posing a great challenge to data integration in nowadays system biology. The traditional clustering approach, although widely used to divide the data into groups sharing common features, is less powerful in the analysis of heterogeneous data from n different sources (n _ 2). The co-clustering approach has been widely used for combined analyses of multiple networks to address the challenge of heterogeneity. In this thesis, novel methods for the co-clustering of large scale heterogeneous data sets are presented in the software package n-CluE: one exact algorithm and two heuristic algorithms based on the model of bi-/n-cluster editing by modeling the input as n-partite graphs and solving the clustering problem with various strategies. In the first part of the thesis, the complexity and the fixed-parameter tractability of the extended bicluster editing model with relaxed constraints are investigated, namely the ?-bicluster editing model and its NP-hardness is proven. Based on the results of this analysis, three strategies within the n-CluE software package are then established and discussed, together with the evaluations on performances and the systematic comparisons against other algorithms of the same type in solving bi-/n-cluster editing problem. To demonstrate the practical impact, three real-world analyses using n-CluE are performed, including (a) prediction of novel genotype-phenotype associations by clustering the data from Genome-Wide Association Studies; (b) comparison between n-CluE and eight other biclustering tools on GEO Omnibus microarray data sets; (c) drug repositioning predictions by co-clustering on drug, gene and disease networks. The outstanding performance of n-CluE in the real-world applications shows its strength and flexibility in integrating heterogeneous data and extracting biological relevant information in bioinformatic analyses.
%U http://scidok.sulb.uni-saarland.de/volltexte/2017/6930/http://scidok.sulb.uni-saarland.de/doku/lic_ohne_pod.php?la=de
191. Sun P, Guo J, Winnenburg R, Baumbach J: Drug Repurposing by Integrated Literature Mining and Drug–Gene–Disease Triangulation. Drug Discovery Today 2017, 22.
Export
BibTeX
@article{Sun_Baumbach2017,
TITLE = {Drug Repurposing by Integrated Literature Mining and Drug--Gene--Disease Triangulation},
AUTHOR = {Sun, Peng and Guo, Jiong and Winnenburg, Rainer and Baumbach, Jan},
LANGUAGE = {eng},
ISSN = {1359-6446},
DOI = {10.1016/j.drudis.2016.10.008},
PUBLISHER = {Elsevier},
ADDRESS = {Amsterdam},
YEAR = {2017},
DATE = {2017},
JOURNAL = {Drug Discovery Today},
VOLUME = {22},
NUMBER = {4},
PAGES = {615--619},
}
Endnote
%0 Journal Article
%A Sun, Peng
%A Guo, Jiong
%A Winnenburg, Rainer
%A Baumbach, Jan
%+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
%T Drug Repurposing by Integrated Literature Mining and Drug–Gene–Disease Triangulation :
%G eng
%U http://hdl.handle.net/11858/00-001M-0000-002D-6E09-3
%R 10.1016/j.drudis.2016.10.008
%7 2016-10-22
%D 2017
%J Drug Discovery Today
%V 22
%N 4
%& 615
%P 615 - 619
%I Elsevier
%C Amsterdam
%@ false
2016
192. Ahmad M, Helms V, Kalinina OV, Lengauer T: The Role of Conformational Changes in Molecular Recognition. The Journal of Physical Chemistry B 2016, 120.
Export
BibTeX
@article{AhmadJPhysChem2016,
TITLE = {The Role of Conformational Changes in Molecular Recognition},
AUTHOR = {Ahmad, Mazen and Helms, Volkhard and Kalinina, Olga V. and Lengauer, Thomas},
LANGUAGE = {eng},
ISSN = {1520-6106},
DOI = {10.1021/acs.jpcb.5b11593},
PUBLISHER = {American Chemical Society},
ADDRESS = {Washington, D.C.},
YEAR = {2016},
DATE = {2016},
JOURNAL = {The Journal of Physical Chemistry B},
VOLUME = {120},
NUMBER = {9},
PAGES = {2138--2144},
}
Endnote
%0 Journal Article
%A Ahmad, Mazen
%A Helms, Volkhard
%A Kalinina, Olga V.
%A Lengauer, Thomas
%+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
%T 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
193. 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).
Export
BibTeX
@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},
ISSN = {0305-1048},
DOI = {10.1093/nar/gkw211},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford},
YEAR = {2016},
DATE = {2016},
JOURNAL = {Nucleic Acids Research},
VOLUME = {44},
NUMBER = {W1/Web Server issue},
PAGES = {W581--W586},
}
Endnote
%0 Journal Article
%A Albrecht, Felipe
%A List, Markus
%A Bock, Christoph
%A Lengauer, Thomas
%+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
%T DeepBlue Epigenomic Data Server: Programmatic Data Retrieval and Analysis of Epigenome Region Sets :
%G eng
%U http://hdl.handle.net/11858/00-001M-0000-002B-42AD-0
%R 10.1093/nar/gkw211
%2 PMC4987868
%7 2016
%D 2016
%* Review method: peer-reviewed
%J Nucleic Acids Research
%O Nucleic Acids Res
%V 44
%N W1/Web Server issue
%& W581
%P W581 - W586
%I Oxford University Press
%C Oxford
%@ false
%U https://doi.org/10.1093/nar/gkw211
194. 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.
Export
BibTeX
@article{ListF1000Research2016,
TITLE = {Robust de novo pathway enrichment with {KeyPathwayMiner} 5},
AUTHOR = {Alcaraz, Nicolas and List, Markus and Dissing-Hansen, Martin and Rehmsmeier, Marc and Tan, Qihua and Mollenhauer, Jan and Ditzel, Henrik J. and Baumbach, Jan},
LANGUAGE = {eng},
DOI = {10.12688/f1000research.9054.1},
PUBLISHER = {BioMed Central},
ADDRESS = {London},
YEAR = {2016},
JOURNAL = {Faculty of 1000 Research},
VOLUME = {5},
EID = {1531},
}
Endnote
%0 Journal Article
%A Alcaraz, Nicolas
%A List, Markus
%A Dissing-Hansen, Martin
%A Rehmsmeier, Marc
%A Tan, Qihua
%A Mollenhauer, Jan
%A Ditzel, Henrik J.
%A Baumbach, Jan
%+ External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
%T Robust de novo pathway enrichment with KeyPathwayMiner 5 :
%G eng
%U http://hdl.handle.net/11858/00-001M-0000-002B-4656-5
%R 10.12688/f1000research.9054.1
%2 PMC4965696
%7 2016
%D 2016
%J Faculty of 1000 Research
%O F1000Research
%V 5
%Z sequence number: 1531
%I BioMed Central
%C London
%U http://f1000research.com/articles/5-1531/
195. 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.
Export
BibTeX
@article{Auffray2016,
TITLE = {Making sense of big data in health research: {T}owards an {EU} action plan},
AUTHOR = {Auffray, Charles and Balling, Rudi and Barroso, In{\^e}s and Bencze, L{\'a}szl{\'o} and Blomberg, Niklas and Bock, Christoph and Conesa, Anna and Del Signore, Susanna and Delogne, Christophe and Deyilee, Peter and Di Meglio, Alberto and Eijkemans, Marinus and Flicek, Paul and Graf, Norbert and Grimm, Vera and Guchelaar, Henk-Jan and Guo, Yi-Ke and Gut, Ivo Glynne and Hanbury, Allan and Hanif, Shahid and Hilgers, Ralf-Dieter and Honrado, {\'A}ngel and Hose, D. Rod and Houwing-Duistermaat, Jeanine and Hubbard, Tim and Janacek, Sophie Helen and Karanikas, Haralampos and Kievits, Tim and Kohler, Manfred and Kremer, Andreas and Lanfear, Jerry and Lengauer, Thomas and Maes, Edith and Meert, Theo and M{\"u}ller, Werner and Nickel, D{\"o}rthe and Oledzki, Peter and Pedersen, Bertrand and Petkovic, Milan and Pliakos, Konstantinos and Rattray, Magnus and Red{\'o}n i M{\`a}s, Josep and Schneider, Reinhard and Sengstag, Thierry and Serra-Picamal, Xavier and Spek, Wouter and Vaas, Lea A. I. and van Batenburg, Okker and Vandelaer, Marc and Varnai, Peter and Villoslada, Pablo and Vizca{\'i}no, Juan Antonio and Wubbe, John Peter Mary and Zanetti, Gianluigi},
LANGUAGE = {eng},
DOI = {10.1186/s13073-016-0323-y},
PUBLISHER = {BioMedCentral},
ADDRESS = {London},
YEAR = {2016},
JOURNAL = {Genome Medicine},
VOLUME = {8},
EID = {71},
}
Endnote
%0 Journal Article
%A Auffray, Charles
%A Balling, Rudi
%A Barroso, Inês
%A Bencze, László
%A Blomberg, Niklas
%A Bock, Christoph
%A Conesa, Anna
%A Del Signore, Susanna
%A Delogne, Christophe
%A Deyilee, Peter
%A Di Meglio, Alberto
%A Eijkemans, Marinus
%A Flicek, Paul
%A Graf, Norbert
%A Grimm, Vera
%A Guchelaar, Henk-Jan
%A Guo, Yi-Ke
%A Gut, Ivo Glynne
%A Hanbury, Allan
%A Hanif, Shahid
%A Hilgers, Ralf-Dieter
%A Honrado, Ángel
%A Hose, D. Rod
%A Houwing-Duistermaat, Jeanine
%A Hubbard, Tim
%A Janacek, Sophie Helen
%A Karanikas, Haralampos
%A Kievits, Tim
%A Kohler, Manfred
%A Kremer, Andreas
%A Lanfear, Jerry
%A Lengauer, Thomas
%A Maes, Edith
%A Meert, Theo
%A Müller, Werner
%A Nickel, Dörthe
%A Oledzki, Peter
%A Pedersen, Bertrand
%A Petkovic, Milan
%A Pliakos, Konstantinos
%A Rattray, Magnus
%A Redón i Màs, Josep
%A Schneider, Reinhard
%A Sengstag, Thierry
%A Serra-Picamal, Xavier
%A Spek, Wouter
%A Vaas, Lea A. I.
%A van Batenburg, Okker
%A Vandelaer, Marc
%A Varnai, Peter
%A Villoslada, Pablo
%A Vizcaíno, Juan Antonio
%A Wubbe, John Peter Mary
%A Zanetti, Gianluigi
%+ External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
%T Making Sense of Big Data in Health Research: Towards an EU Action Plan :
%G eng
%U http://hdl.handle.net/11858/00-001M-0000-002A-F908-8
%R 10.1186/s13073-016-0323-y
%2 PMC4919856
%7 2016
%D 2016
%J Genome Medicine
%V 8
%Z sequence number: 71
%I BioMedCentral
%C London
196. 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.
Export
BibTeX
@article{Auffray2016Erratum,
TITLE = {Erratum to: Making sense of big data in health research: {T}owards an {EU} action plan},
AUTHOR = {Auffray, Charles and Balling, Rudi and Barroso, In{\^e}s and Bencze, L{\'a}szl{\'o} and Blomberg, Niklas and Bock, Christoph and Conesa, Anna and Del Signore, Susanna and Delogne, Christophe and Deyilee, Peter and Di Meglio, Alberto and Eijkemans, Marinus and Flicek, Paul and Graf, Norbert and Grimm, Vera and Guchelaar, Henk-Jan and Guo, Yi-Ke and Gut, Ivo Glynne and Hanbury, Allan and Hanif, Shahid and Hilgers, Ralf-Dieter and Honrado, {\'A}ngel and Hose, D. Rod and Houwing-Duistermaat, Jeanine and Hubbard, Tim and Janacek, Sophie Helen and Karanikas, Haralampos and Kievits, Tim and Kohler, Manfred and Kremer, Andreas and Lanfear, Jerry and Lengauer, Thomas and Maes, Edith and Meert, Theo and M{\"u}ller, Werner and Nickel, D{\"o}rthe and Oledzki, Peter and Pedersen, Bertrand and Petkovic, Milan and Pliakos, Konstantinos and Rattray, Magnus and Red{\'o}n i M{\`a}s, Josep and Schneider, Reinhard and Sengstag, Thierry and Serra-Picamal, Xavier and Spek, Wouter and Vaas, Lea A. I. and van Batenburg, Okker and Vandelaer, Marc and Varnai, Peter and Villoslada, Pablo and Vizca{\'i}no, Juan Antonio and Wubbe, John Peter Mary and Zanetti, Gianluigi},
LANGUAGE = {eng},
DOI = {10.1186/s13073-016-0376-y},
PUBLISHER = {BioMedCentral},
ADDRESS = {London},
YEAR = {2016},
JOURNAL = {Genome Medicine},
VOLUME = {8},
EID = {118},
}
Endnote
%0 Journal Article
%A Auffray, Charles
%A Balling, Rudi
%A Barroso, Inês
%A Bencze, László
%A Blomberg, Niklas
%A Bock, Christoph
%A Conesa, Anna
%A Del Signore, Susanna
%A Delogne, Christophe
%A Deyilee, Peter
%A Di Meglio, Alberto
%A Eijkemans, Marinus
%A Flicek, Paul
%A Graf, Norbert
%A Grimm, Vera
%A Guchelaar, Henk-Jan
%A Guo, Yi-Ke
%A Gut, Ivo Glynne
%A Hanbury, Allan
%A Hanif, Shahid
%A Hilgers, Ralf-Dieter
%A Honrado, Ángel
%A Hose, D. Rod
%A Houwing-Duistermaat, Jeanine
%A Hubbard, Tim
%A Janacek, Sophie Helen
%A Karanikas, Haralampos
%A Kievits, Tim
%A Kohler, Manfred
%A Kremer, Andreas
%A Lanfear, Jerry
%A Lengauer, Thomas
%A Maes, Edith
%A Meert, Theo
%A Müller, Werner
%A Nickel, Dörthe
%A Oledzki, Peter
%A Pedersen, Bertrand
%A Petkovic, Milan
%A Pliakos, Konstantinos
%A Rattray, Magnus
%A Redón i Màs, Josep
%A Schneider, Reinhard
%A Sengstag, Thierry
%A Serra-Picamal, Xavier
%A Spek, Wouter
%A Vaas, Lea A. I.
%A van Batenburg, Okker
%A Vandelaer, Marc
%A Varnai, Peter
%A Villoslada, Pablo
%A Vizcaíno, Juan Antonio
%A Wubbe, John Peter Mary
%A Zanetti, Gianluigi
%+ External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
%T Erratum to: Making Sense of Big Data in Health Research: Towards an EU Action Plan :
%G eng
%U http://hdl.handle.net/11858/00-001M-0000-002C-1D02-C
%R 10.1186/s13073-016-0376-y
%2 PMC5100330
%7 2016-11-07
%D 2016
%8 07.11.2016
%J Genome Medicine
%V 8
%Z sequence number: 118
%I BioMedCentral
%C London
197. 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.
Export
BibTeX
@article{Berger2016,
TITLE = {{ISCB}'s Initial Reaction to {The New England Journal of Medicine} Editorial on Data Sharing},
AUTHOR = {Berger, Bonnie and Gaasterland, Terry and Lengauer, Thomas and Orengo, Christine and Gaeta, Bruno and Markel, Scott and Valencia, Alfonso},
LANGUAGE = {eng},
ISSN = {1553-734X},
DOI = {10.1371/journal.pcbi.1004816},
PUBLISHER = {Public Library of Science},
ADDRESS = {San Francisco, CA},
YEAR = {2016},
JOURNAL = {PLOS Computational Biology},
VOLUME = {12},
NUMBER = {3},
PAGES = {1--2},
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
%O PLOS Comput Biol
%V 12
%N 3
%& 1
%P 1 - 2
%Z sequence number: e1004816
%I Public Library of Science
%C San Francisco, CA
%@ false
%U https://doi.org/10.1371/journal.pcbi.1004816
198. 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.
Export
BibTeX
@article{BockNatureBiotechn2016,
TITLE = {Quantitative comparison of {DNA} methylation assays for biomarker development and clinical applications},
AUTHOR = {Bock, Christoph and Halbritter, Florian and Carmona, Francisco J. and Tierling, Sascha and Datlinger, Paul and Assenov, Yassen and Berdasco, Maria and Bergmann, Anke K. and Booher, Keith and Busato, Florance and Campan, Mihaela and Dahl, Christina and Dahmcke, Christina M. and Diep, Dinh and Fern{\'a}ndez, Agust{\'i}n F. and Gerhauser, Clarissa and Haake, Andrea and Heilmann, Katharina and Holcomb, Thomas and Hussmann, Dianna and Ito, Mitsuteru and Kl{\"a}ver, Ruth and Kreutz, Martin and Kulis, Marta and Lopez, Virginia and Nair, Shalima S. and Paul, Dirk S. and Plongthongkum, Nongluk and Qu, Wenija and Queir{\'o}s, Ana C. and Reinicke, Frank and Sauter, Guido and Schlomm, Thorsten and Statham, Aaron and Stirzaker, Clare and Strogantsev, Ruslan and Urdinguio, Roc{\'i}o G. and Walter, Kimberly and Weichenhan, Dieter and Weisenberger, Daniel J. and Beck, Stephan and Clark, Susan J. and Esteller, Manel and Ferguson-Smith, Anne C. and Fraga, Mario F. and Guldberg, Per and Hansen, Lise Lotte and Laird, Peter W. and Mart{\'i}n-Subero, Jos{\'e} I. and Nygren, Anders O. H. and Peist, Ralf and Plass, Christoph and Shames, David S. and Siebert, Reiner and Sun, Xueguang and Tost, J{\"o}rg and Walter, J{\"o}rn and Zhan, Kun and {BLUEPRINT consortium}},
LANGUAGE = {eng},
ISSN = {1087-0156},
DOI = {10.1038/nbt.3605},
PUBLISHER = {Nature Publishing Group},
ADDRESS = {New York, NY},
YEAR = {2016},
DATE = {2016},
JOURNAL = {Nature Biotechnology},
VOLUME = {34},
PAGES = {726--737},
}
Endnote
%0 Journal Article
%A Bock, Christoph
%A Halbritter, Florian
%A Carmona, Francisco J.
%A Tierling, Sascha
%A Datlinger, Paul
%A Assenov, Yassen
%A Berdasco, Maria
%A Bergmann, Anke K.
%A Booher, Keith
%A Busato, Florance
%A Campan, Mihaela
%A Dahl, Christina
%A Dahmcke, Christina M.
%A Diep, Dinh
%A Fernández, Agustín F.
%A Gerhauser, Clarissa
%A Haake, Andrea
%A Heilmann, Katharina
%A Holcomb, Thomas
%A Hussmann, Dianna
%A Ito, Mitsuteru
%A Kläver, Ruth
%A Kreutz, Martin
%A Kulis, Marta
%A Lopez, Virginia
%A Nair, Shalima S.
%A Paul, Dirk S.
%A Plongthongkum, Nongluk
%A Qu, Wenija
%A Queirós, Ana C.
%A Reinicke, Frank
%A Sauter, Guido
%A Schlomm, Thorsten
%A Statham, Aaron
%A Stirzaker, Clare
%A Strogantsev, Ruslan
%A Urdinguio, Rocío G.
%A Walter, Kimberly
%A Weichenhan, Dieter
%A Weisenberger, Daniel J.
%A Beck, Stephan
%A Clark, Susan J.
%A Esteller, Manel
%A Ferguson-Smith, Anne C.
%A Fraga, Mario F.
%A Guldberg, Per
%A Hansen, Lise Lotte
%A Laird, Peter W.
%A Martín-Subero, José I.
%A Nygren, Anders O. H.
%A Peist, Ralf
%A Plass, Christoph
%A Shames, David S.
%A Siebert, Reiner
%A Sun, Xueguang
%A Tost, Jörg
%A Walter, Jörn
%A Zhan, Kun
%A BLUEPRINT consortium,
%+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
%T Quantitative Comparison of DNA Methylation Assays for Biomarker Development and Clinical Applications :
%G eng
%U http://hdl.handle.net/11858/00-001M-0000-002B-6373-E
%R 10.1038/nbt.3605
%7 2016
%D 2016
%K , Jörg Tost, Jörn Walter & Kun Zhang for The BLUEPRINT consortium
%J Nature Biotechnology
%V 34
%& 726
%P 726 - 737
%I Nature Publishing Group
%C New York, NY
%@ false
199. Bock C, Farlik M, Sheffield NC: Multi-Omics of Single Cells: Strategies and Applications. Trends in Biotechnology 2016, 34.
Export
BibTeX
@article{Bock_TrendsBiotech2016,
TITLE = {Multi-Omics of Single Cells: {S}trategies and Applications},
AUTHOR = {Bock, Christoph and Farlik, Matthias and Sheffield, Nathan C.},
LANGUAGE = {eng},
ISSN = {0167-7799},
DOI = {10.1016/j.tibtech.2016.04.004},
PUBLISHER = {Elsevier},
ADDRESS = {Amsterdam, Netherlands},
YEAR = {2016},
DATE = {2016},
JOURNAL = {Trends in Biotechnology},
VOLUME = {34},
NUMBER = {8},
PAGES = {605--608},
}
Endnote
%0 Journal Article
%A Bock, Christoph
%A Farlik, Matthias
%A Sheffield, Nathan C.
%+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
External Organizations
%T Multi-Omics of Single Cells: Strategies and Applications :
%G eng
%U http://hdl.handle.net/11858/00-001M-0000-002B-4789-D
%R 10.1016/j.tibtech.2016.04.004
%2 PMC4959511
%7 2016
%D 2016
%J Trends in Biotechnology
%O Trends Biotechnol.
%V 34
%N 8
%& 605
%P 605 - 608
%I Elsevier
%C Amsterdam, Netherlands
%@ false
%U http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4959511/http://www.sciencedirect.com/science/article/pii/S0167779916300233
200. 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).
Export
BibTeX
@article{Bracciali2016,
TITLE = {{PWHATSHAP}: {E}fficient Haplotyping for Future Generation Sequencing},
AUTHOR = {Bracciali, Andrea and Aldinucci, Marco and Patterson, Murray and Marschall, Tobias and Pisanti, Nadia and Merelli, Ivan and Torquati, Massimo},
LANGUAGE = {eng},
ISSN = {1471-2105},
DOI = {10.1186/s12859-016-1170-y},
PUBLISHER = {BioMed Central},
YEAR = {2016},
JOURNAL = {BMC Bioinformatics (Proc. CIBB)},
VOLUME = {17},
NUMBER = {Suppl. 11},
EID = {342},
BOOKTITLE = {Selected articles from the 11th International Meeting on Computational Intelligence Methods for Bioinformatics and Selected articles from the 11th International Meeting on Computational Intelligence Methods for Bioinformatics and Biostatistics (CIBB 2014)},
}
Endnote
%0 Journal Article
%A Bracciali, Andrea
%A Aldinucci, Marco
%A Patterson, Murray
%A Marschall, Tobias
%A Pisanti, Nadia
%A Merelli, Ivan
%A Torquati, Massimo
%+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
%T PWHATSHAP: Efficient Haplotyping for Future Generation Sequencing :
%G eng
%U http://hdl.handle.net/11858/00-001M-0000-002B-AEFB-6
%R 10.1186/s12859-016-1170-y
%2 PMC5046197
%7 2016
%D 2016
%J BMC Bioinformatics
%V 17
%N Suppl. 11
%Z sequence number: 342
%I BioMed Central
%@ false
%B Selected articles from the 11th International Meeting on Computational Intelligence Methods for Bioinformatics and Selected articles from the 11th International Meeting on Computational Intelligence Methods for Bioinformatics and Biostatistics
%O CIBB 2014
201. 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.
Export
BibTeX
@article{Carlson2016,
TITLE = {Impact of Pre-adapted {HIV} Transmission},
AUTHOR = {Carlson, Jonathan M. and Du, Victor Y. and Pfeifer, Nico and Bansal, Anju and Tan, Vincent Y. F. and Power, Karen and Brumme, Chanson J. and Kreimer, Anat and DeZiel, Charles E. and Fusi, Nicolo and Schaefer, Malinda and Brockman, Mark A. and Gilmour, Jil and Price, Matt A. and Kilembe, William and Haubrich, Richard and John, Mina and Mallal, Simon and Shapiro, Roger and Frater, John and Harrigan, P. Richard and Ndung'u, Thumbi and Allen, Susan and Heckerman, David and Sidney, John and Allen, Todd M. and Goulder, Philip J. R. and Brumme, Zabrina L. and Hunter, Eric and Goepfert, Paul A.},
LANGUAGE = {eng},
ISSN = {1078-8956},
DOI = {10.1038/nm.4100},
PUBLISHER = {Nature Pub. Co.},
ADDRESS = {New York, NY},
YEAR = {2016},
DATE = {2016},
JOURNAL = {Nature Medicine},
VOLUME = {22},
PAGES = {606--613},
}
Endnote
%0 Journal Article
%A Carlson, Jonathan M.
%A Du, Victor Y.
%A Pfeifer, Nico
%A Bansal, Anju
%A Tan, Vincent Y. F.
%A Power, Karen
%A Brumme, Chanson J.
%A Kreimer, Anat
%A DeZiel, Charles E.
%A Fusi, Nicolo
%A Schaefer, Malinda
%A Brockman, Mark A.
%A Gilmour, Jil
%A Price, Matt A.
%A Kilembe, William
%A Haubrich, Richard
%A John, Mina
%A Mallal, Simon
%A Shapiro, Roger
%A Frater, John
%A Harrigan, P. Richard
%A Ndung'u, Thumbi
%A Allen, Susan
%A Heckerman, David
%A Sidney, John
%A Allen, Todd M.
%A Goulder, Philip J. R.
%A Brumme, Zabrina L.
%A Hunter, Eric
%A Goepfert, Paul A.
%+ External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
%T Impact of Pre-adapted HIV Transmission :
%G eng
%U http://hdl.handle.net/11858/00-001M-0000-002A-ED12-F
%R 10.1038/nm.4100
%7 2016
%D 2016
%J Nature Medicine
%O Nat. Med.
%V 22
%& 606
%P 606 - 613
%I Nature Pub. Co.
%C New York, NY
%@ false
202. 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.
Export
BibTeX
@article{Christiansen2016,
TITLE = {A Systematic Review of Breath Analysis and Detection of Volatile Organic Compounds in {COPD}},
AUTHOR = {Christiansen, Anders and Davidsen, Jesper R{\o}mhild and Titlestad, Ingrid and Vestbo, J{\o}rgen and Baumbach, Jan},
LANGUAGE = {eng},
DOI = {10.1088/1752-7155/10/3/034002},
PUBLISHER = {IOP Publishing},
YEAR = {2016},
DATE = {2016},
JOURNAL = {Journal of Breath Research},
VOLUME = {10},
NUMBER = {3},
EID = {034002},
}
Endnote
%0 Journal Article
%A Christiansen, Anders
%A Davidsen, Jesper Rømhild
%A Titlestad, Ingrid
%A Vestbo, Jørgen
%A Baumbach, Jan
%+ External Organizations
External Organizations
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
%T A Systematic Review of Breath Analysis and Detection of Volatile Organic Compounds in COPD :
%G eng
%U http://hdl.handle.net/11858/00-001M-0000-002B-A5A2-E
%R 10.1088/1752-7155/10/3/034002
%7 2016
%D 2016
%J Journal of Breath Research
%V 10
%N 3
%Z sequence number: 034002
%I IOP Publishing
203. Dheghani Amirabad A, Schulz MH: Multitask Regression for Condition-specific Prioritization of miRNA Targets in Transcripts. PeerJ Preprints 2016, 4.
Export
BibTeX
@article{Amirabad2016,
TITLE = {Multitask Regression for Condition-specific Prioritization of {miRNA} Targets in Transcripts},
AUTHOR = {Dheghani Amirabad, Azim and Schulz, Marcel Holger},
LANGUAGE = {eng},
DOI = {10.7287/peerj.preprints.2377v2},
YEAR = {2016},
JOURNAL = {PeerJ Preprints},
VOLUME = {4},
EID = {e2377v2},
}
Endnote
%0 Journal Article
%A Dheghani Amirabad, Azim
%A Schulz, Marcel Holger
%+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
%T Multitask Regression for Condition-specific Prioritization of miRNA Targets in Transcripts :
%G eng
%U http://hdl.handle.net/11858/00-001M-0000-002B-866A-8
%R 10.7287/peerj.preprints.2377v2
%7 2016-08-22
%D 2016
%8 22.08.2016
%J PeerJ Preprints
%V 4
%Z sequence number: e2377v2
204. Doncheva NT: Network Biology Methods for Functional Characterization and Integrative Prioritization of Disease Genes and Proteins. Universität des Saarlandes; 2016.
Export
BibTeX
@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},
DOI = {10.22028/D291-26665},
SCHOOL = {Universit{\"a}t des Saarlandes},
ADDRESS = {Saarbr{\"u}cken},
YEAR = {2016},
DATE = {2016},
}
Endnote
%0 Thesis
%A Doncheva, Nadezhda Tsankova
%Y Albrecht, Mario
%A referee: Lengauer, Thomas
%A referee: Lenhof, Hans-Peter
%+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
International Max Planck Research School, MPI for Informatics, Max Planck Society
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
%T Network Biology Methods for Functional Characterization and Integrative Prioritization of Disease Genes and Proteins :
%G eng
%U http://hdl.handle.net/11858/00-001M-0000-002B-1921-A
%U urn:nbn:de:bsz:291-scidok-65957
%R 10.22028/D291-26665
%F OTHER: hdl:20.500.11880/26721
%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
205. 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.
Export
BibTeX
@article{DoeringRetro16,
TITLE = {A Genotypic Method for Determining {HIV-2} Coreceptor Usage enables Epidemiological Studies and Clinical Decision Support},
AUTHOR = {D{\"o}ring, Matthias and Borrego, Pedro and B{\"u}ch, Joachim and Martins, Andreia and Friedrich, Georg and Camacho, Ricardo Jorge and Eberle, Josef and Kaiser, Rolf and Lengauer, Thomas and Taveira, Nuno and Pfeifer, Nico},
LANGUAGE = {eng},
ISSN = {1742-4690},
DOI = {10.1186/s12977-016-0320-7},
PUBLISHER = {BioMed Central},
ADDRESS = {London},
YEAR = {2016},
JOURNAL = {Retrovirology},
VOLUME = {13},
EID = {85},
}
Endnote
%0 Journal Article
%A Döring, Matthias
%A Borrego, Pedro
%A Büch, Joachim
%A Martins, Andreia
%A Friedrich, Georg
%A Camacho, Ricardo Jorge
%A Eberle, Josef
%A Kaiser, Rolf
%A Lengauer, Thomas
%A Taveira, Nuno
%A Pfeifer, Nico
%+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
%T A Genotypic Method for Determining HIV-2 Coreceptor Usage enables Epidemiological Studies and Clinical Decision Support :
%G eng
%U http://hdl.handle.net/11858/00-001M-0000-002C-298A-A
%R 10.1186/s12977-016-0320-7
%7 2016-12-20
%D 2016
%8 20.12.2016
%K Human immunodeficiency virus type 2, HIV-2, Coreceptor, Chemokine receptor, Prediction, Statistical learning, V3, V1, V2, Coreceptor antagonists
%J Retrovirology
%V 13
%Z sequence number: 85
%I BioMed Central
%C London
%@ false
206. Durai DA, Schulz MH: Informed kmer Selection for de novo Transcriptome Assembly. Bioinformatics 2016, 32.
Export
BibTeX
@article{Durai2016,
TITLE = {Informed $k$mer Selection for \textit{de novo} Transcriptome Assembly},
AUTHOR = {Durai, Dilip Ariyur and Schulz, Marcel H.},
LANGUAGE = {eng},
ISSN = {1367-4803},
DOI = {10.1093/bioinformatics/btw217},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford},
YEAR = {2016},
DATE = {2016},
JOURNAL = {Bioinformatics},
VOLUME = {32},
NUMBER = {11},
PAGES = {1670--1677},
}
Endnote
%0 Journal Article
%A Durai, Dilip Ariyur
%A Schulz, Marcel H.
%+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
%T Informed kmer Selection for de novo Transcriptome Assembly :
%G eng
%U http://hdl.handle.net/11858/00-001M-0000-002A-F53A-5
%R 10.1093/bioinformatics/btw217
%2 PMC4892416
%7 2016
%D 2016
%J Bioinformatics
%V 32
%N 11
%& 1670
%P 1670 - 1677
%I Oxford University Press
%C Oxford
%@ false
207. 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.
Export
BibTeX
@article{Durek2016,
TITLE = {Epigenomic Profiling of Human {CD4}+ {T} Cells Supports a Linear Differentiation Model and Highlights Molecular Regulators of Memory Development},
AUTHOR = {Durek, Pawel and Nordstr{\"o}m, Karl and Gasparoni, Gilles and Salhab, Abdulrahman and Kressler, Christopher and de Almeida, Melanie and Bassler, Kevin and Ulas, Thomas and Schmidt, Florian and Xiong, Jieyi and Gla{\v z}ar, Petar and Klironomos, Filippos and Sinha, Anupam and Kinkley, Sarah and Yang, Xinyi and Arrigoni, Laura and Dheghani Amirabad, Azim and Behjati Ardakani, Fatemeh and Feuerbach, Lars and Gorka, Oliver and Ebert, Peter and M{\"u}ller, Fabian and Li, Na and Frischbutter, Stefan and Schlickeiser, Stephan and Cendon, Carla and Fr{\"o}hler, Sebastian and Felder, B{\"a}rbel and Gasparoni, Nina and Imbusch, Charles D. and Hutter, Barbara and Zipprich, Gideon and Tauchmann, Yvonne and Reinke, Simon and Wassilew, Georgi and Hoffmann, Ute and Richter, Andreas S. and Sieverling, Lina and {DEEP Consortium} and Chang, Hyun-Dong and Syrbe, Uta and Kalus, Ulrich and Eils, J{\"u}rgen and Brors, Benedikt and Manke, Thomas and Ruland, J{\"u}rgen and Lengauer, Thomas and Rajewsky, Nikolaus and Chen, Wei and Dong, Jun and Sawitzki, Birgit and Chung, Ho-Ryun and Rosenstiel, Philip and Schulz, Marcel H. and Schultze, Joachim L. and Radbruch, Andreas and Walter, J{\"o}rn and Hamann, Alf and Polansky, Julia K.},
LANGUAGE = {eng},
ISSN = {1074-7613},
DOI = {10.1016/j.immuni.2016.10.022},
PUBLISHER = {Cell Press},
ADDRESS = {Cambridge, Mass.},
YEAR = {2016},
DATE = {2016},
JOURNAL = {Immunity},
VOLUME = {45},
NUMBER = {5},
PAGES = {1148--1161},
}
Endnote
%0 Journal Article
%A Durek, Pawel
%A Nordström, Karl
%A Gasparoni, Gilles
%A Salhab, Abdulrahman
%A Kressler, Christopher
%A de Almeida, Melanie
%A Bassler, Kevin
%A Ulas, Thomas
%A Schmidt, Florian
%A Xiong, Jieyi
%A Glažar, Petar
%A Klironomos, Filippos
%A Sinha, Anupam
%A Kinkley, Sarah
%A Yang, Xinyi
%A Arrigoni, Laura
%A Dheghani Amirabad, Azim
%A Behjati Ardakani, Fatemeh
%A Feuerbach, Lars
%A Gorka, Oliver
%A Ebert, Peter
%A Müller, Fabian
%A Li, Na
%A Frischbutter, Stefan
%A Schlickeiser, Stephan
%A Cendon, Carla
%A Fröhler, Sebastian
%A Felder, Bärbel
%A Gasparoni, Nina
%A Imbusch, Charles D.
%A Hutter, Barbara
%A Zipprich, Gideon
%A Tauchmann, Yvonne
%A Reinke, Simon
%A Wassilew, Georgi
%A Hoffmann, Ute
%A Richter, Andreas S.
%A Sieverling, Lina
%A DEEP Consortium,
%A Chang, Hyun-Dong
%A Syrbe, Uta
%A Kalus, Ulrich
%A Eils, Jürgen
%A Brors, Benedikt
%A Manke, Thomas
%A Ruland, Jürgen
%A Lengauer, Thomas
%A Rajewsky, Nikolaus
%A Chen, Wei
%A Dong, Jun
%A Sawitzki, Birgit
%A Chung, Ho-Ryun
%A Rosenstiel, Philip
%A Schulz, Marcel H.
%A Schultze, Joachim L.
%A Radbruch, Andreas
%A Walter, Jörn
%A Hamann, Alf
%A Polansky, Julia K.
%+ External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
%T Epigenomic Profiling of Human CD4+ T Cells Supports a Linear Differentiation Model and Highlights Molecular Regulators of Memory Development :
%G eng
%U http://hdl.handle.net/11858/00-001M-0000-002C-2DF6-1
%R 10.1016/j.immuni.2016.10.022
%7 2016
%D 2016
%J Immunity
%V 45
%N 5
%& 1148
%P 1148 - 1161
%I Cell Press
%C Cambridge, Mass.
%@ false
208. 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.
Export
BibTeX
@article{Farlik:2016ig,
TITLE = {{DNA} Methylation Dynamics of Human Hematopoietic Stem Cell Differentiation},
AUTHOR = {Farlik, Matthias and Halbritter, Florian and M{\"u}ller, Fabian and Choudry, Fizzah A. and Ebert, Peter and Klughammer, Johanna and Farrow, Samantha and Santoro, Antonella and Ciaurro, Valerio and Mathur, Anthony and Uppal, Rakesh and Stunnenberg, Hendrik G. and Ouwehand, Willem H. and Laurenti, Elisa and Lengauer, Thomas and Frontini, Mattia and Bock, Christoph},
LANGUAGE = {eng},
ISSN = {1875-9777},
DOI = {10.1016/j.stem.2016.10.019},
PUBLISHER = {Elsevier},
ADDRESS = {Amsterdam},
YEAR = {2016},
DATE = {2016},
JOURNAL = {Cell Stem Cell},
VOLUME = {19},
NUMBER = {6},
PAGES = {808--822},
}
Endnote
%0 Journal Article
%A Farlik, Matthias
%A Halbritter, Florian
%A Müller, Fabian
%A Choudry, Fizzah A.
%A Ebert, Peter
%A Klughammer, Johanna
%A Farrow, Samantha
%A Santoro, Antonella
%A Ciaurro, Valerio
%A Mathur, Anthony
%A Uppal, Rakesh
%A Stunnenberg, Hendrik G.
%A Ouwehand, Willem H.
%A Laurenti, Elisa
%A Lengauer, Thomas
%A Frontini, Mattia
%A Bock, Christoph
%+ External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
%T DNA Methylation Dynamics of Human Hematopoietic Stem Cell Differentiation :
%G eng
%U http://hdl.handle.net/11858/00-001M-0000-002C-2094-5
%R 10.1016/j.stem.2016.10.019
%7 2016-11-17
%D 2016
%J Cell Stem Cell
%V 19
%N 6
%& 808
%P 808 - 822
%I Elsevier
%C Amsterdam
%@ false
209. Fischer S: Selecting Reads for Haplotype Phasing. Universität des Saarlandes; 2016.
Export
BibTeX
@mastersthesis{FischerMSc2016,
TITLE = {Selecting Reads for Haplotype Phasing},
AUTHOR = {Fischer, Sarah},
LANGUAGE = {eng},
SCHOOL = {Universit{\"a}t des Saarlandes},
ADDRESS = {Saarbr{\"u}cken},
YEAR = {2016},
DATE = {2016},
}
Endnote
%0 Thesis
%A Fischer, Sarah
%+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
%T Selecting Reads for Haplotype Phasing :
%G eng
%U http://hdl.handle.net/11858/00-001M-0000-002C-4839-8
%I Universität des Saarlandes
%C Saarbrücken
%D 2016
%V master
%9 master
210. Forster J: Inferring Horizontal Gene Transfer from NGS Data. Universität des Saarlandes; 2016.
Export
BibTeX
@mastersthesis{ForsterMSc2016,
TITLE = {Inferring Horizontal Gene Transfer from {NGS} Data},
AUTHOR = {Forster, Jan},
LANGUAGE = {eng},
SCHOOL = {Universit{\"a}t des Saarlandes},
ADDRESS = {Saarbr{\"u}cken},
YEAR = {2016},
DATE = {2016},
}
Endnote
%0 Thesis
%A Forster, Jan
%+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
%T Inferring Horizontal Gene Transfer from NGS Data :
%G eng
%U http://hdl.handle.net/11858/00-001M-0000-002C-4845-C
%I Universität des Saarlandes
%C Saarbrücken
%D 2016
%V master
%9 master
211. 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.
Export
BibTeX
@article{Gapp2016,
TITLE = {Parallel Reverse Genetic Screening in Mutant Human Cells Using Transcriptomics},
AUTHOR = {Gapp, Bianca V. and Konopka, Tomasz and Penz, Thomas and Dalal, Vineet and B{\"u}rckst{\"u}mmer, Tilmann and Bock, Christoph and Nijman, Sebastian M. B.},
LANGUAGE = {eng},
ISSN = {1744-4292},
DOI = {10.15252/msb.20166890},
PUBLISHER = {Nature Pub. Group},
ADDRESS = {London},
YEAR = {2016},
JOURNAL = {Molecular Systems Biology},
VOLUME = {12},
NUMBER = {8},
EID = {879},
}
Endnote
%0 Journal Article
%A Gapp, Bianca V.
%A Konopka, Tomasz
%A Penz, Thomas
%A Dalal, Vineet
%A Bürckstümmer, Tilmann
%A Bock, Christoph
%A Nijman, Sebastian M. B.
%+ External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
%T Parallel Reverse Genetic Screening in Mutant Human Cells Using Transcriptomics :
%G eng
%U http://hdl.handle.net/11858/00-001M-0000-002B-5503-8
%R 10.15252/msb.20166890
%7 2016-08-01
%D 2016
%8 01.08.2016
%J Molecular Systems Biology
%V 12
%N 8
%Z sequence number: 879
%I Nature Pub. Group
%C London
%@ false
212. Garg S, Martin M, Marschall T: Read-based Phasing of Related Individuals. Bioinformatics (Proc ISMB 2016) 2016, 32.
Export
BibTeX
@article{GargMarschall2016,
TITLE = {Read-based Phasing of Related Individuals},
AUTHOR = {Garg, Shilpa and Martin, Marcel and Marschall, Tobias},
LANGUAGE = {eng},
ISSN = {1367-4803},
DOI = {10.1093/bioinformatics/btw276},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford},
YEAR = {2016},
DATE = {2016},
JOURNAL = {Bioinformatics (Proc. ISMB)},
VOLUME = {32},
NUMBER = {12},
PAGES = {i234--i242},
BOOKTITLE = {ISMB 2016 Proceedings},
EDITOR = {Baldi, Pierre and Przytycka, Teresa},
}
Endnote
%0 Journal Article
%A Garg, Shilpa
%A Martin, Marcel
%A Marschall, Tobias
%+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
%T Read-based Phasing of Related Individuals :
%G eng
%U http://hdl.handle.net/11858/00-001M-0000-002A-F931-A
%R 10.1093/bioinformatics/btw276
%2 PMC4908360
%7 2016
%D 2016
%J Bioinformatics
%V 32
%N 12
%& i234
%P i234 - i242
%I Oxford University Press
%C Oxford
%@ false
%B ISMB 2016 Proceedings
%O July 8 to July 12, 2016, Orlando, Florida 24th Annual Conference Intelligent Systems for Molecular Biology ISMB 2016
213. 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.
Export
BibTeX
@article{Goetz2016,
TITLE = {Two Sets of {RNA}i Components are Required for Heterochromatin Formation \textsl{in trans} Triggered by Truncated Transgenes},
AUTHOR = {G{\"o}tz, Ulrike and Marker, Simone and Cheaib, Miriam and Andresen, Karsten and Shrestha, Simon and Durai, Dilip Ariyur and Nordstr{\"o}m, Karl and Schulz, Marcel H. and Simon, Martin},
LANGUAGE = {eng},
ISSN = {0301-5610},
DOI = {10.1093/nar/gkw267},
YEAR = {2016},
DATE = {2016},
JOURNAL = {Nucleic Acids Research},
VOLUME = {44},
NUMBER = {12},
PAGES = {5908--5923},
}
Endnote
%0 Journal Article
%A Götz, Ulrike
%A Marker, Simone
%A Cheaib, Miriam
%A Andresen, Karsten
%A Shrestha, Simon
%A Durai, Dilip Ariyur
%A Nordström, Karl
%A Schulz, Marcel H.
%A Simon, Martin
%+ External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
%T Two Sets of RNAi Components are Required for Heterochromatin Formation in Trans Triggered by Truncated Transgenes :
%G eng
%U http://hdl.handle.net/11858/00-001M-0000-002B-16B8-E
%R 10.1093/nar/gkw267
%7 2016
%D 2016
%J Nucleic Acids Research
%O Nucleic Acids Res.
%V 44
%N 12
%& 5908
%P 5908 - 5923
%@ false
214. 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).
Export
BibTeX
@article{Gress_Buech_Kalinina2016,
TITLE = {{StructMAn}: {A}nnotation of Single-nucleotide Polymorphisms in the Structural Context},
AUTHOR = {Gress, Alexander and Ramensky, Vasily and B{\"u}ch, Joachim and Keller, Andreas and Kalinina, Olga V.},
LANGUAGE = {eng},
DOI = {10.1093/nar/gkw364},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford, UK},
YEAR = {2016},
DATE = {2016},
JOURNAL = {Nucleic Acids Research},
VOLUME = {44},
NUMBER = {W1/Web Server issue},
PAGES = {W463--W468},
}
Endnote
%0 Journal Article
%A Gress, Alexander
%A Ramensky, Vasily
%A Büch, Joachim
%A Keller, Andreas
%A Kalinina, Olga V.
%+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
%T StructMAn: Annotation of Single-nucleotide Polymorphisms in the Structural Context :
%G eng
%U http://hdl.handle.net/11858/00-001M-0000-002B-42A2-6
%R 10.1093/nar/gkw364
%2 PMC4987916
%7 2016
%D 2016
%* Review method: peer-reviewed
%J Nucleic Acids Research
%V 44
%N W1/Web Server issue
%& W463
%P W463 - W468
%I Oxford University Press
%C Oxford, UK
215. 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.
Export
BibTeX
@online{HandlarXiv2016,
TITLE = {Partially Blind Domain Adaptation for Age Prediction from {DNA} Methylation Data},
AUTHOR = {Handl, Lisa and Jalali, Adrin and Scherer, Michael and Pfeifer, Nico},
LANGUAGE = {eng},
URL = {http://arxiv.org/abs/1612.06650},
EPRINT = {1612.06650},
EPRINTTYPE = {arXiv},
YEAR = {2016},
ABSTRACT = {Over the last years, huge resources of biological and medical data have become available for research. This data offers great chances for machine learning applications in health care, e.g. for precision medicine, but is also challenging to analyze. Typical challenges include a large number of possibly correlated features and heterogeneity in the data. One flourishing field of biological research in which this is relevant is epigenetics. Here, especially large amounts of DNA methylation data have emerged. This epigenetic mark has been used to predict a donor's 'epigenetic age' and increased epigenetic aging has been linked to lifestyle and disease history. In this paper we propose an adaptive model which performs feature selection for each test sample individually based on the distribution of the input data. The method can be seen as partially blind domain adaptation. We apply the model to the problem of age prediction based on DNA methylation data from a variety of tissues, and compare it to a standard model, which does not take heterogeneity into account. The standard approach has particularly bad performance on one tissue type on which we show substantial improvement with our new adaptive approach even though no samples of that tissue were part of the training data.},
}
Endnote
%0 Report
%A Handl, Lisa
%A Jalali, Adrin
%A Scherer, Michael
%A Pfeifer, Nico
%+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
%T Partially Blind Domain Adaptation for Age Prediction from DNA
Methylation Data :
%G eng
%U http://hdl.handle.net/11858/00-001M-0000-002C-4CDD-3
%U http://arxiv.org/abs/1612.06650
%D 2016
%X Over the last years, huge resources of biological and medical data have
become available for research. This data offers great chances for machine
learning applications in health care, e.g. for precision medicine, but is also
challenging to analyze. Typical challenges include a large number of possibly
correlated features and heterogeneity in the data. One flourishing field of
biological research in which this is relevant is epigenetics. Here, especially
large amounts of DNA methylation data have emerged. This epigenetic mark has
been used to predict a donor's 'epigenetic age' and increased epigenetic aging
has been linked to lifestyle and disease history. In this paper we propose an
adaptive model which performs feature selection for each test sample
individually based on the distribution of the input data. The method can be
seen as partially blind domain adaptation. We apply the model to the problem of
age prediction based on DNA methylation data from a variety of tissues, and
compare it to a standard model, which does not take heterogeneity into account.
The standard approach has particularly bad performance on one tissue type on
which we show substantial improvement with our new adaptive approach even
though no samples of that tissue were part of the training data.
%K Quantitative Biology, Quantitative Methods, q-bio.QM,Statistics, Machine Learning, stat.ML
216. Hauschild A-C: Computational Methods for Breath Metabolomics in Clinical Diagnostics. Universität des Saarlandes; 2016.
Export
BibTeX
@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},
DOI = {10.22028/D291-26662},
SCHOOL = {Universit{\"a}t des Saarlandes},
ADDRESS = {Saarbr{\"u}cken},
YEAR = {2016},
DATE = {2016},
}
Endnote
%0 Thesis
%A Hauschild, Anne-Christin
%Y Helms, Volkhard
%A referee: Baumbach, Jan
%+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
International Max Planck Research School, MPI for Informatics, Max Planck Society
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
%T Computational Methods for Breath Metabolomics in Clinical Diagnostics :
%G eng
%U http://hdl.handle.net/11858/00-001M-0000-002B-0C18-7
%U urn:nbn:de:bsz:291-scidok-65874
%R 10.22028/D291-26662
%F OTHER: hdl:20.500.11880/26718
%I Universität des Saarlandes
%C Saarbrücken
%D 2016
%P 188 p.
%V phd
%9 phd
%U http://scidok.sulb.uni-saarland.de/volltexte/2016/6587/http://scidok.sulb.uni-saarland.de/doku/lic_ohne_pod.php?la=de
217. 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.
Export
BibTeX
@article{Heger_Theis2016,
TITLE = {Development of a Phenotypic Susceptibility Assay for {HIV}-1 Integrase Inhibitors},
AUTHOR = {Heger, Eva and Theis, Alexandra Andr{\'e}e and Remmel, Klaus and Walter, Hauke and Pironti, Alejandro and Knops, Elena and Cristanziano, Veronica Di and Jensen, Bj{\"o}rn and Esser, Stefan and Kaiser, Rolf and L{\"u}bke, Nadine},
LANGUAGE = {eng},
ISSN = {0166-0934},
DOI = {10.1016/j.jviromet.2016.10.002},
PUBLISHER = {Elsevier},
ADDRESS = {Amsterdam},
YEAR = {2016},
DATE = {2016},
JOURNAL = {Journal of Virological Methods},
VOLUME = {238},
PAGES = {29--37},
}
Endnote
%0 Journal Article
%A Heger, Eva
%A Theis, Alexandra Andrée
%A Remmel, Klaus
%A Walter, Hauke
%A Pironti, Alejandro
%A Knops, Elena
%A Cristanziano, Veronica Di
%A Jensen, Björn
%A Esser, Stefan
%A Kaiser, Rolf
%A Lübke, Nadine
%+ External Organizations
External Organizations
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
%T Development of a Phenotypic Susceptibility Assay for HIV-1 Integrase Inhibitors :
%G eng
%U http://hdl.handle.net/11858/00-001M-0000-002C-2DCF-E
%R 10.1016/j.jviromet.2016.10.002
%7 2016
%D 2016
%J Journal of Virological Methods
%V 238
%& 29
%P 29 - 37
%I Elsevier
%C Amsterdam
%@ false
218. 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.
Export
BibTeX
@article{Hehir-Kwa2016,
TITLE = {A High-quality Human Reference Panel Reveals the Complexity and Distribution of Genomic Structural Variants},
AUTHOR = {Hehir-Kwa, Jayne Y. and Marschall, Tobias and Kloosterman, Wigard P. and Francioli, Laurent C. and Baaijens, Jasmijn A. and Dijkstra, Louis J. and Abdellaoui, Abdel and Koval, Vyacheslav and Thung, Dije Tiwan and Wardenaar, Ren{\'e} and Renkens, Ivo and Coe, Bradley P. and Deelen, Patrick and de Ligt, Joep and Lameijer, Eric-Wubbo and van Dijk, Freerk and Hormozdiari, Fereydoun and Uitterlinden, Andr{\'e} G. and van Duijn, Cornelia M. and Eichler, Evan E. and de Bakker, Paul I. W. and Swertz, Morris A. and Wijmenga, Cisca and van Ommen, Gert-Jan and Slagboom, Eline and Boomsma, Dorret I. and Sch{\"o}nhuth, Alexander and Ye, Kai and Guryev, Victor},
LANGUAGE = {eng},
ISSN = {2041-1723},
DOI = {10.1038/ncomms12989},
PUBLISHER = {Nature Publishing Group},
ADDRESS = {London},
YEAR = {2016},
JOURNAL = {Nature Communications},
VOLUME = {7},
EID = {12989},
}
Endnote
%0 Journal Article
%A Hehir-Kwa, Jayne Y.
%A Marschall, Tobias
%A Kloosterman, Wigard P.
%A Francioli, Laurent C.
%A Baaijens, Jasmijn A.
%A Dijkstra, Louis J.
%A Abdellaoui, Abdel
%A Koval, Vyacheslav
%A Thung, Dije Tiwan
%A Wardenaar, René
%A Renkens, Ivo
%A Coe, Bradley P.
%A Deelen, Patrick
%A de Ligt, Joep
%A Lameijer, Eric-Wubbo
%A van Dijk, Freerk
%A Hormozdiari, Fereydoun
%A Uitterlinden, André G.
%A van Duijn, Cornelia M.
%A Eichler, Evan E.
%A de Bakker, Paul I. W.
%A Swertz, Morris A.
%A Wijmenga, Cisca
%A van Ommen, Gert-Jan
%A Slagboom, Eline
%A Boomsma, Dorret I.
%A Schönhuth, Alexander
%A Ye, Kai
%A Guryev, Victor
%+ External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
%T A High-quality Human Reference Panel Reveals the Complexity and Distribution of Genomic Structural Variants :
%G eng
%U http://hdl.handle.net/11858/00-001M-0000-002B-AF0A-B
%R 10.1038/ncomms12989
%7 2016
%D 2016
%J Nature Communications
%O Nat. Commun.
%V 7
%Z sequence number: 12989
%I Nature Publishing Group
%C London
%@ false
219. 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.
Export
BibTeX
@article{Heller2016,
TITLE = {Next-generation sequencing identifies major {DNA} methylation changes during progression of {Ph}+ chronic myeloid leukemia},
AUTHOR = {Heller, G. and Topakian, T. and Altenberger, C. and Cerny-Reiterer, S. and Herndlhofer, S. and Ziegler, B. and Datlinger, P. and Byrgazov, K. and Bock, Christoph and Mannhalter, C. and H{\"o}rmann, G. and Sperr, W. R. and Lion, T. and Zielinski, C. C. and Valent, P. and Z{\"o}chbauer-M{\"u}ller, S.},
LANGUAGE = {eng},
ISSN = {0887-6924},
DOI = {10.1038/leu.2016.143},
PUBLISHER = {NPG},
ADDRESS = {London},
YEAR = {2016},
DATE = {2016},
JOURNAL = {Leukemia},
VOLUME = {30},
PAGES = {1861--1868},
}
Endnote
%0 Journal Article
%A Heller, G.
%A Topakian, T.
%A Altenberger, C.
%A Cerny-Reiterer, S.
%A Herndlhofer, S.
%A Ziegler, B.
%A Datlinger, P.
%A Byrgazov, K.
%A Bock, Christoph
%A Mannhalter, C.
%A Hörmann, G.
%A Sperr, W. R.
%A Lion, T.
%A Zielinski, C. C.
%A Valent, P.
%A Zöchbauer-Müller, S.
%+ External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
%T Next-generation Sequencing Identifies Major DNA Methylation Changes during Progression of Ph+ Chronic Myeloid Leukemia :
%G eng
%U http://hdl.handle.net/11858/00-001M-0000-002B-9AEC-3
%R 10.1038/leu.2016.143
%7 2016-06-17
%D 2016
%J Leukemia
%V 30
%& 1861
%P 1861 - 1868
%I NPG
%C London
%@ false
220. Jalali A, Pfeifer N: Interpretable Per Case Weighted Ensemble Method for Cancer Associations. BMC Genomics 2016, 17.
Export
BibTeX
@article{JalaliPfeifer2016,
TITLE = {Interpretable Per Case Weighted Ensemble Method for Cancer Associations},
AUTHOR = {Jalali, Adrin and Pfeifer, Nico},
LANGUAGE = {eng},
ISSN = {1471-2164},
DOI = {10.1186/s12864-016-2647-9},
PUBLISHER = {BioMed Central},
ADDRESS = {London},
YEAR = {2016},
JOURNAL = {BMC Genomics},
VOLUME = {17},
EID = {501},
}
Endnote
%0 Journal Article
%A Jalali, Adrin
%A Pfeifer, Nico
%+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
%T Interpretable Per Case Weighted Ensemble Method for Cancer Associations :
%G eng
%U http://hdl.handle.net/11858/00-001M-0000-002B-16A3-D
%R 10.1186/s12864-016-2647-9
%7 2016
%D 2016
%J BMC Genomics
%V 17
%Z sequence number: 501
%I BioMed Central
%C London
%@ false
221. Kalaghatgi P, Pfeifer N, Lengauer T: Family-Joining: A Fast Distance-Based Method for Constructing Generally Labeled Trees. Molecular Biology and Evolution 2016, 33.
Export
BibTeX
@article{Kalaghatgi2016,
TITLE = {Family-Joining: A Fast Distance-Based Method for Constructing Generally Labeled Trees},
AUTHOR = {Kalaghatgi, Prabhav and Pfeifer, Nico and Lengauer, Thomas},
LANGUAGE = {eng},
ISSN = {0737-4038},
DOI = {10.1093/molbev/msw123},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford},
YEAR = {2016},
DATE = {2016},
JOURNAL = {Molecular Biology and Evolution},
VOLUME = {33},
NUMBER = {10},
PAGES = {2720--2734},
}
Endnote
%0 Journal Article
%A Kalaghatgi, Prabhav
%A Pfeifer, Nico
%A Lengauer, Thomas
%+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
%T Family-Joining: A Fast Distance-Based Method for Constructing Generally Labeled Trees :
%G eng
%U http://hdl.handle.net/11858/00-001M-0000-002B-8268-E
%R 10.1093/molbev/msw123
%7 2016
%D 2016
%J Molecular Biology and Evolution
%O Mol. Biol. Evol.
%V 33
%N 10
%& 2720
%P 2720 - 2734
%I Oxford University Press
%C Oxford
%@ false
%U http://mbe.oxfordjournals.org/content/33/10/2720/suppl/DC1
222. 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.
Export
BibTeX
@article{KalaghatgiPLOSone2016,
TITLE = {{Geno2pheno} [{HCV}] -- A Web-based Interpretation System to Support Hepatitis {C} Treatment Decisions in the Era of Direct-Acting Antiviral Agents},
AUTHOR = {Kalaghatgi, Prabhav and Sikorski, Anna Maria and Knops, Elena and Rupp, Daniel and Sierra, Saleta and Heger, Eva and Neumann-Fraune, Maria and Beggel, Bastian and Walker, Andreas and Timm, J{\"o}rg and Walter, Hauke and Obermeier, Martin and Kaiser, Rolf and Bartenschlager, Ralf and Lengauer, Thomas},
LANGUAGE = {eng},
ISSN = {1932-6203},
DOI = {10.1371/journal.pone.0155869},
PUBLISHER = {Public Library of Science},
ADDRESS = {San Francisco, CA},
YEAR = {2016},
JOURNAL = {PLoS One},
VOLUME = {11},
NUMBER = {5},
EID = {e0155869},
}
Endnote
%0 Journal Article
%A Kalaghatgi, Prabhav
%A Sikorski, Anna Maria
%A Knops, Elena
%A Rupp, Daniel
%A Sierra, Saleta
%A Heger, Eva
%A Neumann-Fraune, Maria
%A Beggel, Bastian
%A Walker, Andreas
%A Timm, Jörg
%A Walter, Hauke
%A Obermeier, Martin
%A Kaiser, Rolf
%A Bartenschlager, Ralf
%A Lengauer, Thomas
%+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
%T Geno2pheno [HCV] -- A Web-based Interpretation System to Support Hepatitis C Treatment Decisions in the Era of Direct-Acting Antiviral Agents :
%G eng
%U http://hdl.handle.net/11858/00-001M-0000-002A-EB8A-2
%R 10.1371/journal.pone.0155869
%2 PMC4873220
%7 2016-05-19
%D 2016
%8 19.05.2016
%J PLoS One
%V 11
%N 5
%Z sequence number: e0155869
%I Public Library of Science
%C San Francisco, CA
%@ false
223. 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.
Export
BibTeX
@article{Kartashev2016,
TITLE = {New findings in {HCV} genotype distribution in selected {West European}, {Russian} and {Israeli} regions},
AUTHOR = {Kartashev, Vladimir and D{\"o}ring, Matthias and Nieto, Leonardo and Coletta, Eleda and Kaiser, Rolf and Sierra, Saleta},
LANGUAGE = {eng},
ISSN = {1386-6532},
DOI = {10.1016/j.jcv.2016.05.010},
PUBLISHER = {Elsevier},
ADDRESS = {Amsterdam},
YEAR = {2016},
DATE = {2016},
JOURNAL = {Journal of Clinical Virology},
VOLUME = {81},
PAGES = {82--89},
}
Endnote
%0 Journal Article
%A Kartashev, Vladimir
%A Döring, Matthias
%A Nieto, Leonardo
%A Coletta, Eleda
%A Kaiser, Rolf
%A Sierra, Saleta
%+ External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
External Organizations
External Organizations
External Organizations
%T New Findings in HCV Genotype Distribution in Selected West European, Russian and Israeli Regions :
%G eng
%U http://hdl.handle.net/11858/00-001M-0000-002A-F8EB-0
%R 10.1016/j.jcv.2016.05.010
%7 2016-05-24
%D 2016
%J Journal of Clinical Virology
%V 81
%& 82
%P 82 - 89
%I Elsevier
%C Amsterdam
%@ false
224. Keller S: Finding Common Substructures in Viral Proteins Using Frequent Subgraph Mining. Universität des Saarlandes; 2016.
Export
BibTeX
@mastersthesis{Keller2016,
TITLE = {Finding Common Substructures in Viral Proteins Using Frequent Subgraph Mining},
AUTHOR = {Keller, Sebastian},
LANGUAGE = {eng},
SCHOOL = {Universit{\"a}t des Saarlandes},
ADDRESS = {Saarbr{\"u}cken},
YEAR = {2016},
DATE = {2016},
}
Endnote
%0 Thesis
%A Keller, Sebastian
%+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
%T Finding Common Substructures in Viral Proteins Using Frequent Subgraph Mining :
%G eng
%U http://hdl.handle.net/11858/00-001M-0000-002C-2881-6
%I Universität des Saarlandes
%C Saarbrücken
%D 2016
%V master
%9 master
225. 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.
Export
BibTeX
@article{Lawyer2016BMC,
TITLE = {Measuring the Potential of Individual Airports for Pandemic Spread over the World Airline Network},
AUTHOR = {Lawyer, Glenn},
LANGUAGE = {eng},
ISSN = {1471-2334},
DOI = {10.1186/s12879-016-1350-4},
PUBLISHER = {BioMed Central Ltd.},
ADDRESS = {London, UK},
YEAR = {2016},
ABSTRACT = {ABSTRACT: BACKGROUND: Massive growth in human mobility has dramatically increased the risk and rate of pandemic spread. Macro-level descriptors of the topology of the World Airline Network (WAN) explains middle and late stage dynamics of pandemic spread mediated by this network, but necessarily regard early stage variation as stochastic. We propose that much of this early stage variation can be explained by appropriately characterizing the local network topology surrounding an outbreak{\textquoteright}s debut location. METHODS: Based on a model of the WAN derived from public data, we measure for each airport the expected force of infection (AEF) which a pandemic originating at that airport would generate, assuming an epidemic process which transmits from airport to airport via scheduled commercial flights. We observe, for a subset of world airports, the minimum transmission rate at which a disease becomes pandemically competent at each airport. We also observe, for a larger subset, the time until a pandemically competent outbreak achieves pandemic status given its debut location. Observations are generated using a highly sophisticated metapopulation reaction-diffusion simulator under a disease model known to well replicate the 2009 influenza pandemic. The robustness of the AEF measure to model misspecification is examined by degrading the underlying model WAN. RESULTS: AEF powerfully explains pandemic risk, showing correlation of 0.90 to the transmission level needed to give a disease pandemic competence, and correlation of 0.85 to the delay until an outbreak becomes a pandemic. The AEF is robust to model misspecification. For 97 % of airports, removing 15 % of airports from the model changes their AEF metric by less than 1 %. CONCLUSIONS: Appropriately summarizing the size, shape, and diversity of an airport{\textquoteright}s local neighborhood in the WAN accurately explains much of the macro-level stochasticity in pandemic outcomes.},
JOURNAL = {BMC Infectious Diseases},
VOLUME = {16},
NUMBER = {1},
EID = {70},
}
Endnote
%0 Journal Article
%A Lawyer, Glenn
%+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
%T Measuring the Potential of Individual Airports for Pandemic Spread over the World Airline Network :
%G eng
%U http://hdl.handle.net/11858/00-001M-0000-0029-C693-A
%R 10.1186/s12879-016-1350-4
%7 2016-02-09
%D 2016
%8 09.02.2016
%X ABSTRACT: BACKGROUND: Massive growth in human mobility has dramatically increased the risk and rate of pandemic spread. Macro-level descriptors of the topology of the World Airline Network (WAN) explains middle and late stage dynamics of pandemic spread mediated by this network, but necessarily regard early stage variation as stochastic. We propose that much of this early stage variation can be explained by appropriately characterizing the local network topology surrounding an outbreak’s debut location. METHODS: Based on a model of the WAN derived from public data, we measure for each airport the expected force of infection (AEF) which a pandemic originating at that airport would generate, assuming an epidemic process which transmits from airport to airport via scheduled commercial flights. We observe, for a subset of world airports, the minimum transmission rate at which a disease becomes pandemically competent at each airport. We also observe, for a larger subset, the time until a pandemically competent outbreak achieves pandemic status given its debut location. Observations are generated using a highly sophisticated metapopulation reaction-diffusion simulator under a disease model known to well replicate the 2009 influenza pandemic. The robustness of the AEF measure to model misspecification is examined by degrading the underlying model WAN. RESULTS: AEF powerfully explains pandemic risk, showing correlation of 0.90 to the transmission level needed to give a disease pandemic competence, and correlation of 0.85 to the delay until an outbreak becomes a pandemic. The AEF is robust to model misspecification. For 97 % of airports, removing 15 % of airports from the model changes their AEF metric by less than 1 %. CONCLUSIONS: Appropriately summarizing the size, shape, and diversity of an airport’s local neighborhood in the WAN accurately explains much of the macro-level stochasticity in pandemic outcomes.
%J BMC Infectious Diseases
%V 16
%N 1
%Z sequence number: 70
%I BioMed Central Ltd.
%C London, UK
%@ false
226. 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.
Export
BibTeX
@article{Li2015EMBO,
TITLE = {Single-cell Transcriptomes Reveal Characteristic Features of Human Pancreatic Islet Cell Types},
AUTHOR = {Li, Jin and Klughammer, Johanna and Farlik, Matthias and Penz, Thomas and Spittler, Andreas and Barbieux, Charlotte and Berishvili, Ekaterine and Bock, Christoph and Kubicek, Stefan},
LANGUAGE = {eng},
ISSN = {1469-221X},
DOI = {10.15252/embr.201540946},
PUBLISHER = {Published for EMBO by Oxford University Press},
ADDRESS = {Oxford, UK},
YEAR = {2016},
DATE = {2016},
JOURNAL = {EMBO Reports},
VOLUME = {17},
NUMBER = {2},
PAGES = {178--187},
}
Endnote
%0 Journal Article
%A Li, Jin
%A Klughammer, Johanna
%A Farlik, Matthias
%A Penz, Thomas
%A Spittler, Andreas
%A Barbieux, Charlotte
%A Berishvili, Ekaterine
%A Bock, Christoph
%A Kubicek, Stefan
%+ External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
%T Single-cell Transcriptomes Reveal Characteristic Features of Human Pancreatic Islet Cell Types :
%G eng
%U http://hdl.handle.net/11858/00-001M-0000-0029-4243-A
%R 10.15252/embr.201540946
%7 2015-12-21
%D 2016
%J EMBO Reports
%O EMBO Rep.
%V 17
%N 2
%& 178
%P 178 - 187
%I Published for EMBO by Oxford University Press
%C Oxford, UK
%@ false
%U http://onlinelibrary.wiley.com/doi/10.15252/embr.201540946/pdf
227. 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).
Export
BibTeX
@article{List:Baumbach2016,
TITLE = {{KeyPathwayMinerWeb}: {O}nline Multi-omics Network Enrichment},
AUTHOR = {List, Markus and Alcaraz, Nicolas and Dissing-Hansen, Martin and Ditzel, Henrik J. and Mollenhauer, Jan and Baumbach, Jan},
LANGUAGE = {eng},
DOI = {10.1093/nar/gkw373},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford, UK},
YEAR = {2016},
DATE = {2016},
JOURNAL = {Nucleic Acids Research},
VOLUME = {44},
NUMBER = {W1/Web Server issue},
PAGES = {W98--W104},
}
Endnote
%0 Journal Article
%A List, Markus
%A Alcaraz, Nicolas
%A Dissing-Hansen, Martin
%A Ditzel, Henrik J.
%A Mollenhauer, Jan
%A Baumbach, Jan
%+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
External Organizations
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
%T KeyPathwayMinerWeb: Online Multi-omics Network Enrichment :
%G eng
%U http://hdl.handle.net/11858/00-001M-0000-002B-42F8-8
%R 10.1093/nar/gkw373
%2 PMC4987922
%7 2016
%D 2016
%* Review method: peer-reviewed
%J Nucleic Acids Research
%V 44
%N W1/Web Server issue
%& W98
%P W98 - W104
%I Oxford University Press
%C Oxford, UK
228. 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.
Export
BibTeX
@article{ListNAR2016,
TITLE = {Comprehensive analysis of high-throughput screens with {HiTSeekR}},
AUTHOR = {List, Markus and Schmidt, Steffen and Christiansen, Helle and Rehmsmeier, Marc and Tan, Oihua and Mollenhauer, Jan and Baumbach, Jan},
LANGUAGE = {eng},
ISSN = {0301-5610},
DOI = {10.1093/nar/gkw554},
YEAR = {2016},
DATE = {2016},
JOURNAL = {Nucleic Acids Research},
VOLUME = {44},
NUMBER = {14},
PAGES = {6639--6648},
}
Endnote
%0 Journal Article
%A List, Markus
%A Schmidt, Steffen
%A Christiansen, Helle
%A Rehmsmeier, Marc
%A Tan, Oihua
%A Mollenhauer, Jan
%A Baumbach, Jan
%+ External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
%T Comprehensive Analysis of High-throughput Screens with HiTSeekR :
%G eng
%U http://hdl.handle.net/11858/00-001M-0000-002B-4666-3
%R 10.1093/nar/gkw554
%7 2016
%D 2016
%J Nucleic Acids Research
%O Nucleic Acids Res.
%V 44
%N 14
%& 6639
%P 6639 - 6648
%@ false
229. Lüssem H: Identifying Structural Variants Using Variant Graphs. Universität des Saarlandes; 2016.
Export
BibTeX
@mastersthesis{LuessemBachelor2016,
TITLE = {Identifying Structural Variants Using Variant Graphs},
AUTHOR = {L{\"u}ssem, Helene},
LANGUAGE = {eng},
SCHOOL = {Universit{\"a}t des Saarlandes},
ADDRESS = {Saarbr{\"u}cken},
YEAR = {2016},
DATE = {2016},
TYPE = {Bachelor's thesis},
}
Endnote
%0 Thesis
%A Lüssem, Helene
%+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
%T Identifying Structural Variants Using Variant Graphs :
%G eng
%U http://hdl.handle.net/11858/00-001M-0000-002C-480F-A
%I Universität des Saarlandes
%C Saarbrücken
%D 2016
%V bachelor
%9 bachelor
230. 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.
Export
BibTeX
@article{Magiorkinis2016,
TITLE = {The global spread of {HIV}-1 subtype {B} epidemic},
AUTHOR = {Magiorkinis, Gkikas and Angelis, Konstantinos and Mamais, Ioannis and Katzourakis, Aris and Hatzakis, Angelo and Albert, Jan and Lawyer, Glenn and Hamouda, Osamah and Struck, Daniel and Vercauteren, Jurgen and Wensing, Annemarie and Alexiev, Ivailo and {\AA}sj{\"o}, Birgitta and Balotta, Claudia and Gomes, Perp{\'e}tua and Camacho, Ricardo J. and Coughlan, Suzie and Griskevicius, Algirdas and Grossman, Zehava and Horban, Anders and Kostrikis, Leondios G. and Lepej, Snjezana J. and Liitsola, Kirsi and Linka, Marek and Nielsen, Claus and Otelea, Dan and Paredes, Roger and Poljak, Mario and Puchhammer-St{\"o}ckl, Elizabeth and Schmit, Jean Claude and S{\"o}nnerborg, Anders and Stanekov{\'a}, Danica and Stanojevic, Maja and Stylianou, Dora C. and Boucher, Charles A. B. and Nikolopoulos, Georgios and Vasylyeva, Tetyana and Friedman, Samuel R. and van de Vijver, David and Angarano, Gioacchino and Chaix, Marie-Laure and de Luca, Andrea and Korn, Klaus and Loveday, Clive and Soriano, Vincent and Yerly, Sabine and Zazzi, Mauricio and Vandamm, Anne-Mieke and Paraskevis, Dimitrios},
LANGUAGE = {eng},
DOI = {10.1016/j.meegid.2016.05.041},
PUBLISHER = {Elsevier},
ADDRESS = {Amsterdam},
YEAR = {2016},
DATE = {2016},
JOURNAL = {Infection, Genetics and Evolution},
VOLUME = {46},
PAGES = {169--179},
}
Endnote
%0 Journal Article
%A Magiorkinis, Gkikas
%A Angelis, Konstantinos
%A Mamais, Ioannis
%A Katzourakis, Aris
%A Hatzakis, Angelo
%A Albert, Jan
%A Lawyer, Glenn
%A Hamouda, Osamah
%A Struck, Daniel
%A Vercauteren, Jurgen
%A Wensing, Annemarie
%A Alexiev, Ivailo
%A Åsjö, Birgitta
%A Balotta, Claudia
%A Gomes, Perpétua
%A Camacho, Ricardo J.
%A Coughlan, Suzie
%A Griskevicius, Algirdas
%A Grossman, Zehava
%A Horban, Anders
%A Kostrikis, Leondios G.
%A Lepej, Snjezana J.
%A Liitsola, Kirsi
%A Linka, Marek
%A Nielsen, Claus
%A Otelea, Dan
%A Paredes, Roger
%A Poljak, Mario
%A Puchhammer-Stöckl, Elizabeth
%A Schmit, Jean Claude
%A Sönnerborg, Anders
%A Staneková, Danica
%A Stanojevic, Maja
%A Stylianou, Dora C.
%A Boucher, Charles A. B.
%A Nikolopoulos, Georgios
%A Vasylyeva, Tetyana
%A Friedman, Samuel R.
%A van de Vijver, David
%A Angarano, Gioacchino
%A Chaix, Marie-Laure
%A de Luca, Andrea
%A Korn, Klaus
%A Loveday, Clive
%A Soriano, Vincent
%A Yerly, Sabine
%A Zazzi, Mauricio
%A Vandamm, Anne-Mieke
%A Paraskevis, Dimitrios
%+ External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
External Organizations
%T The Global Spread of HIV-1 Subtype B Epidemic :
%G eng
%U http://hdl.handle.net/11858/00-001M-0000-002C-2F82-8
%R 10.1016/j.meegid.2016.05.041
%7 2016
%D 2016
%J Infection, Genetics and Evolution
%V 46
%& 169
%P 169 - 179
%I Elsevier
%C Amsterdam
231. Malek M, Ibragimov R, Albrecht M, Baumbach J: CytoGEDEVO-global Alignment of Biological Networks with Cytoscape. Bioinformatics 2016, 32.
Export
BibTeX
@article{Malek2016,
TITLE = {{CytoGEDEVO}-global alignment of biological networks with {Cytoscape}},
AUTHOR = {Malek, Maximilian and Ibragimov, Rashid and Albrecht, Mario and Baumbach, Jan},
LANGUAGE = {eng},
ISSN = {1367-4803},
DOI = {10.1093/bioinformatics/btv732},
PUBLISHER = {Oxford University Press},
ADDRESS = {Oxford},
YEAR = {2016},
DATE = {2016},
JOURNAL = {Bioinformatics},
VOLUME = {