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Year

Author(s) [non member]

Title

Type

Lucius, Ralph

2005

[Costello, Christine M.]
[Mah, Nancy]
[Häsler, Robert]
[Rosenstiel, Philip]
[Waetzig, Georg H.]
Hahn, Andreas
[Lu, Tim]
[Gurbuz, Yesim]
[Nikolaus, Susanna]
Albrecht, Mario
[Hampe, Jochen]
[Lucius, Ralph]
[Klöppel, Günther]
[Eickhoff, Holger]
[Lehrach, Hans]
Lengauer, Thomas
[Schreiber, Stefan]

Dissection of the inflammatory bowel disease transcriptome using genome-wide cDNA microarrays identifies novel candidate disease genes
In: PLoS Medicine [2], 771-787

Journal Article

Ludwig, Jost

2006

[Heil, Burkhard]
[Ludwig, Jost]
[Lichtenberg-Fraté, Hella]
Lengauer, Thomas

Computational recognition of potassium channel sequences
In: Bioinformatics [13], 1562-1568

Journal Article

Lundegaard, C.

2009

Adams, Ben
McHardy, Alice
[Lundegaard, C.]
Lengauer, Thomas

Viral Bioinformatics
In: Modern Genome Annotation - The BioSapiens Network, 429-452

Part of a Book

Lupas, Andrei (ed.)

2006

Schlicker, Andreas
Huthmacher, Carola
Ramírez, Fidel
Lengauer, Thomas
Albrecht, Mario

Functional evaluation of domain-domain interactions and human protein interaction networks
In: German Conference on Bioinformatics (GCB 2006), 115-126

Proceedings Article

Lurz, Rudi

2006

[Boeddrich, Annett]
[Gaumer, Sébastien]
[Haacke, Annette]
[Tzvetkov, Nikolay]
Albrecht, Mario
[Evert, Bernd O.]
[Müller, Eva C.]
[Lurz, Rudi]
[Breuer, Peter]
[Schugardt, Nancy]
[Plaßmann, Stephanie]
[Xu, Kexiang]
[Warrick, John M.]
[Suopanki, Jaana]
[Wüllner, Ullrich]
[Frank, Ronald]
[Hartl, Ulrich F.]
[Bonini, Nancy M.]
[Wanker, Erich E.]

An arginine/lysine-rich motif is crucial for VCP/p97-mediated modulation of ataxin-3 fibrillogenesis
In: EMBO Journal [25], 1547-1558

Journal Article

Lutsik, Pavlo

2011

[Lutsik, Pavlo]
Feuerbach, Lars
[Arand, Julia]
Lengauer, Thomas
[Walter, Jörn]
Bock, Christoph

BiQ Analyzer HT: locus-specific analysis of DNA methylation by high-throughput bisulfite sequencing
In: Nucleic Acids Research [39], W551-W556

Journal Article

2010

Lutsik, Pavlo

Processing of high-throughput DNA methylation data
Universität des Saarlandes

Thesis - Masters thesis

Luz, H.

2004

[Crass, T.]
Antes, Iris
[Basekow, R.]
[Bork, P.]
Buning, Christian
[Christensen, M.]
[Claußen, H.]
[Ebeling, C.]
[Ernst,P.]
[Gailus-Durner, V.]
[Glatting, K.-H.]
[Gohla, R.]
[Gößling, F.]
[Grote, K.]
[Heidtke, K.]
[Herrmann, A.]
[O Keefe, S.]
[Kießlich, O.]
[Kolibal, S.]
[Korbel, J.O.]
Lengauer, Thomas
[Liebich, I.]
[van der Linden, M.]
[Luz, H.]
[Meissner, K.]
[von Mering, C.]
[Mevissen, T.]
[Mewes, H.-W.]
[Michael, H.]
[Mokrejs, M.]
[Müller, T.]
[Pospisil, H.]
[Rarey, Matthias]
[Reich, J.G.]
[Schneider, R.]
[Schomburg, D.]
[Schulze-Kremer, S.]
[Schwarzer, K.]
Sommer, Ingolf
[Springstubbe, S.]
[Suhai, S.]
[Thoppae, G.]
[Vingron, M.]
[Warfsmann, J.]
[Werner, T.]
[Wetzler, D.]
[Wingender, E.]
[Zimmer, Ralf]

The Helmholtz Network for Bioinformatics: an integrative web portal for bioinformatics resources
In: Bioinformatics [20], 268-270

Journal Article

Lu, Tim

2005

Dissection of the inflammatory bowel disease transcriptome using genome-wide cDNA microarrays identifies novel candidate disease genes
In: PLoS Medicine [2], 771-787

Journal Article

2004

Hahn, Andreas
[Costello, Christine M.]
[Lu, Tim]
Lengauer, Thomas
[Schreiber, Stefan]

Expression analysis for inflammatory bowel disease
In: Workshop Poster Competition, ?

Poster

2002

Hahn, Andreas
[Costello, Christine M.]
[Lu, Tim]
Lengauer, Thomas
[Schreiber, Stefan]

Expression analysis for inflammatory bowel disease
In: Proceedings of the n?th Conference on, ?

Poster

Lyngsoe, Rune

2010

Feuerbach, Lars
Lyngsoe, Rune
Lengauer, Thomas
[Hein, Jotun]

Comparative Epigenomiocs - Towards Ancestral Germline Methylome Reconstruction
In: Abstracts of papers presented at the 2010 meeting on The Biology of genomes, 87

Poster

Lyngso, Rune B.

2011

Feuerbach, Lars
[Lyngso, Rune B.]
Lengauer, Thomas
[Hein, Jotun]

Reconstructing the ancestral germline methylation state of young repeats
In: Molecular Biology and Evolution [28], 1777-1784

Journal Article

Lynn, David J.

2011

[Aranda, Bruno]
Blankenburg, Hagen
[Kerrien, Samuel]
[Brinkman, Fiona S.]
[Ceol, Arnaud]
[Chautard, Emilie]
[Dana, Jose M.]
[De Las Rivas, Javier]
[Dumousseau, Marine]
[Galeota, Eugenia]
[Gaulton, Anna]
[Goll, Johannes]
[Hancock, Robert E. W.]
[Isserlin, Ruth]
[Jimenez, Rafael C.]
[Kerssemakers, Jules]
[Khadake, Jyoti]
[Lynn, David J.]
[Michaut, Magali]
[O'Kelly, Gavin]
[Ono, Keiichiro]
[Orchard, Sandra]
[Prieto, Carlos]
[Razick, Sabry]
[Rigina, Olga]
[Salwinski, Lukasz]
[Simonovic, Milan]
[Velankar, Sameer]
[Winter, Andrew]
[Wu, Guanming]
[Bader, Gary D.]
[Cesareni, Gianni]
[Donaldson, Ian M.]
[Eisenberg, David]
[Kleywegt, Gerard J.]
[Overington, John]
[Ricard-Blum, Sylvie]
[Tyers, Mike]
Albrecht, Mario
[Hermjakob, Henning]

PSICQUIC and PSISCORE: accessing and scoring molecular interactions
In: Nature Methods [8], 528-529

Journal Article

Macías, José R.

2008

[Jenkinson, Andrew M.]
Albrecht, Mario
[Birney, Ewan]
Blankenburg, Hagen
[Down, Thomas]
[Finn, Robert D.]
[Hermjakob, Henning]
[Hubbard, Tim J. P.]
[Jimenez, Rafael C.]
[Jones, Philip]
[Kähäri, Andreas]
[Kulesha, Eugene]
[Macías, José R.]
[Reeves, Gabrielle A.]
[Prlić, Andreas]

Integrating biological data - the Distributed Annotation System
In: BMC Bioinformatics [9], S3.1-7

Journal Article

Macintyre, Elizabeth

2012

[Adams, David]
[Altucci, Lucia]
[Antonarakis, Stylianos E]
[Ballesteros, Juan]
[Beck, Stephan]
[Bird, Adrian]
Bock, Christoph
[Boehm, Bernhard]
[Campo, Elias]
[Caricasole, Andrea]
[Dahl, Fredrik]
[Dermitzakis, Emmanouil T]
[Enver, Tariq]
[Esteller, Manel]
[Estivill, Xavier]
[Ferguson-Smith, Anne]
[Fitzgibbon, Jude]
[Flicek, Paul]
[Giehl, Claudia]
[Graf, Thomas]
[Grosveld, Frank]
[Guigó, Roderic]
[Gut, Ivo]
[Helin, Kristian]
[Jarvius, Jonas]
[Küppers, Ralf]
[Lehrach, Hans]
Lengauer, Thomas
[Lernmark, Åke]
[Leslie, David]
[Loeffler, Markus]
[Macintyre, Elizabeth]
[Mai, Antonello]
[Martens, Joost H A]
[Minucci, Saverio]
[Ouwehand, Willem H]
[Pelicci, Pier Giuseppe]
[Pendeville, Hèléne]
[Porse, Bo]
[Rakyan, Vardhman]
[Reik, Wolf]
[Schrappe, Martin]
[Schübeler, Dirk]
[Seifert, Martin]
[Siebert, Reiner]
[Simmons, David]
[Soranzo, Nicole]
[Spicuglia, Salvatore]
[Stratton, Michael]
[Stunnenberg, Hendrik G]
[Tanay, Amos]
[Torrents, David]
[Valencia, Alfonso]
[Vellenga, Edo]
[Vingron, Martin]
[Walter, Jörn]
[Willcocks, Spike]

BLUEPRINT to decode the epigenetic signature written in blood
In: Nature Biotechnology [30], 224-226

Journal Article

Mahlich, Yannick

2013

[Radivojac, Predrag]
[Clark, Wyatt T]
[Oron, Tal Ronnen]
[Schnoes, Alexandra M]
[Wittkop, Tobias]
[Sokolov, Artem]
[Graim, Kiley]
[Funk, Christopher]
[Verspoor, Karin]
[Ben-Hur, Asa]
[Pandey, Gaurav]
[Yunes, Jeffrey M]
[Talwalkar, Ameet S]
[Repo, Susanna]
[Souza, Michael L]
[Piovesan, Damiano]
[Casadio, Rita]
[Wang, Zheng]
[Cheng, Jianlin]
[Fang, Hai]
[Gough, Julian]
[Koskinen, Patrik]
[T\"{o}r\"{o}nen, Petri]
[Nokso-Koivisto, Jussi]
[Holm, Liisa]
[Cozzetto, Domenico]
[Buchan, Daniel W A]
[Bryson, Kevin]
[Jones, David T]
[Limaye, Bhakti]
[Inamdar, Harshal]
[Datta, Avik]
[Manjari, Sunitha K]
[Joshi, Rajendra]
[Chitale, Meghana]
[Kihara, Daisuke]
[Lisewski, Andreas M]
[Erdin, Serkan]
[Venner, Eric]
[Lichtarge, Olivier]
[Rentzsch, Robert]
[Yang, Haixuan]
[Romero, Alfonso E]
[Bhat, Prajwal]
[Paccanaro, Alberto]
[Hamp, Tobias]
[Ka\ss ner, Rebecca]
[Seemayer, Stefan]
[Vicedo, Esmeralda]
[Schaefer, Christian]
[Achten, Dominik]
[Auer, Florian]
[Boehm, Ariane]
[Braun, Tatjana]
[Hecht, Maximilian]
[Heron, Mark]
[H\"{o}nigschmid, Peter]
[Hopf, Thomas A]
[Kaufmann, Stefanie]
[Kiening, Michael]
[Krompass, Denis]
[Landerer, Cedric]
[Mahlich, Yannick]
[Roos, Manfred]
[Bj\"{o}rne, Jari]
[Salakoski, Tapio]
[Wong, Andrew]
[Shatkay, Hagit]
Gatzmann, Fanny
Sommer, Ingolf
[Wass, Mark N]
[Sternberg, Michael J E]
[Skunca, Nives]
[Supek, Fran]
[Bo\v{s}njak, Matko]
[Panov, Pan\v{c}e]
[D\v{z}eroski, Sa\v{s}o]
[Smuc, Tomislav]
[Kourmpetis, Yiannis A I]
[van Dijk, Aalt D J]
[Braak, Cajo J F Ter]
[Zhou, Yuanpeng]
[Gong, Qingtian]
[Dong, Xinran]
[Tian, Weidong]
[Falda, Marco]
[Fontana, Paolo]
[Lavezzo, Enrico]
[{Di Camillo}, Barbara]
[Toppo, Stefano]
[Lan, Liang]
[Djuric, Nemanja]
[Guo, Yuhong]
[Vucetic, Slobodan]
[Bairoch, Amos]
[Linial, Michal]
[Babbitt, Patricia C]
[Brenner, Steven E]
[Orengo, Christine]
[Rost, Burkhard]
[Mooney, Sean D]
[Friedberg, Iddo]

A large-scale evaluation of computational protein function prediction
In: Nature Methods [10], 221-227

Journal Article

Mah, Nancy

2005

Dissection of the inflammatory bowel disease transcriptome using genome-wide cDNA microarrays identifies novel candidate disease genes
In: PLoS Medicine [2], 771-787

Journal Article

Mai, Antonello

2012

BLUEPRINT to decode the epigenetic signature written in blood
In: Nature Biotechnology [30], 224-226

Journal Article

Maldener, Esther

2007

[Flockerzi, Aline]
Maydt, Jochen
[Frank, Oliver]
[Ruggieri, Alessia]
[Maldener, Esther]
[Seifarth, Wolfgang]
[Medstrand, Patrik]
Lengauer, Thomas
[Meyerhans, Andreas]
[Leib-Mosch, Christine]
[Meese, Eckart]
[Mayer, Jens]

Expression pattern analysis of transcribed HERV sequences is complicated by ex vitvo recombination
In: Retrovirology [4], 39

Journal Article

Mallick, Bani (ed.)

2003

Rahnenführer, Jörg

Statistical Inference for Clustering Microarrays
In: Proceedings of the MSRI Workshop: Nonlinear Estimation and Classification, 323-332

Proceedings Article

Mammano, Fabrizio

2007

[Skrabal, Katharina]
[Low, Andrew J.]
[Dong, Winnie]
Sing, Tobias
[Cheung, Peter K.]
[Mammano, Fabrizio]
[Harrigan, P. Richard]

Determining human immunodeficiency virus coreceptor use in a clinical setting: Degree of correlation between two phenotypic assays and a bioinformatic model
In: Journal of Clinical Microbiology [45], 279-284

Journal Article

Mangadu, Vidya

2003

Talwar, Priti
Lengauer, Thomas
[Wittmann, Christoph]
[Mangadu, Vidya]
[Heinzle, Elmar]

Towards cellular function through metabolite screening
In: Proceedings of the 3rd Annual Conference on Metabolic Profiling: Pathways in Discovery, 7

Proceedings Article

Mangas, Cristina

2012

[Calvanese, Vincenzo]
[Fernandez, Agustín F.]
[Urdinguio, Rocío G.]
[Suarez-Álvarez, Beatriz]
[Mangas, Cristina]
[Pérez-García, Vicente]
[Bueno, Clara]
[Montes, Rosa]
[Ramos-Mejía, Verónica]
[Martínez-Camblor, Pablo]
[Ferrero, Cecilia]
Assenov, Yassen
Bock, Christoph
[Menendez, Pablo]
[Carrera, Ana Clara]
[Lopez-Larrea, Carlos]
[Fraga, Mario F.]

A promoter DNA demethylation landscape of human hematopoietic differentiation
In: Nucleic Acids Research [40], 116-131

Journal Article

Mangels, Miriam

2009

Mangels, Miriam

In Silico Models for the Prediction of Metabolism by Cytochrome P450 Enzymes
Universität des Saarlandes

Thesis - Bachelor thesis

Manjari, Sunitha K

2013

A large-scale evaluation of computational protein function prediction
In: Nature Methods [10], 221-227

Journal Article

Manns, Michael P.

2013

[Liu, Jimmy Z.]
[Hov, Johannes Roksund]
[Folseraas, Trine]
[Ellinghaus, Eva]
[Rushbrook, Simon M.]
Doncheva, Nadezhda T.
[Andreassen, Ole A.]
[Weersma, Rinse K.]
[Weismuller, Tobias J.]
[Eksteen, Bertus]
[Invernizzi, Pietro]
[Hirschfield, Gideon M.]
[Gotthardt, Daniel Nils]
[Pares, Albert]
[Ellinghaus, David]
[Shah, Tejas]
[Juran, Brian D.]
[Milkiewicz, Piotr]
[Rust, Christian]
[Schramm, Christoph]
[Muller, Tobias]
[Srivastava, Brijesh]
[Dalekos, Georgios]
[Nothen, Markus M.]
[Herms, Stefan]
[Winkelmann, Juliane]
[Mitrovic, Mitja]
[Braun, Felix]
[Ponsioen, Cyriel Y.]
[Croucher, Peter J. P.]
[Sterneck, Martina]
[Teufel, Andreas]
[Mason, Andrew L.]
[Saarela, Janna]
[Leppa, Virpi]
[Dorfman, Ruslan]
[Alvaro, Domenico]
[Floreani, Annarosa]
[Onengut-Gumuscu, Suna]
[Rich, Stephen S.]
[Thompson, Wesley K.]
[Schork, Andrew J.]
[Naess, Sigrid]
[Thomsen, Ingo]
Mayr, Gabriele
[Konig, Inke R.]
[Hveem, Kristian]
[Cleynen, Isabelle]
[Gutierrez-Achury, Javier]
[Ricano-Ponce, Isis]
[van Heel, David]
[Bjornsson, Einar]
[Sandford, Richard N.]
[Durie, Peter R.]
[Melum, Espen]
[Vatn, Morten H.]
[Silverberg, Mark S.]
[Duerr, Richard H.]
[Padyukov, Leonid]
[Brand, Stephan]
[Sans, Miquel]
[Annese, Vito]
[Achkar, Jean-Paul]
[Boberg, Kirsten Muri]
[Marschall, Hanns-Ulrich]
[Chazouilleres, Olivier]
[Bowlus, Christopher L.]
[Wijmenga, Cisca]
[Schrumpf, Erik]
[Vermeire, Severine]
Albrecht, Mario
[The UK-PSCSC Consortium,]
[The International IBD Genetics Consortium,]
[Rioux, John D.]
[Alexander, Graeme]
[Bergquist, Annika]
[Cho, Judy]
[Schreiber, Stefan]
[Manns, Michael P.]
[Farkkila, Martti]
[Dale, Anders M.]
[Chapman, Roger W.]
[Lazaridis, Konstantinos N.]
[The International PSC Study Group,]
[Franke, Andre]
[Anderson, Carl A.]
[Karlsen, Tom H.]

Dense genotyping of immune-related disease regions identifies nine new risk loci for primary sclerosing cholangitis
In: Nature Genetics [45], 670-677

Journal Article

Marcelin, Anne-Genevieve

2011

[Alcaro, Stefano]
[Alteri, Claudia]
[Artese, Anna]
[Ceccherini-Silberstein, Francesca]
[Costa, Giosuè]
[Ortuso, Francesco]
[Forbici, Federica]
[Santoro, Maria Mercedes]
[Parrotta, Lucia]
[Flandre, Philippe]
[Descamps, Diane]
[Calvez, Vincent]
[Marcelin, Anne-Genevieve]
[Perno, Carlo Federico]
Sing, Tobias
[Svicher, Valentina]

Docking Analysis and Resistance Evaluation of Clinically Relevant Mutations Associated with the HIV-1 Nonnucleoside Reverse Transcriptase Inhibitors Nevirapine, Efavirenz and Etravirine
In: ChemMedChem [6], 2203-2213

Journal Article

Marchais-Oberwinkler, Sandrine

2006

[Voets, Marieke]
Antes, Iris
[Scherer, Christiane]
[Müller-Vieira, Ursula]
[Biemel, Klaus]
[Marchais-Oberwinkler, Sandrine]
[Hartmann, Rolf W.]

Synthesis and evaluation of heteroaryl substituted dihydronaphthalenes and indenes: potent and selective inhibitors of aldosterone synthase (CYP11B2) for the treatment of congestive heart failure and myocardial fibrosis
In: Journal of Medicinal Chemistry [49], 2222-2231

Journal Article

Marchais-Oberwinkler, S.

2005

[Voets, Marieke]
Antes, Iris
[Scherer, C]
[Mueller-Vieira, U.]
[Biemel, K.]
[Barrassin, C.]
[Marchais-Oberwinkler, S.]
[Hartmann, R. W.]

Heteroaryl-substituted naphthalenes and structurally modified derivatives: selective inhibitors of CYP11B2 for the treatment of congestive heart failure and myocardial fibrosis
In: Journal of Medicinal Chemistry [48], 6632-6642

Journal Article

Marcil, Michel

2002

[Wellington, Cheryl L.]
[Yang, Yu-Zhou]
[Zhou, Stephen]
[Clee, Susanne M.]
[Tan, Bing]
[Hirano, Kenichi]
[Zwarts, K.Y.]
[Kwok, Anita]
[Gelfer, Allison]
[Marcil, Michel]
[Newman, Scott]
Roomp, Kirsten
[Singaraja, Roshni]
[Collins, Jennifer A.]
[Zhang, Lin-Hua]
[Groen, Albert K.]
[Hovingh, Kees]
[Brownlie, Alison]
[Tafuri, Sherrie]
[Genest, Jacques Jr]
[Kastelein, J.J.P.]
[Hayden, Michael R.]

Truncation mutations in ABCA1 suppress normal upregulation of full-length ABCA1 by 9-cis-retinoic acid and 22-R-hydroxycholesterol
In: Journal of Lipid Research [43], 1939-1949

Journal Article

2000

[Clee, Susanne M.]
[Kastelein, J.J.P.]
[van Dam, M]
[Marcil, Michel]
Roomp, Kirsten
[Zwarts, K.Y.]
[Collins, Jennifer A.]
[Roelants, R]
[Tamasawa, N]
[Stulc, T]
[Suda, T]
[Ceska, R]
[Boucher, B]
[Rondeau, C]
[DeSouich, C]
[Brooks-Wilson, A]
[Molhuizen, H.O.]
[Frohlich, J]
[Genest, Jacques Jr]
[Hayden, Michael R.]

Age and residual cholesterol efflux affect HDL cholesterol levels and coronary artery disease in ABCA1 heterozygotes
In: Journal of Clinical Investigation [106], 1263-70

Journal Article

1999

[Brooks-Wilson, A]
[Marcil, Michel]
[Clee, Susanne M.]
[Zhang, Lin-Hua]
Roomp, Kirsten
[van Dam, M]
[Yu, L]
[Brewer, C]
[Collins, Jennifer A.]
[Molhuizen, H.O.]
[Loubser, O]
[Ouelette, B.F.]
[Fichter, K]
[Ashbourne-Excoffon, K.J.]
[Sensen, C.W.]
[Scherer, S]
[Mott, S]
[Denis, M]
[Martindale, D]
[Frohlich, J]
[Morgan, K]
[Koop, B]
[Pimstone, S]
[Kastelein, J.J.P.]
[Hayden, Michael R.]

Mutations in ABC1 in Tangier disease and familial high-density lipoprotein
In: Nature Genetics [22], 336-45

Journal Article

1999

[Marcil, Michel]
[Brooks-Wilson, A.]
[Clee, Susanne M.]
Roomp, Kirsten
[Zhang, Lin-Hua]
[Yu, L.]
[Collins, Jennifer A.]
[van Dam, M.]
[Molhuizen, H. O.]
[Loubser, O.]
[Ouelette, B. F.]
[Sensen, C. W.]
[Fichter, K.]
[Mott, S.]
[Denis, M.]
[Boucher, B.]
[Pimstone, S.]
[Genest, Jacques]
[Kastelein, J. J. P.]
[Hayden, Michael R.]

Mutations in the ABC1 gene in familial HDL deficiency with defective cholesterol efflux
In: The Lancet [354], 1341-6

Journal Article

Marconi, Patrizia

2009

[Trignetti, Maria]
Sing, Tobias
[Svicher, Valentina]
[Santoro, Maria Mercedes]
[Forbici, Federica]
[D'Arrigo, Roberta]
[Bellocchi, Maria Concetta]
[Santoro, Mario]
[Marconi, Patrizia]
[Zaccarelli, Mauro]
[Trotta, Maria Paola]
[Bellagamba, Rita]
[Narciso, Pasquale]
[Antinori, Andrea]
Lengauer, Thomas
[Perno, Carlo Federico]
[Ceccherini-Silberstein, Francesca]

Dynamics of NRTI resistance mutations during therapy interruption
In: AIDS Research and Human Retroviruses [25], 57-64

Journal Article

Marenholz, Ingo

2007

[Söderhäll, Cilla]
[Marenholz, Ingo]
[Kerscher, Tamara]
[Rüschendorf, Franz]
[Esparza-Gordillo, Jorge]
[Worm, Margitta]
[Gruber, Christoph]
Mayr, Gabriele
Albrecht, Mario
[Rohde, Klaus]
[Schulz, Herbert]
[Wahn, Ulrich]
[Hubner, Norbert]
[Lee, Young-Ae]

Variants in a novel epidermal collagen gene (COL29A1) are associated with atopic dermatitis
In: PLoS Biology [5], e242.1952-1961

Journal Article

Margeridon-Thermet, Severin

2010

[Rhee, Soo-Yon]
[Margeridon-Thermet, Severin]
[Nguyen, Mindie]
[Liu, Tommy]
[Kagan, Ron]
Beggel, Bastian
[Verheyen, Jens]
[Kaiser, Rolf]
[Shafer, Robert]

Hepatitis B virus reverse transcriptase sequence variant database for sequence analysis and mutation discovery
In: Antiviral Research [88], 269-275

Journal Article

Marian, Christel Maria

2006

Kämper, Andreas
[Apostolakis, Joannis]
[Rarey, Matthias]
[Marian, Christel Maria]
Lengauer, Thomas

Fully Automated Flexible Docking of Ligands into Flexible Synthetic Receptors Using Forward and Inverse Docking Strategies
In: Journal of Chemical Information and Modeling [46], 903-911

Journal Article

2001

Kämper, Andreas
[Apostolakis, Joannis]
[Rarey, Matthias]
[Marian, Christel Maria]
Lengauer, Thomas

Docking of Ligands into Artificial Receptors

Miscellaneous

2001

[Kämper, Andreas]
[Apostolakis, Joannis]
[Rarey, Matthias]
[Marian, Christel Maria]
[Lengauer, Thomas]

Docking of Ligands into Artificial Receptors
In: Electronically Excited Molecules: Structure and Dynamics, 37th Symposium for Theoretical Chemistry, P76

Proceedings Article

Marinoj, Nicoletta

2011

[Svichera, Valentina]
[Centoa, Valeria]
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Association between variants of PRDM1 and NDP52 and Crohn's disease, based on exome sequencing and functional studies
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Journal Article

2010

Genome-wide association study for ulcerative colitis identifies risk loci at 7q22 and 22q13 (IL17REL)
In: Nature Genetics [42], 292-294

Journal Article

2008

Sequence variants in IL10, ARPC2, and multiple other loci contribute to ulcerative colitis
In: Nature Genetics [40], 1319-1323

Journal Article

McCallum, Andrew (ed.)

2008

Bickel, Steffen
Bogojeska, Jasmina
Lengauer, Thomas
Sheffer, Tobias

Multi-Task Learning for HIV Therapy Screening
In: Proceedings, Twenty-Fifth International Conference on Machine Learning, 56-63

Proceedings Article

McCauley, Brenna MM

2013

[Le, Hai-Son]
Schulz, Marcel Holger
[McCauley, Brenna MM]
[Hinman, Veronica F]
[Bar-Joseph, Ziv]

Probabilistic error correction for RNA sequencing
In: Nucleic Acids Researcb [41], e109

Journal Article

McCulloch, John

2011

[Ruiz, Jeronimo C.]
[D'Afonseca, Vivian]
[Silva, Artur]
[Ali, Amjad]
[Pinto, Anne C.]
[Santos, Anderson R.]
[Rocha, Aryanne A. M. C.]
[Lopes, Debora O.]
[Dorella, Fernanda A.]
[Pacheco, Luis G. C.]
[Costa, Marcilia P.]
[Turk, Meritxell Z.]
[Seyffert, Nubia]
[Moraes, Pablo M. R. O.]
[Soares, Siomar C.]
[Almeida, Sintia S.]
[Castro, Thiago L. P.]
[Abreu, Vinicius A. C.]
[Trost, Eva]
Baumbach, Jan
[Tauch, Andreas]
[Schneider, Maria P. C.]
[McCulloch, John]
[Cerdeira, Louise T.]
[Ramos, Rommel T. J.]
[Zerlotini, Adhemar]
[Dominitini, Anderson]
[Resende, Daniela M.]
[Coser, Elisangela M.]
[Oliveira, Luciana M.]
[Pedrosa, Andre L.]
[Vieira, Carlos U.]
[Guimaraes, Claudia T.]
[Bartholomeu, Daniela C.]
[Oliveira, Diana M.]
[Santos, Fabricio R.]
[Rabelo, Elida Mara]
[Lobo, Francisco P.]
[Franco, Gloria R.]
[Costa, Ana Flavia]
[Castro, Ieso M.]
[Dias, Silvia Regina]
[Ferro, Jesus A.]
[Ortega, Jose Miguel]
[Paiva, Luciano V.]
[Goulart, Luiz R.]
[Almeida, Juliana Franco]
[Ferro, Maria Ines]
[Carneiro, Newton P.]
[Falcao, Paula R. K.]
[Grynberg, Priscila]
[Teixeira, Santuza M. R.]
[Brommonschenkel, Sergio]
[Oliveira, Sergio C.]
[Meyer, Roberto]
[Moore, Robert J.]
[Miyoshi, Anderson]
[Oliveira, Guilherme C.]
[Azevedo, Vaco]

Evidence for Reductive Genome Evolution and Lateral Acquisition of Virulence Functions in two Corynebacterium pseudotuberculosis strains
In: PLoS One [6], e18551

Electronic Journal Article

McCulloch, John A

2011

[Santos, Anderson R]
[Santos, Marcos A]
Baumbach, Jan
[McCulloch, John A]
[Oliveira, Guilherme C]
[Silva, Artur]
[Miyoshi, Anderson]
[Azevedo, Vasco]

A singular value decomposition approach for improved taxonomy classification of biological sequences
In: BMC Genomics [12], S11,1-S11,15

Journal Article

McCulloch, John Anthony

2011

[Cerdeira, Louise Teixeira]
[Carneir, Aadriana Ribeiro]
[Ramos, Rommel Thiago Juca]
[de Almeida, Sintia Silva]
[D'Afonseca, Vivian]
[Schneider, Maria Paula Cruz]
Baumbach, Jan
[Tauch, Andreas]
[McCulloch, John Anthony]
[Azevedo, Vasco Ariston Carvalho]
[Silva, Aartur]

Rapid hybrid de novo assembly of a microbial genome using only short reads: Corynebacterium pseudotuberculosis I19 as a case study
In: Journal of Microbiological Methods [86], 218-223

Journal Article

McGivern, David R.

2011

[Shimakami, Tetsuro]
Welsch, Christoph
[Yamane, Daisuke]
[McGivern, David R.]
[Yi, MinKyung]
[Zeuzem, Stefan]
[Lemon, Stanley M.]

Protease Inhibitor-Resistant Hepatitis C Virus Mutants With Reduced Fitness From Impaired Production of Infectious Virus
In: Gastroenterology [140], 667-675

Journal Article

McGovern, Rachel

2009

[Harrigan, P Richard]
[McGovern, Rachel]
[Dong, Winnie]
Thielen, Alexander
[Jensen, Mark]
[Mo, Theresa]
[Chapman, Douglas]
[Lewis, Marilyn]
[James, Ian]
[Valdez, Hernan]

Screening for HIV tropism using population-based V3 genotypic analysis: a retrospective outcome analysis using stored plasma screening samples from MOTIVATE-1
In: Abstracts presented at the XVIII International HIV Drug Resistance Workshop : Basic Principles & Clinical Implications, A17-A17

Poster

McGovern, Rachel A

2011

Thielen, Alexander
Lengauer, Thomas
[Swenson, Luke C]
[Dong, Winnie W.Y.]
[McGovern, Rachel A]
[Lewis, Marilyn]
[James, Ian]
[Heera, Jayvant]
[Valdez, Hernan]
[Harrigan, P Richard]

Mutations in gp41 are correlated with coreceptor tropism but do not improve prediction methods substantially
In: Antiviral Therapy [16], 319-328

Journal Article

2010

Thielen, Alexander
Lengauer, Thomas
[Harrigan, P Richard]
[Swenson, Luke]
[Dong, Winnie WY]
[McGovern, Rachel A]
[Lewis, Marilyn]
[James, Ian]
[Heera, Jayvant]
[Valdez, Hernan]

Mutations within GP41 are correlated with coreceptor tropism but do not substantially improve coreceptor usage prediction
In: Reviews in Antiviral Therapy & Infectious Diseases, 47-47

Poster

2010

[McGovern, Rachel A]
Thielen, Alexander
[Mo, Theresa]
[Dong, Winnie]
[Woods, Conan K]
[Chapman, Douglass]
[Lewis, Marilyn]
[James, Ian]
[Heera, Jayvant]
[Valdez, Hernan]
[Harrigan, P Richard]

Population-based V3 genotypic tropism assay: a retrospective analysis using screening samples from the A4001029 and MOTIVATE studies
In: AIDS [24], 2517-2525

Journal Article

McGovern, Rachel A.

2010

[Swenson, Luke C.]
[Boehme‌, Richard]
Thielen, Alexander
[McGovern‌, Rachel A.]
[Harrigan, P. Richard]

Genotypic determination of HIV-1 tropism in the clinical setting
In: HIV Therapy [4], 293-303

Journal Article

McHardy, Alice

2009

Adams, Ben
McHardy, Alice
[Lundegaard, C.]
Lengauer, Thomas

Viral Bioinformatics
In: Modern Genome Annotation - The BioSapiens Network, 429-452

Part of a Book

McHardy, Alice C.

2009

McHardy, Alice C.
Adams, Ben

The role of genomics in tracking the evolution of influenza A virus
In: PLoS Pathog [5], e1000566

Electronic Journal Article

McKay, B. J. Morrison

2012

[Rost, Burkhard]
[Gaasterland, Terry]
Lengauer, Thomas
[Linial, Michal]
[Markel, Scott]
[McKay, B. J. Morrison]
[Schneider, Reinhard]
[Horton, Paul]
[Kelso, Janet]

Paving the future: finding suitable ISMB venues
In: Bioinformatics [28], 2556-2559

Journal Article

McKeown, Astrid

2007

Fifteen years of env C2V3C3 evolution in six individuals clonally infected with human immunodeficiency virus type 1
In: Journal of Medical Virology [79], 1629-1639

Journal Article

Medstrand, Patrik

2007

Expression pattern analysis of transcribed HERV sequences is complicated by ex vitvo recombination
In: Retrovirology [4], 39

Journal Article

Meese, Eckart

2007

Expression pattern analysis of transcribed HERV sequences is complicated by ex vitvo recombination
In: Retrovirology [4], 39

Journal Article

2005

[Wemmert, Silke]
[Ketter, Ralf]
Rahnenführer, Jörg
Beerenwinkel, Niko
[Strowitzki, Martin]
[Feiden, Wolfgang]
[Hartmann, Christian]
Lengauer, Thomas
[Stockhammer, Florian]
[Zang, Klaus D.]
[Meese, Eckart]
[Steudel, Wolf-Ingo]
[von Deimling, Andreas]
[Urbschat, Steffi]

Patients with high grade gliomas harboring delections of chromosomes 9p and 10q benefit from temozolomide treatment
In: Neoplasia [7], 883-893

Journal Article

Meijer, Gerrit (ed.)

2009

Feuerbach, Lars
Halachev, Konstantin
Lengauer, Thomas
Bock, Christoph

An exhaustive methode for CpG island annotation
In: Special Issue: Abstracts of the 3rd MC-GARD Meeting, 146-146

Poster

2008

Feuerbach, Lars
Christopher, Bock
Halachev, Konstantin
Büch, Joachim
Lengauer, Thomas

Towards Comparative Epigenomics: A Software Toolkit For Cross-Species Epigenome Data Analysis
In: Abstracts of the 2nd MC-GARD Meeting, 230

Electronic Proceedings Article

Meiser, Ina

2005

Meiser, Ina

Identification of functionally important regions in cytochrome P450 systems and a systematic analysis of various CYP P450 homology models
Universität des Saarlandes

Thesis - Bachelor thesis

Meissner, Alex

2011

[Zacharek, Sima J.]
[Fillmore, Christine M.]
[Lau, Allison N.]
[Gludish, David W.]
[Chou, alan]
[Ho, Joshua W. K.]
[Zamponi, Raffaella]
[Gazit, Roi]
Bock, Christoph
[Jäger, Natalie]
[Smith, Zachary D.]
[Kim, Tae-min]
[Saunders, Arven H.]
[Wong, Janice]
[Lee, Joo-Hyeon]
[Roach, Rebecca R.]
[Rossi, Derrick J.]
[Meissner, Alex]
[Gimelbrant, Alexander A.]
[Park, Peter J.]
[Kim, Carla F.]

Lung stem cell self-renewal relies on BMI1-dependent control of expression at imprinted loci
In: Cell Stem Cell [9], 272-280

Journal Article

Meissner, Alexander

2013

[Ziller, Michael J.]
[Gu, Hongcang]
Müller, Fabian
[Donaghey, Julie]
[Tsai, Linus T.-Y.]
[Kohlbacher, Oliver]
[De Jager, Philip L.]
[Rosen, Evan D.]
[Bennett, David A.]
[Bernstein, Bradley E.]
[Gnirke, Andreas]
[Meissner, Alexander]

Charting a dynamic DNA methylation landscape of the human genome
In: Nature [500], 477–481

Journal Article

2012

[Mekhubad, Shila]
Bock, Christoph
[de Boer, A. Sophie]
[Kiskinis, Evangelos]
[Meissner, Alexander]
[Eggan, Kevin]

Erosion of dosage compensation impacts human iPSC disease modeling
In: Cell Stem Cell [10], 595-609

Journal Article

2012

[Xi, Yuanxin]
Bock, Christoph
Müller, Fabian
[Sun, Deqiang]
[Meissner, Alexander]
[Li, Wei]

RRBSMAP: a fast, accurate and user-friendly alignment tool for reduced representation bisulfite sequencing
In: Bioinformatics [28], 430-432

Journal Article

2011

[Ziller, Michael J.]
Müller, Fabian
[Liao, Jing]
[Zhang, Yingying]
[Gu, Hongcang]
Bock, Christoph
[Boyle, Patrick]
[Epstein, Charles B.]
[Bernstein, Bradley E.]
Lengauer, Thomas
[Gnirke, Andreas]
[Meissner, Alexander]

Genomic distribution and inter-sample variation of non-CpG methylation across human cell types
In: PLoS Genetics [17], e1002389,1-e1002389,15

Electronic Journal Article

2011

[Gu, Hongcang]
[Smith, Zachary D.]
Bock, Christoph
[Boyle, Patrick]
[Gnirke, Andreas]
[Meissner, Alexander]

Preparation of reduced representation bisulfite sequencing libraries for genome-scale DNA methylation profiling
In: Nature Protocols [6], 468-481

Journal Article

2011

Bock, Christoph
[Kiskinis, Evangelos]
[Verstappen, Griet]
[Gu, Hongcang]
[Boulting, Gabriella]
[Smith, Zachary D.]
[Ziller, Michael]
[Croft, Gist F.]
[Amoroso, MacKenzie W.]
[Oakley, Derek H.]
[Gnirke, Andreas]
[Eggan, Kevin]
[Meissner, Alexander]

Reference Maps of Human ES and iPS Cell Variation Enable High-Throughput Characterization of Pluripotent Cell Lines
In: Cell [144], 439-452

Journal Article

2011

[Xi, Yuanxin]
Bock, Christoph
Müller, Fabian
[Sun, Deqiang]
[Meissner, Alexander]
[Li, Wei]

RRBSMAP: A Fast, Accurate and User-friendly Alignment Tool for Reduced Representation Bisulfite Sequencing
In: Bioinformatics [28], 430-432

Journal Article

2010

Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications
In: Nature Biotechnology [28], 1097-1105

Journal Article

2010

[Gu, Hongcang]
Bock, Christoph
[Mikkelsen, Tarjei S.]
[Jäger, Natalie]
[Smith, Zachary D.]
[Tomazou, Eleni]
[Gnirke, Andreas]
[Lander, Eric S.]
[Meissner, Alexander]

Genome-scale DNA methylation mapping of clinical samples at single-nucleotide resolution
In: Nature Methods [7], 133-136

Journal Article

2010

Bock, Christoph
[Tomazou, Eleni M.]
[Brinkman, Arie B.]
Müller, Fabian
[Simmer, Femke]
[Gu, Hongcang]
[Jäger, Natalie]
[Gnirke, Andreas]
[Stunnenberg, Hendrik G.]
[Meissner, Alexander]

Quantitative comparison of genome-wide DNA methylation mapping technologies
In: Nature Biotechnology [28], 1106-1114

Journal Article

Meissner, K.

2004

The Helmholtz Network for Bioinformatics: an integrative web portal for bioinformatics resources
In: Bioinformatics [20], 268-270

Journal Article

Mekhubad, Shila

2012

[Mekhubad, Shila]
Bock, Christoph
[de Boer, A. Sophie]
[Kiskinis, Evangelos]
[Meissner, Alexander]
[Eggan, Kevin]

Erosion of dosage compensation impacts human iPSC disease modeling
In: Cell Stem Cell [10], 595-609

Journal Article

Mellgard, Bjorn

2004

Genetic variation in DLG5 is associated with inflammatory bowel disease
In: Nature Genetics [36], 376-380

Journal Article

Mellors, John (ed.)

2004

Beerenwinkel, Niko
Sing, Tobias
[Däumer, Martin]
[Kaiser, Rolf]
Lengauer, Thomas

Computing the genetic barrier
In: XII International HIV Drug resistance Workshop, S125-S125

Proceedings Article

2003

Beerenwinkel, Niko
[Kaiser, Rolf]
Rahnenführer, Jörg
[Däumer, Martin]
[Hoffmann, Daniel]
[Selbig, Joachim]
Lengauer, Thomas

Tree models for the evolution of drug resistance
In: XII International HIV Drug resistance Workshop, S107-S107

Proceedings Article

Meltzer, Paul

2007

[Kamradt, Jörn]
[Jung, Volker]
[Wahrheit, Kerstin]
Tolosi, Laura
Rahnenführer, Jörg
[Schilling, Martin]
[Walker, Robert]
[Davis, Sean]
[Stöckle, Michael]
[Meltzer, Paul]
[Wullich, Bernd]

Detection of Novel Amplicons in Prostate Cancer by Comprehensive Genomic Profiling of Prostate Cancer Cell Lines Using Oligonucleotide-Based ArrayCGH
In: PLoS ONE [2], e769

Electronic Journal Article

Meltzer, Stephen J.

2012

A DNA methylation fingerprint of 1628 human samples
In: Genome Research [22], 407-419

Journal Article

Melum, Espen

2013

Dense genotyping of immune-related disease regions identifies nine new risk loci for primary sclerosing cholangitis
In: Nature Genetics [45], 670-677

Journal Article

Mendez-Gonzales, Jesus

2013

[Sandoval, Juan]
[Mendez-Gonzales, Jesus]
[Nadal, Ernest]
[Chen, Guoan]
[Carmona, F. Javier]
[Sayols, Sergi]
[Moran, Sebastian]
[Heyn, Holger]
[Vizoso, Miguel]
[Gomez, Antonio]
[Sanchez-Cespedes, Montse]
Assenov, Yassen
Müller, Fabian
Bock, Christoph
[Taron, Miquel]
[Mora, Josefina]
[Muscarella, Lucia A.]
[Liloglou, Triantafillos]
[Davies, Michael]
[Pollan, Marina]
[Pajares, Maria J.]
[Torre, Wenceslao]
[Montuenga, Luis M.]
[Brambilla, Elisabeth]
[Field, John K.]
[Roz, Luca]
[Lo Iacono, Marco]
[Scagliotti, Giorgio V.]
[Rosell, Rafael]
[Beer, David G.]
[Esteller,Manel]

A Prognostic DNA Methylation Signature for Stage I Non-Small-Cell Lung Cancer
In: Journal of Clinical Oncology [31], 4140-4147

Journal Article

Menendez, Pablo

2012

A promoter DNA demethylation landscape of human hematopoietic differentiation
In: Nucleic Acids Research [40], 116-131

Journal Article

Mercurioa, Fabio

2011

Role of hepatitis B virus genetic barrier in drug-resistance and immune-escape development
In: Digestive and Liver Disease [43], 975–983

Journal Article

Mercurio, Fabio

2011

Role of hepatitis B virus genetic barrier in drug-resistance and immune-escape development
In: Digestive and Liver Disease [43], 975-983

Journal Article

Merkwirth, Christian

2006

[Neumann, Dirk]
[Kohlbacher, Oliver]
[Merkwirth, Christian]
Lengauer, Thomas

A Fully Computational Model for Predicting Percutaneous Drug Absorption
In: Journal of Chemical Information and Modeling [1], 424-429

Journal Article

2006

[Neumann, Dirk]
[Kohlbacher, Oliver]
[Merkwirth, Christian]
Lengauer, Thomas

Prediction of percutaneous drug absorption
In: Journal of Chemical Information and Modeling [1], 424-429

Journal Article

2005

Lengauer, Thomas
[Merkwirth, Christian]

Automatic Generation of complementary descriptors with molecular graph networks
In: Journal of Chemical Information and Modeling [45], 1159-1168

Journal Article

2005

Antes, Iris
Merkwirth, Christian
Lengauer, Thomas

POEM: Parameter Optimization using Ensemble Methods: Application to target specific scoring functions
In: Journal of Chemical Information and Modeling [45], 1291-1302

Journal Article

2004

[Hofmann, W.P.]
[Herrmann, E.]
[Kronenberger, B.]
Merkwirth, Christian
Welsch, Christoph
Lengauer, Thomas
[Zeuzem, S.]
[Sarrazin, C.]

Association of HCV-related mixed cryoglobulinemia with specific mutational patterns of the HCV E2 protein and CD81 expression on peripheral B lymphocytes
In: Blood [104], 1228-1229

Journal Article

2004

Merkwirth, Christian
[Mauser, H.]
[Schulz-Gasch, T.]
[Roche, O.]
[Stahl, M.]
Lengauer, Thomas

Ensemble methods for classification in cheminformatics
In: Journal of Chemical Information and Modeling [44], 1971-1978

Journal Article

2004

Merkwirth, Christian
[Bröcker, J.]
[Ogorzalek, Maciej]
Wichard, J.D.

Finite iteration DT-CNN - new design and operation principles
In: Proceedings (ISCAS-04) : 2004 IEEE International Symposium on Circuits and Systems. - Vol. 5, Blind signal processing, computer-aided network design, invited sessions, neural sytems and applications, power systems and power electronic circuits, 504-507

Proceedings Article

2004

[Wichard, J.D.]
[Ogorzalek, Maciej]
Merkwirth, Christian
[Bröcker, J.]

Finite iteration DT-CNN with stationary templates
In: Proceedings of the 8th IEEE International Workshop on Cellular Neural Networks and their Applications (CNNA 2004), 459-464

Proceedings Article

2003

Merkwirth, Christian
[Ogorzalek, Maciej]
[Wichard, Jörg Daniel]

Stochastic Gradient Descent Training of Ensembles of DT-CNN Classifiers for Digit Recognition
In: Proceedings of the 16th European Conference on Circuit Theory and Design ECCTD'03, 337-341

Proceedings Article

Mermel, Craig

2009

[Sos, Martin L.]
[Michel, Kathrin]
[Zander, Thomas]
[Weiss, Jonathan]
[Frommolt, Peter]
[Pfeifer, Martin]
[Li, Danan]
[Ullrich, Roland]
[Koker, Mirjam]
[Fischer, Florian]
[Shimamura, Takeshi]
[Rauh, Daniel]
[Mermel, Craig]
[Fischer, Stefanie]
[Stückrath, Isabel]
[Heynck, Stefanie]
[Beroukhim, Rameen]
[Lin, William]
[Winckler, Wendy]
[Shah, Kinjal]
[LaFramboise, Thomas]
[Moriarty, Whei F.]
Hanna, megan
Tolosi, Laura
[Rahnenführer, Jörg]
[Verhaak, Roel]
[Chiang, Derek]
[Getz, Gad]
[Hellmich, Martin]
[Wolf, Jürgen]
[Girard, Luc]
[Peyton, Michael]
[Weir, Barbara A.]
[Chen, Tzu-Hsiu]
[Greulich, Heidi]
[Barretina, Jordi]
[Shapiro, Geoffrey I.]
[Garraway, Levi A.]
[Gazdar, Adi F.]
[Minna, John D.]
[Meyerson, Matthew]
[Wong, Kwok-Kin]
[Thomas, Roman K.]

Predicting drug susceptibility of non-small cell lung cancers based on genetic lesions
In: Journal of Clinical Investigation [119], 1727-1740

Journal Article

Mestre, Julián

2011

Schelhorn, Sven-Eric
Mestre, Julián
Zotenko, Elena
Albrecht, Mario

Inferring physical protein contacts from large-scale purification data of protein complexes
In: Molecular & Cellular Proteomics [10], M110.004929,1-M110.004929,15

Electronic Journal Article

2008

Zotenko, Elena
Mestre, Julian
[O'Leary, Dianne]
[Przytycka, Teresa]

Why Do Hubs in the Yeast Protein Interaction Network Tend To Be Essential: Reexamining the Connection between the Network Topology and Essentiality
In: PLoS Computational Biology [4], e1000140

Journal Article

Metzner, Karin J

2011

[Knoepfel, Stefanie]
[Di Giallonardoc, Francesca]
[Däumer, Martin]
Thielen, Alexander
[Metzner, Karin J]

In-depth analysis of G-to-A hypermutation rate in HIV-1 env DNA induced by endogenous APOBEC3 proteins using massively parallel sequencing
In: Journal of Virological Methods [71], 329-338

Journal Article

Mevissen, T.

2004

The Helmholtz Network for Bioinformatics: an integrative web portal for bioinformatics resources
In: Bioinformatics [20], 268-270

Journal Article

Mewes, H.-W.

2004

The Helmholtz Network for Bioinformatics: an integrative web portal for bioinformatics resources
In: Bioinformatics [20], 268-270

Journal Article

Meyerhans, Andreas

2007

Expression pattern analysis of transcribed HERV sequences is complicated by ex vitvo recombination
In: Retrovirology [4], 39

Journal Article

2007

[Scheller, Nicoletta]
[Resa-Infante, Patricia]
[de la Luna, Susana]
[Galao, Rui Pedro]
Albrecht, Mario
[Kaestner, Lars]
[Lipp, Peter]
Lengauer, Thomas
[Meyerhans, Andreas]
[Díez, Juana]

Identification of PatL1, a human homolog to yeast P body component Pat1
In: Biochimica et Biophysica Acta - Molecular Cell Research [1773], 1786-1792

Journal Article

Meyerson, Matthew

2009

Predicting drug susceptibility of non-small cell lung cancers based on genetic lesions
In: Journal of Clinical Investigation [119], 1727-1740

Journal Article

Meyers, Robert A. (ed.)

2012

Lengauer, Thomas
Albrecht, Mario
Domingues, Francisco S.

Computational Biology
In: Encyclopedia of Molecular Cell Biology and Molecular Medicine, 1-71

Part of a Book

2005

Lengauer, Thomas

Informatics (Computational Biology)
In: Growth Factors and Oncogenes in Gastrointestinal Cancers to Informatics (Computational Biology), 567-626

Part of a Book

Meyer, Aline

2010

[Welker, Martin-Walter]
[Welsch, Christoph]
[Meyer, Aline]
Antes, Iris
Albrecht, Mario
[Forestier, Nicole]
[Kronenberger, Bernd]
Lengauer, Thomas
[Piiper, Albrecht]
[Zeuzem, Stefan]
[Sarrazin, Christoph]

Dimerization of the hepatitis C virus nonstructural protein 4B depends on the integrity of an aminoterminal basic leucine zipper
In: Protein Science [19], 1327-1336

Journal Article

Meyer, Jobst

2009

[Moser, Dirk]
[Ekawardhani, Savira]
[Kumsta, Robert]
[Palmason, Haukur]
Bock, Christoph
[Athanassiadou, Zoi]
[Lesch, Klaus-Peter]
[Meyer, Jobst]

Functional Analysis of a Potassium-Chloride Co-Transporter 3 (SLC12A6) Promoter Polymorphism Leading to an Additional DNA Methylation Site
In: Neuropsychopharmacology [34], 458-467

Journal Article

Meyer, Roberto

2011

Evidence for Reductive Genome Evolution and Lateral Acquisition of Virulence Functions in two Corynebacterium pseudotuberculosis strains
In: PLoS One [6], e18551

Electronic Journal Article

Michael, H.

2004

The Helmholtz Network for Bioinformatics: an integrative web portal for bioinformatics resources
In: Bioinformatics [20], 268-270

Journal Article

Michalk, Monika

2010

[Lange, Christian Markus]
Roomp, Kirsten
[Dragan, Anette]
[Nattermann, Jacob]
[Michalk, Monika]
[Spengler, Ulrich]
[Weich, Viola]
Lengauer, Thomas
[Zeuzem, Stefan]
[Berg, Thoma]
[Sarrazin, Christoph]

HLA class I allele associations with HCV genetic variants in patients with chronic HCV genotypes 1a or 1b infection
In: Journal of Hepatology [53], 1022-1028

Journal Article

Michaut, Magali

2011

PSICQUIC and PSISCORE: accessing and scoring molecular interactions
In: Nature Methods [8], 528-529

Journal Article

Michelig, Valeria

2011

Role of hepatitis B virus genetic barrier in drug-resistance and immune-escape development
In: Digestive and Liver Disease [43], 975–983

Journal Article

Micheli, Valeria

2011

Role of hepatitis B virus genetic barrier in drug-resistance and immune-escape development
In: Digestive and Liver Disease [43], 975-983

Journal Article

Michel, Kathrin

2009

Predicting drug susceptibility of non-small cell lung cancers based on genetic lesions
In: Journal of Clinical Investigation [119], 1727-1740

Journal Article

Middaugh, C. Russell

2007

[Salamat-Miller, Nazila]
[Fang, Jianwen]
[Seidel, Christopher W.]
Assenov, Yassen
Albrecht, Mario
[Middaugh, C. Russell]

A network-based analysis of polyanion-binding proteins utilizing human protein arrays
In: Journal of Biological Chemistry [282], 10153-10163

Journal Article

2006

[Salamat-Miller, Nazila]
[Fang, Jianwen]
[Seidel, Christopher W.]
[Smalter, Aaron M.]
[Assenov, Yassen]
Albrecht, Mario
[Middaugh, C. Russell]

A network-based analysis of polyanion-binding proteins utilizing yeast protein arrays
In: Molecular and Cellular Proteomics [5], 2263-2278

Journal Article

Mihm, Ulrike

2011

[Hofmann, Wolf Peter]
[Chung, Tje Lin]
[Osbahr, Carola]
[Susser, Simone]
[Karey, Ursel]
[Mihm, Ulrike]
Welsch, Christoph
[Lötsch, Jörn]
[Sarrazin, Christoph]
[Zeuzem, Stefan]
[Herrmann, Eva]

Impact of ribavirin on HCV replicon RNA decline during treatment with interferon-α and the protease inhibitors boceprevir or telaprevir
In: Antiviral Therapy [16], 695-704

Journal Article

2010

[Mihm, Ulrike]
[Hofmann, W.P.]
Welsch, Christoph
[Polta, A.]
Lengauer, Thomas
[Zeuzem, Stefan]
[Sarrazin, Christoph]
[Herrmann, E.]

Effect of ribavirin on the frequency of RNAse L cleavage sites within the hepatitis C viral genome
In: Journal of Viral Hepatitis [17], 217-221

Journal Article

2009

[Mihm, Ulrike]
[Ackermann, Oliver]
Welsch, Christoph
[Herrmann, Eva]
[Hofmann, Wolf Peter]
[Grigorian, Natalia]
[Welker, Martin Walter]
Lengauer, Thomas
[Zeuzem, Stefan]
[Sarrazin, Christoph]

Clinical relevance of the 2'-5'-oligoadenylate synthetase/RNase L system for treatment response in chronic hepatitis C
In: Journal of Hepatology [50], 49-58

Journal Article

2007

[Hofmann, Wolf Peter]
Welsch, Christoph
[Takahashi, Yoshitomo]
[Miyajima, Hiroaki]
[Mihm, Ulrike]
[Krick, Christoph]
[Zeuzem, Stefan]
[Sarrazin, Christoph]

Identification and in silico characterization of a novel compound heterozygosty associated with hereditary aceruloplasminemia
In: Scandinavian Journal of Gastroenterology [42], 1088-1094

Journal Article

2007

[Hofmann, Wolf Peter]
[Fernandez, B.]
[Herrmann, E.]
Welsch, Christoph
[Mihm, Ulrike]
[Kronenberg, B.]
[Feldmann, G.]
[Spengler, U.]
[Zeuzem, Stefan]
[Sarrazin, Christoph]

Somatic hypermutation and mRNA expression levels of the BCL-6 gene in patients with hepatitis C virus-associated lymphoproliferative diseases
In: Journal of Viral Hepatitis [14], 484-491

Journal Article

2006

[Mihm, Ulrike]
[Grigorian, Natalia]
[Welsch, Christoph]
[Herrmann, Eva]
[Kronenberger, Bernd]
[Teuber, Gerlinde]
[von Wagner, Michael]
[Hofmann, Wolf-Peter]
Albrecht, Mario
Lengauer, Thomas
[Zeuzem, Stefan]
[Sarrazin, Christoph]

Amino acid variations in hepatitis C virus p7 and sensitivity to antiviral combination therapy with amantadine in chronic hepatitis C
In: Antiviral Therapy [11], 507-519

Journal Article

2005

[Sarrazin, Christoph]
[Mihm, Ulrike]
[Herrmann, Eva]
[Welsch, Christoph]
Albrecht, Mario
[Sarrazin, Ulrike]
[Traver, Stella]
Lengauer, Thomas
[Zeuzem, Stefan]

Clinical significance of in vitro replication-enhancing mutations of the hepatitis C virus (HCV) replicon in patients with chronic HCV infection
In: The Journal of Infectious Diseases [192], 1710-1719

Journal Article

Mihm, U.

2013

[Dietz, J.]
Schelhorn, Sven-Eric
[Fitting, D.]
[Mihm, U.]
[Susser, S.]
[Welker, M.-W.]
[Füller, C.]
[Däumer, M.]
[Teuber, G.]
[Wedemeyer, H.]
[Berg, T.]
Lengauer, Thomas
[Z., Stefan]
[Herrmann, E.]
[Sarrazin, C.]

Deep sequencing reveals mutagenic effects of ribavirin during monotherapy of HCV genotype 1-infected patients
In: Journal of Virology [87], 6172-6181

Journal Article

2005

Lengauer, Thomas
Albrecht, Mario
[Sarrazin, C.]
[Mihm, U.]
[Herrmann, E.]
Welsch, Christoph
[Sarrazin, U.]
[Traver, S.]
[Zeuzem, S.]

Clinical significance of in vitro replication-enhancing mutations of the hepatitis C virus (HCV) replicon in patients with chronic HCV infection.
In: Journal of Infectious Diseases [192], 1710-1719

Journal Article

Mikeska, Thomas

2012

[Mikeska, Thomas]
Bock, Christoph
[Do, Hongdo]
[Dobrovic, Alexander]

DNA methylation biomarkers in cancer: Progress towards clinical implementation
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Journal Article

2009

Schüffler, Peter
[Mikeska, Thomas]
[Waha, Andreas]
Lengauer, Thomas
Bock, Christoph

MethMarker: User-friendly design and optimization of gene-specific DNA methylation assays
In: Genome Biology [10], R105:1-R105:10

Journal Article

2007

[Mikeska, Thomas]
Bock, Christoph
[El-Maarri, Osman]
[Hübner, Anika]
[Ehrentraut, Denise]
[Schramm, Johannes]
[Felsberg, Jörg]
[Kahl, Philip]
[Büttner, Reinhard]
[Pietsch, Torsten]
[Waha, Andreas]

Optimization of Quantitative MGMT Promoter Methylation Analysis Using Pyrosequencing and Combined Bisulfite Restriction Analysis
In: Journal of Molecular Diagnostics [9], 368-381

Journal Article

2006

Bock, Christoph
[Paulsen, Martina]
[Tierling, Sascha]
[Mikeska, Thomas]
Lengauer, Thomas
[Walter, Jörn]

CpG Island Methylation in Human Lymphocytes Is Highly Correlated with DNA Sequence, Repeats, and Predicted DNA Structure
In: PLoS Genetics [2], 0243-0252

Electronic Journal Article

2005

Bock, Christoph
Lengauer, Thomas
[Reither, Sabine]
[Mikeska, Thomas]
[Paulsen, Martina]
[Walter, Jörn]

BiQ Analyzer: visualization and quality control for DNA methylation data from bisulfite sequencing
In: Bioinformatics [21], 4067-4068

Journal Article

Mikkelsen, Tarjei S.

2010

[Gu, Hongcang]
Bock, Christoph
[Mikkelsen, Tarjei S.]
[Jäger, Natalie]
[Smith, Zachary D.]
[Tomazou, Eleni]
[Gnirke, Andreas]
[Lander, Eric S.]
[Meissner, Alexander]

Genome-scale DNA methylation mapping of clinical samples at single-nucleotide resolution
In: Nature Methods [7], 133-136

Journal Article

Milkiewicz, Piotr

2013

Dense genotyping of immune-related disease regions identifies nine new risk loci for primary sclerosing cholangitis
In: Nature Genetics [45], 670-677

Journal Article

Milosavljevic, Aleksandar

2010

Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications
In: Nature Biotechnology [28], 1097-1105

Journal Article

Minna, John D.

2009

Predicting drug susceptibility of non-small cell lung cancers based on genetic lesions
In: Journal of Clinical Investigation [119], 1727-1740

Journal Article

Minucci, Saverio

2012

BLUEPRINT to decode the epigenetic signature written in blood
In: Nature Biotechnology [30], 224-226

Journal Article

Misugi, Susumu

2002

Journal Article

Mitrenga, Markus

2005

[Ulmschneider, Sarah]
[Mueller-Vieira, Ursula]
[Mitrenga, Markus]
[Hartmann, Rolf W.]
[Oberwinkler-Marchais, S]
[Klein, Christian D.]
[Bureik, M.]
[Bernhardt, R.]
Antes, Iris
Lengauer, Thomas

Synthesis and Evaluation of Imidazolylmethylenetetrahydronaphthalenes and Imidazolylmethyleneindanes: Potent Inhibitors of Aldosterone Synthase
In: Journal of Medicinal Chemistry [48], 1796-1805

Journal Article

Mitrovic, Mitja

2013

Dense genotyping of immune-related disease regions identifies nine new risk loci for primary sclerosing cholangitis
In: Nature Genetics [45], 670-677

Journal Article

Miyajima, Hiroaki

2007

[Hofmann, Wolf Peter]
Welsch, Christoph
[Takahashi, Yoshitomo]
[Miyajima, Hiroaki]
[Mihm, Ulrike]
[Krick, Christoph]
[Zeuzem, Stefan]
[Sarrazin, Christoph]

Identification and in silico characterization of a novel compound heterozygosty associated with hereditary aceruloplasminemia
In: Scandinavian Journal of Gastroenterology [42], 1088-1094

Journal Article

Miyano, Satoru (ed.)

2008

Sander, Oliver
Domingues, Francisco S.
Zhu, Hongbo
Lengauer, Thomas
Sommer, Ingolf

Structural descriptors of protein-protein binding sites
In: Proceedings of 6th Asia-Pacific Bioinformatics Conference, 79-88

Proceedings Article

Miyoshi, Anderson

2012

PIPS: Pathogenicity Island Prediction Software
In: PLoS One [7], e30848,1-e30848,10

Electronic Journal Article

2011

[Santos, Anderson R]
[Santos, Marcos A]
Baumbach, Jan
[McCulloch, John A]
[Oliveira, Guilherme C]
[Silva, Artur]
[Miyoshi, Anderson]
[Azevedo, Vasco]

A singular value decomposition approach for improved taxonomy classification of biological sequences
In: BMC Genomics [12], S11,1-S11,15

Journal Article

2011

Evidence for Reductive Genome Evolution and Lateral Acquisition of Virulence Functions in two Corynebacterium pseudotuberculosis strains
In: PLoS One [6], e18551

Electronic Journal Article

Mokrejs, M.

2004

The Helmholtz Network for Bioinformatics: an integrative web portal for bioinformatics resources
In: Bioinformatics [20], 268-270

Journal Article

Molhuizen, H. O.

1999

Mutations in the ABC1 gene in familial HDL deficiency with defective cholesterol efflux
In: The Lancet [354], 1341-6

Journal Article

Molhuizen, H.O.

2001

[Clee, Susanne M.]
[Zwinderman, A.H.]
[Engert, J.C.]
[Zwarts, K.Y.]
[Molhuizen, H.O.]
Roomp, Kirsten
[Jukema, J.W.]
[van Wijland, M]
[van Dam, M]
[Hudson, T.J.]
[Brooks-Wilson, A]
[Genest, Jacques Jr]
[Kastelein, J.J.P.]
[Hayden, Michael R.]

Common genetic variation in ABCA1 is associated with altered lipoprotein levels and a modified risk for coronary artery disease
In: Circulation [103], 1198-205

Journal Article

2000

Age and residual cholesterol efflux affect HDL cholesterol levels and coronary artery disease in ABCA1 heterozygotes
In: Journal of Clinical Investigation [106], 1263-70

Journal Article

1999

Mutations in ABC1 in Tangier disease and familial high-density lipoprotein
In: Nature Genetics [22], 336-45

Journal Article

Monforte, Antonella d'Arminio

2007

[Ceccherini-Silberstein, Francesca]
[Svicher, Valentina]
Sing, Tobias
[Artese, Anna]
[Santoro, Maria Mercedes]
[Forbici, Federica]
[Bertoli, Ada]
[Alcaro, Stefano]
[Palamara, Guido]
[Monforte, Antonella d'Arminio]
[Balzarini, Jan]
[Antinori, Andrea]
Lengauer, Thomas
[Perno, Carlo Federico]

Characterization and structural analysis of novel mutations in human immunodeficiency virus type 1 reverse transcriptase involved in the regulation of restistance to nonnucleoside inhibitors
In: Journal of Virology [81], 11507-11519

Journal Article

Monk, David

2012

A DNA methylation fingerprint of 1628 human samples
In: Genome Research [22], 407-419

Journal Article

Montes, Rosa

2012

A promoter DNA demethylation landscape of human hematopoietic differentiation
In: Nucleic Acids Research [40], 116-131

Journal Article

Montuenga, Luis M.

2013

A Prognostic DNA Methylation Signature for Stage I Non-Small-Cell Lung Cancer
In: Journal of Clinical Oncology [31], 4140-4147

Journal Article

Mooney, Sean D

2013

A large-scale evaluation of computational protein function prediction
In: Nature Methods [10], 221-227

Journal Article

Moores, A

2008

Thielen, Alexander
[Harrigan, P Richard]
Low, Andrew J.
[Moores, A]
Altmann, Andre
Bozek, Kasia
[Heger, Eva]
[Sichtig, Nadine]
[Kaiser, Rolf]
Lengauer, Thomas

Improved genotypic prediction of HIV-1 coreceptor usage by incorporating V2 loop sequence variation
In: Antiviral Therapy, A100

Poster

Moores, Andrew

2010

[Swenson, Luke C.]
[Moores, Andrew]
[Low, Andrew J.]
Thielen, Alexander
[Dong, Winnie]
[Woods, Conan]
[Jensen, Mark A.]
[Wynhoven, Brian]
[Chan, Dennison]
[Glascock, Christopher]
[Harrigan, P. Richard]

Improved detection of CXCR4-using HIV by V3 genotyping: application of population-based and "deep" sequencing to plasma RNA and proviral DNA
In: Journal of Acquired Immune Deficiency Syndromes [54], 506-510

Journal Article

2008

[Moores, Andrew]
Thielen, Alexander
[Dong, Winnie]
Low, Andrew J.
[Woods, Conan]
[Jensen, Mark]
[Wynhoven, Brian]
[Chan, Dennison]
[Glascock, Christopher]
[Harrigan, P Richard]

Improved detection of X4 virus by V3 genotyping: application to plasma RNA and proviral DNA
In: Antiviral Therapy, A99

Poster

Moore, Robert J.

2011

Evidence for Reductive Genome Evolution and Lateral Acquisition of Virulence Functions in two Corynebacterium pseudotuberculosis strains
In: PLoS One [6], e18551

Electronic Journal Article

Mora-Oberlaender, Julian (ed.)

2004

Ramírez, Fidel

Evolucion de la Evolucionalidad
In: Biologos lejos del equilibrio: Nuevas metaforas evolutivas, 59-87

Part of a Book

Moraes, Pablo M. R. O.

2011

Evidence for Reductive Genome Evolution and Lateral Acquisition of Virulence Functions in two Corynebacterium pseudotuberculosis strains
In: PLoS One [6], e18551

Electronic Journal Article

Moran, Sebastian

2013

A Prognostic DNA Methylation Signature for Stage I Non-Small-Cell Lung Cancer
In: Journal of Clinical Oncology [31], 4140-4147

Journal Article

Mora, Jaume

2012

A DNA methylation fingerprint of 1628 human samples
In: Genome Research [22], 407-419

Journal Article

Mora, Josefina

2013

A Prognostic DNA Methylation Signature for Stage I Non-Small-Cell Lung Cancer
In: Journal of Clinical Oncology [31], 4140-4147

Journal Article

Moreno, Victor

2012

A DNA methylation fingerprint of 1628 human samples
In: Genome Research [22], 407-419

Journal Article

Morgan, K

1999

Mutations in ABC1 in Tangier disease and familial high-density lipoprotein
In: Nature Genetics [22], 336-45

Journal Article

Moriarty, Whei F.

2009

Predicting drug susceptibility of non-small cell lung cancers based on genetic lesions
In: Journal of Clinical Investigation [119], 1727-1740

Journal Article

Morris, John H.

2011

[Morris, John H.]
[Apeltsin, Leonard]
[Newman, Aaron M.]
Baumbach, Jan
[Wittkop, Tobias]
[Su, Gang]
[Bader, Gary D.]
[Ferrin, Thomas E.]

clusterMaker: A Multi-algorithm Clustering Plugin for Cytoscape
In: BMC Bioinformatics [12], 436,1-436,14

Journal Article

2010

[Wittkop, Tobias]
Emig, Dorothea
[Lange, Sita]
[Rahmann, Sven]
Albrecht, Mario
[Morris, John H.]
[Böcker, Sebastian]
[Stoye, Jens]
Baumbach, Jan

Partitioning biological data with transitivity clustering
In: Nature Methods [7], 419-420

Journal Article

Morris, Lynn

2010

[Zazzi, Maurizio]
[Kaiser, Rolf]
[Sönnerborg, Anders]
[Struck, Daniel]
Altmann, Andre
[Prosperi, Mattia C. F.]
[Rosen-Zvi, Michal]
[Petroczi, Andrea]
[Peres, Yardena]
[Schülter, Eugen]
[Boucher, Charles]
[Brun-Vezinet, Francoise]
[Harigan, Richard]
[Morris, Lynn]
[Obermeier, Martin]
[Perno, Federico]
[Shafer, Robert]
[Vandamme, Anne-Mieke]
[van Laethem, Kristel]
[Wensing, Annemarie]
Lengauer, Thomas
[Incardona, Francesca]

Prediction of Response to Antiretroviral Therapy by Human Experts and by the EuResist Data-Driven Expert System (the EVE Study)
In: HIV Medicine [Early View], 1-8

Electronic Journal Article

Morris, L.

2011

[Zazzi, M.]
[Kaiser, R.]
[Sönnerborg, A.]
[Struck, D]
Altmann, Andre
[Prosperi, M.]
[Rosen-Zvi, M.]
[Petroczi, A.]
[Peres, Y.]
[Schülter, E.]
[Boucher, C.A.]
[Brun-Vezinet, F.]
[Harrigan, R.]
[Morris, L.]
[Obermeier, M.]
[Perno, C.-F.]
[Phanuphak, P.]
[Pillay, D]
[Shafer, R.W.]
[Vandamme, A.-M.]
[Van Laethem, K.]
[Wensing, A.]
Lengauer, Thomas
[Incardona, F.]

Prediction of Response to Antiretroviral Therapy by Human Experts and by the EuResist Data-Driven Expert System (the EVE study)
In: HIV Medicine [12], 211-218

Journal Article

Mortazavi, A

2013

[Steijger, T]
[Abril, JF]
[Engström,PG]
[Kokocinski, F]
[Abril, JF]
[Akerman, M]
[Alioto, T]
[Ambrosini, G]
[Antonarakis, SE]
[Behr, J]
[Bohnert, R]
[Bucher, P]
[Cloonan, N]
[Derrien, T]
[Djebali, S]
[Du, J]
[Dudoit, S]
[Engström, PG]
[Gerstein, M]
[Gingeras, TR]
[Gonzalez, D]
[Grimmond, SM]
[Habegger, L]
[Iseli, C]
[Jean, G]
[Kahles, A]
[Kokocinski, F]
[Lagarde, J]
[Leng, J]
[Lefebvre, G]
[Lewis, S]
[Mortazavi, A]
[Niermann, P]
[Rätsch, G]
[Reymond, A]
[Ribeca, P]
[Richard, H]
[Rougemont, J]
[Rozowsky, J]
[Sammeth, M]
[Sboner, A]
Schulz, Marcel Holger
[Searle, SM]
[Solorzano, ND]
[Solovyev, V]
[Stanke, M]
[Steijger, T]
[Stevenson, BJ]
[Stockinger, H]
[Valsesia, A]
[Weese, D]
[White, S]
[Wold, BJ]
[Wu, J]
[Wu, TD]
[Zeller, G]
[Zerbino, D]
[Zhang, MQ]
[Hubbard, TJ]
[Guigó, R]
[Harrow, J]
[Bertone, P]

Assessment of transcript reconstruction methods for RNA-seq
In: Nature Methods [10], 1177-84

Journal Article

Moser, Dirk

2009

[Moser, Dirk]
[Ekawardhani, Savira]
[Kumsta, Robert]
[Palmason, Haukur]
Bock, Christoph
[Athanassiadou, Zoi]
[Lesch, Klaus-Peter]
[Meyer, Jobst]

Functional Analysis of a Potassium-Chloride Co-Transporter 3 (SLC12A6) Promoter Polymorphism Leading to an Additional DNA Methylation Site
In: Neuropsychopharmacology [34], 458-467

Journal Article

Mott, S

1999

Mutations in ABC1 in Tangier disease and familial high-density lipoprotein
In: Nature Genetics [22], 336-45

Journal Article

Mott, S.

1999

Mutations in the ABC1 gene in familial HDL deficiency with defective cholesterol efflux
In: The Lancet [354], 1341-6

Journal Article

Mo, Theresa

2011

[Swenson, Luke C.]
[Mo, Theresa]
[Dong, Winnie W. Y.]
[Zhong, Xiaoyin]
[Woods, Conan K.]
[Jensen, Mark A.]
Thielen, Alexander
[Chapman, Douglass]
[Lewis, Marilyn]
[James, Ian]
[Heera, Jayvant]
[Valdez, Hernan]
[Harrigan, P. Richard]

Deep Sequencing to Infer HIV-1 Co-Receptor Usage: Application to Three Clinical Trials of Maraviroc in Treatment-Experienced Patients
In: The Journal of Infectious Diseases [203], 237-245

Journal Article

2011

[Swenson, Luke C]
[Mo, Theresa]
[Dong, Winnie WY]
[Zhong, Xiaoyin]
[Woods, Conan K]
Thielen, Alexander
[Jensen, Mark A]
[Knapp, David JHF]
[Chapman, Douglass]
[Lewis, Marilyn]
[James, Ian]
[Heera, Jayvant]
[Valdez, Hernan]
[Harrigan, P Richard]

Deep V3 sequencing for HIV type 1 tropism in treatment-naive patients: a reanalysis of the MERIT trial of maraviroc.
In: Clinical Infectious Diseases [53], 732-742

Journal Article

2010

[McGovern, Rachel A]
Thielen, Alexander
[Mo, Theresa]
[Dong, Winnie]
[Woods, Conan K]
[Chapman, Douglass]
[Lewis, Marilyn]
[James, Ian]
[Heera, Jayvant]
[Valdez, Hernan]
[Harrigan, P Richard]

Population-based V3 genotypic tropism assay: a retrospective analysis using screening samples from the A4001029 and MOTIVATE studies
In: AIDS [24], 2517-2525

Journal Article

2009

[Harrigan, P Richard]
[McGovern, Rachel]
[Dong, Winnie]
Thielen, Alexander
[Jensen, Mark]
[Mo, Theresa]
[Chapman, Douglas]
[Lewis, Marilyn]
[James, Ian]
[Valdez, Hernan]

Poster

Mrowietz, Ulrich

2010

Genome-wide association study identifies a psoriasis susceptibility locus at TRAF3IP2
In: Nature Genetics [42], 991-995

Journal Article

Mueller-Vieira, Ursula

2005

[Ulmschneider, Sarah]
[Mueller-Vieira, Ursula]
[Mitrenga, Markus]
[Hartmann, Rolf W.]
[Oberwinkler-Marchais, S]
[Klein, Christian D.]
[Bureik, M.]
[Bernhardt, R.]
Antes, Iris
Lengauer, Thomas

Synthesis and Evaluation of Imidazolylmethylenetetrahydronaphthalenes and Imidazolylmethyleneindanes: Potent Inhibitors of Aldosterone Synthase
In: Journal of Medicinal Chemistry [48], 1796-1805

Journal Article

2005

[Ulmschneider, Sarah]
[Mueller-Vieira, Ursula]
[Klein, Christian D.]
Antes, Iris
Lengauer, Thomas
[Hartmann, Rolf W.]

Synthesis and Evaluation of Pyridylmethylene-tetrahydronaphthalenes and -indanes: Potent and Selective Inhibitors of Aldosterone Synthase (CYP11B2)
In: Journal of Medicinal Chemistry [48], 4489-4490

Journal Article

Mueller-Vieira, U.

2005

[Voets, Marieke]
Antes, Iris
[Scherer, C]
[Mueller-Vieira, U.]
[Biemel, K.]
[Barrassin, C.]
[Marchais-Oberwinkler, S.]
[Hartmann, R. W.]

Journal Article

Mueller, Fabian

2012

[Feuerbach, Lars]
Halachev, Konstantin
Assenov, Yassen
Mueller, Fabian
Bock, Christoph
Lengauer, Thomas

Analyzing epigenome data in context of genome evolution and human diseases
In: Evolutionary Genomics : Statistical and Computational Methods, Volume 2, 431-467
In: Methods of Molecular Biology [856], 431-467

Part of a Book

Mueller, Ursula

2003

Antes, Iris
Lengauer, Thomas
Mueller, Ursula
[Ulmschneider, Sarah]
[Hartmann, Rolf]

Docking into the homology models of CYP11B1 and CYP11B2
In: Proceedings of the German Conference on Bioinformatics 2003, 13

Poster

Müller-Quernheim, Joachim

2005

[Valentonyte, Ruta]
[Hampe, Jochen]
[Huse, Klaus]
[Rosenstiel, Philip]
Albrecht, Mario
[Stenzel, Annette]
[Nagy, Marion]
[Gaede, Karoline I.]
[Franke, Andre]
[Haesler, Robert]
[Koch, Andreas]
Lengauer, Thomas
[Seegert, Dirk]
[Reiling, Norbert]
[Ehlers, Stefan]
[Schwinger, Eberhard]
[Platzer, Mathias]
[Krawczak, Michael]
[Müller-Quernheim, Joachim]
[Schürmann, Manfred]
[Schreiber, Stefan]

Sarcoidosis is associated with a truncating splice site mutation in BTNL2
In: Nature Genetics [37], 357-364

Journal Article

Müller-Vieira, Ursula

2006

[Voets, Marieke]
Antes, Iris
[Scherer, Christiane]
[Müller-Vieira, Ursula]
[Biemel, Klaus]
[Marchais-Oberwinkler, Sandrine]
[Hartmann, Rolf W.]

Journal Article

Müller, Barbara

2012

Bozek, Katarzyna
[Eckhardt, Manon]
[Sierra, Saleta]
[Kaiser, Rolf]
[Kräusslich, Hans-Georg]
[Müller, Barbara]
Lengauer, Thomas

An expanded model of HIV cell entry phenotype based on multi-parameter single-cell data
In: Retrovirology [9], 60.1-60.15

Journal Article

Müller, Eva C.

2006

An arginine/lysine-rich motif is crucial for VCP/p97-mediated modulation of ataxin-3 fibrillogenesis
In: EMBO Journal [25], 1547-1558

Journal Article

Müller, Fabian

2013

A Prognostic DNA Methylation Signature for Stage I Non-Small-Cell Lung Cancer
In: Journal of Clinical Oncology [31], 4140-4147

Journal Article

2013

Charting a dynamic DNA methylation landscape of the human genome
In: Nature [500], 477–481

Journal Article

2012

[Xi, Yuanxin]
Bock, Christoph
Müller, Fabian
[Sun, Deqiang]
[Meissner, Alexander]
[Li, Wei]

RRBSMAP: a fast, accurate and user-friendly alignment tool for reduced representation bisulfite sequencing
In: Bioinformatics [28], 430-432

Journal Article

2011

Genomic distribution and inter-sample variation of non-CpG methylation across human cell types
In: PLoS Genetics [17], e1002389,1-e1002389,15

Electronic Journal Article

2011

Saigo, Hiroto
Altmann, André
Bogojeska, Jasmina
Müller, Fabian
[Nowozin, Sebastian]
Lengauer, Thomas

Learning from past treatments and their outcome improves prediction of In Vivo response to anti-HIV therapy
In: Statistical Applications in Genetics and Molecular Biology [10], 1-32

Electronic Journal Article

2011

[Xi, Yuanxin]
Bock, Christoph
Müller, Fabian
[Sun, Deqiang]
[Meissner, Alexander]
[Li, Wei]

RRBSMAP: A Fast, Accurate and User-friendly Alignment Tool for Reduced Representation Bisulfite Sequencing
In: Bioinformatics [28], 430-432

Journal Article

2010

Bock, Christoph
[Tomazou, Eleni M.]
[Brinkman, Arie B.]
Müller, Fabian
[Simmer, Femke]
[Gu, Hongcang]
[Jäger, Natalie]
[Gnirke, Andreas]
[Stunnenberg, Hendrik G.]
[Meissner, Alexander]

Quantitative comparison of genome-wide DNA methylation mapping technologies
In: Nature Biotechnology [28], 1106-1114

Journal Article

2009

Müller, Fabian

Assessing Antibody Neutralization of HIV-1 as an Initial Step in the Search for gp160-based Immunogens
Universität des Saarlandes

Thesis - Masters thesis

2008

Müller, Fabian

Inferring virological response to antiretroviral combination therapy based on past treatment lines
Universität des Saarlandes

Thesis - Bachelor thesis

Müller, Harm

2012

[Obermeier, Martin]
Pironti, Alejandro
[Berg, Thomas]
[Braun, Patrick]
[Däumer, Martin]
[Eberle, Josef]
[Ehret, Robert]
[Kaiser, Rolf]
[Kleinkauf, Niels]
[Korn, Klaus]
[Kücherer, Claudia]
[Müller, Harm]
[Noah, Christian]
[Stürmer, Martin]
Thielen, Alexander
[Wolf, Eva]
[Walter, Hauke]

HIV-GRADE: A Publicly Available, Rules-Based Drug Resistance Interpretation Algorithm Integrating Bioinformatic Knowledge
In: Intervirology [55], 102-107

Journal Article

2009

Thielen, Alexander
[Sichtig, Nadine]
[Braun, Patrick]
[Däumer, Martin]
[Walter, Hauke]
[Noah, Christian]
[Wolf, Eva]
[Müller, Harm]
[Stürmer, Martin]
Lengauer, Thomas
[Kaiser, Rolf]
[Obermeier, Martin]

Performance of genotypic coreceptor measurement using geno2pheno[coreceptor] in B- and non-B HIV subtypes in a large cohort of therapy-experienced patients in Germany
In: Reviews in Antiviral Therapy, 99-99

Poster

2008

[Obermeier, Martin]
[Berg, Thomas]
[Sichtig, Nadine]
[Braun, Patrick]
[Däumer, Martin]
[Walter, Hauke]
[Noah, Christian]
[Wolf, Eva]
[Müller, Harm]
[Stürmer, Martin]
Thielen, Alexander
[Kaiser, Rolf]

Determination of HIV-1 co-receptor usage in German patients – comparison of genotypic methods with the TROFILE® phenotypic assay
In: Abstracts of the Ninth International Congress on Drug Therapy in HIV Infection, 123

Poster

2008

[Obermeier, Martin]
[Sichtig, Nadine]
[Braun, Patrick]
[Däumer, Martin]
[Walter, Hauke]
[Noah, Christian]
[Wolf, Eva]
[Müller, Harm]
[Stürmer, Martin]
[Kaiser, Rolf]
Thielen, Alexander

Determination of HIV-1 coreceptor usage in German patients - comparison of genotypic methods with the TROFILE phenotypic assay
In: Antiviral Therapy, A112

Poster

Müller, Joachim

2012

Müller, Joachim

Extracting pathways from biological networks incorporating omics data, introducing a webinterface for KeyPathwayMiner
Universität des Saarlandes

Thesis - Masters thesis

Müller, Mirko

2008

[Hornstein, Max]
[Hoffmann, Michele J.]
Alexa, Adrian
[Yamanaka, Masanori]
[Müller, Mirko]
[Jung, Volker]
[Rahnenführer, Jörg]
[Schulz, Wolfgang A.]

Protein phosphatase and TRAIL receptor genes as new candidate tumor genes on chromosome 8p in prostate cancer
In: Cancer Genomics & Proteomics [5], 123-136

Journal Article

2007

[Schulz, Wolfgang A.]
Alexa, Adrian
[Jung, Volker]
[Hader, Christiane]
[Hoffmann, Michele J.]
[Yamanaka, Masanori]
[Fritzsche, Sandy]
[Wlazlinski, Agnes]
[Müller, Mirko]
Lengauer, Thomas
[Engers, Rainer]
[Florl, Andrea R.]
[Wullich, Bernd]
Rahnenführer, Jörg

Factor interaction analysis for chromosome 8 and DNA methylation alterations highlights innate immune response suppression and cytoskeletal changes in prostate cancer
In: Molecular Cancer [6], 1-16

Journal Article

Müller, Oliver

2007

Sommer, Ingolf
Müller, Oliver
Domingues, Francisco S.
Sander, Oliver
[Weickert, Joachim]
Lengauer, Thomas

Moment invariants as shape recognition technique for comparing protein binding sites
In: Bioinformatics [23], 3139-3146

Journal Article

2007

Müller, Oliver

Using Shape Retrieval Techniques for Identifying Similar Protein Binding Sites
Universität des Saarlandes

Thesis - Masters thesis

Muller, Tobias

2013

Dense genotyping of immune-related disease regions identifies nine new risk loci for primary sclerosing cholangitis
In: Nature Genetics [45], 670-677

Journal Article

Müller, T.

2004

The Helmholtz Network for Bioinformatics: an integrative web portal for bioinformatics resources
In: Bioinformatics [20], 268-270

Journal Article

Münk, C.

2013

Beggel, Bastian
[Münk, C.]
[Däumer, M.]
[Hauck, K.]
[Häussinger, D.]
Lengauer, Thomas
[Ehrhardt, A.]

Full genome ultra-deep pyrosequencing associates G-to-A-hypermutation of the hepatitis B virus genome with the natural progression of hepatitis B
In: Journal of Viral Hepatitis [12], 882-889

Journal Article

Mun, Y. (ed.)

2002

[Bozinov, Daniel]
Rahnenführer, Jörg
[Burson, Cathy]
[Spiegelstein, Ofer]

Automated Grid Alignment for High-Throughput Analysis of Microarray Images (CIIST-02)
In: Proceedings of the 2002 International Conference on Imaging Science, Systems, and Technology, 161-167

Proceedings Article

Muscarella, Lucia A.

2013

A Prognostic DNA Methylation Signature for Stage I Non-Small-Cell Lung Cancer
In: Journal of Clinical Oncology [31], 4140-4147

Journal Article

Mutzel, Petra

2010

Albrecht, Mario
[Kerren, Andreas]
[Klein, Karsten]
[Kohlbacher, Oliver]
[Mutzel, Petra]
[Paul, Wolfgang]
[Schreiber, Falk]
[Wybrow, Michael]

On open problems in biological network visualization
In: Graph Drawing : 17th International Symposium, GD 2009, 256-267

Proceedings Article

2008

Emig, Dorothea
[Cline, Melissa S.]
[Klein, Karsten]
[Kunert, Anne]
[Mutzel, Petra]
Lengauer, Thomas
Albrecht, Mario

Integrative visual analysis of the effects of alternative splicing on protein domain interaction networks
In: Journal of Integrative Bioinformatics [5], 101-115

Journal Article

2008

Emig, Dorothea
[Klein, Karsten]
[Kunert, Anne]
[Mutzel, Petra]
Albrecht, Mario

Visualizing domain interaction networks and the impact of alternative splicing events
In: Proceedings of the 5th International Conference on BioMedical Visualization (MediVis): Information Visualization in Medical and Biomedical Informatics, 36-43

Proceedings Article

Myers, Gene (ed.)

2002

[Zien, Alexander]
[Fluck, Juliane]
[Zimmer, Ralf]
Lengauer, Thomas

Microarrays: How Many Do You Need?
In: Proceedings of the Sixth Annual Conference on Research in Computational Molecular Biology (RECOMB2002), 321-330

Proceedings Article

Myers, G. (ed.)

2004

Proceedings Twelfth International Conference on Intelligent Systems for Molecular Biology/Third European Conference on Computional Biology 2004 (ISMB/ECCB 2004)

Proceedings

Nadal, Ernest

2013

A Prognostic DNA Methylation Signature for Stage I Non-Small-Cell Lung Cancer
In: Journal of Clinical Oncology [31], 4140-4147

Journal Article

Naess, Sigrid

2013

Dense genotyping of immune-related disease regions identifies nine new risk loci for primary sclerosing cholangitis
In: Nature Genetics [45], 670-677

Journal Article

Nagano, Makoto

2002

Journal Article

Nagarajan, Raman P.

2010

Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications
In: Nature Biotechnology [28], 1097-1105

Journal Article

Nagy, Alinda

2007

The implications of alternative splicing in the ENCODE protein complement
In: Proceedings of the National Academy of Sciences [104], 5495-5500

Journal Article

Nagy, Marion

2005

Sarcoidosis is associated with a truncating splice site mutation in BTNL2
In: Nature Genetics [37], 357-364

Journal Article

Nair, Rajan P.

2010

Genome-wide association study identifies a psoriasis susceptibility locus at TRAF3IP2
In: Nature Genetics [42], 991-995

Journal Article

Nakayama, Emi E.

2010

[Kuroishi, Ayumu]
Bozek, Katarzyna
[Shioda, Tatsuo]
[Nakayama, Emi E.]

A single amino acid substitution of the human immunodeficiency virus type 1 capsid protein affects viral sensitivity to TRIM5 alpha.
In: Retrovirology [7], 58,1-58,10

Electronic Journal Article

2009

[Kono, Ken]
Bozek, Kasia
Domingues, Francisco S.
[Shioda, Tatsuo]
[Nakayama, Emi E.]

Impact of a single amino acid in the variable region 2 of the Old World monkey TRIM5alpha SPRY (B30.2) domain on anti-human immunodeficiency virus type 2 activity
In: Virology [388], 160-168

Journal Article

Narciso, Pasquale

2009

Dynamics of NRTI resistance mutations during therapy interruption
In: AIDS Research and Human Retroviruses [25], 57-64

Journal Article

Nattermann, Jacob

2010

[Lange, Christian Markus]
Roomp, Kirsten
[Dragan, Anette]
[Nattermann, Jacob]
[Michalk, Monika]
[Spengler, Ulrich]
[Weich, Viola]
Lengauer, Thomas
[Zeuzem, Stefan]
[Berg, Thoma]
[Sarrazin, Christoph]

HLA class I allele associations with HCV genetic variants in patients with chronic HCV genotypes 1a or 1b infection
In: Journal of Hepatology [53], 1022-1028

Journal Article

Nattermann, T.

2007

[Ahlenstiel, G.]
Roomp, Kirsten
Däumer, Martin
[Nattermann, T.]
[Vogel, M.]
[Rockstroh, J.K.]
Beerenwinkel, Niko
Kaiser, R.
[Nischalke, H.-D.]
[Sauerbruch, T.]
Lengauer, Thomas
[Spengler, U.]

Selective pressures of HLA genotypes and antiviral therapy on human immunodeficiency virus type 1 sequence mutation at a population level
In: Clinical and Vaccine Immunology [14], 1266-1273

Journal Article

Naumann, T.

2005

[Hessler, G.]
[Zimmermann, M.]
[Matter, H.]
[Evers, A.]
[Naumann, T.]
Lengauer, Thomas
[Rarey, M.]

Multiple-Ligand-Based Virtual Screening: Methods and Applications of the MTree Approach
In: Journal of Medicinal Chemistry [48], 6575-6584

Journal Article

Nebot, Victoria

2011

Nebot, Victoria
Ye, Min
Albrecht, Mario
Eom, Jae-Hong
Weikum, Gerhard

DIDO: a disease-determinants ontology from web sources
In: Proceedings of the 20th International Conference on World Wide Web (WWW 2011), 237-240

Proceedings Article

Negri, Matthias

2008

[Lucas, Simon]
[Heim, Ralph]
[Negri, Matthias]
Antes, Iris
[Ries, Christina]
[Schewe, Katarzyna E.]
[Bisi, Alessandra]
[Gobbi, Silvia]
[Hartmann, Rolf W.]

Novel Aldosterone Synthase Inhibitors with Extended Carbocyclic Skeleton by a Combined Ligand-Based and Structure-Based Drug Design Approach
In: Journal of Medical Chemistry [51], 6138-6149

Journal Article

Nekrutenko, Anton

2010

Bock, Christoph
[Von Kuster, Greg]
Halachev, Konstantin
[Taylor, James]
[Nekrutenko, Anton]
Lengauer, Thomas

Web-based analysis of (epi-) genome data using EpiGRAPH and Galaxy.
In: Genetic Variation : Methods and Protocols, 275-296
In: Methods of Molecular Biology [628], 275-296

Part of a Book

Nepusz, T

2007

[Zazzi, Maurizio]
[Aharoni, Ehud]
[Altmann, Andre]
[Baszó, Fulop]
[Bidgood, Penny]
[Borgulya, Gabór]
[Denholm-Prince, J]
[Fielder, M]
[Kaiser, Rolf]
[Kent, Carmel]
[Lengauer, Thomas]
[Nepusz, T]
[Neuvirth, Hanni]
[Peres, Yardena]
[Petroczi, Andrea]
[Prosperi, Mattia]
[Romano, L]
[Rosen-Zvi, Michal]
[Schülter, Eugen]
Sing, Tobias
[Sonnerborg, Andras]
[Thompson, R]
[Ulivi, G]
[Zalány, L]
[Incardona, Francesca]

EuResist: exploration of multiple modeling techniques for prediction of response to treatment
In: Proceedings of the 5th European HIV Drug Resistance Workshop, -

Poster

Nesvåg, Ragnar

2009

[Lawyer, Glenn]
[Nesvåg, Ragnar]
[Varnäs, Katarina]
[Okugawa, Gaku]
[Agartz, Ingrid]

Grey and white matter proportional relationships in the cerebellar vermis altered in schizophrenia
In: Cerebellum [8], 52-60

Journal Article

Nesvåg, Rangan

2009

[Lawyer, Glenn]
[Ferkingstad, Egil]
[Nesvåg, Rangan]
[Varnäs, Katarina]
[Agartz, Ingrid]

Local and covariate-modulated false discovery rates applied in neuroimaging
In: NeuroImage [47], 213-219

Journal Article

Neumann-Fraune, Maria

2013

[Neumann-Fraune, Maria]
Beggel, Bastian
[Pfister, Herbert]
[Kaiser, Rolf]
[Verheyen, Jens]

High frequency of complex mutational patterns in lamivudine resistant hepatitis B virus isolates
In: Journal of Medical Virology [200], 39-49

Journal Article

2012

Beggel, Bastian
[Neumann-Fraune, Maria]
[Doering, Matthias]
Lawyer, Glenn
[Kaiser, Rolf]
[Verheyen, Jens]
Lengauer, Thomas

Genotyping hepatitis B virus dual infections using population-based sequence data
In: Journal of General Virology [9], 1899-1907

Journal Article

Neumann, Britta

2010

[Kamp, Christel]
[Wolf, Timo]
[Bravo, Ignacio G]
[Kraus, Benjamin]
[Krause, Birgit]
[Neumann, Britta]
[Winskowsky, Gudrun]
Thielen, Alexander
[Werner, Albrecht]
[Schnierle, Barbara S]

Decreased HIV diversity after allogeneic stem cell transplantation of an HIV-1 infected patient: a case report.
In: Virology Journal [7], 55,1-55,9

Electronic Journal Article

Neumann, Dirk

2006

[Neumann, Dirk]
[Kohlbacher, Oliver]
[Merkwirth, Christian]
Lengauer, Thomas

A Fully Computational Model for Predicting Percutaneous Drug Absorption
In: Journal of Chemical Information and Modeling [1], 424-429

Journal Article

2006

[Neumann, Dirk]
[Kohlbacher, Oliver]
[Merkwirth, Christian]
Lengauer, Thomas

Prediction of percutaneous drug absorption
In: Journal of Chemical Information and Modeling [1], 424-429

Journal Article

Neuner, Andreas

2012

Pauling, Josch
Röttger, Richard
[Neuner, Andreas]
[Salgado, Heladia]
[Collado-Vides, Julio]
Kalaghatgi, Prabhav
[Azevedo, Vasco]
[Tauch, Andreas]
[Pühler, Alfred]
Baumbach, Jan

On the trail of EHEC/EAEC - unraveling the gene regulatory networks of human pathogenic Escherichia coli bacteria
In: Integrative Biology [4], 728-733

Journal Article

Neuvirth, Hani

2008

Altmann, Andre
[Rosen-Zvi, Michal]
[Prosperi, Mattia]
[Aharoni, Ehud]
[Neuvirth, Hani]
[Sönnerborg, Anders]
[Schülter, Eugen]
Büch, Joachim
[Struck, Daniel]
[Peres, Yardena]
[Incardona, Francesca]
[Kaiser, Rolf]
[Zazzi, Maurizio]
Lengauer, Thomas

Comparison of Classifier Fusion Methods for Predicting Response to Anti HIV-1 Therapy
In: PLoS ONE [3], e3470

Journal Article

2008

[Rosen-Zvi, Michal]
Altmann, Andre
[Prosperi, Mattia]
[Aharoni, Ehud]
[Neuvirth, Hani]
[Sönnerborg, Anders]
[Schülter, Eugen]
[Struck, Daniel]
[Peres, Yardena]
[Incardona, Francesca]
[Kaiser, Rolf]
[Zazzi, Maurizio]
Lengauer, Thomas

Selecting anti-HIV therapies based on a variety of genomic and clinical factors
In: Proceedings of the 16th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB 2008), i399-406

Proceedings Article

2008

Altmann, Andre
[Rosen-Zvi, Michal]
[Prosperi, Mattia]
[Aharoni, Ehud]
[Neuvirth, Hani]
[Schülter, Eugen]
Büch, Joachim
[Peres, Yardena]
[Incardona, Incardona]
[Sönnerborg, Anders]
[Kaiser, Rolf]
[Zazzi, Maurizio]
Lengauer, Thomas

The EuResist approach for predicting response to anti HIV-1 therapy
In: Reviews in Antiviral Therapy, 107

Poster

Neuvirth, Hanni

2007

EuResist: exploration of multiple modeling techniques for prediction of response to treatment
In: Proceedings of the 5th European HIV Drug Resistance Workshop, -

Poster

Newman, Aaron M.

2011

[Morris, John H.]
[Apeltsin, Leonard]
[Newman, Aaron M.]
Baumbach, Jan
[Wittkop, Tobias]
[Su, Gang]
[Bader, Gary D.]
[Ferrin, Thomas E.]

clusterMaker: A Multi-algorithm Clustering Plugin for Cytoscape
In: BMC Bioinformatics [12], 436,1-436,14

Journal Article

Newman, Scott

2002

Truncation mutations in ABCA1 suppress normal upregulation of full-length ABCA1 by 9-cis-retinoic acid and 22-R-hydroxycholesterol
In: Journal of Lipid Research [43], 1939-1949

Journal Article

Nguyen, Mindie

2010

[Rhee, Soo-Yon]
[Margeridon-Thermet, Severin]
[Nguyen, Mindie]
[Liu, Tommy]
[Kagan, Ron]
Beggel, Bastian
[Verheyen, Jens]
[Kaiser, Rolf]
[Shafer, Robert]

Hepatitis B virus reverse transcriptase sequence variant database for sequence analysis and mutation discovery
In: Antiviral Research [88], 269-275

Journal Article

Nickels, Stefan

2005

Nickels, Stefan

Generating Molecular Hashcodes for
Finding Duplicates in Virtual Screening
Libraries
Universität des Saarlandes

Thesis - Bachelor thesis

Niermann, P

2013

Assessment of transcript reconstruction methods for RNA-seq
In: Nature Methods [10], 1177-84

Journal Article

Nieselt, Kay (ed.)

2006

Schlicker, Andreas
Huthmacher, Carola
Ramírez, Fidel
Lengauer, Thomas
Albrecht, Mario

Functional evaluation of domain-domain interactions and human protein interaction networks
In: German Conference on Bioinformatics (GCB 2006), 115-126

Proceedings Article

Nikolaus, Susanna

2013

Association between variants of PRDM1 and NDP52 and Crohn's disease, based on exome sequencing and functional studies
In: Gastroenterology [145], 339-347

Journal Article

2010

Genome-wide association study for ulcerative colitis identifies risk loci at 7q22 and 22q13 (IL17REL)
In: Nature Genetics [42], 292-294

Journal Article

2008

Sequence variants in IL10, ARPC2, and multiple other loci contribute to ulcerative colitis
In: Nature Genetics [40], 1319-1323

Journal Article

2005

Dissection of the inflammatory bowel disease transcriptome using genome-wide cDNA microarrays identifies novel candidate disease genes
In: PLoS Medicine [2], 771-787

Journal Article

2004

Genetic variation in DLG5 is associated with inflammatory bowel disease
In: Nature Genetics [36], 376-380

Journal Article

Nischalke, H.-D.

2007

[Ahlenstiel, G.]
Roomp, Kirsten
Däumer, Martin
[Nattermann, T.]
[Vogel, M.]
[Rockstroh, J.K.]
Beerenwinkel, Niko
Kaiser, R.
[Nischalke, H.-D.]
[Sauerbruch, T.]
Lengauer, Thomas
[Spengler, U.]

Selective pressures of HLA genotypes and antiviral therapy on human immunodeficiency virus type 1 sequence mutation at a population level
In: Clinical and Vaccine Immunology [14], 1266-1273

Journal Article

Nishida, Yoshiharu

2002

Journal Article

Noah, Christian

2012

HIV-GRADE: A Publicly Available, Rules-Based Drug Resistance Interpretation Algorithm Integrating Bioinformatic Knowledge
In: Intervirology [55], 102-107

Journal Article

2009

Poster

2008

Poster

2008

[Obermeier, Martin]
[Sichtig, Nadine]
[Braun, Patrick]
[Däumer, Martin]
[Walter, Hauke]
[Noah, Christian]
[Wolf, Eva]
[Müller, Harm]
[Stürmer, Martin]
[Kaiser, Rolf]
Thielen, Alexander

Determination of HIV-1 coreceptor usage in German patients - comparison of genotypic methods with the TROFILE phenotypic assay
In: Antiviral Therapy, A112

Poster

Nokso-Koivisto, Jussi

2013

A large-scale evaluation of computational protein function prediction
In: Nature Methods [10], 221-227

Journal Article

Nonhoff, Ute

2005

[Ralser, Markus]
Albrecht, Mario
[Nonhoff, Ute]
Lengauer, Thomas
[Lehrach, Hans]
[Krobitsch, Sylvia]

An integrative approach to gain insights into the cellular function of human ataxin-2
In: Journal of Molecular Biology [346], 203-214

Journal Article

2005

[Ralser, Markus]
[Nonhoff, Ute]
Albrecht, Mario
Lengauer, Thomas
[Wanker, Erich E.]
[Lehrach, Hans]
[Krobitsch, Sylvia]

Ataxin-2 and huntingtin interact with endophilin-A complexes to function in plastin-associated pathways
In: Human Molecular Genetics [14], 2893-2909

Journal Article

Nöthen, Markus M.

2013

Association between variants of PRDM1 and NDP52 and Crohn's disease, based on exome sequencing and functional studies
In: Gastroenterology [145], 339-347

Journal Article

2013

Dense genotyping of immune-related disease regions identifies nine new risk loci for primary sclerosing cholangitis
In: Nature Genetics [45], 670-677

Journal Article

Nothnagel, Michael

2013

Association between variants of PRDM1 and NDP52 and Crohn's disease, based on exome sequencing and functional studies
In: Gastroenterology [145], 339-347

Journal Article

2008

Sequence variants in IL10, ARPC2, and multiple other loci contribute to ulcerative colitis
In: Nature Genetics [40], 1319-1323

Journal Article

Novoselov, Sergey V.

2005

[Castellano, Sergi]
[Lobanov, Alexey V.]
[Chapple, Charles]
[Novoselov, Sergey V.]
Albrecht, Mario
[Hua, Deame]
[Lescure, Alain]
Lengauer, Thomas
[Krol, Alain]
[Gladyshev, Vadim N.]
[Guigó, Roderic]

Diversity and functional plasticity of eukaryotic selenoproteins: Identification and characterization of the SelJ family
In: Proceedings of the National Academy of Sciences [102], 16188-16193

Journal Article

Nowozin, Sebastian

2011

Saigo, Hiroto
Altmann, André
Bogojeska, Jasmina
Müller, Fabian
[Nowozin, Sebastian]
Lengauer, Thomas

Learning from past treatments and their outcome improves prediction of In Vivo response to anti-HIV therapy
In: Statistical Applications in Genetics and Molecular Biology [10], 1-32

Electronic Journal Article

Nürnberg, Peter

2007

Systematic association mapping identifies NELL1 as a novel IBD disease gene
In: PLoS ONE [2], e691.1-13

Journal Article

Nürnberg, P.

2013

Schelhorn, Sven-Eric
[Fischer, M.]
[Tolosi, Laura]
[Altmüller, J.]
[Nürnberg, P.]
[Pfister, H.]
Lengauer, Thomas
Berthold, F.

Sensitive detection of viral transcripts in human tumor transcriptomes
In: PLOS Computational Biology [9], xx

Journal Article

Nykter, Matti (ed.)

2010

Emig, Dorothea
Kacprowski, Tim
Albrecht, Mario

Measuring and analyzing tissue specificity of human genes and protein complexes
In: Seventh International Workshop on Computational Systems
Biology, WCSB 2010, 27-30

Proceedings Article

O'Geen, Heriette

2010

Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications
In: Nature Biotechnology [28], 1097-1105

Journal Article

O'Kelly, Gavin

2011

PSICQUIC and PSISCORE: accessing and scoring molecular interactions
In: Nature Methods [8], 528-529

Journal Article

O'Leary, Dianne

2008

Zotenko, Elena
Mestre, Julian
[O'Leary, Dianne]
[Przytycka, Teresa]

Why Do Hubs in the Yeast Protein Interaction Network Tend To Be Essential: Reexamining the Connection between the Network Topology and Essentiality
In: PLoS Computational Biology [4], e1000140

Journal Article

O Keefe, S.

2004

The Helmholtz Network for Bioinformatics: an integrative web portal for bioinformatics resources
In: Bioinformatics [20], 268-270

Journal Article

Oakley, Derek H.

2011

Reference Maps of Human ES and iPS Cell Variation Enable High-Throughput Characterization of Pluripotent Cell Lines
In: Cell [144], 439-452

Journal Article

Obermeier, Martin

2012

[Heger, Eva]
[Thielen, Alexander]
[Gilles, Ramona]
[Obermeier, Martin]
Lengauer, Thomas
[Kaiser, Rolf]
[Trapp, Susanna]

APOBEC3G/F a one possible driving source for co-receptor switch of the human immunodeficiency virus-1
In: Medical Microbiology and Immunology [201], 7-16

Journal Article

2012

HIV-GRADE: A Publicly Available, Rules-Based Drug Resistance Interpretation Algorithm Integrating Bioinformatic Knowledge
In: Intervirology [55], 102-107

Journal Article

2012

[Obermeier, Martin]
[Camacho, Ricardo]
[Charpentier, Charlotte]
[Deschamps, Diane]
[Eberle, Joseph]
[Gürtler, Lutz]
[Ruelle, Jean]
Pironti, Alejandro
[Brun-Veziet, Francoise]
[Stürmer, Martin]
[Kaiser, Rolf]

HIV2EU: supporting standardized HIV-2 drug resistance interpretation in Europe
In: Journal of the International AIDS Society, 135

Poster

2011

[Heger, Eva]
Thielen, Alexander
[Gilles, Ramona]
[Obermeier, Martin]
Lengauer, Thomas
[Kaiser, Rolf]
[Trapp, Susanna]

APOBEC3G/F as one possible driving force for co-receptor switch of the human immunodeficiency virus-1
In: Medical Microbiology and Immunology [201], 7-16

Journal Article

2010

Prediction of Response to Antiretroviral Therapy by Human Experts and by the EuResist Data-Driven Expert System (the EVE Study)
In: HIV Medicine [Early View], 1-8

Electronic Journal Article

2009

Poster

2008

Poster

2008

[Obermeier, Martin]
[Sichtig, Nadine]
[Braun, Patrick]
[Däumer, Martin]
[Walter, Hauke]
[Noah, Christian]
[Wolf, Eva]
[Müller, Harm]
[Stürmer, Martin]
[Kaiser, Rolf]
Thielen, Alexander

Determination of HIV-1 coreceptor usage in German patients - comparison of genotypic methods with the TROFILE phenotypic assay
In: Antiviral Therapy, A112

Poster

Obermeier, M.

2011

Prediction of Response to Antiretroviral Therapy by Human Experts and by the EuResist Data-Driven Expert System (the EVE study)
In: HIV Medicine [12], 211-218

Journal Article

Oberwinkler-Marchais, S

2005

[Ulmschneider, Sarah]
[Mueller-Vieira, Ursula]
[Mitrenga, Markus]
[Hartmann, Rolf W.]
[Oberwinkler-Marchais, S]
[Klein, Christian D.]
[Bureik, M.]
[Bernhardt, R.]
Antes, Iris
Lengauer, Thomas

Synthesis and Evaluation of Imidazolylmethylenetetrahydronaphthalenes and Imidazolylmethyleneindanes: Potent Inhibitors of Aldosterone Synthase
In: Journal of Medicinal Chemistry [48], 1796-1805

Journal Article

Oberwinkler, Heike

2012

Kalinina, Olga V.
[Oberwinkler, Heike]
[Glass, Bärbel]
[Kräusslich, Hans-Georg]
[Russell, Robert B.]
[Briggs, John A. G.]

Computational Identification of Novel Amino-Acid Interactions in HIV Gag via Correlated Evolution
In: PLoS ONE [7], e42468,1-e42468,5

Electronic Journal Article

Ochs, D.

2011

[Welker, M.-W.]
Welsch, Christoph
[Ochs, D.]
[Hofmann, W. P.]
[Herrmann, E.]
[Piiper, A.]
[Hartmann, R. W.]
[Zeuzem, S.]
[Sarrazin, C.]
[Kronenberger, Bernd]

Comparison of Envelope 2 CD81 binding regions in PBMC-derived versus serum-derived hepatitis C virus isolates: higher conservation of CD81 region 2 in PBMC isolates
In: Journal of Viral Hepatitis [18], 181-192

Journal Article

Oette, Mark

2012

[Oette, Mark]
[Schulter, Eugen]
[Rosen-Zvi, Michal]
[Peres, Yardena]
[Zazzi, Maurizio]
[Sonnerborg, Anders]
[Struck, Daniel]
Altmann, Andre
[Kaiser, Rolf]

Efficacy of antiretroviral therapy switch in HIV-infected patients: A 10-year analysis of the EuResist cohort
In: Intervirology [55], 160-166

Journal Article

2012

Lawyer, Glenn
[Schülter, Eugen]
[Kaiser, Rolf]
[Reuter, Stefan]
[Oette, Mark]
Lengauer, Thomas

Endogenous or exogenous spreading of HIV-1 in Nordrhein-Westfalen, Germany, investigated by phylodynamic analysis of the RESINA Study cohort
In: Medical Microbiology and Immunology [201], 259-269

Journal Article

2012

[Reuter, Stefan]
[Oette, Mark]
[Kaiser, Rolf]
Lengauer, Thomas
[Fätkenheuer, Gerd]
[Rockstroh, Jürgen]
[Knechten, Heribert]
[Häussinger, Dieter]

Risk factors associated with older age in treatment-naive HIV-positive patients
In: Intervirology [55], 147-153

Journal Article

2011

[Reuter, Stefan]
[Oette, Mark]
[Wilhelm, Frank Clemens]
Beggel, Bastian
[Kaiser, Rolf]
[Balduin, Melanie]
[Schweitzer, Finja]
[Verheyen, Jens]
[Adams, Ortwin]
Lengauer, Thomas
[Faetkenheuer, Gerd]
[Pfister, Herbert]
[Haeussinger, Dieter]

Erratum to: Prevalence and characteristics of hepatitis B and C virus infections in treatment-naïve HIV-infected patients.
In: Medical Microbiology and Immunology [200], 51-51

Journal Article

2011

[Schülter, Eugen]
[Oette, Mark]
[Balduin, Melanie]
[Reuter, Stefan]
[Rockstroh, Jürgen]
[Fätkenheuer, Gerd]
[Esser, Stefan]
Lengauer, Thomas
[Agacfidan, Ali]
[Pfister, Herbert]
[Kaiser, Rolf]
[Akgul, Baki]

HIV prevalence and route of transmission in Turkish immigrants
living in North-Rhine Westphalia, Germany
In: Medical Microbiology and Immunology [200], 219-223

Journal Article

2011

[Sierra, Saleta]
[Kaiser, Rolf]
[Lübke, Nadine]
Thielen, Alexander
[Schuelter, Eugen]
[Heger, Eva]
[Däumer, Martin]
[Reuter, Stefan]
[Esser, Stefan]
[Fätkenheuer, Gerd]
[Pfister, Herbert]
[Oette, Mark]
Lengauer, Thomas

Prediction of HIV-1 coreceptor usage (tropism) by sequence analysis using a genotypic approach
In: Journal of Visualized Experiments [58], e3264,1-e3264,9

Electronic Journal Article

2011

Prevalence and characteristics of hepatitis B and C virus infections in treatment-naïve HIV-infected patients
In: Medical Microbiology and Immunology [200], 39-49

Journal Article

2008

[Rosen-Zvi, Michal]
[Schülter, Eugen]
Altmann, Andre
[Sierra-Aragon, Saleta]
[Zazzi, Maurizio]
[Sönnerborg, Anders]
[Oette, Mark]
Lengauer, Thomas
[Kaiser, Rolf]

Sustaining lamivudine/emtricitabine, abacavir, zidovudine or atazanavir from a previous treatment shows a clinical benefit
In: Antiviral Therapy, A86

Poster

2006

[Verheyen, Jens]
[Litau, Elena]
Sing, Tobias
[Däumer, Martin]
[Balduin, Melanie]
[Oette, Mark]
[Fätkenheuer, Gerd]
[Rockstroh, Jürgen K.]
[Schuldenzucker, Ulrike]
[Hoffmann, Daniel]
[Pfister, Herbert]
[Kaiser, Rolf]

Compensatory mutations at the HIV cleavage sites p7/p1 and p1/p6-gag in therapy-naive and therapy-experienced patients
In: Antiviral Therapy [11], 879-887

Journal Article

2005

Sing, Tobias
[Svicher, Valentina]
Beerenwinkel, Niko
[Ceccherini-Silberstein, Francesca]
[Däumer, Martin]
[Kaiser, Rolf]
[Walter, Hauke]
[Korn, Klaus]
[Hoffmann, Daniel]
[Oette, Mark]
[Rockstroh, Jürgen K.]
Fätkenheuer, Gerd
[Perno, Carlo-Federico]
Lengauer, Thomas

Characterization of novel HIV Drug Resistance Mutations using clustering, multidimensional scaling and SVM-based feature ranking
In: Knowledge Discovery in Databases: PKDD 2005., 285-296

Proceedings Article

2005

[Beerenwinkel, Niko]
Sing, Tobias
Lengauer, Thomas
Rahnenführer, Jörg
Roomp, Kirsten
Savenkov, Igor
[Fischer, Roman]
[Hoffmann, Daniel]
[Selbig, Joachim]
[Korn, Klaus]
[Walter, Hauke]
[Berg, Thomas]
[Braun, Patrick]
[Fätkenheuer, Gerd]
[Oette, Mark]
[Rockstroh, Jürgen]
[Kupfer, Bernd]
[Kaiser, Rolf]
[Däumer, Martin]

Computational methods for the design of effective therapies against drug resistant HIV strains
In: Bioinformatics [21], 3943-3950

Journal Article

2005

[Balduin, Melanie]
Beerenwinkel, Niko
[Sierra, Saleta]
[Däumer, Martin]
[Rockstroh, Jürgen]
[Oette, Mark]
[Fätkenheuer, Gerd]
[Kupfer, Bernd]
[Hoffmann, Daniel]
[Selbig, Joachim]
[Pfister, Herbert]
[Kaiser, Rolf]

Evolution of HIV resistance during treatment interruption in experienced patients and after restarting a new therapy
In: J Clin Virol [34], 277-287

Journal Article

2003

Beerenwinkel, Niko
[Däumer, Martin]
[Oette, Mark]
[Korn, Klaus]
[Hoffmann, Daniel]
[Kaiser, Rolf]
Lengauer, Thomas
[Selbig, Joachim]
[Walter, Hauke]

Geno2pheno: estimating phenotypic drug resistance from HIV-1 genotypes
In: Nucleic Acids Research [31], 3850-3855

Journal Article

2002

Beerenwinkel, Niko
Lengauer, Thomas
[Däumer, Martin]
[Sierra, S.]
[Schmidt, Barbara]
[Walter, Hauke]
[Korn, Klaus]
[Oette, Mark]
Fätkenheuer, Gerd
[Rockstroh, J.]
[Hoffmann, Daniel]
[Kaiser, Rolf]
[Selbig, Joachim]

Geno2pheno is predictive of short-term virological response
In: Proceedings from the 5th International Workshop on HIV Drug Resistance & Treatment Strategies, 74-74

Proceedings Article

Oette, Mark (ed.)

2004

Beerenwinkel, Niko

Das Arevir-Projekt : neue Wege zur Optimierung von Anti-HIV-Therapien
In: Resistenz in der HIV-Therapie : Diagnostik und Management, 94-98

Part of a Book

2004

Beerenwinkel, Niko

Methoden zur Interpretation genotypischer Resistenztests
In: Resistenz in der HIV-Therapie : Diagnostik und Management, 66-68

Part of a Book

Oette, M. (ed.)

2007

European Journal of Medical Research

Journal

Ogorzalek, Maciej

2004

Merkwirth, Christian
[Bröcker, J.]
[Ogorzalek, Maciej]
Wichard, J.D.

Proceedings Article

2004

[Wichard, J.D.]
[Ogorzalek, Maciej]
Merkwirth, Christian
[Bröcker, J.]

Finite iteration DT-CNN with stationary templates
In: Proceedings of the 8th IEEE International Workshop on Cellular Neural Networks and their Applications (CNNA 2004), 459-464

Proceedings Article

2003

Merkwirth, Christian
[Ogorzalek, Maciej]
[Wichard, Jörg Daniel]

Stochastic Gradient Descent Training of Ensembles of DT-CNN Classifiers for Digit Recognition
In: Proceedings of the 16th European Conference on Circuit Theory and Design ECCTD'03, 337-341

Proceedings Article

Ogorzalek, Maciej (ed.)

2003

Merkwirth, Christian
[Ogorzalek, Maciej]
[Wichard, Jörg Daniel]

Stochastic Gradient Descent Training of Ensembles of DT-CNN Classifiers for Digit Recognition
In: Proceedings of the 16th European Conference on Circuit Theory and Design ECCTD'03, 337-341

Proceedings Article

Ohama, Tohru

2002

Journal Article

Öhsen von, Niklas

2004

[Öhsen von, Niklas]
Sommer, Ingolf
[Zimmer, Ralf]
Lengauer, Thomas

Arby: Automatic protein structure prediction using profile-profile alignment and confidence measures
In: Bioinformatics [20], 2228-2235

Journal Article

2002

Sommer, Ingolf
[Zien, Alexander]
[Öhsen von, Niklas]
[Zimmer, Ralf]
Lengauer, Thomas

Confidence measures for protein fold recognition
In: Bioinformatics [18], 802-812

Journal Article

Okugawa, Gaku

2009

[Lawyer, Glenn]
[Nesvåg, Ragnar]
[Varnäs, Katarina]
[Okugawa, Gaku]
[Agartz, Ingrid]

Grey and white matter proportional relationships in the cerebellar vermis altered in schizophrenia
In: Cerebellum [8], 52-60

Journal Article

Ólason, Páll Í.

2007

The implications of alternative splicing in the ENCODE protein complement
In: Proceedings of the National Academy of Sciences [104], 5495-5500

Journal Article

Oldenburg, Johannes

2007

Fifteen years of env C2V3C3 evolution in six individuals clonally infected with human immunodeficiency virus type 1
In: Journal of Medical Virology [79], 1629-1639

Journal Article

Oliveira, Diana M.

2011

Evidence for Reductive Genome Evolution and Lateral Acquisition of Virulence Functions in two Corynebacterium pseudotuberculosis strains
In: PLoS One [6], e18551

Electronic Journal Article

Oliveira, Guilherme C

2011

[Santos, Anderson R]
[Santos, Marcos A]
Baumbach, Jan
[McCulloch, John A]
[Oliveira, Guilherme C]
[Silva, Artur]
[Miyoshi, Anderson]
[Azevedo, Vasco]

A singular value decomposition approach for improved taxonomy classification of biological sequences
In: BMC Genomics [12], S11,1-S11,15

Journal Article

Oliveira, Guilherme C.

2011

Evidence for Reductive Genome Evolution and Lateral Acquisition of Virulence Functions in two Corynebacterium pseudotuberculosis strains
In: PLoS One [6], e18551

Electronic Journal Article

Oliveira, Luciana M.

2011

Evidence for Reductive Genome Evolution and Lateral Acquisition of Virulence Functions in two Corynebacterium pseudotuberculosis strains
In: PLoS One [6], e18551

Electronic Journal Article

Oliveira, Sergio C.

2011

Evidence for Reductive Genome Evolution and Lateral Acquisition of Virulence Functions in two Corynebacterium pseudotuberculosis strains
In: PLoS One [6], e18551

Electronic Journal Article

Olsen, Lars

2003

[Olsen, Lars]
[Antony, Jens]
[Ryde, Ulf]
Adolph, Hans-Werner
[Hemmingsen, Lars]

Lactam hydrolysis catalyzed by mononuclear metallo-beta-lactamases: a density functional study
In: Journal of Physical Chemistry / B [107], 2366-2375

Journal Article

Olshen, Adam

2010

Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications
In: Nature Biotechnology [28], 1097-1105

Journal Article

Onengut-Gumuscu, Suna

2013

Dense genotyping of immune-related disease regions identifies nine new risk loci for primary sclerosing cholangitis
In: Nature Genetics [45], 670-677

Journal Article

Onnie, Clive M.

2010

Genome-wide association study for ulcerative colitis identifies risk loci at 7q22 and 22q13 (IL17REL)
In: Nature Genetics [42], 292-294

Journal Article

2008

Sequence variants in IL10, ARPC2, and multiple other loci contribute to ulcerative colitis
In: Nature Genetics [40], 1319-1323

Journal Article

2007

A genome-wide association scan of nonsynonymous SNPs identifies a susceptibility variant for Crohn disease in ATG16L1
In: Nature Genetics [39], 207-211

Journal Article

2007

Systematic association mapping identifies NELL1 as a novel IBD disease gene
In: PLoS ONE [2], e691.1-13

Journal Article

Ono, Keiichiro

2011

PSICQUIC and PSISCORE: accessing and scoring molecular interactions
In: Nature Methods [8], 528-529

Journal Article

Orchard, Sandra

2011

PSICQUIC and PSISCORE: accessing and scoring molecular interactions
In: Nature Methods [8], 528-529

Journal Article

2007

The implications of alternative splicing in the ENCODE protein complement
In: Proceedings of the National Academy of Sciences [104], 5495-5500

Journal Article

Orengo, Christine

2013

A large-scale evaluation of computational protein function prediction
In: Nature Methods [10], 221-227

Journal Article

Orengo, Christine A.

2008

[Watson, James D.]
[Thornton, Janet M.]
[Tress, Michael L.]
[Lopez, Gonzalo]
[Valencia, Alfonso]
[Redfern, Oliver]
[Orengo, Christine A.]
Sommer, Ingolf
Domingues, Francisco S.

Structure to function
In: Modern Genome Annotation, 239-262

Part of a Book

2007

The implications of alternative splicing in the ENCODE protein complement
In: Proceedings of the National Academy of Sciences [104], 5495-5500

Journal Article

Oron, Tal Ronnen

2013

A large-scale evaluation of computational protein function prediction
In: Nature Methods [10], 221-227

Journal Article

Orsini, Massimiliano

2007

The implications of alternative splicing in the ENCODE protein complement
In: Proceedings of the National Academy of Sciences [104], 5495-5500

Journal Article

Ortega, Jose Miguel

2011

Evidence for Reductive Genome Evolution and Lateral Acquisition of Virulence Functions in two Corynebacterium pseudotuberculosis strains
In: PLoS One [6], e18551

Electronic Journal Article

Ortuso, Francesca

2009

[Alcaro, Stefano]
[Artese, Anna]
[Ceccherini-Silberstein, Francesca]
[Ortuso, Francesca]
[Perno, Carlo Federico]
Sing, Tobias
[Svicher, Valentina]

Molecular Dynamics and Free Energy Studies on the Wild-Type and Mutated HIV-1
Protease Complexed with Four Approved Drugs: Mechanism of Binding and
In: Journal of Chemical Information and Modeling [49], 1751-1761

Journal Article

Ortuso, Francesco

2011

Journal Article

Osbahr, Carola

2011

[Hofmann, Wolf Peter]
[Chung, Tje Lin]
[Osbahr, Carola]
[Susser, Simone]
[Karey, Ursel]
[Mihm, Ulrike]
Welsch, Christoph
[Lötsch, Jörn]
[Sarrazin, Christoph]
[Zeuzem, Stefan]
[Herrmann, Eva]

Impact of ribavirin on HCV replicon RNA decline during treatment with interferon-α and the protease inhibitors boceprevir or telaprevir
In: Antiviral Therapy [16], 695-704

Journal Article

Oster, George

2003

Antes, Iris
[Wang, Hongyun]
[Chandler, David]
[Oster, George]

The unbinding of ATP from F1-ATPase
In: Biophysical Journal [85], 695-706

Journal Article

2002

Antes, Iris
[Chandler, David]
[Oster, George]

A classical dynamics study of the unbinding of ATP from the F0F1-ATPase
In: Poster book of the European Conference on Computational Biology, Saarbrücken, Germany 2002, -

Poster

Ouelette, B. F.

1999

Mutations in the ABC1 gene in familial HDL deficiency with defective cholesterol efflux
In: The Lancet [354], 1341-6

Journal Article

Ouelette, B.F.

1999

Mutations in ABC1 in Tangier disease and familial high-density lipoprotein
In: Nature Genetics [22], 336-45

Journal Article

Ouwehand, Willem H

2012

BLUEPRINT to decode the epigenetic signature written in blood
In: Nature Biotechnology [30], 224-226

Journal Article

Overington, John

2011

PSICQUIC and PSISCORE: accessing and scoring molecular interactions
In: Nature Methods [8], 528-529

Journal Article

Paccanaro, Alberto

2013

A large-scale evaluation of computational protein function prediction
In: Nature Methods [10], 221-227

Journal Article

Pacheco, Luis G. C.

2011

Evidence for Reductive Genome Evolution and Lateral Acquisition of Virulence Functions in two Corynebacterium pseudotuberculosis strains
In: PLoS One [6], e18551

Electronic Journal Article

Padyukov, Leonid

2013

Dense genotyping of immune-related disease regions identifies nine new risk loci for primary sclerosing cholangitis
In: Nature Genetics [45], 670-677

Journal Article

Pagel, Philipp

2009

[Frishman, Dmitrij]
Albrecht, Mario
Blankenburg, Hagen
[Bork, Peer]
[Harrington, Eoghan D.]
[Hermjakob, Henning]
[Jensen, Lars J.]
[Juan, David A.]
Lengauer, Thomas
[Pagel, Philipp]
[Schachter, Vincent]
[Valencia, Alfonso]

Protein-protein interactions: analysis and prediction
In: Modern Genome Annotation - The Biosapiens Network, 353-410

Part of a Book

Paiva, Luciano V.

2011

Evidence for Reductive Genome Evolution and Lateral Acquisition of Virulence Functions in two Corynebacterium pseudotuberculosis strains
In: PLoS One [6], e18551

Electronic Journal Article

Pajares, Maria J.

2013

A Prognostic DNA Methylation Signature for Stage I Non-Small-Cell Lung Cancer
In: Journal of Clinical Oncology [31], 4140-4147

Journal Article

Palamara, Guido

2007

Journal Article

Palmason, Haukur

2009

[Moser, Dirk]
[Ekawardhani, Savira]
[Kumsta, Robert]
[Palmason, Haukur]
Bock, Christoph
[Athanassiadou, Zoi]
[Lesch, Klaus-Peter]
[Meyer, Jobst]

Functional Analysis of a Potassium-Chloride Co-Transporter 3 (SLC12A6) Promoter Polymorphism Leading to an Additional DNA Methylation Site
In: Neuropsychopharmacology [34], 458-467

Journal Article

Palmer, Leslie

2011

[Kumar, Vinod]
Sun, Peng
[Vamathevan, Jessica]
[Li, Yong]
[Ingraham, Karen]
[Palmer, Leslie]
[Huang, Jianzhong]
[Brown, James R.]

Comparative Genomics of Klebsiella pneumoniae Strains with Different Antibiotic Resistance Profiles
In: Antimicrobial Agents and Chemotherapy [55], 4267-4276

Journal Article

Pandey, Gaurav

2013

A large-scale evaluation of computational protein function prediction
In: Nature Methods [10], 221-227

Journal Article

Pandit, Kusum V

2013

Schulz, Marcel Holger
[Pandit, Kusum V]
[Lino Cardenas, Christian L]
[Ambalavanan,Namasivayam]
[Kaminski, Naftali]
[Bar-Joseph, Ziv]

Reconstructing dynamic microRNA-regulated interaction networks
In: Proceedings of the National Academy of Sciences of the United States [110], 15686–15691

Journal Article

Panov, Pan

v{c}e

2013

A large-scale evaluation of computational protein function prediction
In: Nature Methods [10], 221-227

Journal Article

Paredes, Roger

2011

[Codoner, Francisco]
[Pou, Christian]
Thielen, Alexander
[García, Federico]
[Delgado, Rafael]
[Dalmau, David]
[Álvarez-Tejado, Miguel]
[Ruiz, Lidia]
[Clotet, Bonaventura]
[Paredes, Roger]

Added value of deep sequencing relative to population sequencing in heavily pre-treated HIV-1-infected subjects
In: PLoS One [6], e19461,1-e19461,5

Electronic Journal Article

2010

Dynamic escape of pre-existing raltegravir-resistant HIV-1 from raltegravir selection pressure
In: Antiviral Research [88], 281-286

Journal Article

Pares, Albert

2013

Dense genotyping of immune-related disease regions identifies nine new risk loci for primary sclerosing cholangitis
In: Nature Genetics [45], 670-677

Journal Article

Parkes, Miles

2013

Association between variants of PRDM1 and NDP52 and Crohn's disease, based on exome sequencing and functional studies
In: Gastroenterology [145], 339-347

Journal Article

Park, Peter J.

2011

Lung stem cell self-renewal relies on BMI1-dependent control of expression at imprinted loci
In: Cell Stem Cell [9], 272-280

Journal Article

Parrotta, Lucia

2011

Journal Article

Patil, Kaustubh Raosaheb

2013

Patil, Kaustubh Raosaheb

Genome Signature based Sequence Comparison for Taxonomic Assignment and tree inference
Universität des Saarlandes

Thesis - PhD thesis

Patthy, László

2007

The implications of alternative splicing in the ENCODE protein complement
In: Proceedings of the National Academy of Sciences [104], 5495-5500

Journal Article

Pauling, Josch

2012

Hauschild, Anne-Christin
[Schneider, Till]
Pauling, Josch
[Rupp, Kathrin]
[Jang, Mi]
[Baumbach, Jörg Ingo]
Baumbach, Jan

Computational Methods for Metabolomic Data Analysis of Ion Mobility Spectrometry Data - Reviewing the State of the Art
In: Metabolites [2], 733-755

Electronic Journal Article

2012

Pauling, Josch
Röttger, Richard
[Tauch, Andreas]
[Azevedo, Vasco]
Baumbach, Jan

CoryneRegNet 6.0 - Updated database content, new analysis methods and novel features focusing on community demands
In: Nucleic Acids Research [40], D610-D614

Journal Article

2012

Pauling, Josch
Röttger, Richard
[Neuner, Andreas]
[Salgado, Heladia]
[Collado-Vides, Julio]
Kalaghatgi, Prabhav
[Azevedo, Vasco]
[Tauch, Andreas]
[Pühler, Alfred]
Baumbach, Jan

On the trail of EHEC/EAEC - unraveling the gene regulatory networks of human pathogenic Escherichia coli bacteria
In: Integrative Biology [4], 728-733

Journal Article

Paulsen, Martina

2008

Bock, Christoph
[Walter, Jörn]
[Paulsen, Martina]
Lengauer, Thomas

Inter-individual variation of DNA methylation and its implications for large-scale epigenome mapping
In: Nucleic Acids Research [36], e55

Journal Article

2008

Kircher, Martin
Bock, Christoph
Paulsen, Martina

Structural conservation versus functional divergence of maternally expressed microRNAs in the Dlk1/Gtl2 imprinting region
In: BMC Genomics [9], 346

Journal Article

2007

Bock, Christoph
[Walter, Jörn]
[Paulsen, Martina]
Lengauer, Thomas

CpG Island Mapping by Epigenome Prediction
In: PLoS Computational Biology [3], 1055-1070

Journal Article

2006

Bock, Christoph
[Paulsen, Martina]
[Tierling, Sascha]
[Mikeska, Thomas]
Lengauer, Thomas
[Walter, Jörn]

CpG Island Methylation in Human Lymphocytes Is Highly Correlated with DNA Sequence, Repeats, and Predicted DNA Structure
In: PLoS Genetics [2], 0243-0252

Electronic Journal Article

2005

Bock, Christoph
Lengauer, Thomas
[Reither, Sabine]
[Mikeska, Thomas]
[Paulsen, Martina]
[Walter, Jörn]

BiQ Analyzer: visualization and quality control for DNA methylation data from bisulfite sequencing
In: Bioinformatics [21], 4067-4068

Journal Article

Paul, Wolfgang

2010

Albrecht, Mario
[Kerren, Andreas]
[Klein, Karsten]
[Kohlbacher, Oliver]
[Mutzel, Petra]
[Paul, Wolfgang]
[Schreiber, Falk]
[Wybrow, Michael]

On open problems in biological network visualization
In: Graph Drawing : 17th International Symposium, GD 2009, 256-267

Proceedings Article

Pauwels, Edouard

2011

[Yamanishi, Yoshihiro]
[Pauwels, Edouard]
Saigo, Hiroto
[Stovent, Veronique]

Extracting Sets of Chemical Substructures and Protein Domains Governing Drug-Target Interactions
In: Journal of Chemical Information and Modeling [51], 1183-1194

Journal Article

Pedrosa, Andre L.

2011

Evidence for Reductive Genome Evolution and Lateral Acquisition of Virulence Functions in two Corynebacterium pseudotuberculosis strains
In: PLoS One [6], e18551

Electronic Journal Article

Peinado, M.

2003

[Peinado, M.]
Lengauer, Thomas

Parallel "go with the winners algorithms" in Distributed Memory Models
In: Journal of Parallel and Distributed Processing [63], 801-814

Journal Article

Pelicci, Pier Giuseppe

2012

BLUEPRINT to decode the epigenetic signature written in blood
In: Nature Biotechnology [30], 224-226

Journal Article

Pelizzola, Mattia

2010

Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications
In: Nature Biotechnology [28], 1097-1105

Journal Article

Pendeville, Hèléne

2012

BLUEPRINT to decode the epigenetic signature written in blood
In: Nature Biotechnology [30], 224-226

Journal Article

Pepperkok, Rainer

2011

Recruitment and activation of a lipid kinase by hepatitis C virus NS5A is essential for integrity of the membranous replication compartment
In: Cell Host & Microbe [9], 32-45

Journal Article

Pereira, Fernando (ed.)

2011

Bogojeska, Jasmina

History distribution matching method for predicting effectiveness of HIV combination therapies
In: Neural Information Processing Systems (NIPS 2011), 424-432

Electronic Proceedings Article

Peres, Yardena

2012

[Oette, Mark]
[Schulter, Eugen]
[Rosen-Zvi, Michal]
[Peres, Yardena]
[Zazzi, Maurizio]
[Sonnerborg, Anders]
[Struck, Daniel]
Altmann, Andre
[Kaiser, Rolf]

Efficacy of antiretroviral therapy switch in HIV-infected patients: A 10-year analysis of the EuResist cohort
In: Intervirology [55], 160-166

Journal Article

2010

Prediction of Response to Antiretroviral Therapy by Human Experts and by the EuResist Data-Driven Expert System (the EVE Study)
In: HIV Medicine [Early View], 1-8

Electronic Journal Article

2009

Altmann, André
Sing, Tobias
[Vermeiren, Hans]
[Winters, Bart]
[Van Craenenbroeck, Elke]
[Van der Borght, Koen]
[Rhee, Soo-Yon]
Shafer, Robert W.
[Schülter, Eugen]
[Kaiser, Rolf]
[Peres, Yardena]
[Sönnerborg, Anders]
Fessel, W. Jeffrey
[Incardona, Francesca]
[Zazzi, Maurizio]
[Bacheler, Lee]
[Van Vlijmen, Hermann]
Lengauer, Thomas

Advantages of Predicted Phenotypes and Statistical Learning Models in Inferring Virological Response to Antiretroviral Therapy from HIV Genotype
In: Antiviral Therapy [14], 273-283

Journal Article

2009

Altmann, André
[Däumer, Martin]
[Beerenwinkel, Niko]
[Peres, Yardena]
[Schülter, Eugen]
Büch, Joachim
[Rhee, Soo-Yon]
[Sönnerborg, Anders]
[Fessel, W. Jeffrey]
[Shafer, Robert W.]
[Zazzi, Maurizio]
[Kaiser, Rolf]
Lengauer, Thomas

Predicting the Response to Combination Antiretroviral Therapy: Retrospective Validation of
geno2pheno-THEO on a Large Clinical Database
In: The Journal of Infectious Diseases [199], 999-1006

Journal Article

2008

Comparison of Classifier Fusion Methods for Predicting Response to Anti HIV-1 Therapy
In: PLoS ONE [3], e3470

Journal Article

2008

Proceedings Article

2008

The EuResist approach for predicting response to anti HIV-1 therapy
In: Reviews in Antiviral Therapy, 107

Poster

2007

EuResist: exploration of multiple modeling techniques for prediction of response to treatment
In: Proceedings of the 5th European HIV Drug Resistance Workshop, -

Poster

2007

Altmann, Andre
Sing, Tobias
[Vermeiren, Hans]
[Winters, Bart]
[Van Craenenbroeck, Elke]
[Van der Borght, Koen]
[Rhee, Soo-Yon]
[Shafer, Robert W]
[Schülter, Eugen]
[Kaiser, Rolf]
[Peres, Yardena]
[Sonnerborg, Anders]
[Fessel, W Jeffrey]
[Incardona, Francesca]
[Zazzi, Maurizio]
[Bacheler, Lee]
[Van Vlijmen, Hermann]
Lengauer, Thomas

Inferring virological response from genotype: with or without predicted phenotypes?
In: Proceedings of the 16th International HIV Drug Resistance Workshop, S169

Poster

Peres, Y.

2011

Prediction of Response to Antiretroviral Therapy by Human Experts and by the EuResist Data-Driven Expert System (the EVE study)
In: HIV Medicine [12], 211-218

Journal Article

Pérez-García, Vicente

2012

A promoter DNA demethylation landscape of human hematopoietic differentiation
In: Nucleic Acids Research [40], 116-131

Journal Article

Perez-Jurado, Luis

2012

A DNA methylation fingerprint of 1628 human samples
In: Genome Research [22], 407-419

Journal Article

Pérez Rodríguez, Paulino (ed.)

2010

Ramirez, Fidel

Tutorial Cytoscape
In: Bioinformática: Aplicaciones a la genómica y proteómica, 73-98

Part of a Book

Perner, Juliane

2010

Altmann, Andre
Pironti, Alejandro
Perner, Juliane
Büch, Joachim
Lengauer, Thomas

Determination of clinically relevant cutoffs for HIV-1 phenotypic resistance estimates through a combined analysis of clinical trial and cohort data
In: Abstract Book. 8th European Drug Resistance Workshop, 46

Poster

2010

Perner, Juliane

Finding local similarities in gene expression patterns between partially reprogrammed cells and know cell types using a module network approach
Universität des Saarlandes

Thesis - Masters thesis

2008

Perner, Juliane

Semi-Supervised Learning for Predicting Anti-HIV Drug Resistance
Universität des Saarlandes

Thesis - Bachelor thesis

Pernoa, Carlo Federico

2011

Role of hepatitis B virus genetic barrier in drug-resistance and immune-escape development
In: Digestive and Liver Disease [43], 975–983

Journal Article

Perno, Carlo-Federico

2006

[Svicher, Valentina]
Sing, Tobias
[Santoro, Maria Mercedes]
[Forbici, Federica]
[Rodriguez- Barrios, Fátima]
[Bertoli, Ada]
[Beerenwinkel, Niko]
[Bellocchi, Maria Concetta]
[Gago, Federigo]
[d´Arminio Monforte, Antonella]
[Antinori, Andrea]
Lengauer, Thomas
Ceccherini-Silberstein, Francesca
[Perno, Carlo-Federico]

Involvement of novel HIV-1 reverse transcriptase mutations in the regulation of resistance to nucleoside inhibitors
In: Journal of Virology [80], 7186-7198

Journal Article

2005

[Svicher, Valentina]
[Ceccherini-Silberstein, Francesca]
Sing, Tobias
[Santoro, Maria Mercedes]
[Gori, C.]
Beerenwinkel, Niko
[Gago, F.]
[D'Arrigo, R.]
[Bellochi, M.C.]
[Giannella, S.]
[Bertoli, A.]
[D'Arminio Monforte, A.]
[Antinori, A.]
[Perno, Carlo-Federico]

A highly ordered network of HIV-1 RT mutations regulates the continuous escape from antiviral drugs
In: International Workshop in HIV Dynamics and Evolution, -

Proceedings Article

2005

[Svicher, Valentina]
[Ceccherini-Silberstein, Francesca]
Sing, Tobias
[Santoro, Maria Mercedes]
[Gori, C.]
Beerenwinkel, Niko
[Gago, F.]
[D'Arrigo, R.]
[Bellocchi, M. C.]
[Giannella, S.]
[Bertoli, A.]
[D'Arminio Monforte, A.]
[Antinori, A.]
[Perno, Carlo-Federico]

Additional Mutations in HIV-1 Reverse Transcriptase are Involved in the Highly Ordered Regulation of NRTI Resistance
In: Proceedings of the 3rd European HIV Drug Resistance Workshop, -

Proceedings Article

2005

Characterization of novel HIV Drug Resistance Mutations using clustering, multidimensional scaling and SVM-based feature ranking
In: Knowledge Discovery in Databases: PKDD 2005., 285-296

Proceedings Article

Perno, Carlo Federico

2011

Journal Article

2011

Role of hepatitis B virus genetic barrier in drug-resistance and immune-escape development
In: Digestive and Liver Disease [43], 975-983

Journal Article

2009

Dynamics of NRTI resistance mutations during therapy interruption
In: AIDS Research and Human Retroviruses [25], 57-64

Journal Article

2009

[Alcaro, Stefano]
[Artese, Anna]
[Ceccherini-Silberstein, Francesca]
[Ortuso, Francesca]
[Perno, Carlo Federico]
Sing, Tobias
[Svicher, Valentina]

Journal Article

2007

Journal Article

Perno, C.-F.

2011

Prediction of Response to Antiretroviral Therapy by Human Experts and by the EuResist Data-Driven Expert System (the EVE study)
In: HIV Medicine [12], 211-218

Journal Article

Perno, Federico

2010

Prediction of Response to Antiretroviral Therapy by Human Experts and by the EuResist Data-Driven Expert System (the EVE Study)
In: HIV Medicine [Early View], 1-8

Electronic Journal Article

Pesquita, Catia

2012

[Faria, Daniel]
Schlicker, Andreas
[Pesquita, Catia]
[Bastos, Hugo]
[Ferreira, António E N]
Albrecht, Mario
[Falcão, André O]

Mining GO annotations for improving annotation consistency
In: PLoS ONE [7], e40519,1-e40519,7

Electronic Journal Article

Petroczi, Andrea

2010

Prediction of Response to Antiretroviral Therapy by Human Experts and by the EuResist Data-Driven Expert System (the EVE Study)
In: HIV Medicine [Early View], 1-8

Electronic Journal Article

2007

EuResist: exploration of multiple modeling techniques for prediction of response to treatment
In: Proceedings of the 5th European HIV Drug Resistance Workshop, -

Poster

Petroczi, A.

2011

Prediction of Response to Antiretroviral Therapy by Human Experts and by the EuResist Data-Driven Expert System (the EVE study)
In: HIV Medicine [12], 211-218

Journal Article

Pevzner, Pavel (ed.)

2004

Beerenwinkel, Niko
Rahnenführer, Jörg
Däumer, Martin
Hoffmann, Daniel
Kaiser, Rolf
Selbig, Joachim
Lengauer, Thomas

Learning multiple evolutionary pathways from cross-sectional data
In: RECOMB 2004 : proceedings of the Eighth Annual International Conference on Research in Computational Molecular Biology, 36-44

Proceedings Article

2002

[Zien, Alexander]
[Fluck, Juliane]
[Zimmer, Ralf]
Lengauer, Thomas

Microarrays: How Many Do You Need?
In: Proceedings of the Sixth Annual Conference on Research in Computational Molecular Biology (RECOMB2002), 321-330

Proceedings Article

Pevzner, P. (ed.)

2001

Proceedings of the 5th Annual Conference on Research in Computational Molecular Biology (RECOMB2001)

Book

Peyton, Michael

2009

Predicting drug susceptibility of non-small cell lung cancers based on genetic lesions
In: Journal of Clinical Investigation [119], 1727-1740

Journal Article

Pfeifer, Martin

2009

Predicting drug susceptibility of non-small cell lung cancers based on genetic lesions
In: Journal of Clinical Investigation [119], 1727-1740

Journal Article

Pfeifer, Nico

2014

Pironti, Alejandro
Pfeifer, Nico
Lengauer, Thomas

Accurate prediction of drug-exposure without using established drug-resistance mutations
In: Antiviral Therapy, A75

Poster

2014

Pironti, Alejandro
Pfeifer, Nico
Kaiser, Rolf
Walter, Hauke
Lengauer, Thomas

Accurate prediction of drug-exposure without using established drug-resistance mutations
In: Antiviral Therapy, A75

Poster

2014

Pironti, Alejandro
Pfeifer, Nico
Lengauer, Thomas

Improved HIV-1 drug-exposure reconstruction with linear support vector machines
In: Reviews in Antiviral Therapy & Infectious Diseases, 67

Poster

2014

Pironti, Alejandro
Pfeifer, Nico
Kaiser, Rolf
Walter, Hauke
Lengauer, Thomas

Improved HIV-1 drug-exposure reconstruction with linear support vector machines
In: Reviews in Antiviral Therapy & Infectious Diseases, 67

Poster

2014

Pironti, Alejandro
Pfeifer, Nico
[Kaiser, Rolf]
[Walter, Hauke]
Lengauer, Thomas

Improved therapy-success prediction with GSS estimated from clinical HIV-1 sequences
In: Abstract Supplement of the HIV Drug Therapy Glasgow Congress 2014, 155

Poster

2014

Pironti, Alejandro
Lengauer, Thomas
Pfeifer, Nico

Simulation of Sanger-sequencing errors in the context of genotypic tropism determination
In: Antiviral Therapy, A81

Poster

2014

Pironti, Alejandro
Sierra, Saleta
Kaiser, Rolf
Lengauer, Thomas
Pfeifer, Nico

Simulation of Sanger-sequencing errors in the context of genotypic tropism determination
In: Antiviral Therapy, A81

Poster

2013

Pfeifer, Nico
Lengauer, Thomas

Association Between HIV-1 Coreceptor Usage and Resistance to Some Broadly Neutralizing Antibodies
In: Proceedings of the AIDS Vaccine Conference 2013, A-1-A-208

Poster

2013

Pironti, Alejandro
Lengauer, Thomas
Pfeifer, Nico

Effects of sequencing errors on geno2pheno[coreceptor] predictions
In: Abstract Book 11th European Meeting on HIV & Hepatitis, 23-24

Poster

2013

Pironti, Alejandro
Lengauer, Thomas
Pfeifer, Nico

In silico analysis of the effects of sequencing errors on geno2pheno[coreceptor]
In: Abstract Book of the International Workshop on HIV&Hepatitis Virus, A142

Poster

2013

Kalinina, Olga
Pfeifer, Nico
Lengauer, Thomas

Modelling binding between CCR5 and CXCR4 receptors and their ligands suggests the surface electrostatic potential of the co-receptor to be a key player in the HIV-1 tropism
In: Retrovirology [10], 130

Journal Article

2012

Pfeifer, Nico
Lengauer, Thomas

Improving coreceptor usage prediction in the clinic using hints from next generation sequencing data
In: Bioinformatics [28], i589-i595

Journal Article

2012

Pfeifer, Nico
Lengauer, Thomas

Improving HIV coreceptor usage prediction in the clinic using hints from next-generation sequencing data
In: Bioinformatics [28], i589-i595

Journal Article

Pfeifer, Susanne

2006

Pfeifer, Susanne

Development of a fast
geometry-based screening
compound prefiltering technique
Universität des Saarlandes

Thesis - Bachelor thesis

Pfister, Herbert

2013

[Neumann-Fraune, Maria]
Beggel, Bastian
[Pfister, Herbert]
[Kaiser, Rolf]
[Verheyen, Jens]

High frequency of complex mutational patterns in lamivudine resistant hepatitis B virus isolates
In: Journal of Medical Virology [200], 39-49

Journal Article

2011

Erratum to: Prevalence and characteristics of hepatitis B and C virus infections in treatment-naïve HIV-infected patients.
In: Medical Microbiology and Immunology [200], 51-51

Journal Article

2011

HIV prevalence and route of transmission in Turkish immigrants
living in North-Rhine Westphalia, Germany
In: Medical Microbiology and Immunology [200], 219-223

Journal Article

2011

Prediction of HIV-1 coreceptor usage (tropism) by sequence analysis using a genotypic approach
In: Journal of Visualized Experiments [58], e3264,1-e3264,9

Electronic Journal Article

2011

Prevalence and characteristics of hepatitis B and C virus infections in treatment-naïve HIV-infected patients
In: Medical Microbiology and Immunology [200], 39-49

Journal Article

2010

[Däumer, Martin]
[Awerkiew, Sabine]
[Sierra Aragon, Saleto]
[Kartashev, Vladimir]
[Poplavskaja, Tatjana]
[Klein, Rolf]
[Sichtig, Nadine]
[Thielen, Bernhard]
Lengauer, Thomas
Roomp, Kirsten
[Pfister, Herbert]
[Kaiser, Rolf]

Short Communication: Selection of Thymidine Analogue Resitance Mutational Patterns in Children from a Common HIV Type 1 Subtype G Source
In: AIDS Research and Human Retroviruses [26], 275-278

Journal Article

2009

[Sichtig, Nadine]
[Sierra, Saleta]
[Kaiser, Rolf]
[Däumer, Martin]
[Reuter, Stefan]
[Schülter, Eugen]
Altmann, André
[Fätkenheuer, Gerd]
[Dittmer, Ulf]
[Pfister, Herbert]
[Esser, Stefan]

Evolution of raltegravir resistance during therapy
In: Journal of antimicrobial chemotherapy [64], 25-32

Journal Article

2008

[Verheyen, Jens]
Altmann, Andre
[Knops, Elena]
[Schülter, Eugen]
[Sichtig, Nadine]
[Reuter, Stefan]
[Fätkenheuer, Gerd]
[Pfister, Herbert]
[Kaiser, Rolf]

Relevance of HIV gag cleavage site mutations in failures of protease inhibitor therapies
In: Antiviral Therapy, A53

Poster

2006

Compensatory mutations at the HIV cleavage sites p7/p1 and p1/p6-gag in therapy-naive and therapy-experienced patients
In: Antiviral Therapy [11], 879-887

Journal Article

2005

Evolution of HIV resistance during treatment interruption in experienced patients and after restarting a new therapy
In: J Clin Virol [34], 277-287

Journal Article

Pfister, Holger

2012

[Sierra, Saleta]
[Dzbowski, Jan Nikolaj]
Pironti, Alejandro
[Gueney, L]
Thielen, Alexander
[Reuter, Stefan]
[Esser, Stefan]
[Fätkenheuer, Gerd]
Lengauer, Thomas
[Hider, Dominik]
[Hoffmann, Daniel]
[Pfister, Holger]
[Jensen, Björn]
[Kaiser, Rolf]

Optimisation of baseline genotypic testing for safe and efficient maraviroc administration
In: Journal of the International AIDS Society, 101-102

Poster

Pfister, H.

2013

Schelhorn, Sven-Eric
[Fischer, M.]
[Tolosi, Laura]
[Altmüller, J.]
[Nürnberg, P.]
[Pfister, H.]
Lengauer, Thomas
Berthold, F.

Sensitive detection of viral transcripts in human tumor transcriptomes
In: PLOS Computational Biology [9], xx

Journal Article

Phanuphak, P.

2011

Prediction of Response to Antiretroviral Therapy by Human Experts and by the EuResist Data-Driven Expert System (the EVE study)
In: HIV Medicine [12], 211-218

Journal Article

Pichler, Irene

2013

[Zanon, Alessandra]
[Rakovic, Aleksandar]
[Blankenburg, Hagen]
Doncheva, Nadezhda T.
[Schwienbacher, Christine]
[Serafin, Alice]
Alexa, Adrian
[Weichenberger, Christian X.]
Albrecht, Mario
[Klein, Christine]
[Hicks, Andrew A.]
[Pramstaller, Peter P.]
[Domingues, Francisco S.]
[Pichler, Irene]

Profiling of parkin-binding partners using tandem affinity purification
In: PLoS ONE [8], 1-17

Journal Article

Pierrou, Stefan

2004

Genetic variation in DLG5 is associated with inflammatory bowel disease
In: Nature Genetics [36], 376-380

Journal Article

Pietsch, Torsten

2007

[Mikeska, Thomas]
Bock, Christoph
[El-Maarri, Osman]
[Hübner, Anika]
[Ehrentraut, Denise]
[Schramm, Johannes]
[Felsberg, Jörg]
[Kahl, Philip]
[Büttner, Reinhard]
[Pietsch, Torsten]
[Waha, Andreas]

Optimization of Quantitative MGMT Promoter Methylation Analysis Using Pyrosequencing and Combined Bisulfite Restriction Analysis
In: Journal of Molecular Diagnostics [9], 368-381

Journal Article

Piiper, Albrecht

2010

Dimerization of the hepatitis C virus nonstructural protein 4B depends on the integrity of an aminoterminal basic leucine zipper
In: Protein Science [19], 1327-1336

Journal Article

2006

[Plotz, Guido]
[Welsch, Christoph]
[Giron-Monzon, Luis]
[Friedhoff, Peter]
Albrecht, Mario
[Piiper, Albrecht]
Biondi, Ricardo M.
Lengauer, Thomas
[Zeuzem, Stefan]
[Raedle, Jochen]

Mutations in the MutSalpha interaction interface of MLH1 can abolish DNA mismatch repair
In: Nucleic Acids Research [34], 6574-6586

Journal Article

Piiper, A.

2011

[Welker, M.-W.]
Welsch, Christoph
[Ochs, D.]
[Hofmann, W. P.]
[Herrmann, E.]
[Piiper, A.]
[Hartmann, R. W.]
[Zeuzem, S.]
[Sarrazin, C.]
[Kronenberger, Bernd]

Journal Article

Pillai, Satish

2007

[Low, Andrew J.]
[Dong, Winnie]
[Chan, Dennison]
Sing, Tobias
[Swanstrom, Ronald]
[Jensen, Mark]
[Pillai, Satish]
[Good, Benjamin]
[Harrigan, P. Richard]

Current V3 genotyping algorithms are inadequate for predicting X4 co-receptor usage in clinical isolates
In: AIDS [21], F19-F26

Journal Article

Pillay, D

2011

Prediction of Response to Antiretroviral Therapy by Human Experts and by the EuResist Data-Driven Expert System (the EVE study)
In: HIV Medicine [12], 211-218

Journal Article

Pimstone, S

1999

Mutations in ABC1 in Tangier disease and familial high-density lipoprotein
In: Nature Genetics [22], 336-45

Journal Article

Pimstone, S.

1999

Mutations in the ABC1 gene in familial HDL deficiency with defective cholesterol efflux
In: The Lancet [354], 1341-6

Journal Article

Pinto, Anne C.

2011

Evidence for Reductive Genome Evolution and Lateral Acquisition of Virulence Functions in two Corynebacterium pseudotuberculosis strains
In: PLoS One [6], e18551

Electronic Journal Article

Piovesan, Damiano

2013

A large-scale evaluation of computational protein function prediction
In: Nature Methods [10], 221-227

Journal Article

Pironti, Alejandro

2014

Pironti, Alejandro
Pfeifer, Nico
Lengauer, Thomas

Accurate prediction of drug-exposure without using established drug-resistance mutations
In: Antiviral Therapy, A75

Poster

2014

Pironti, Alejandro
Pfeifer, Nico
Kaiser, Rolf
Walter, Hauke
Lengauer, Thomas

Accurate prediction of drug-exposure without using established drug-resistance mutations
In: Antiviral Therapy, A75

Poster

2014

Pironti, Alejandro
Pfeifer, Nico
Lengauer, Thomas

Improved HIV-1 drug-exposure reconstruction with linear support vector machines
In: Reviews in Antiviral Therapy & Infectious Diseases, 67

Poster

2014

Pironti, Alejandro
Pfeifer, Nico
Kaiser, Rolf
Walter, Hauke
Lengauer, Thomas

Improved HIV-1 drug-exposure reconstruction with linear support vector machines
In: Reviews in Antiviral Therapy & Infectious Diseases, 67

Poster

2014

Pironti, Alejandro
Pfeifer, Nico
[Kaiser, Rolf]
[Walter, Hauke]
Lengauer, Thomas

Improved therapy-success prediction with GSS estimated from clinical HIV-1 sequences
In: Abstract Supplement of the HIV Drug Therapy Glasgow Congress 2014, 155

Poster

2014

Pironti, Alejandro
Lengauer, Thomas
Pfeifer, Nico

Simulation of Sanger-sequencing errors in the context of genotypic tropism determination
In: Antiviral Therapy, A81

Poster

2014

Pironti, Alejandro
Sierra, Saleta
Kaiser, Rolf
Lengauer, Thomas
Pfeifer, Nico

Simulation of Sanger-sequencing errors in the context of genotypic tropism determination
In: Antiviral Therapy, A81

Poster

2013

Pironti, Alejandro
Lengauer, Thomas
Pfeifer, Nico

Effects of sequencing errors on geno2pheno[coreceptor] predictions
In: Abstract Book 11th European Meeting on HIV & Hepatitis, 23-24

Poster

2013

Pironti, Alejandro

HIV-1 fitness landscape models for indinavir treatment pressure using observed evolution in longitudinal sequence data are predictive for treatment failure
In: Infection, Genetics and Evolution [19], 349–360

Journal Article

2013

Pironti, Alejandro
Lengauer, Thomas
Pfeifer, Nico

In silico analysis of the effects of sequencing errors on geno2pheno[coreceptor]
In: Abstract Book of the International Workshop on HIV&Hepatitis Virus, A142

Poster

2012

Pironti, Alejandro
Lengauer, Thomas
[Kaiser, Rolf]
[Schülter, Eugen]
[Verheyen, Jens]

Characterization of HIV-1 Gag Subtype C
In: Abstract Book. 9th Workshop on HIV \& Hepatitis Treatment Strategies \& Antiviral Drug Resistance, 40-41

Poster

2012

[Schuelter, Eugen]
[Lübcke, Nadine]
[Jensen, Björn]
[Zazzi, Maurizio]
[Sönnerborg, Anders]
Lengauer, Thomas
[Incardona, Francesca]
[Camacho, Richardo]
[Schmit, J]
[Clotet, Bonaventura]
[Kaiser, Rolf]
Pironti, Alejandro

Etravirine in protease inhibitor-free antiretroviral combination therapies
In: Journal of the International AIDS Society, 155-156

Poster

2012

HIV-GRADE: A Publicly Available, Rules-Based Drug Resistance Interpretation Algorithm Integrating Bioinformatic Knowledge
In: Intervirology [55], 102-107

Journal Article

2012

HIV2EU: supporting standardized HIV-2 drug resistance interpretation in Europe
In: Journal of the International AIDS Society, 135

Poster

2012

Optimisation of baseline genotypic testing for safe and efficient maraviroc administration
In: Journal of the International AIDS Society, 101-102

Poster

2011

Pironti, Alejandro
Altmann, André
Büch, Joachim
Lengauer, Thomas

A Computational Method for Predicting First-Line Antiretroviral Therapy Success
In: Abstract Book. 9th Workshop on HIV & Hepatitis Treatment Strategies & Antiviral Drug Resistance, 94

Poster

2010

Altmann, Andre
Pironti, Alejandro
Perner, Juliane
Büch, Joachim
Lengauer, Thomas

Poster

2009

Pironti, Alejandro

Probabilistic disease gene prioritization
Universität des Saarlandes

Thesis - Masters thesis

Plaßmann, Stephanie

2006

An arginine/lysine-rich motif is crucial for VCP/p97-mediated modulation of ataxin-3 fibrillogenesis
In: EMBO Journal [25], 1547-1558

Journal Article

Platt, J. (ed.)

2007

Sing, Tobias
[Beerenwinkel, Niko]

Mutagenetic tree Fisher kernel improves prediction of HIV drug resistance from viral genotype
In: Advances in Neural Information Processing Systems 19, 1-9

Proceedings Article

Platzer, Mathias

2005

Sarcoidosis is associated with a truncating splice site mutation in BTNL2
In: Nature Genetics [37], 357-364

Journal Article

Platzer, Matthias

2007

A genome-wide association scan of nonsynonymous SNPs identifies a susceptibility variant for Crohn disease in ATG16L1
In: Nature Genetics [39], 207-211

Journal Article

2007

Systematic association mapping identifies NELL1 as a novel IBD disease gene
In: PLoS ONE [2], e691.1-13

Journal Article

Plotz, Guido

2006

[Plotz, Guido]
[Welsch, Christoph]
[Giron-Monzon, Luis]
[Friedhoff, Peter]
Albrecht, Mario
[Piiper, Albrecht]
Biondi, Ricardo M.
Lengauer, Thomas
[Zeuzem, Stefan]
[Raedle, Jochen]

Mutations in the MutSalpha interaction interface of MLH1 can abolish DNA mismatch repair
In: Nucleic Acids Research [34], 6574-6586

Journal Article

Podswiadek, Marta

2005

[Van Duist, Marjan M.]
Albrecht, Mario
[Podswiadek, Marta]
[Giachino, Daniela]
Lengauer, Thomas
[Punzi, Leonardo]
[De Marchi, Mario]

A new CARD15 mutation in Blau syndrome
In: European Journal of Human Genetics [13], 742-747

Journal Article

Poenisch, Marion

2011

Recruitment and activation of a lipid kinase by hepatitis C virus NS5A is essential for integrity of the membranous replication compartment
In: Cell Host & Microbe [9], 32-45

Journal Article

Poggensee, G. (ed.)

2007

European Journal of Medical Research

Journal

Pollan, Marina

2013

A Prognostic DNA Methylation Signature for Stage I Non-Small-Cell Lung Cancer
In: Journal of Clinical Oncology [31], 4140-4147

Journal Article

Polta, A.

2010

[Mihm, Ulrike]
[Hofmann, W.P.]
Welsch, Christoph
[Polta, A.]
Lengauer, Thomas
[Zeuzem, Stefan]
[Sarrazin, Christoph]
[Herrmann, E.]

Effect of ribavirin on the frequency of RNAse L cleavage sites within the hepatitis C viral genome
In: Journal of Viral Hepatitis [17], 217-221

Journal Article

Ponsioen, Cyriel Y.

2013

Association between variants of PRDM1 and NDP52 and Crohn's disease, based on exome sequencing and functional studies
In: Gastroenterology [145], 339-347

Journal Article

2013

Dense genotyping of immune-related disease regions identifies nine new risk loci for primary sclerosing cholangitis
In: Nature Genetics [45], 670-677

Journal Article

Poplavskaja, Tatjana

2010

Short Communication: Selection of Thymidine Analogue Resitance Mutational Patterns in Children from a Common HIV Type 1 Subtype G Source
In: AIDS Research and Human Retroviruses [26], 275-278

Journal Article

Porse, Bo

2012

BLUEPRINT to decode the epigenetic signature written in blood
In: Nature Biotechnology [30], 224-226

Journal Article

Pospisil, H.

2004

The Helmholtz Network for Bioinformatics: an integrative web portal for bioinformatics resources
In: Bioinformatics [20], 268-270

Journal Article

Pou, Christian

2011

[Codoner, Francisco]
[Pou, Christian]
Thielen, Alexander
[García, Federico]
[Delgado, Rafael]
[Dalmau, David]
[Álvarez-Tejado, Miguel]
[Ruiz, Lidia]
[Clotet, Bonaventura]
[Paredes, Roger]

Added value of deep sequencing relative to population sequencing in heavily pre-treated HIV-1-infected subjects
In: PLoS One [6], e19461,1-e19461,5

Electronic Journal Article

2010

Dynamic escape of pre-existing raltegravir-resistant HIV-1 from raltegravir selection pressure
In: Antiviral Research [88], 281-286

Journal Article

Poveda, Eva

2011

[Seclen, Eduardo]
[Soriano, Vincente]
[González, Maria M]
[Gómez, Sagrario]
Thielen, Alexander
[Poveda, Eva]

High Concordance between the Position-Specific Scoring Matrix and Geno2pheno Algorithms for Genotypic Interpretation of HIV-1 Tropism: V3 Length as the Major Cause of Disagreement
In: Journal of Clinical Microbiology [49], 3380-3382

Journal Article

Pramstaller, Peter P.

2013

Profiling of parkin-binding partners using tandem affinity purification
In: PLoS ONE [8], 1-17

Journal Article

Prat, Jaime

2012

A DNA methylation fingerprint of 1628 human samples
In: Genome Research [22], 407-419

Journal Article

Prescott, Natalie J.

2007

A genome-wide association scan of nonsynonymous SNPs identifies a susceptibility variant for Crohn disease in ATG16L1
In: Nature Genetics [39], 207-211

Journal Article

2007

Systematic association mapping identifies NELL1 as a novel IBD disease gene
In: PLoS ONE [2], e691.1-13

Journal Article

Prieto, Carlos

2011

PSICQUIC and PSISCORE: accessing and scoring molecular interactions
In: Nature Methods [8], 528-529

Journal Article

Prlic, Andreas

2004

[Prlic, Andreas]
Domingues, Francisco S.
[Lackner, Peter]
[Sippl, Manfred J.]

WILMA-automated annotation of protein sequences
In: Bioinformatics [20], 127-128

Journal Article

Prlić, Andreas

2009

Blankenburg, Hagen
[Finn, Robert D.]
[Prlić, Andreas]
[Jenkinson, Andrew M.]
Ramírez, Fidel
Emig, Dorothea
Schelhorn, Sven-Eric
Büch, Joachim
Lengauer, Thomas
Albrecht, Mario

DASMI: exchanging, annotating and assessing molecular interaction data
In: Bioinformatics [25], 1321-1328

Journal Article

2008

Integrating biological data - the Distributed Annotation System
In: BMC Bioinformatics [9], S3.1-7

Journal Article

Propping, Peter (ed.)

2001

Lengauer, Thomas

Bioinformatik an der Schwelle zur postgenomischen Ära
In: Was wissen wir, wenn wir das menschliche Genom kennen, 56-62

Part of a Book

Prosperi, Mattia

2012

[Zazzi, Maurizio]
[Incardona, Francesca]
[Rosen-Zvi, Michal]
[Prosperi, Mattia]
Lengauer, Thomas
Altmann, Andre
[Sonnerborg, Anders]
[Lavee, Tamar]
[Schülter, Eugen]
[Kaiser, Rolf]

Predicting Response to Antiretroviral Treatment by Machine Learning:
The EuResist Project
In: Intervirology [55], 123-127

Journal Article

2008

Comparison of Classifier Fusion Methods for Predicting Response to Anti HIV-1 Therapy
In: PLoS ONE [3], e3470

Journal Article

2008

Proceedings Article

2008

The EuResist approach for predicting response to anti HIV-1 therapy
In: Reviews in Antiviral Therapy, 107

Poster

2007

EuResist: exploration of multiple modeling techniques for prediction of response to treatment
In: Proceedings of the 5th European HIV Drug Resistance Workshop, -

Poster

Prosperi, Mattia C. F.

2010

[Prosperi, Mattia C. F.]
[Rosen-Zvi, Michal]
Altmann, Andre
[Zazzi, Maurizio]
[Di Giambenedetto, Simona]
[Kaiser, Rolf]
[Schülter, Eugen]
[Struck, Daniel]
[Sloot, Peter]
[van de Vijver, David A.]
[Vandamme, Anne-Mieke]
[Sönnerborg, Anders]

Antiretroviral Therapy Optimisation without Genotype Resistance Testing: A Perspective on Treatment History Based Models
In: PLoS ONE [5], e13753,1-e13753,8

Electronic Journal Article

2010

Prediction of Response to Antiretroviral Therapy by Human Experts and by the EuResist Data-Driven Expert System (the EVE Study)
In: HIV Medicine [Early View], 1-8

Electronic Journal Article

2009

[Prosperi, Mattia C. F.]
Altmann, André
[Rosen-Zvi, Michal]
[Aharoni, Ehud]
[Gabor, Borgulya]
[Fulop, Bazso]
[Sonnerborg, Anders]
[Schulter, Eugen]
[Struck, Daniel]
[Ulivi, Giovanni]
[Vandamme, Anne-Mieke]
[Vercauteren, Jurgen]
[Zazzi, Maurizio]

Investigation of expert rule bases, logistic regression, and non-linear machine learning techniques for predicting response to antiretroviral treatment
In: Antiviral Therapy [14], 433-442

Journal Article

Prosperi, M.

2011

Prediction of Response to Antiretroviral Therapy by Human Experts and by the EuResist Data-Driven Expert System (the EVE study)
In: HIV Medicine [12], 211-218

Journal Article

Prosper, Felipe

2012

A DNA methylation fingerprint of 1628 human samples
In: Genome Research [22], 407-419

Journal Article

Przytycka, Teresa

2008

Zotenko, Elena
Mestre, Julian
[O'Leary, Dianne]
[Przytycka, Teresa]

Why Do Hubs in the Yeast Protein Interaction Network Tend To Be Essential: Reexamining the Connection between the Network Topology and Essentiality
In: PLoS Computational Biology [4], e1000140

Journal Article

Psihoyios, George (ed.)

2012

Reppas, Andreas
Lawyer, Glenn

Low k-shells identify bridge elements critical to disease flow in small-world networks
In: Numerical Analysis and Applied Mathematics (ICNAAM 2012), 1426-1429

Proceedings Article

Puca, Annibale A.

2012

A DNA methylation fingerprint of 1628 human samples
In: Genome Research [22], 407-419

Journal Article

Pühler, Alfred

2012

Pauling, Josch
Röttger, Richard
[Neuner, Andreas]
[Salgado, Heladia]
[Collado-Vides, Julio]
Kalaghatgi, Prabhav
[Azevedo, Vasco]
[Tauch, Andreas]
[Pühler, Alfred]
Baumbach, Jan

On the trail of EHEC/EAEC - unraveling the gene regulatory networks of human pathogenic Escherichia coli bacteria
In: Integrative Biology [4], 728-733

Journal Article

Puig, Susana

2012

A DNA methylation fingerprint of 1628 human samples
In: Genome Research [22], 407-419

Journal Article

Punzi, Leonardo

2005

[Van Duist, Marjan M.]
Albrecht, Mario
[Podswiadek, Marta]
[Giachino, Daniela]
Lengauer, Thomas
[Punzi, Leonardo]
[De Marchi, Mario]

A new CARD15 mutation in Blau syndrome
In: European Journal of Human Genetics [13], 742-747

Journal Article

Putz, H.

2004

[Hannemann, A.]
[Schön, J.C.]
[Jansen, M.]
[Putz, H.]
Lengauer, Thomas

Modelling amorphous Si3B3N7: Structure and elastic properties
In: Physical Review [B 70], 144201-144201

Journal Article

Quackenbush, J. (ed.)

2004

Proceedings Twelfth International Conference on Intelligent Systems for Molecular Biology/Third European Conference on Computional Biology 2004 (ISMB/ECCB 2004)

Proceedings

Rabelo, Elida Mara

2011

Evidence for Reductive Genome Evolution and Lateral Acquisition of Virulence Functions in two Corynebacterium pseudotuberculosis strains
In: PLoS One [6], e18551

Electronic Journal Article

Radelof, Uwe

2007

Systematic association mapping identifies NELL1 as a novel IBD disease gene
In: PLoS ONE [2], e691.1-13

Journal Article

Radivojac, Predrag

2013

A large-scale evaluation of computational protein function prediction
In: Nature Methods [10], 221-227

Journal Article

Raedle, Jochen

2006

[Plotz, Guido]
[Welsch, Christoph]
[Giron-Monzon, Luis]
[Friedhoff, Peter]
Albrecht, Mario
[Piiper, Albrecht]
Biondi, Ricardo M.
Lengauer, Thomas
[Zeuzem, Stefan]
[Raedle, Jochen]

Mutations in the MutSalpha interaction interface of MLH1 can abolish DNA mismatch repair
In: Nucleic Acids Research [34], 6574-6586

Journal Article

Raelson, John V.

2010

Genome-wide association study identifies a psoriasis susceptibility locus at TRAF3IP2
In: Nature Genetics [42], 991-995

Journal Article

Ragozin, Sergey

2009

[Zhang, Yingying]
[Rohde, Christian]
[Tierling, Sascha]
[Jurkowski, Tomasz P.]
Bock, Christoph
[Santacruz, Diana]
[Ragozin, Sergey]
[Reinhardt, Richard]
[Groth, Marco]
[Walter, Jörn]
[Jeltsch, Albert]

DNA methylation analysis of chromosome 21 gene promoters at single base pair and single allele resolution
In: PLoS Genetics [5], e1000438:1-e1000438:15

Electronic Journal Article

Rahmann, Sven

2013

Hauschild, Anne-Christin
[Kopczynski, Dominik]
[D'Addario, Marianna]
[Baumbach, Joerg Ingo]
[Rahmann, Sven]
Baumbach, Jan

Peak Detection Method Evaluation for Ion Mobility Spectrometry by using Machine Learning Approaches
In: Metabolites [3], 277-293

Electronic Journal Article

2011

[Wittkop, Tobias]
[Rahmann, Sven]
Roettger, Richard
[Boecker, Sebastian]
Baumbach, Jan

Extension and robustness of Transitivity Clustering for protein-protein interaction network analysis
In: Internet Mathematics [7], 255-273

Journal Article

2010

[Wittkop, Tobias]
[Rahmann, Sven]
Baumbach, Jan

Efficient Online Transcription Factor Binding Site Adjustment by Integrating Transitive Graph Projection with MoRAine 2.0
In: Special Issue: 6th International Symposium on Integrative Bioinformatics, 117,1-117,11

Electronic Proceedings Article

2010

[Wittkop, Tobias]
Emig, Dorothea
[Lange, Sita]
[Rahmann, Sven]
Albrecht, Mario
[Morris, John H.]
[Böcker, Sebastian]
[Stoye, Jens]
Baumbach, Jan

Partitioning biological data with transitivity clustering
In: Nature Methods [7], 419-420

Journal Article

Rahman, Proton

2010

Genome-wide association study identifies a psoriasis susceptibility locus at TRAF3IP2
In: Nature Genetics [42], 991-995

Journal Article

Rahnenführer, Jörg

2009

Predicting drug susceptibility of non-small cell lung cancers based on genetic lesions
In: Journal of Clinical Investigation [119], 1727-1740

Journal Article

2008

[Hornstein, Max]
[Hoffmann, Michele J.]
Alexa, Adrian
[Yamanaka, Masanori]
[Müller, Mirko]
[Jung, Volker]
[Rahnenführer, Jörg]
[Schulz, Wolfgang A.]

Protein phosphatase and TRAIL receptor genes as new candidate tumor genes on chromosome 8p in prostate cancer
In: Cancer Genomics & Proteomics [5], 123-136

Journal Article

2008

Bogojeska, Jasmina
Alexa, Adrian
Altmann, André
Lengauer, Thomas
[Rahnenführer, Jörg]

Rtreemix: an R package for estimating evolutionary pathways and genetic progression scores
In: Bioinformatics [24], 2391-2392

Journal Article

2008

Bogojeska, Jasmina
Lengauer, Thomas
[Rahnenführer, Jörg]

Stability analysis of mixtures of mutagenetic trees
In: BMC Bioinformatics [9], 165-181

Journal Article

2007

Rahnenführer, Jörg
Lengauer, Thomas

Analysis of Expression Data: Classification of genes
In: Bioinformatics - From Genomes to Therapies 2. Getting at the Inner Workings: Molecular Interactions, 993-1021

Part of a Book

2007

[Ketter, Ralf]
[Urbschat, Steffi]
[Henn, Wolfram]
[Feiden, Wolfgang]
Beerenwinkel, Niko
Lengauer, Thomas
[Steudel, Wolf-Ingo]
[Zang, Klaus D.]
Rahnenführer, Jörg

Application of oncogenetic trees mixtures as a biostatistical model of the clonal cytogenetic evolution of meningiomas
In: International Journal of Cancer [121], 1473-1480

Journal Article

2007

Domingues, Francisco S.
[Rahnenführer, Jörg]
Lengauer, Thomas

Conformational analysis of alternative protein structures
In: Bioinformatics [23], 3131-3138

Journal Article

2007

[Kamradt, Jörn]
[Jung, Volker]
[Wahrheit, Kerstin]
Tolosi, Laura
Rahnenführer, Jörg
[Schilling, Martin]
[Walker, Robert]
[Davis, Sean]
[Stöckle, Michael]
[Meltzer, Paul]
[Wullich, Bernd]

Detection of Novel Amplicons in Prostate Cancer by Comprehensive Genomic Profiling of Prostate Cancer Cell Lines Using Oligonucleotide-Based ArrayCGH
In: PLoS ONE [2], e769

Electronic Journal Article

2007

Factor interaction analysis for chromosome 8 and DNA methylation alterations highlights innate immune response suppression and cytoskeletal changes in prostate cancer
In: Molecular Cancer [6], 1-16

Journal Article

2007

Schlicker, Andreas
Rahnenführer, Jörg
Albrecht, Mario
Lengauer, Thomas
Domingues, Francisco S.

GOTax: investigating biological processes and biochemical activities along the taxonomic tree
In: Genome Biology [8], R33.1-10

Electronic Journal Article

2007

[Ketter, Ralf]
[Kim, Yoo-Jin]
[Storck, Simone]
Rahnenführer, Jörg
[Romeike, Bernd F.M.]
[Steudel, Wolf-Ingo]
[Zang, Klaus D.]
[Henn, Wolfram]

Hyperdiploidy defines a distinct cytogenetic entity of meningiomas
In: Journal of Neuro-Oncology [83], 213-221

Journal Article

2006

Schlicker, Andreas
Domingues, Francisco S.
Rahnenführer, Jörg
Lengauer, Thomas

A new measure for functional similarity of gene products based on Gene Ontology
In: BMC Bioinformatics [7], 1-16

Electronic Journal Article

2006

Alexa, Adrian
Rahnenführer, Jörg
Lengauer, Thomas

Improved Scoring of Functional Groups from Gene Expression Data by Decorrelating GO Graph Structure
In: Bioinformatics [22], 1600-1607

Journal Article

2006

[Yin, Junming]
[Beerenwinkel, Niko]
Rahnenführer, Jörg
Lengauer, Thomas

Model Selection for Mixtures of Mutagenetic Trees
In: Statistical Applications in Genetics and Molecular Biology [5], Article 17

Journal Article

2006

Rahnenführer, Jörg

Statistical methods for the biological interpretation of genome-wide measurements
Universität des Saarlandes

Thesis - Habilitation thesis

2005

Rahnenführer, Jörg

Clustering algorithms and other exploratory methods for microarray data analysis
In: Methods of Information in Medicine [44], 444-448

Journal Article

2005

Talwar, Priti
Lengauer, Thomas
Rahnenführer, Jörg
[Wittmann, Christoph]
[Velagapudi, VR]
[Heinzle, Elmar]

Computational Methods for Protein Function Prediction using Metabolomics Data
In: Proceedings of International Workshop on Systems Biology 2005, 1

Poster

2005

Computational methods for the design of effective therapies against drug resistant HIV strains
In: Bioinformatics [21], 3943-3950

Journal Article

2005

Hahn, Andreas
Rahnenführer, Jörg
Talwar, Priti
Lengauer, Thomas

Confirmation of human protein interaction data by human expression data
In: BMC Bioinformatics [6], 1-11

Journal Article

2005

Rahnenführer, Jörg
Beerenwinkel, Niko
[Schulz, Wolfgang A.]
[Hartmann, Christian]
[von Deimling, Andreas]
[Wullich, Bernd]
Lengauer, Thomas

Estimating cancer survival and clinical outcome based on genetic tumor progression scores
In: Bioinformatics [21], 2438-2446

Journal Article

2005

Beerenwinkel, Niko
[Däumer, Martin]
Sing, Tobias
Rahnenführer, Jörg
Lengauer, Thomas
[Selbig, Joachim]
[Hoffmann, Daniel]
[Kaiser, Rolf]

Estimating HIV evolutionary pathways and the genetic barrier to drug resistance
In: The Journal of Infectious Diseases [191], 1953-1960

Journal Article

2005

Rahnenführer, Jörg

Image analysis for cDNA microarrays
In: Methods of Information in Medicine [44], 405-407

Journal Article

2005

Beerenwinkel, Niko
Rahnenführer, Jörg
[Däumer, Martin]
[Hoffmann, Daniel]
[Kaiser, Rolf]
[Selbig, Joachim]
Lengauer, Thomas

Learning multiple evolutionary pathways from cross-sectional data
In: Journal of Computational Biology [12], 584-598

Journal Article

2005

Beerenwinkel, Niko
Rahnenführer, Jörg
[Kaiser, Rolf]
[Hoffmann, Daniel]
[Selbig, Joachim]
Lengauer, Thomas

Mtreemix: a software package for learning and using mixture models of mutagenetic trees
In: Bioinformatics [21], 2106-2107

Journal Article

2005

Patients with high grade gliomas harboring delections of chromosomes 9p and 10q benefit from temozolomide treatment
In: Neoplasia [7], 883-893

Journal Article

2005

[Das, Ani V.]
[James, Jackson]
Rahnenführer, Jörg
[Thoresona, Wallace B.]
[Bhattacharyaa, Sumitra]
[Zhao, Xing]
[Ahmad, Iqbal]

Retinal properties and potential of the adult mammalian ciliary epithelium stem cells
In: Vision Research [45], 1653-1666

Journal Article

2005

Talwar, Priti
Lengauer, Thomas
Rahnenführer, Jörg
[Heinzle, Elmar]
[Velagapudi, VR]
[Wittmann, Christoph]

Towards computational analysis of metabolic profiling data for protein function prediction.
In: Proceedings of the Yeast Systems Biology, 6th International Conference on Systems Biology (ICSB 2005), 1

Poster

2004

Domingues, Francisco S.
Rahnenführer, Jörg
Lengauer, Thomas

Automated clustering of ensembles of alternative models in protein structure databases
In: Protein Engineering Design and Selection [17], 537-543

Journal Article

2004

Rahnenführer, Jörg
Domingues, Francisco S.
Maydt, Jochen
Lengauer, Thomas

Calculating the statistical significance of changes in pathway activity from gene expression data
In: Statistical Applications in Genetics and Molecular Biology [3], Article 16

Electronic Journal Article

2004

[James, Jackson]
[Das, Ani V.]
Rahnenführer, Jörg
[Ahmad, Iqbal]

Cellular and Molecular Characterization of Early and Late Retinal Stem Cells/Progenitors: Differential Regulation of Proliferation and Context Dependent Role of Notch Signaling
In: Journal of Neurobiology [61], 359-376

Journal Article

2004

Talwar, Priti
Lengauer, Thomas
Rahnenführer, Jörg
[Velagapudi, VR]
[Wittmann, Christoph]
[Heinzle, Elmar]

Computational Methods For Metabolite Screening
In: Proceedings of the 12th International Conference on Intelligent Systems for Molecular Biology + 3rd European Conference on Computational Biology (ISMB/ECCB 2004), 1

Poster

2004

Talwar, Priti
Lengauer, Thomas
Rahnenführer, Jörg
[Velagapudi, VR]
[Wittmann, Christoph]
[Heinzle, Elmar]

Computational Methods For Metabolite Screening
In: Proceedings of the 5th International Conference on Systems Biology (ICSB 2004), 1

Poster

2004

Rahnenführer, Jörg
[Bozinov, Daniel]

Hybrid clustering for microarray image analysis combining intensity and shape features
In: BMC Bioinformatics [5], 1-11

Journal Article

2004

[James, Jackson]
[Das, Ani V.]
[Zhao, Xing]
Rahnenführer, Jörg
[Ahmad, Iqbal]

Identification of c-Kit receptor as a regulator of adult neural stem cells in the mammalian eye: interactions with Notch signaling
In: Developmental Biology [273], 87-105

Journal Article

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