%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

%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

%0 Thesis %A Hake, Anna %Y Pfeifer, Nico %A referee: Kalinina, Olga V. %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %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

%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

%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

%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

%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

%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

%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

%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

%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

%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

%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

%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

%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

%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

%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

%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

%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

%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

%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

%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

%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

%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

%0 Thesis %A Metzler, Saskia %Y Miettinen, Pauli %Y Weikum, Gerhard %Y G&#252;nnemann, 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 Universit&#228;t des Saarlandes %C Saarbr&#252;cken %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&#8211;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 &#8211; valid for many real-world data, in particular time-evolving networks &#8211; 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

%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

%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

%0 Journal Article %A Scherer, Michael %A Schmidt, Florian %A Lazareva, Olga %A Walter, J&#246;rn %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

%0 Thesis %A Scherer, Michael %Y Lengauer, Thomas %A referee: Walther, J&#246;rn %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 Universit&#228;t des Saarlandes %C Saarbr&#252;cken %D 2021 %P 147 p. %V phd %9 phd %U https://publikationen.sulb.uni-saarland.de/handle/20.500.11880/31186

%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, J&#246;rn %+ 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

%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 G&#246;ke, 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

%0 Conference Proceedings %A &#220;nal, Ali Burak %A Akg&#252;n, 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

%0 Journal Article %A Akg&#252;n, Mete %A &#220;nal, Ali Burak %A Erg&#252;ner, 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

%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

%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

%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

%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 Universit&#228;t des Saarlandes %C Saarbr&#252;cken %D 2020 %P 170 p. %V phd %9 phd %U https://publikationen.sulb.uni-saarland.de/handle/20.500.11880/29766

%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, Bj&#246;rn %A D&#246;ring, Matthias %A St&#252;rmer, Martin %A Rockstroh, J&#252;rgen %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

%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

%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

%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, Andr&#233; 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

%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 Sir&#233;n, 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

%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

%0 Journal Article %A Karunanithi, Sivarajan %A Oruganti, Vidya %A de Wijn, Raphael %A Drews, Franziska %A Cheaib, Miriam %A Nordstr&#246;m, 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

%0 Journal Article %A Kreer, Christoph %A D&#246;ring, 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

%0 Journal Article %A L&#228;hnemann, David %A K&#246;ster, 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 Sch&#246;nhuth, 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

%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

%0 Journal Article %A Porubsky, David %A Sanders, Ashley D. %A H&#246;ps, 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

%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

%0 Journal Article %A Rosser, Elizabeth C. %A Piper, Christopher J. M. %A Matei, Diana E. %A Blair, Paul A. %A Rendeiro, Andr&#233; 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

%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, J&#246;rn %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

%0 Journal Article %A Scherer, Michael %A Nebel, Almut %A Franke, Andre %A Walter, J&#246;rn %A Lengauer, Thomas %A Bock, Christoph %A M&#252;ller, 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

%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

%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

%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

%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

%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

%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

%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 H&#228;sler, 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

%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

%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

%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 Universit&#228;t des Saarlandes %C Saarbr&#252;cken %D 2019 %P 240 p. %V phd %9 phd %U https://publikationen.sulb.uni-saarland.de/handle/20.500.11880/28473

%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

%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

%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

%0 Journal Article %A De Luca, Andrea %A Pezzotti, Patrizio %A Boucher, Charles %A D&#246;ring, Matthias %A Incardona, Francesca %A Kaiser, Rolf %A Lengauer, Thomas %A Pfeifer, Nico %A Sch&#252;lter, 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

%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 Universit&#228;t des Saarlandes %C Saarbr&#252;cken %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

%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

%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

%0 Thesis %A D&#246;ring, 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 Universit&#228;t des Saarlandes %C Saarbr&#252;cken %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

%0 Journal Article %A D&#246;ring, 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, &#916;G, is the key driver of amplifcation (p=7.35e-12) and that<br>3&#8242; mismatches should be considered in dependence on &#916;G and the mismatch closest to the 3&#8242; 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

%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

%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 Universit&#228;t des Saarlandes %C Saarbr&#252;cken %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

%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

%0 Journal Article %A G&#233;rard, Deborah %A Schmidt, Florian %A Ginolhac, Aur&#233;lien %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

%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&#8211;25, 2019

%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

%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

%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

%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&#8211;25, 2019.

%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

%0 Journal Article %A Karunanithi, Sivarajan %A Oruganti, Vidya %A Marker, Simone %A Rodriguez-Viana, Angela M. %A Drews, Franziska %A Pirritano, Marcello %A Nordstr&#246;m, 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

%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

%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

%0 Journal Article %A Kr&#246;hler, 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 M&#252;ller, Rolf %A Helms, Volkhard %A Schulz, Marcel Holger %A Hoppst&#228;dter, 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

%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&#8211;25, 2019

%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

%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

%0 Journal Article %A M&#252;ller, Fabian %A Scherer, Michael %A Assenov, Yassen %A Lutsik, Pavlo %A Walter, J&#246;rn %A Lengauer, Thomas %A Bock, Christoph %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society 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

%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

%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 Universit&#228;t des Saarlandes %C Saarbr&#252;cken %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

%0 Journal Article %A Nordstr&#246;m, Karl J. V. %A Schmidt, Florian %A Gasparoni, Nina %A Salhab, Abdulrahman %A Gasparoni, Gilles %A Kattler, Kathrin %A M&#252;ller, Fabian %A Ebert, Peter %A Costa, Ivan G. %A DEEP Consortium, %A Pfeifer, Nico %A Lengauer, Thomas %A Schulz, Marcel Holger %A Walter, J&#246;rn %+ 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

%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 M&#252;ller, 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

%0 Journal Article %A Piper, Christopher J.M. %A Rosser, Elizabeth C. %A Oleinika, Kristine %A Nistala, Kiran %A Krausgruber, Thomas %A Rendeiro, Andr&#233; 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

%0 Journal Article %A Rautiainen, Mikko %A M&#228;kinen, 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

%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

%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

%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

%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

%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

%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

%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

%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

%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

%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

%0 Conference Proceedings %A &#220;nal, Ali Burak %A Akg&#252;n, 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

%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

%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

%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

%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

%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

%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

%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

%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 Universit&#228;t des Saarlandes %C Saarbr&#252;cken %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

%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.

%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

%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

%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

%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

%0 Journal Article %A D&#246;ring, Matthias %A B&#252;ch, Joachim %A Friedrich, Georg %A Pironti, Alejandro %A Kalaghatgi, Prabhav %A Knops, Elena %A Heger, Eva %A Obermeier, Martin %A D&#228;umer, 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

%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

%0 Journal Article %A Fr&#246;hlich, 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 R&#246;st, 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

%0 Journal Article %A Fun, Axel %A Leitner, Thomas %A Vandekerckhove, Linos %A D&#228;umer, 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

%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

%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 Universit&#228;t des Saarlandes %C Saarbr&#252;cken %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

%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

%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

%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

%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 &#8220;Killer Trait&#8221;: 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

%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

%0 Journal Article %A Hor&#328;&#225;kov&#225;, 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

%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

%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

%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

%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

%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

%0 Thesis %A Nazarieh, Maryam %Y Helms, Volker %A referee: Lengauer, Thomas %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T Understanding Regulatory Mechanisms Underlying Stem Cells Helps to Identify Cancer Biomarkers : %G eng %U http://hdl.handle.net/21.11116/0000-0001-9D69-9 %R 10.22028/D291-27265 %U urn:nbn:de:bsz:291-scidok-ds-272650 %F OTHER: hdl:20.500.11880/27104 %I Universit&#228;t des Saarlandes %C Saarbr&#252;cken %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

%0 Journal Article %A Palanisamy, Navaneethan %A Kalaghatgi, Prabhav %A Akaberi, Dario %A Lundkvist, &#197;ke %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

%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 M&#252;ller, 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

%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

%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

%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

%0 Journal Article %A Sikandar, Asfandyar %A Cirnski, Katarina %A Testolin, Giambattista %A Volz, Carsten %A Broenstrup, Mark %A Kalinina, Olga V. %A M&#252;ller, 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

%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

%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

%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

%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

%0 Journal Article %A Almeida, Diogo %A Skov, Ida %A Silva, Artur %A Vandin, Fabio %A Tan, Qihua %A R&#246;ttger, 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

%0 Journal Article %A Bader, Jo&#235;lle %A D&#228;umer, Martin %A Sch&#246;ni-Affolter, Franziska %A B&#246;ni, J&#252;rg %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

%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

%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&#8217;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

%0 Journal Article %A Busch, Clara Jana-Lui %A Hendrikx, Tim %A Weismann, David %A J&#228;ckel, Sven %A Walenbergh, Sofie M. A. %A Rendeiro, Andr&#233; F. %A Wei&#223;er, Juliane %A Puhm, Florian %A Hladik, Anastasiya %A G&#246;derle, 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

%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&#8217;Brien, Cecilia %A Weiland, Daniela %A Robles, Alexander %A K&#252;mmerle, 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 F&#228;tkenheuer, 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

%0 Journal Article %A Datlinger, Paul %A Rendeiro, Andr&#233; 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

%0 Journal Article %A Demirci, M&#252;&#351;erref Duygu Sa&#231;ar %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

%0 Journal Article %A Ebler, Jana %A Sch&#246;nhuth, 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

%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

%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

%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

%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

%0 Journal Article %A J&#252;hling, 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

%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

%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

%0 Journal Article %A Kehl, Tim %A Schneider, Lara %A Schmidt, Florian %A St&#246;ckel, 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

%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

%0 Journal Article %A Knops, Elena %A Sch&#252;bel, 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

%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 M&#252;ller, Andr&#233; C. %A Caldera, Michael %A Wagner, Anja %A Herzog, Rebecca %A Penz, Thomas %A Schuster, Michael %A Boidol, Bernd %A D&#252;rnberger, Gerhard %A Folkvaljon, Yasin %A Stattin, P&#228;r %A Ivanov, Vladimir %A Colinge, Jacques %A Bock, Christoph %A Kratochwill, Klaus %A Menche, J&#246;rg %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

%0 Journal Article %A Li, Jin %A Casteels, Tamara %A Frogne, Thomas %A Ingvorsen, Camilla %A Honor&#233;, 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, Fran&#231;ois %A Baburin, Igor %A M&#225;jek, 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-S&#248;rensen, 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 &#945; 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

%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

%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

%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

%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

%0 Thesis %A M&#252;ller, 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 Universit&#228;t des Saarlandes %C Saarbr&#252;cken %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

%0 Journal Article %A M&#252;ller, 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

%0 Journal Article %A Neogi, Ujjwal %A Siddik, Abu Bakar %A Kalaghatgi, Prabhav %A Gissl&#233;n, Magnus %A Bratt, G&#246;ran %A Marrone, Gaetano %A S&#246;nnerborg, 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

%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

%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

%0 Journal Article %A Pironti, Alejandro %A Walter, Hauke %A Pfeifer, Nico %A Knops, Elena %A L&#252;bke, Nadine %A B&#252;ch, 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

%0 Journal Article %A Pironti, Alejandro %A Pfeifer, Nico %A Walter, Hauke %A Jensen, Bj&#246;rn-Erik O. %A Zazzi, Maurizio %A Gomes, Perp&#233;tua %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 &#8211; 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

%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

%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 Nordstr&#246;m, Karl %A Barann, Matthias %A Sinha, Anupam %A Fr&#246;hler, Sebastian %A Xiong, Jieyi %A Dheghani Amirabad, Azim %A Behjati Ardakani, Fatemeh %A Hutter, Barbara %A Zipprich, Gideon %A Felder, B&#228;rbel %A Eils, J&#252;rgen %A Brors, Benedikt %A Chen, Wei %A Hengstler, Jan G. %A Hamann, Alf %A Lengauer, Thomas %A Rosenstiel, Philip %A Walter, J&#246;rn %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

%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, J&#246;rn %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

%0 Journal Article %A Sheffield, Nathan C. %A Pierron, Gaelle %A Klughammer, Johanna %A Datlinger, Paul %A Sch&#246;negger, 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 &#193;lava, 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, Val&#233;rie %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

%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 Universit&#228;t des Saarlandes %C Saarbr&#252;cken %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