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#	Y		Author/Editor		Title
11	2014
7		Poster
			Pironti, Alejandro Lengauer, Thomas Pfeifer, Nico		Simulation of Sanger-sequencing errors in the context of genotypic tropism determination In: Antiviral Therapy, A81
			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
			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
			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
			Pironti, Alejandro Pfeifer, Nico Lengauer, Thomas		Accurate prediction of drug-exposure without using established drug-resistance mutations In: Antiviral Therapy, A75
			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
			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
2		Journal Article
			Lawyer, Glenn		COMET: Adaptive context-based modeling for ultrafast HIV-1 subtype identification. In: Nucleic Acids Research [42], e144
			Maurer, Felix Hauschild, Anne-Christin Eisinger, Kathrin Baumbach, Jan Mayor, Arno Baumbach, Jörg Ingo		MIMA - A software for analyte identification in MCC/IMS chromatograms by mapping accompanying GC/MS measurements In: International Journal for Ion Mobility Spectrometry [?], ?
2		Unpublished/Draft
			Eckel, Sandrah Baumbach, Jan Hauschild, Anne-Christin		On the importance of statistics in breath analysis - Hope or curse?
			Smolinska, Agnieszka Hauschild, Anne-Christin Fijten, Rianne Dallinga, Jan Baumbach, Jan van Schooten, Frederik		Current breathomics – A review on data pre-processing techniques and machine learning in metabolomics breath analysis
31	2013
4		Poster
			Kalaghatgi, Prabhav Lawyer, Glenn		Inter-country mixing in HIV transmission clusters: a pan-European phylodynamics study In: Abstract Book 11th European HIV & Hepatitis Workshop, 9
			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
			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
			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
22		Journal Article
			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
			Bhadra, T. Battacharya, M. Feuerbach, L. Lengauer, Thomas Bandyopadhyay, S.		DNA Methylation Patterns Facilitate the Identification of Transcription Start Sites: A Brain-specofoc Study In: PLOSONE [8], xx
			Bozek, K. Lengauer, Thomas Sierra, S. Kaiser, Rolf Domingues, F.S.		Analysis of physicochemical and structural properties determining HIV-1 coreceptor usage In: PLoS Computational Biology [x], x
			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
			Ellinghaus, David Zhang, Hu Zeissig, Sebastian Lipinski, Simone Till, Andreas Jiang, Tao Stade, Björn Bromberg, Yana Ellinghaus, Eva Keller, Andreas Rivas, Manuel A. Skieceviciene, Jurgita Doncheva, Nadezhda T. Liu, Xiao Liu, Qing Jiang, Fuman Forster, Michael Mayr, Gabriele Albrecht, Mario Häsler, Robert Boehm, Bernhard O. Goodall, Jane Berzuini, Carlo R. Lee, James Andersen, Vibeke Vogel, Ulla Kupcinskas, Limas Kayser, Manfred Krawczak, Michael Nikolaus, Susanna Weersma, Rinse K. Ponsioen, Cyriel Y. Sans, Miquel Wijmenga, Cisca Strachan, David P. McArdle, Wendy L. Vermeire, Séverine Rutgeerts, Paul Sanderson, Jeremy D. Mathew, Christopher G. Vatn, Morten H. Wang, Jun Nöthen, Markus M. Duerr, Richard H. Büning, Carsten Brand, Stephan Glas, Jürgen Winkelmann, Juliane Illig, Thomas Latiano, Anna Annese, Vito Halfvarson, Jonas D'Amato, Mauro Daly, Mark J. Nothnagel, Michael Karlsen, Tom H. Subramani, Suresh Rosenstiel, Philip Schreiber, Stefan Parkes, Miles Franke, Andre		Association between variants of PRDM1 and NDP52 and Crohn's disease, based on exome sequencing and functional studies In: Gastroenterology [145], 339-347
			Halachev, Konstantin Bast, H. Lengauer, Thomas Bock, Christoph		Interactive exploration of large genome and epigenome datasets in real time In: Genome Biology [13], xx
			Kacprowski, Tim Doncheva, Nadezhda T. Albrecht, Mario		NetworkPrioritizer: a versatile tool for network-based prioritization of candidate disease genes or other molecules In: Bioinformatics [29], 1471-1473
			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
			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
			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
			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
			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
			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
			Röttger, Richard Kalaghatgi, Prabhav Sun, Peng de Castro Soares, Siomar Azevedo, Vasco Wittkop, Tobias Baumbach, Jan		Density Parameter Estimation for Finding Clusters of Homologous Proteins - Tracing Actinobacterial Pathogenicity Life Styles In: Bioinformatics [29], 215-222
			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
			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
			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
			Simmer, F. Brinkmann, A.B. Assenov, Yassen Matarese, F. Kaan, A. Lengauer, Thomas Bock, Christoph Colantuoni, V. Altucci, L. Stunnenberg, H.G.		Comparative genome-wide DNA methylation analysis of colorectal tumor and matched human tissue In: Epigenetics [7], 1355-1367
			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
			Tolosi, Laura Theißen, J. Halachev, Konstantin Hero, B. Berthold, F. Lengauer, Thomas		A method for finding consensus breakpoints in the cancer genome from copy number data In: Bioinformatics [29], 1793-1800
			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
			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
3		Electronic Journal Article
			Beggel, Bastian Lengauer, Thomas		Inferring short-range linkage information from sequencing chromatograms In: PLoS One,
			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
			Schneider, Till Hauschild, Anne-Christin Baumbach, Joerg Ingo Baumbach, Jan		An Integrative Clinical Database and Diagnostics Platform for Biomarker Identification and Analysis in Ion Mobility Spectra of Human Exhaled Air In: Journal of Integrative Bioinformatics [10],
1		Thesis - PhD thesis
			Patil, Kaustubh Raosaheb		Genome Signature based Sequence Comparison for Taxonomic Assignment and tree inference Universität des Saarlandes
1		Miscellaneous
			Hauschild, Anne-Christin Baumbach, Joerg Ingo Baumbach, Jan		Paving the Way for Automated Clinical Breath Analysis and Biomarker Detection
69	2012
3		Part of a Book
			Emig, Dorothea Blankenburg, Hagen Ramírez, Fidel Albrecht, Mario		Functional characterization of human genes from exon expression and RNA interference results In: Bioinformatics and Drug Discovery, 33-53
			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
			Lengauer, Thomas Albrecht, Mario Domingues, Francisco S.		Computational Biology In: Encyclopedia of Molecular Cell Biology and Molecular Medicine, 1-71
2		Proceedings Article
			Bogojeska, Jasmina Stöckel, Daniel Zazzi, Maurizio Kaiser, Rolf Incardona, Francesca Rosen-Zvi, Michal Lengauer, Thomas		History-alignment models for bias-aware prediction of virological response to HIV combination therapy In: Proceedings of the Fifteenth International Conference on Artificial Intelligence and Statistics (AISTATS 2012), 118-126
			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
1		Electronic Proceedings Article
			Röttger, Richard Kreutzer, Christoph Duong Vu, Thuy Wittkop, Tobias Baumbach, Jan		Online Transitivity Clustering of Biological Data with Missing Values In: German Conference on Bioinformatics 2012 (GCB 2012), 57-68
4		Poster
			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
			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
			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
			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
40		Journal Article
			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
			Alcaraz, Nicolas Kucuk, Hande Weile, Jochen Wipat, Anil Baumbach, Jan		KeyPathwayMiner - Detecting case-specific biological pathways by using expression data In: Internet Mathematics [7], 299-313
			Baumbach, Jan		Integrative computational biology In: Integrative Biology [4], 713-714
			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
			Bhattacharyya, Malay Feuerbach, Lars Bhadra, Tapas Bandyopadhyay, Sanghamitra		MicroRNA Transcription Start Site Prediction with Multi-objective Feature Selection In: Statistical Applications in Genetics and Molecular Biology [11], 6.1-6.25
			Bock, Christoph		Analysing and interpreting DNA methylation data In: Nature Reviews Genetics [13], 705-719
			Bock, Christoph Lengauer, Thomas		Epigenom-Karten erstellen und nutzen In: BIOspektrum [18], 138-141
			Bock, Christoph Lengauer, Thomas		Managing drug resistance in cancer: lessons from HIV therapy In: Nature Reviews Cancer [12], 494-501
			Bogojeska, Jasmina Lengauer, Thomas		Hierarchical Bayes Model for Predicting Effectiveness of HIV Combination Therapies In: Statistical Applications in Genetics and Molecular Biology [11], 11.1-11.19
			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
			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
			Dietzen, Matthias Zotenko, Elena Hildebrandt, Andreas Lengauer, Thomas		On the Applicability of Elastic Network Normal Modes in Small-Molecule Docking In: Journal of Chemical Information and Modeling [52], 844-856
			Doncheva, Nadezhda T Assenov, Yassen Domingues, Francisco S. Albrecht, Mario		Topological analysis and interactive visualization of biological networks and protein structures In: Nature Protocols [7], 670-685
			Doncheva, Nadezhda T Kacprowski, Tim Albrecht, Mario		Recent approaches to the prioritization of candidate disease genes In: Wiley Interdisciplinary Reviews: Systems Biology and Medicine [4], 429-442
			Fernandez, Agustin F. Assenov, Yassen Martin-Subero, Jose Ignacio Balint, Balazs Siebert, Reiner Taniguchi, Hiroaki Yamamoto, Hiroyuki Hidalgo, Manuel Tan, Aik-Choon Galm, Oliver Ferrer, Isidre Sanchez-Cespedes, Montse Villanueva, Alberto Carmona, Javier Sanchez-Mut, Jose V. Berdasco, Maria Moreno, Victor Capella, Gabriel Monk, David Ballestar, Esteban Ropero, Santiago Martinez, Ramon Sanchez-Carbayo, Marta Prosper, Felipe Agirre, Xabier Fraga, Mario F. Gran˜a, Osvaldo Perez-Jurado, Luis Mora, Jaume Puig, Susana Prat, Jaime Badimon, Lina Puca, Annibale A. Meltzer, Stephen J. Lengauer, Thomas Bridgewater, John Bock, Christoph Esteller, Manel		A DNA methylation fingerprint of 1628 human samples In: Genome Research [22], 407-419
			Garai, Ágnes Zeke, András Gógl, Gergo Töro, Imre Fördos, Ferenc Blankenburg, Hagen Bárkai, Tünde Varga, János Alexa, Anita Emig, Dorothea Albrecht, Mario Reményi, Attila		Specificity of linear motifs that bind to a common mitogen-activated protein kinase docking groove In: Science Signaling [5], ra74,1-ra74,14
			Halachev, K. Bast, H. Albrecht, F. Lengauer, Thomas Bock, Christoph		EpiExplorer: live exploration and global analysis of large epigenomic datasets In: Genome Biology [13], R96,1-R96,14
			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
			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
			Lengauer, Thomas		Bioinformatical Assistance of Selecting Anti-HIV Therapies: Where Do We Stand? In: Intervirology [55], 108-112
			Lengauer, Thomas Bock, Christoph		Managing drug resistance in cancer: lessons from HIV therapy In: Nature Reviews Cancer [12], 494-501
			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
			Mikeska, Thomas Bock, Christoph Do, Hongdo Dobrovic, Alexander		DNA methylation biomarkers in cancer: Progress towards clinical implementation In: Expert Reviews of Molecular Diagnostics [12], 473-487
			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
			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
			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
			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
			Pfeifer, Nico Lengauer, Thomas		Improving coreceptor usage prediction in the clinic using hints from next generation sequencing data In: Bioinformatics [28], i589-i595
			Pfeifer, Nico Lengauer, Thomas		Improving HIV coreceptor usage prediction in the clinic using hints from next-generation sequencing data In: Bioinformatics [28], i589-i595
			Ramírez, Fidel Lawyer, Glenn Albrecht, Mario		Novel search method for the discovery of functional relationships In: Bioinformatics [28], 269-276
			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
			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
			Röttger, Richard Rueckert, Ulrich Taubert, Jan Baumbach, Jan		How Little Do We Actually Know? - On the Size of Gene Regulatory Networks. In: IEEE/ACM transactions on computational biology and bioinformatics [9], 1293-1300
			Setty, Yaki		Multi-scale computational modeling of developmental biology In: Bioinformatics [28], 2022-2028
			Simmer, Femke Brinkman, Arie B. Assenov, Yassen Matarese, Filomena Kaan, Anita Sabatino, Lina Villanueva, Alberto Huertas, Dori Esteller, Manel Lengauer, Thomas Bock, Christoph Colantuoni, Vittorio Altucci, Lucia Stunnenberg, Henk G.		Comparative genome-wide DNA methylation analysis of colorectal tumor and matched normal tissues In: Epigenetics [7], 1355-1367
			Thielen, Alexander Lengauer, Thomas		Geno2pheno[454]: A Web Server for the Prediction of HIV-1 Coreceptor Usage from Next-Generation Sequencing Data In: Intervirology [55], 113-117
			Welsch, Christoph Schweizer, Sabine Shimakami, Testsuro Domingues, Francisco S. Kim, Seungtaek Lemon, Stanley, M. Antes, Iris		Ketoamide Resistance and Hepatitis C Virus Fitness in Val55 Variants of the NS3 Serine Protease In: Antimicrobial Agents and Chemotherapy [56], 1907-1915
			Welsch, Christoph Shimakami, Tetsuro Hartmann, Christoph Yang, Yan Domingues, Francisco S. Lengauer, Thomas Zeuzem, Stefan Lemon, Stanley M.		Peptidomimetic Escape Mechanisms Arise via Genetic Diversity in the Ligand-Binding Site of the Hepatitis C Virus NS3/4A Serine Protease In: Gastroenterology [142], 654-663
			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
			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
6		Electronic Journal Article
			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
			Halachev, Konstantin Bast, Hannah Albrecht, Felipe Lengauer, Thomas Bock, Christoph		EpiExplorer: live exploration and global analysis of large epigenomic datasets In: Genome Biology [13], R96,1-R96,14
			Hauschild, Anne-Christin Baumbach, Jörg Ingo Baumbach, Jan		Integrated statistical learning of metabolic ion mobility spectrometry profiles for pulmonary disease identification In: Genetics and Molecular Research [11], 2733-2744
			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
			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
			Soares, Siomar C. Abreu, Vinícius A. C. Ramos, Rommel T. J. Cerdeira, Louise Silva, Artur Baumbach, Jan Trost, Eva Tauch, Andreas Hirata, Raphael Mattos-Guaraldi, Ana L. Miyoshi, Anderson Azevedo, Vasco		PIPS: Pathogenicity Island Prediction Software In: PLoS One [7], e30848,1-e30848,10
3		Thesis - Bachelor thesis
			Galata, Valentina		Applying Lasso regression to related cell types for gene network astimation Universität des Saarlandes
			Klingen, Thorsten		Automatic Recombination Analysis Using Recoo and Mebitoo Universität des Saarlandes
			Zeidler, Michael		Cloudbasierte Analyse von viralen Sequenzdaten der neuesten Generation Universität des Saarlandes
8		Thesis - Masters thesis
			Bader, Mathias		Clustering epigenetic data using a Dirichlet process prior Universität des Saarlandes
			Bastys, Tomas		MAP Kinase Docking Motifs in HIV Proteins Universität des Saarlandes
			Eldarov, Nasimi		Modeling influenza evolution in response to immune system pressure Universität des Saarlandes
			Kalaghatgi, Prabhav		A Phylodynamic Study of HIV Transmission Networks in Europe Universität des Saarlandes
			König, Eva		Automatic detection of loss of heterozygosity in cancer Universität des Saarlandes
			Koser, Sandra		Reconstructing anecestral methylation states in phylogenetic trees Universität des Saarlandes
			Müller, Joachim		Extracting pathways from biological networks incorporating omics data, introducing a webinterface for KeyPathwayMiner Universität des Saarlandes
			Speicher, Nora		Towards the identification of cancer subtypes by integrative clustering of molecular data Universität des Saarlandes
2		Thesis - PhD thesis
			Ramirez, Fidel		Novel Approaches to the Integration and Analysis of Systems Biology Universität des Saarlandes
			Tolosi, Laura		Finding Regions of Aberrant DNA Copy Number Associated With Tumor Phenotype Universität des Saarlandes
67	2011
1		Book
			Lengauer (ed.)		Computermodelle in der Wissenschaft - zwischen Analyse, Vorhersage und Suggestion
1		Proceedings Article
			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
1		Electronic Proceedings Article
			Bogojeska, Jasmina		History distribution matching method for predicting effectiveness of HIV combination therapies In: Neural Information Processing Systems (NIPS 2011), 424-432
1		Poster
			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
40		Journal Article
			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
			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
			Bleif, Sabrina Hannemann, Frank Lisurek, Michael von Kries, Jens Peter Zapp, Josef Dietzen, Matthias Antes, Iris Bernhardt, Rita		Identification of CYP106A2 as a Regioselective Allylic Bacterial Diterpene Hydroxylase In: ChemBioChem [12], 576-582
			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
			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
			Doncheva, Nadezhda T. Klein, Karsten Domingues, Francisco S. Albrecht, Mario		Analyzing and visualizing residue networks of protein structures In: Trends in Biochemical Sciences [36], 179-182
			Emig, Dorothea Albrecht, Mario		Tissue-specific proteins and functional implications In: Journal of Proteome Research [10], 1893-1903
			Emig, Dorothea Kacprowski, Tim Albrecht, Mario		Measuring and analyzing tissue specificity of human genes and protein complexes In: EURASIP Journal on Bioinformatics and Systems Biology [2011], 5,1-5,6
			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
			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
			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
			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
			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
			Krol, Elizaveta Blom, Jochen Winnebald, Jörn Berhörster, Alexander Barnett, Melanie J. Goesmann, Alexander Baumbach, Jan Becker, Anke		RhizoRegNet - A database of rhizobial transcription factors and regulatory networks. In: Journal of Biotechnology [155], 127-134
			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
			Lawyer, Glenn Altmann, André Thielen, Alex Zazzi, Maurizio Sönnerborg, Anders Lengauer, Thomas		HIV-1 mutational pathways under multidrug therapy In: AIDS Research and Therapy [8], 1-13
			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
			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
			Ramos, Rommel T.J. Carneiro, Adriana R. Baumbach, Jan Azevedo, Vasco Schneider, Maria P.C. Silva, Artur		Analysis of quality raw data of second generation sequencers with Quality Assessment Software In: BMC Research Notes [4], 130,1-130,6
			Reiss, Simon Rebhan, Ilka Backes, Perdita Romero-Brey, Ines Erfle, Holger Matula, Petr Kaderali, Lars Poenisch, Marion Blankenburg, Hagen Hiet, Marie-Sophie Longerich, Thomas Diehl, Sarah Ramírez, Fidel Balla, Tamas Rohr, Karl Kaul, Artur Bühler, Sandra Pepperkok, Rainer Lengauer, Thomas Albrecht, Mario Eils, Roland Schirmacher, Peter Lohmann, Volker Bartenschlager, Ralf		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
			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
			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		Prevalence and characteristics of hepatitis B and C virus infections in treatment-naïve HIV-infected patients In: Medical Microbiology and Immunology [200], 39-49
			Roomp, Kirsten Domingues, Francisco S.		Predicting interactions between T cell receptors and MHC-peptide complexes In: Molecular Immunology [48], 553-562
			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
			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
			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
			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
			Svichera, Valentina Centoa, Valeria Salpinia, Romina Mercurioa, Fabio Fraune, Maria Beggel, Bastian Hanc, Yue Gorid, Caterina Wittkope, Linda Bertolif, Ada Michelig, Valeria Gubertinig, Guido Longoh, Roberta Romanoh, Sara Viscah, Michela Gallinaroi, Valentina Marinoj, Nicoletta Mazzottaj, Francesco De Sanctisi, Giuseppe Maria Fleurye, Hervè Trimoulete, Pascale Angelicoa, Mario Cappielloh, Giuseppina Zhangc, Xin Xin Verheyenb, Jens Ceccherini-Silbersteina, Francesca Pernoa, Carlo Federico		Role of hepatitis B virus genetic barrier in drug-resistance and immune-escape development In: Digestive and Liver Disease [43], 975–983
			Svicher, Valentina Cento, Valeria Salpini, Romina Mercurio, Fabio Fraune, Maria Beggel, Bastian Han, Yue Gori, Caterina Wittkop, Linda Bertoli, Ada Micheli, Valeria Gubertini, Guido Longo, Roberta Romano, Sara Visca, Michela Gallinaro, Valentina Marino, Nicoletta Mazzotta, Francesco De Sanctis, Giuseppe Maria Fleury, Hervè Trimoulet, Pascale Angelico, Mario Cappiello, Giuseppina Zhang, Xin Xin Verheyen, Jens Ceccherini-Silberstein, Francesca Perno, Carlo Federico		Role of hepatitis B virus genetic barrier in drug-resistance and immune-escape development In: Digestive and Liver Disease [43], 975-983
			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
			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
			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
			Tolosi, Laura Lengauer, Thomas		Classification with correlated features: unreliability of feature ranking and solutions In: Bioinformatics [27], 1986-1994
			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
			Wittkop, Tobias Emig, Dorothea Truss, Anke Albrecht, Mario Böcker, Sebastian Baumbach, Jan		Comprehensive cluster analysis with Transitivity Clustering In: Nature Protocols [6], 285-295
			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
			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
			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
			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
			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
9		Electronic Journal Article
			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
			Däumer, Martin Kaiser, Rolf Klein, Rolf Lengauer, Thomas Thiele, Bernhard Thielen, Alexander		Genotypic tropism testing by massively parallel sequencing: qualitative and quantitative analysis In: BMC Medical Informatics and Decision Making [11], 30,1-30,8
			Ebrahimi, Mansou Lakizadeh, Amir Agha-Golzadeh, Esmaeil Ebrahimi, Mahdi		Prediction of Thermostability from Amino Acid Attributes by Combination of Clustering with Attribute Weighting: A New Vista in Engineering Enzymes In: PLoS One [6], e23146,1-e23146,11
			Emig, Dorothea Sander, Oliver Mayr, Gabriele Albrecht, Mario		Structure collisions between interacting proteins In: PLoS ONE [6], e19581,1-e19581,7
			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
			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
			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
			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
			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
3		Thesis - Bachelor thesis
			Döring, Matthias		Web Implementation of the HBV Dual Infection Model Universität des Saarlandes
			Junge, Alexander		Unsupervised dissection of cancer types based on genomic, epigenomic and transciptomic features Universität des Saarlandes
			Reuter, Kerstin		Estimating and Using the Uncertainty in the Phenotypic Resistance Assay of the Hepatitis B Virus to Improve IC-50 Prediction from Genotype Universität des Saarlandes
6		Thesis - Masters thesis
			Hauschild, Anne-Christin		Modeling HIV Neutralization Universität des Saarlandes
			Hoinka, Jan-Malte		Finding the Hairpin in the Haystack: Towards an High Throughput in Silico Pipeline for Aptamer Motif Identification using SELEX Data Universität des Saarlandes
			Ivanova, Violeta		Comparison of methods for discovering genomic aberrations relevant for cancer Universität des Saarlandes
			Jing, Cui		A comprehensive analysis of the illumina Infinium assay Universität des Saarlandes
			Kacprowski, Tim		Disease gene prioritization by combining network information and functional knowledge Universität des Saarlandes
			Weimann, Aaron		Functional Profiling in Metagenomics Universität des Saarlandes
5		Thesis - PhD thesis
			Bogojeska, Jasmina		Statistical Learning Methods for Bias-aware HIV Therapy Screening Universität des Saarlandes
			Bozek, Katarzyna		Analysis of HIV-host interaction on different scales. Universität des Saarlandes
			Emig, Dorothea		Novel analysis approaches to context-dependent molecular networks Universität des Saarlandes
			Kunert, Lars		Maximal Common Subgraph DAGs: Theory and Application to Virtual Screening in Drug Development Universität des Saarlandes
			Thielen, Alexander		Genotypic Analysis of HIV-1 Coreceptor Usage Universität des Saarlandes
59	2010
2		Part of a Book
			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
			Ramirez, Fidel		Tutorial Cytoscape In: Bioinformática: Aplicaciones a la genómica y proteómica, 73-98
2		Proceedings Article
			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
			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
1		Electronic Proceedings Article
			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
4		Poster
			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
			Feuerbach, Lars Lengauer, Thomas		Ancestral germline methylation reconstruction of young repeats In: Transcription, chromatin structure and DNA repair in development and differentiation, 81
			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
			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
28		Journal Article
			Albrecht, Mario		Color blindness In: Nature Methods [7], 775
			Altmann, André Tolosi, Laura Sander, Oliver Lengauer, Thomas		Permutation importance: an unbiased feature importance measure In: Bioinformatics [26], 1340-1347
			Baumbach, Jan		On the power and limits of evolutionary conservation - unraveling bacterial gene regulatory networks In: Nucleic Acids Research [38], 7877-7884
			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
			Bogojeska, Jasmina Bickel, Steffen Altmann, André Lengauer, Thomas		Dealing with sparse data in predicting outcomes of HIV combination therapies In: Bioinformatics [26], 2085-2092
			Bozek, Katarzyna Rosahl, A. L. Gaub, S. Lorenzen, S. Herzel, H.		Circadian transcription in liver In: Biosystems [102], 61-69
			Brunner, Susanne Hurni, Severine Streckeisen, Philipp Mayr, Gabriele Albrecht, Mario Yahiaoui, Nabila Keller, Beat		Intragenic allele pyramiding combines different specificities of wheat Pm3 resistance alleles In: The Plant Journal [64], 433-445
			Codoñer, Francisco M Pou, Christian Thielen, Alexander García, Federico Delgado, Rafael Dalmau, David Santos, José Ramon Buzón, Maria José Martínez-Picado, Javier Alvarez-Tejado, Miguel Clotet, Bonaventura Ruiz, Lidia Paredes, Roger		Dynamic escape of pre-existing raltegravir-resistant HIV-1 from raltegravir selection pressure In: Antiviral Research [88], 281-286
			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
			Ellinghaus, Eva Ellinghaus, David Stuart, Philip E. Nair, Rajan P. Debrus, Sophie Raelson, John V. Belouchi, Majid Fournier, Hélène Reinhard, Claudia Ding, Jun Li, Yun Tejasvi, Trilokraj Gudjonsson, Johann Stoll, Stefan W. Voorhees, John J. Lambert, Sylviane Weidinger, Stephan Eberlein, Bernadette Kunz, Manfred Rahman, Proton Gladman, Dafna D. Gieger, Christian Wichmann, H. Erich Karlsen, Tom H. Mayr, Gabriele Albrecht, Mario Kabelitz, Dieter Mrowietz, Ulrich Abecasis, Gonçalo R. Elder, James T. Schreiber, Stefan Weichenthal, Michael Franke, Andre		Genome-wide association study identifies a psoriasis susceptibility locus at TRAF3IP2 In: Nature Genetics [42], 991-995
			Emig, Dorothea Salomonis, Nathan Baumbach, Jan Lengauer, Thomas Conklin, Bruce R. Albrecht, Mario		AltAnalyze and DomainGraph: analyzing and visualizing exon expression data In: Nucleic Acids Research [38], W755-W762
			Franke, Andre Balschun, Tobias Sina, Christian Ellinghaus, David Häsler, Robert Mayr, Gabriele Albrecht, Mario Wittig, Michael Buchert, Eva Nikolaus, Susanna Gieger, Christian Wichmann, H. Erich Sventoraityte, Jurgita Kupcinskas, Limas Onnie, Clive M. Gazouli, Maria Anagnou, Nicholas P. Strachan, David McArdle, Wendy L. Mathew, Christopher G. Rutgeerts, Paul Vermeire, Séverine Vatn, Morten H. Krawczak, Michael Rosenstiel, Philip Karlsen, Tom H. Schreiber, Stefan		Genome-wide association study for ulcerative colitis identifies risk loci at 7q22 and 22q13 (IL17REL) In: Nature Genetics [42], 292-294
			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
			Harris, R. Alan Wang, Ting Coarfa, Cristian Nagarajan, Raman P. Hong, Chibo Downey, Sara L. Johnson, Brett E. Fouse, Shaun D. Delaney, Allen Zhao, Yongjun Olshen, Adam Ballinger, Tracy Zhou, Xin Forsberg, Kevin J. Gu, Junchen Echipare, Lorigail O'Geen, Heriette Lister, Ryan Pelizzola, Mattia Xi, Yuanxin Epstein, Charles B. Bernstein, Bradley E. Hawkins, R. David Ren, Bing Chung, Wen-Yu Gu, Hongcang Bock, Christoph Gnirke, Andreas Zhang, Michael Q. Haussler, David Ecker, Joseph R. Li, Wei Farnham, Peggy J. Waterland, Robert a. Meissner, Alexander Marra, Marco A. Hirst, Martin Milosavljevic, Aleksandar Costello, Joseph F.		Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications In: Nature Biotechnology [28], 1097-1105
			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
			Lengauer, Thomas Altmann, André Thielen, Alexander Kaiser, Rolf		Chasing the AIDS Virus In: Communications of the ACM [53], 66-74
			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
			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
			Ramírez, Fidel Albrecht, Mario		Finding scaffold proteins in interactomes In: Trends in Cell Biology [20], 2-4
			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
			Schlicker, Andreas Albrecht, Mario		FunSimMat update: new features for exploring functional similarity In: Nucleic Acids Research [38], D244-D248
			Schlicker, Andreas Lengauer, Thomas Albrecht, Mario		Improving disease gene prioritization using the semantic similarity of Gene Ontology terms In: Bioinformatics [26], i561-i567
			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
			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
			Thielen, Alexander Sichtig, Nadine Kaiser, Rolf Lam, Jeffrey Harrigan, P. Richard Lengauer, Thomas		Improved prediction of HIV-1 coreceptor usage with sequence information from the second hypervariable loop of gp120 In: Journal of Infectious Diseases [202], 1435-1443
			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
			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
			Wohlers, Inken Domingues, Francisco S. Klau, Gunnar W.		Towards optimal alignment of protein structure distance matrices In: Bioinformatics [26], 2273-2280
8		Electronic Journal Article
			Bozek, Katarzyna Lengauer, Thomas		Positive selection of HIV host factors and the evolution of lentivirus genes In: BMC Evolutionary Biology [10], 186,1-186,15
			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
			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
			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
			Roomp, Kirsten Antes, Iris Lengauer, Thomas		Predicting MHC class I epitopes in large datasets In: BMC Bioinformatics [11], 90,1-90,11
			Saigo, Hiroto Hattori, Masahiro Kashima, Hisashi Tsuda, Koji		Reaction graph kernels predict EC numbers of unknown enzymatic reactions in plant secondary metabolism In: BMC Bioinformatics [11], S31,1-S31,7
			Weisser, Hendrik Altmann, André Sierra, Saleta Incardona, Francesca Struck, Daniel Sönnerborg, Anders Kaiser, Rolf Zazzi, Maurizio Tschochner, Monika Walter, Hauke Lengauer, Thomas		Only Slight Impact of Predicted Replicative Capacity for Therapy Response Prediction In: PLoSOne [5], e9044,1-e9044,10
			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
5		Thesis - Bachelor thesis
			Dörr, Barbara		Using copy number variation fpr predicting susceptibility to glioblastoma Universität des Saarlandes
			Gatzmann, Fanny		GOdot Sequence - function prediction from protein sequence Universität des Saarlandes
			Kacprowski, Tim		Analysis of protein complexes and tissue-spedific expression Universität des Saarlandes
			König, Eva		Env-wide analysis of coreceptor determining sites and subtype-specific differences in HIV-1 Universität des Saarlandes
			Speicher, Nora K.		Network analysis of viral host factors Universität des Saarlandes
5		Thesis - Masters thesis
			Kuhn Cuellar, Luis Eugenio		A probabilistic algorithm for matching protein structures - and its application to detecting functionally relevant patterns Universität des Saarlandes
			Loi, Luu Phuc		Identifying discriminative motifs for molecular function of proteins Universität des Saarlandes
			Lutsik, Pavlo		Processing of high-throughput DNA methylation data Universität des Saarlandes
			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
			Stöckel, Daniel		History Based HIV Therapy Outcome Prediction Universität des Saarlandes
4		Thesis - PhD thesis
			Altmann, André		Bioinformatical approaches to ranking of anti-HIV combination therapies and planning of treatment schedules Universität des Saarlandes
			Johannsen, Daniel		Random Combinatorial Structures and Randomized Search Heuristics Universität des Saarlandes
			Schlicker, Andreas		Ontology-based Similarity Measures and their Application in Bioinformatics Universität des Saarlandes
			Zhu, Hongbo		Characterization, classification and alignment of protein-protein interfaces Universität des Saarlandes
43	2009
2		Part of a Book
			Adams, Ben McHardy, Alice Lundegaard, C. Lengauer, Thomas		Viral Bioinformatics In: Modern Genome Annotation - The BioSapiens Network, 429-452
			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
4		Poster
			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
			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
			Thielen, Alexander Altmann, André Bogojeska, Jasmina Kaiser, Rolf Lengauer, Thomas		Estimating evolutionary pathways to 7CXCR4 usage from cross-sectional data In: Abstracts presented at the XVIII International HIV Drug Resistance Workshop : Basic Principles & Clinical Implications, A16-A16
			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
22		Journal Article
			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
			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
			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
			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
			Bock, Christoph		Epigenetic biomarker development In: Epigenomics [1], 99-110
			Bock, Christoph Halachev, Konstantin Büch, Joachim Lengauer, Thomas		EpiGRAPH: user-friendly software for statistical analysis and prediction of (epi)genomic data In: Genome Biology [10], R14.1-R14.14
			Hartmann, Christoph Antes, Iris Lengauer, Thomas		Docking and scoring with alternative side-chain conformations In: Proteins: Structure, Function, and Bioinformatics [74], 712-726
			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
			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
			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
			Lengauer, Thomas Altmann, André Thielen, Alexander		Bioinformatische Unterstützung der Auswahl von HIV Therapien In: Informatik Spektrum [32], 320-331
			Lengauer, Thomas Kaiser, Rolf		Computerjagd auf das AIDSVIRUS In: Spektrum der Wissenschaft [08], 62-67
			Lengauer, Thomas Sierra, S. Kaiser, Rolf		Resistenzbestimmung In: MMW Fortschritte in der Medizin [151], 74-75
			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
			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
			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
			Roomp, Kirsten Rand, Jacquie		Intensive blood glucose control is safe and effective in diabetic cats using home monitoring and treatment with glargine In: Journal of feline medicine and surgery [11], 668-682
			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
			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
			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
			Susser, Simone Welsch, Christoph Wang, Yalan Zettler, Markus Domingues, Francisco S. Karey, Ursula Hughes, Eric Ralston, Robert Tong, Xiao Herrmann, Eva Zeuzem, Stefan Sarrazin, Christoph		Characterization of resistance to the protease inhibitor boceprevir in hepatitis C virus-infected patients. In: Hepatology [50], 1709-1718
			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
5		Electronic Journal Article
			Blankenburg, Hagen Ramírez, Fidel Büch, Joachim Albrecht, Mario		DASMIweb: online integration, analysis and assessment of distributed protein interaction data In: Nucleic Acids Research [37], W122-W128
			Bozek, Kasia Relógio, Angela Kielbasa, Szymon M. Heine, Markus Dame, Christof Kramer, Achim Herzel, Hanspeter		Regulation of clock-controlled genes in mammals. In: PLoS One [4], e4882:1-e4882:12
			Bozek, Kasia Thielen, Alexander Sierra, Saleta Kaiser, Rolf Lengauer, Thomas		V3 loop sequence space analysis suggests different evolutionary patterns of CCR5- and CXCR4-tropic HIV. In: PLoS One [4], e7387:1-e.7387:14
			McHardy, Alice C. Adams, Ben		The role of genomics in tracking the evolution of influenza A virus In: PLoS Pathog [5], e1000566
			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
3		Thesis - Bachelor thesis
			Ebert, Peter		Computational Analysis of genomic HPV data Universität des Saarlandes
			Mangels, Miriam		In Silico Models for the Prediction of Metabolism by Cytochrome P450 Enzymes Universität des Saarlandes
			Weimann, Aaron		Using multidimensional Scaling for visualizing similarities of proteins Universität des Saarlandes
5		Thesis - Masters thesis
			Diehl, Sarah		Analysis and reconstruction of protein complex topology Universität des Saarlandes
			Doncheva, Nadezhda, T.		Analysis and visualization of residue interaction networks Universität des Saarlandes
			Gwinner, Frederik		Assessing the Conservation of Protein Function on Evolutionary Defined Patches Universität des Saarlandes
			Müller, Fabian		Assessing Antibody Neutralization of HIV-1 as an Initial Step in the Search for gp160-based Immunogens Universität des Saarlandes
			Pironti, Alejandro		Probabilistic disease gene prioritization Universität des Saarlandes
2		Thesis - Habilitation thesis
			Antes, Iris		Computational Methods for the Investigation of Protein-Ligand Interactions Universität des Saarlandes
			Sommer, Ingolf		From Protein Structure to Function Universität des Saarlandes
54	2008
2		Part of a Book
			Sierra, Saleta Kaiser, Rolf Thielen, Alexander Sander, Oliver Lengauer, Thomas		Genotypic Analysis of HIV Co-Receptor Usage In: Entry Inhibitoren - Neue Formen der HIV-Therapie, 31-39
			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
5		Proceedings Article
			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
			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
			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
			Saigo, Hiroto Tsuda, Koji		Iterative Subgraph Mining for Principal Component Analysis. In: Proceedings of the IEEE International Conference on Data Mining (ICDM2008), DM934
			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
1		Electronic Proceedings Article
			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
10		Poster
			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
			Däumer, Martin Kaiser, Rolf Klein, Rolf Lengauer, Thomas Thiele, Bernhard Thielen, Alexander		Inferring viral tropism from genotype with massively parallel sequencing; qualitative and quantitative analysis In: Antiviral Therapy, A101
			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
			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
			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
			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
			Sander, Oliver Altmann, Andre Lengauer, Thomas		Computational analysis of covariation and interactions between HIV-1 reverse transcriptase and Integrase In: Reviews in Antiviral Therapy, 113-114
			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
			Thielen, Alexander Kaiser, Rolf Lengauer, Thomas		Improving HIV-1 coreceptor usage prediction from genotype with regions outside of V3 In: Reviews in Antiviral Therapy, 81-82
			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
23		Journal Article
			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
			Assenov, Yassen Ramírez, Fidel Schelhorn, Sven-Eric Lengauer, Thomas Albrecht, Mario		Computing topological parameters of biological networks In: Bioinformatics [24], 282-284
			Bock, Christoph		IVF: stars may have to consider the risk of stolen parenthood In: Nature [454], 938
			Bock, Christoph Lengauer, Thomas		Computational epigenetics In: Bioinformatics [24], 1-10
			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
			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
			Bogojeska, Jasmina Lengauer, Thomas Rahnenführer, Jörg		Stability analysis of mixtures of mutagenetic trees In: BMC Bioinformatics [9], 165-181
			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
			Emig, Dorothea Cline, Melissa S. Lengauer, Thomas Albrecht, Mario		Integrating expression data with domain interaction networks In: Bioinformatics [24], 2546-2548
			Franke, Andre Balschun, Tobias Karlsen, Tom H. Sventoraityte, Jurgita Nikolaus, Susanna Mayr, Gabriele Domingues, Francisco S. Albrecht, Mario Nothnagel, Michael Ellinghaus, David Sina, Christian Onnie, Clive M. Weersma, Rinse K. Stokkers, Pieter C. F. Wijmenga, Cisca Gazouli, Maria Strachan, David McArdle, Wendy L. Vermeire, Séverine Rutgeers, Paul Rosenstiel, Philip Krawczak, Michael Vatn, Morten H. IBSEN study group, the Mathew, Christopher G. Schreiber, Stefan		Sequence variants in IL10, ARPC2, and multiple other loci contribute to ulcerative colitis In: Nature Genetics [40], 1319-1323
			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
			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
			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
			Lisurek, Michael Simgen, Birgit Antes, Iris Bernhardt, Rita		Theoretical and Experimental Evaluation of a CYP106A2 Low Homology Model and Production of Mutants with Changed Activity and Selectivity of Hydroxylation In: ChemBioChem [9], 1439-1449
			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
			Schelhorn, Sven-Eric Lengauer, Thomas Albrecht, Mario		An integrative approach for predicting interactions of protein regions In: Bioinformatics [24], i35-i41
			Schlicker, Andreas Albrecht, Mario		FunSimMat: a comprehensive functional similarity database In: Nucleic Acids Research [36], D434-D439
			Van Ooijen, Gerben Mayr, Gabriele Albrecht, Mario Cornelissen, Ben J. C. Takken, Frank L. W.		Transcomplementation, but not physical association of the CC-NB-ARC and LRR domains of tomato R protein Mi-1.2 is altered by mutations in the ARC2 subdomain In: Molecular Plant [1], 401-410
			Van Ooijen, Gerben Mayr, Gabriele Kasiem, Mobien M. A. Albrecht, Mario Cornelissen, Ben J. C. Takken, Frank L. W.		Structure-function analysis of the NB-ARC domain of plant disease resistance proteins In: Journal of Experimental Botany [59], 1383-1397
			Weinhold, Nils Sander, Oliver Domingues, Francisco S. Lengauer, Thomas Sommer, Ingolf		Local function conservation in sequence and structure space In: PLoS Computational Biology [4], e1000105
			Welsch, Christoph Domingues, Francisco S. Susser, Simone Antes, Iris Hartmann, Christoph Mayr, Gabriele Schlicker, Andreas Sarrazin, Christoph Albrecht, Mario Zeuzem, Stefan Lengauer, Thomas		Molecular basis of telaprevir resistance due to V36 and T54 mutations in the NS3-4A protease of HCV In: Genome Biology [9], R16
			Zhu, Hongbo Sommer, Ingolf Lengauer, Thomas Domingues, Francisco S.		Alignment of Non-Covalent Interactions at Protein-Protein Interfaces In: PLoS ONE [3], e1926
			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
3		Thesis - Bachelor thesis
			Müller, Fabian		Inferring virological response to antiretroviral combination therapy based on past treatment lines Universität des Saarlandes
			Perner, Juliane		Semi-Supervised Learning for Predicting Anti-HIV Drug Resistance Universität des Saarlandes
			Stöckel, Daniel		Protein Surface Remeshing and Characterisation Using Morse-Smale Complexes Universität des Saarlandes
3		Thesis - Masters thesis
			Djoumbou, Yannick		Molecular Dynamics based prediction of HIV-1 drug resistance Universität des Saarlandes
			Fischer, Sandra		Structure-based prediction of HIV-1 drug resistance Universität des Saarlandes
			Schüffler, Peter		MethMarker – A toolkit for design, optimization and validation of DNA methylation biomarkers for cancer diagnosis and therapy optimization Universität des Saarlandes
7		Thesis - PhD thesis
			Bock, Christoph		Computational Epigenetics - Bioinformatic methods for epigenome prediction, DNA methylation mapping and cancer epigenetics Universität des Saarlandes
			Hartmann, Christoph		Modeling of Flexible Side Chains for Protein-Ligand Docking Universität des Saarlandes
			Maydt, Jochen		Analysis of recombination in Molecular Sequence Data Universität des Saarlandes
			Sander, Oliver		Structural Descriptors for the Analysis of Protein Structure, Function, and Evolution Universität des Saarlandes
			Sing, Tobias		Model-Based Anti HIV Therapy Universität des Saarlandes
			Steffen, Andreas		Computational Approaches in Supramolecular Chemistry with a special Focus on Virtual Screening Universität des Saarlandes
			Talwar, Priti		Development of Computational Methods for Metabolic Network Analysis based on Metabolomics Data Universität des Saarlandes
68	2007
3		Book
			Lengauer (ed.)		Bioinformatics - From Genomes to Therapies 1. The Building Blocks: Molecular Sequences and Structures
			Lengauer (ed.)		Bioinformatics - From Genomes to Therapies 2. Getting at the Inner Workings: Molecular Interactions
			Lengauer (ed.)		Bioinformatics - From Genomes to Therapies 3. The Holy Grail: Molecular Function
10		Part of a Book
			Bock, Christoph Lengauer, Thomas		Computational Epigenetics: Bioinformatik für neue Wege in der Krebsforschung In: Jahrbuch 2007, 271-277
			Domingues, Francisco S. Lengauer, Thomas		Inferring Protein Function from Protein Structure In: Bioinformatics - From Genomes to Therapies 3. The Holy Grail: Molecular Function, 1211-1252
			Kämper, Andreas Rognan, Didier Lengauer, Thomas		Lead Identification by Virtual Screening In: Bioinformatics - From Genomes to Therapies 2. Getting at the Inner Workings: Molecular Interactions, 651-704
			Lengauer, Thomas		Bioinformatik In: Technologiefüher - Grundlagen, Anwendungen, Trends, 4
			Lengauer, Thomas		Future Trends In: Bioinformatics - From Genomes to Therapies 3. The Holy Grail: Molecular Function, 1651-1687
			Lengauer, Thomas		Introduction In: Bioinformatics - From Genomes to Therapies 1. The Building Blocks: Molecular Sequences and Structures, 1-24
			Lengauer, Thomas		Strategiekonzept "Molekulare Bioinformatik" In: Informatikforschung in Deutschland, 9
			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
			Roomp, Kirsten		Evolution of Drug Resistance in HIV In: Bioinformatics - From Genomes to Therapies 3. The Holy Grail: Molecular Function, 1457-1496
			Sommer, Ingolf		Protein Fold Recognition Based on Distant Homologs In: Bioinformatics - From Genomes to Therapies 1. The Building Blocks: Molecular Sequences and Structures, 351-388
1		Proceedings
			Lengauer, Rost, Schuster (ed.)		Proceedings ISMB2007
1		Proceedings Article
			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
3		Poster
			Altmann, Andre Däumer, Martin Sing, Tobias Beerenwinkel, Niko Walter, Hauke Kaiser, Rolf Lengauer, Thomas		Validation of geno2pheno and THEO on a large independent clinical dataset In: Proceedings of the 5th European HIV Drug Resistance Workshop, -
			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
			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, -
35		Journal Article
			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
			Altmann, Andre Beerenwinkel, Niko Sing, Tobias Savenkov, Igor Däumer, Martin Kaiser, Rolf Rhee, Soo-Yon Fessel, W Jeffrey Shafer, Robert W Lengauer, Thomas		Improved prediction of response to antiretroviral combination therapy using the genetic barrier to drug resistance In: Antiviral Therapy [12], 169-178
			Bock, Christoph Walter, Jörn Paulsen, Martina Lengauer, Thomas		CpG Island Mapping by Epigenome Prediction In: PLoS Computational Biology [3], 1055-1070
			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
			Domingues, Francisco S. Rahnenführer, Jörg Lengauer, Thomas		Conformational analysis of alternative protein structures In: Bioinformatics [23], 3131-3138
			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
			Franke, Andre Hampe, Jochen Rosenstiel, Philip Becker, Christoph Wagner, Florian Häsler, Robert Little, Randall D. Huse, Klaus Ruether, Andreas Balschun, Tobias Wittig, Michael ElSharawy, Abdou Mayr, Gabriele Albrecht, Mario Prescott, Natalie J. Onnie, Clive M. Fournier, Hélène Keith, Tim Radelof, Uwe Platzer, Matthias Mathew, Christopher G. Stoll, Monika Krawczak, Michael Nürnberg, Peter Schreiber, Stefan		Systematic association mapping identifies NELL1 as a novel IBD disease gene In: PLoS ONE [2], e691.1-13
			Hampe, Jochen Franke, Andre Rosenstiel, Philip Till, Andreas Teuber, Markus Huse, Klaus Albrecht, Mario Mayr, Gabriele De La Vega, Francisco M. Briggs, Jason Günther, Simone Prescott, Natalie J. Onnie, Clive M. Häsler, Robert Sipos, Bence Fölsch, Ulrich R. Lengauer, Thomas Platzer, Matthias Mathew, Christopher G. Krawczak, Michael Schreiber, Stefan		A genome-wide association scan of nonsynonymous SNPs identifies a susceptibility variant for Crohn disease in ATG16L1 In: Nature Genetics [39], 207-211
			Hartmann, Christoph Antes, Iris Lengauer, Thomas		IRECS: A new algorithm for the selection of most probable ensembles of side-chain conformations in protein models. In: Protein Science [16], 1294-1307
			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
			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
			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
			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
			Kupfer, Bernd Sing, Tobias Schüffler, Peter Hall, Rabea Kurz, Ralf McKeown, Astrid Schneweis, Karl-Eduard Eberl, Wolfgang Oldenburg, Johannes Brackmann, Hans H. Rockstroh, Jürgen K. Spengler, Ulrich Däumer, Martin Kaiser, Rolf Lengauer, Thomas Matz, Bertfried		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
			Lengauer, Thomas Sander, Oliver Sierra, Saleta Thielen, Alexander Kaiser, Rolf		Bioinformatics prediction of HIV coreceptor usage In: Nature Biotechnology [25], 1407-1410
			Liu, Fang Tostesen, Eivind Sundet, Jostein K. Jenssen, Tor-Kristian Bock, Christoph Jerstad, Geir Ivar Thilly, William G. Hovig, Eivind		The human genomic melting map In: PLoS Computational Biology [3], e93
			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
			Mayr, Gabriele Domingues, Francisco S. Lackner, Peter		Comparative Analysis of Protein Structure Alignments In: BMC Structural Biology [7], 1
			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
			Ramírez, Fidel Schlicker, Andreas Assenov, Yassen Lengauer, Thomas Albrecht, Mario		Computational analysis of human protein interaction networks In: Proteomics [7], 2541-2552
			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
			Sander, Oliver Sing, Tobias Sommer, Ingolf Low, Andrew J. Cheung, Peter K. Harrigan, P. Richard Lengauer, Thomas Domingues, Francisco S.		Structural Descriptors of gp120 V3 Loop for the Prediction of HIV-1 Coreceptor Usage In: PLoS Computational Biology [3], 555-564
			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
			Schlicker, Andreas Huthmacher, Carola Ramírez, Fidel Lengauer, Thomas Albrecht, Mario		Functional evaluation of domain-domain interactions and human protein interaction networks In: Bioinformatics [23], 859-865
			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
			Sierra, Saleta Kaiser, Rolf Thielen, Alexander Lengauer, Thomas		Genotypic coreceptor analysis. In: European Journal of Medical Research [12], 453-462
			Sing, Tobias Low, Andrew J. Beerenwinkel, Niko Sander, Oliver Cheung, Peter K. Domingues, Francisco S. Büch, Joachim Däumer, Martin Kaiser, Rolf Lengauer, Thomas Harrigan, P. Richard		Predicting HIV coreceptor usage on the basis of genetic and clinical covariates In: Antiviral Therapy [12], 1097-1106
			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
			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
			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
			Steffen, Andreas Karasz, Maximilian Thiele, Carolin Lengauer, Thomas Kämper, Andreas Wenz, Gerhard Apostolakis, Joannis		Combined similarity and QSPR virtual screening for guest molecules of $\beta$-cyclodextrin In: New Journal of Chemistry [31], 1941-1949
			Steffen, Andreas Thiele, Carolin Tietze, Simon Strassnig, Christian Kämper, Andreas Lengauer, Thomas Wenz, Gerhard Apostolakis, Joannis		Improved cyclodextrin-based receptors for camptothecin by inverse virtual screening In: Chemistry [13], 6801-6809
			Tress, Michael L. Martelli, Pier L. Frankish, Adam Reeves, Gabrielle A. Wesselink, Jan J. Yeats, Corin Ólason, Páll Í. Albrecht, Mario Hegyi, Hedi Giorgetti, Alejandro Raimondo, Domenico Lagarde, Julien Laskowski, Roman A. López, Gonzalo Sadowski, Michael I. Watson, James D. Fariselli, Piero Rossi, Ivan Nagy, Alinda Kai, Wang Størling, Zenia Orsini, Massimiliano Assenov, Yassen Blankenburg, Hagen Huthmacher, Carola Ramírez, Fidel Schlicker, Andreas Denoued, France Jones, Phil Kerrien, Samuel Orchard, Sandra Antonarakis, Stylianos E. Reymond, Alexandre Birney, Ewan Brunak, Søren Casadio, Rita Guigo, Roderic Harrow, Jennifer Hermjakob, Henning Jones, David T. Lengauer, Thomas Orengo, Christine A. Patthy, László Thornton, Janet M. Tramontano, Anna Valencia, Alfonso		The implications of alternative splicing in the ENCODE protein complement In: Proceedings of the National Academy of Sciences [104], 5495-5500
			Welker, Martin W. Hofmann, Wolf-Peter Welsch, Christoph von Wagner, Michael Herrmann, Eva Lengauer, Thomas Zeuzem, Stefan Sarrazin, Christoph		Correlation nonstructural (NS)4B amino acid variations with initial viral kinetics during interferon-alpha-based therapy in HCV-1b-infected patients In: Journal of Viral Hepatitis [14], 338-349
			Welsch, Christoph Albrecht, Mario Maydt, Jochen Herrmann, E. Welker, M.W. Sarrazin, C. Scheidig, A. Lengauer, Thomas Zeuzem, S.		Structural and functional comparison of the non-structural protein 4B of flaviviridae In: Journal of Molecular Graphics and Modeling [26], 546-557
2		Electronic Journal Article
			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
			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
1		Journal
			Lengauer, Oette, Selbig, Hoffmann, Poggensee, Hamouda, Häussinger, Kaiser (ed.)		European Journal of Medical Research
10		Thesis - Masters thesis
			Bogojeska, Jasmina		Stability analysis of oncogenetic trees mixture models Universität des Saarlandes
			Dietzen, Matthias		An additive tree-based approach to the prediction of the strength of acidity for drug-like molecules Universität des Saarlandes
			Feuerbach, Lars		Towards Comparative Epigenomics: A Pilot Study on DNA Methylation of CpG Islands on Human Chromosome 21 Universität des Saarlandes
			Haid, Carla		BSIFlex: Binding Site Identification including protein flexibility Universität des Saarlandes
			Kircher, Martin		In silico analysis of microRNA genes on human chromosome 14 and mouse chromosome 12 Universität des Saarlandes
			Korbel, Ulli S.		Identification of Symmetries in Molecules and Complexes Universität des Saarlandes
			Müller, Oliver		Using Shape Retrieval Techniques for Identifying Similar Protein Binding Sites Universität des Saarlandes
			Schelhorn, Sven-Eric		Prediction of Domain and Motif Interactions from Protein Networks Universität des Saarlandes
			Volkamer, Andrea		Automated generation of pharmacophore type constraints to improve FlexX docking Universität des Saarlandes
			Weisser, Hendrik		Estimating the local variance of protein structure models Universität des Saarlandes
2		Thesis - other
			Blankenburg, Hagen		A Distributed Annotation System for Molecular Interactions Ruprecht Karl Universität Heidelberg; Universität Heilbronn
			Emig, Dorothea		The Impact of Alternative Splicing on Protein Interaction Networks Eberhard Karls Universität Tübingen
57	2006
1		Part of a Book
			Bock, Christoph Halachev, Konstantin Lengauer, Thomas		Bioinformatisches Data Mining erschließt neue Strategien gegen Krebs In: Aktuelle Trends in der Softwareforschung, 91-99
3		Proceedings Article
			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
			Steffen, Andreas Kämper, Andreas Lengauer, Thomas		Virtual screening for guest molecules of a biosensor In: Biosensors 2006: The ninth world congress on biosensors, O66
			Talwar, Priti Lengauer, Thomas Wittmann, Christoph Velagapudi, V. R. Heinzle, Elmar		Development of Computational Methods for Analysis of Metabolic Profiling Data In: Proceedings of International Conference on Systems Biology (ICSB 2006), Japan, 42-42
1		Poster
			Antes, Iris Lengauer, Thomas		Refinement of homology modeled protein structures for molecular docking In: Proceedings of the 367. WE-Heraeus Seminar on Biomolecular Simulations, 1
29		Journal Article
			Albrecht, Mario Takken, Frank L. W.		Update on the domain architectures of NLRs and R proteins In: Biochemical and Biophysical Research Communications [339], 459-462
			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
			Antes, Iris Siu, Shirley Weng-In Lengauer, Thomas		DynaPred: A structure and sequence based method for the prediction of MHC class I binding peptide sequence and conformations In: Bioinformatics [22], 16-24
			Bock, Christoph		Bioinformatik: Neue Strategien gegen Krebs In: Deutsches Ärzteblatt PRAXiS [103], 10-11
			Bock, Christoph Hesser, Jürgen		Analysis and Prediction of Helix Shift Errors in Homology Modeling In: In Silico Biology [6], 131-145
			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
			Heckmann-Pohl, Dorothee M. Bastian, Sabine Altmeier, S. Antes, Iris		Improvement of the fungal enzyme pyranose 2-oxidase using protein engineering In: Journal of Biotechnology [124], 26-40
			Heil, Burkhard Ludwig, Jost Lichtenberg-Fraté, Hella Lengauer, Thomas		Computational recognition of potassium channel sequences In: Bioinformatics [13], 1562-1568
			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
			Lehmann, Clara Däumer, Martin Bousaad, Ibrahim Sing, Tobias Beerenwinkel, Niko Lengauer, Thomas Schmeisser, Norbert Wyen, Christoph Fätkenheuer, Gerd Kaiser, Rolf		Stable coreceptor usage of HIV in patients with ongoing treatment failure on HAART In: Journal of Clinical Virology [37], 300-304
			Lengauer, Thomas Domingues, F.S. Sommer, Ingolf Zhu, Hongbo		Analysis and prediction of protein-protein-interaction types In: BMC Bioinformatics [7], -
			Lengauer, Thomas Sing, Tobias		Bioinformatics-assisted anti-HIV therapy In: Nature Reviews Microbiology [4], 790-797
			Maydt, Jochen Lengauer, Thomas		Recco: recombination analysis using cost optimization In: Bioinformatics [22], 1064-1071
			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
			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
			Neumann, Dirk Kohlbacher, Oliver Merkwirth, Christian Lengauer, Thomas		Prediction of percutaneous drug absorption In: Journal of Chemical Information and Modeling [1], 424-429
			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
			Roomp, Kirsten Beerenwinkel, Niko Sing, Tobias Schülter, Eugen Büch, Joachim Sierra-Aragon, Saleta Däumer, Martin Hoffmann, Daniel Kaiser, Rolf Lengauer, Thomas Selbig, Joachim		Arevir: A Secure Platform for Designing Personalized Antiretroviral Therapies Against HIV In: Lecture Notes in Computer Science [4075], 185-194
			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
			Sing, Tobias Sander, Oliver Beerenwinkel, Niko Lengauer, Thomas		ROCR: Visualizing classifier performance in R In: Bioinformatics [21], 3940-3941
			Steffen, Andreas Kämper, Andreas Lengauer, Thomas		Flexible Docking of Ligands into Synthetic Receptors Using a Two-Sided Incremental Construction Algorithm In: Journal of Chemical Information and Modeling [46], 1695-1703
			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
			Takken, Frank L. W. Albrecht, Mario Tameling, Wladimir I.		Resistance proteins: molecular switches of plant defence In: Current Opinion in Plant Biology [9], 383-390
			Tameling, Wladimir I. Vossen, Jack H. Albrecht, Mario Lengauer, Thomas Berden, Jan A. Haring, Michel A. Cornelissen, Ben J.C. Takken, Frank L. W.		Mutations in the NB-ARC domain of I-2 that impair ATP hydrolysis cause autoactivation In: Plant Physiology [140], 1233-1245
			Torda, Andrew E. Lengauer, Thomas		Editorial: Selection of papers of the German Conference of Bioinformatics (GCB) 2005 In: Bioinformatics [22], 1
			Velagapudi, Vidya R. Wittmann, Christoph Lengauer, Thomas Talwar, Priti Heinzle, Elmar		Metabolic high- content screening of Saccharomyces cerevisiae reveals superior performance of single gene deletion strains In: Process Biochemistry [41], 2170-2179
			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
			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
			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
5		Electronic Journal Article
			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
			Sander, Oliver Sommer, Ingolf Lengauer, Thomas		Local protein structure prediction using discriminative models In: BMC Bioinformatics [7], 1-13
			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
			Sommer, Ingolf Toppo, Stefano Sander, Oliver Lengauer, Thomas Tosatto, Silvio C. E.		Improving the quality of protein structure models by selecting from alignment alternatives In: BMC Bioinformatics [7], 1-11
			Zhu, Hongbo Domingues, Francisco S. Sommer, Ingolf Lengauer, Thomas		NOXclass: prediction of protein-protein interaction types In: BMC Bioinformatics [7], 1-15
7		Thesis - Bachelor thesis
			Frings, Oliver		Development of a Smith-Waterman-Like Multi-Aspect Alignment Tool Universität des Saarlandes
			Glaab, Enrico		On the predictability of CpG methylation in human tissue at single basepair resolution Universität des Saarlandes
			Hobler, Anna		Docking of monosaccharids into the wild type and mutants of pyranose 2-oxidase Universität des Saarlandes
			Jung, Holger		Yamada Analyzer - A tool for fast calculation of genomic attributes Universität des Saarlandes
			Pfeifer, Susanne		Development of a fast geometry-based screening compound prefiltering technique Universität des Saarlandes
			Reimer, Daniela		Docking studies to investigate the effect of correlated mutations in the HIV-Protease on the drug resistance of HIV Universität des Saarlandes
			Zimmer, Tobias		Functional Site Scaffolds Universität des Saarlandes
8		Thesis - Masters thesis
			Assenov, Yassen		Topological Analysis of Biological Networks Universität des Saarlandes
			Binsl, Thomas		Feature Prints: A new method for calculating molecular similarities Universität des Saarlandes
			Guo, Xin		Improving Fold Recognition Using Protein and Domain Interactions Universität des Saarlandes
			Halachev, Konstantin		EpiGRAPHregression: A toolkit for (epi-)genomic correlation analysis and prediction of quantitative attributes Universität des Saarlandes
			Kaspar, Melanie		Automated conformational analysis of macrocyclic ring systems Universität des Saarlandes
			Thielen, Alexander		Prediction of linear B-cell epitopes and MHC class II binding peptides Eberhardt-Karls-Universität Tübingen
			Tolosi, Laura		Analysis of Array CGH Data for the Estimation of Genetic Tumor Progression Universität des Saarlandes
			Weinhold, Nils		Inference of Protein Function based on Functionally Conserved Regions in Sequence and Structure Space Universität des Saarlandes
1		Thesis - PhD thesis
			Albrecht, Mario		Combining protein structure prediction with experiments and functional information Universität des Saarlandes
1		Thesis - Habilitation thesis
			Rahnenführer, Jörg		Statistical methods for the biological interpretation of genome-wide measurements Universität des Saarlandes
1		Thesis - other
			Huthmacher, Carola		Decomposing Protein Networks Into Domain-Domain Interactions Eberhard Karls University Tübingen
57	2005
1		Part of a Book
			Lengauer, Thomas		Informatics (Computational Biology) In: Growth Factors and Oncogenes in Gastrointestinal Cancers to Informatics (Computational Biology), 567-626
6		Proceedings Article
			Kaiser, Rolf Boussaad, Ibo Lehmann, C. Däumer, Martin Sing, Tobias Schmeisser, N. Wyen, C. Fätkenheuer, Gerd		Stable coreceptor usage of HIV-1 in patients with ongoing treatment failure on HAART In: Proceedings of the 3rd European HIV Drug Resistance Workshop, -
			Kämper, Andreas Kaspar, Melanie Lengauer, Thomas		Efficient conformational analysis of synthetic receptors with macrocyclic and fused ring systems In: Synthetic Receptors 2005: Second World Congress on Synthetic Receptors, O4
			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
			Steffen, Andreas Kämper, Andreas Lengauer, Thomas		FlexR - A new tool for predicting the structure of synthetic host-guest complexes In: Synthetic Receptors 2005: Second World Congress on Synthetic Receptors, O7
			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, -
			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, -
4		Poster
			Sing, Tobias Beerenwinkel, Niko Kaiser, Rolf Hoffmann, Daniel Däumer, Martin Lengauer, Thomas		Geno2pheno[coreceptor]: a tool for predicting coreceptor usage from genotype and for monitoring coreceptor-associated sequence alterations In: Proceedings of the 3rd European HIV Drug Resistance Workshop, -
			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
			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
			Zhu, Hongbo Domingues, Francisco S. Sommer, Ingolf Lengauer, Thomas		Analysis and prediction of protein-protein interaction types In: 4th European Conference on Computational Biology (ECCB05), 1
32		Journal Article
			Albrecht, Mario		LRRK2 mutations and parkinsonism In: The Lancet [365], 1230
			Albrecht, Mario Choubey, Divaker Lengauer, Thomas		The HIN domain of IFI-200 proteins consists of two OB folds In: Biochemical and Biophysical Research Communications [327], 679-687
			Albrecht, Mario Huthmacher, Carola Tosatto, Silvio C.E. Lengauer, Thomas		Decomposing protein networks into domain-domain interactions In: Bioinformatics [21], ii220-ii221
			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
			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
			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
			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
			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
			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
			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
			Bojunga, Jörg Welsch, Christoph Antes, Iris Albrecht, Mario Lengauer, Thomas Zeuzem, Stefan		Structural and functional analysis of a novel mutation of CYP21B in a heterozygote carrier of 21-hydroxylase deficiency In: Human Genetics [117], 558-564
			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
			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
			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
			Gu, Wei Kofler, Michael Antes, Iris Freund, Christian Helms, Volkhard		Alternative Binding Modes of Polyproline Peptides Binding to the GYF Domain In: Biochemistry [44], 6404-6415
			Hahn, Andreas Rahnenführer, Jörg Talwar, Priti Lengauer, Thomas		Confirmation of human protein interaction data by human expression data In: BMC Bioinformatics [6], 1-11
			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
			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
			Lengauer, Thomas Merkwirth, Christian		Automatic Generation of complementary descriptors with molecular graph networks In: Journal of Chemical Information and Modeling [45], 1159-1168
			Rahnenführer, Jörg		Clustering algorithms and other exploratory methods for microarray data analysis In: Methods of Information in Medicine [44], 444-448
			Rahnenführer, Jörg		Image analysis for cDNA microarrays In: Methods of Information in Medicine [44], 405-407
			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
			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
			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
			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
			Schreiber, Stefan Rosenstiel, Philip Albrecht, Mario Hampe, Jochen Krawczak, Michael		Genetics of Crohn disease, an archetypal inflammatory barrier disease In: Nature Reviews Genetics [6], 376-388
			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
			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
			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
			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
			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
			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
9		Thesis - Bachelor thesis
			Djoumbou, Yannick		Docking studies to investigate the effect of correlated mutations in the HIV-Protease on the drug resistance of HIV Universität des Saarlandes
			Immesberger, Stefan		A Prefiltering Method to Speed up Protein Structure Prediction Universität des Saarlandes
			Kaspar, Melanie		Conformational Analysis of Macrocyclic Ring Systems Universität des Saarlandes
			Krier, Markus		Motif Search in Protein Sequences for Protein Structure Prediction Universität des Saarlandes
			Meiser, Ina		Identification of functionally important regions in cytochrome P450 systems and a systematic analysis of various CYP P450 homology models Universität des Saarlandes
			Nickels, Stefan		Generating Molecular Hashcodes for Finding Duplicates in Virtual Screening Libraries Universität des Saarlandes
			Volkamer, Andrea		Implementation of a method to filter out compounds with toxic, reactive and unsuitable functional groups Universität des Saarlandes
			Weiss, Julia		Generating Frequency Profiles from Multiple Structure Alignments Universität des Saarlandes
			Yalak, Garif		Analysis of Mutations in the Death Domains, Death Effector Domains, Caspase Recruitment Domains, and Pyrin Domains Universität des Saarlandes
5		Thesis - Masters thesis
			Alexa, Adrian		Integrating the GO graph structure in scoring the significance of Gene Ontology terms Universität des Saarlandes
			Ifrim, Georgiana		A Bayesian Learning Approach to Concept-Based Document Classification Universität des Saarlandes
			Schlicker, Andreas		A Global Approach to Comparative Genomics: Comparison of Functional Annotation over the Taxonomic Tree Universität des Saarlandes
			Siu, Shirley Weng-In		Computational prediction of MHC-peptide interactions Universität des Saarlandes
			Yin, Junming		Model Selection for Mixtures of Mutagenetic Trees Universität des Saarlandes
41	2004
1		Book
			Beerenwinkel, Niko		Computational Analysis of HIV Drug resistance Data
4		Part of a Book
			Beerenwinkel, Niko		Das Arevir-Projekt : neue Wege zur Optimierung von Anti-HIV-Therapien In: Resistenz in der HIV-Therapie : Diagnostik und Management, 94-98
			Beerenwinkel, Niko		Methoden zur Interpretation genotypischer Resistenztests In: Resistenz in der HIV-Therapie : Diagnostik und Management, 66-68
			Domingues, Francisco S. Lengauer, Thomas Sommer, Ingolf		Protein Structure Prediction and Databases In: Nature Encyclopedia of the Human Genome, 864-867
			Ramírez, Fidel		Evolucion de la Evolucionalidad In: Biologos lejos del equilibrio: Nuevas metaforas evolutivas, 59-87
1		Proceedings
			Thornton, Bourne, Gilbert, Goble, Goldman, Gribskov, Hide, Higgins, Kanehisa, Lengauer, Linial, Myers, Quackenbush, Rebholz-Schuhmann, Rost, Sowdhamini, Valencia, Vingron, Xu (ed.)		Proceedings Twelfth International Conference on Intelligent Systems for Molecular Biology/Third European Conference on Computional Biology 2004 (ISMB/ECCB 2004)
5		Proceedings Article
			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
			Beerenwinkel, Niko Sing, Tobias Däumer, Martin Kaiser, Rolf Lengauer, Thomas		Computing the genetic barrier In: XII International HIV Drug resistance Workshop, S125-S125
			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
			Sing, Tobias Beerenwinkel, Niko Lengauer, Thomas		Learning mixtures of localized rules by maximizing the area under the ROC curve In: ROCAI-2004: 1st International Workshop on ROC Analysis in Artificial Intelligence, 89-96
			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
5		Poster
			Hahn, Andreas Costello, Christine M. Lu, Tim Lengauer, Thomas Schreiber, Stefan		Expression analysis for inflammatory bowel disease In: Workshop Poster Competition, ?
			Steffen, Andreas Kämper, Andreas Lengauer, Thomas		Development of a new tool for predicting the structure of host-guest complexes In: Proceedings of the 2nd Summer School Medicinal Chemistry Regensburg 2004, 83
			Steffen, Andreas Kämper, Andreas Lengauer, Thomas		FlexR - Predicting the structure of host-guest complexes In: Proceedings of the Annual Meeting of the German Pharmaceutical Society - Joint Meeting 2004 (DPhG 2004), 130
			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
			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
16		Journal Article
			Albrecht, Mario Golatta, Michael Wüllner, Ullrich Lengauer, Thomas		Structural and functional analysis of ataxin-2 and ataxin-3 In: European Journal of Biochemistry [271], 3155-3170
			Albrecht, Mario Lengauer, Thomas		Novel Sm-like proteins with long C-terminal tails and associated methyltransferases In: FEBS Letters [569], 18-26
			Albrecht, Mario Lengauer, Thomas		Survey on the PABC recognition motif PAM2 In: Biochemical and Biophysical Research Communications [316], 129-138
			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
			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
			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
			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
			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
			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
			Lengauer, Thomas Lemmen, Christian Rarey, Matthias Zimmermann, M.		Novel technologies for virtual screening In: Drug Discovery Today [9], 27-34
			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
			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
			Prlic, Andreas Domingues, Francisco S. Lackner, Peter Sippl, Manfred J.		WILMA-automated annotation of protein sequences In: Bioinformatics [20], 127-128
			Rahnenführer, Jörg Bozinov, Daniel		Hybrid clustering for microarray image analysis combining intensity and shape features In: BMC Bioinformatics [5], 1-11
			Sommer, Ingolf Rahnenführer, Jörg Domingues, Francisco S. de Lichtenberg, Ulrik Lengauer, Thomas		Predicting Protein Structure Classes from Function Predictions In: Bioinformatics [20], 770-776
			Stoll, Monika Corneliussen, Brit Costello, Christine M. Waetzig, Georg H. Mellgard, Bjorn Koch, W. Andreas Rosenstiel, Philip Albrecht, Mario Croucher, Peter J.P. Seegert, Dirk Nikolaus, Susanna Hampe, Jochen Lengauer, Thomas Pierrou, Stefan Foelsch, Ulrich R. Mathew, Christopher G. Lagerstrom-Fermer, Maria Schreiber, Stefan		Genetic variation in DLG5 is associated with inflammatory bowel disease In: Nature Genetics [36], 376-380
1		Electronic Journal Article
			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
3		Thesis - Bachelor thesis
			Binsl, Thomas		Implementation of a Generic Fragment Based Method for Automated Calculation of the Octanol-Water Partition Coefficient Universität des Saarlandes
			Eyrisch, Susanne		Fun2Struc-A Tool For Predicting Protein Structure Classes from Function Predictions Universität des Saarlandes
			Schlicker, Andreas		Automated Differential Analysis of Proteomes Universität des Saarlandes
4		Thesis - Masters thesis
			Bayjanov, Jumamurat		Scoring pathway activity from gene expression data Universität des Saarlandes
			Ramírez, Fidel		Hacia una comprension de la accion de la recombinacion genetica y la mutacion en el origen de la variacion fenotipica, mediante el analisis de la computacion evolutiva Universidad Nacional de Colombia
			Sing, Tobias		Learning localized rule mixtures by maximizing the area under the ROC curve, with an application to the prediction of HIV-1 coreceptor usage Universität Freiburg
			Trajkovski, Igor		Analysis of protein binding pocket flexibility Universität des Saarlandes
1		Thesis - other
			Sander, Oliver		Local sequence-structure relationships in proteins Friedrich-Alexander-Universität Erlangen-Nürnberg
35	2003
2		Part of a Book
			Beerenwinkel, Niko Däumer, Martin Hoffmann, Daniel Kaiser, Rolf Selbig, Joachim Lengauer, Thomas		Bioinformatikmethoden für die Optimierung antiviraler Kombinationstherapien In: MPG Jahrbuch, 481-486
			Lengauer, Thomas Schäfer, M.		Combinatorial Optimization Techniques for Three-Dimensional Arrangement Problems In: Mathematics - Key Technology for the Future, 63-73
8		Proceedings Article
			Beerenwinkel, Niko Däumer, Martin Kaiser, Rolf Walter, Hauke Korn, Klaus Hoffmann, Daniel Selbig, Joachim Lengauer, Thomas		Estimating effective drug combinations against drug-resistant mutants from genotypes In: Proceedings of the 1st European HIV Drug Resistamce Workshop, 18-18
			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
			Jose, Joachim Betschieder, Dirk Ray, Somak Lengauer, Thomas Zangen, D		New inhibitors of human cathepsin G identified by surface display library screening and peptide-protein docking In: 7th International Symposium on Pharmaceutical Sciences (ISOPS-7), 46-49
			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
			Rahnenführer, Jörg		Efficient Clustering Methods for Tumor Classification with Microarrays In: Proceedings of the 26th Annual Conference of the Gesellschaft für Klassifikation, 670-679
			Rahnenführer, Jörg		Statistical Inference for Clustering Microarrays In: Proceedings of the MSRI Workshop: Nonlinear Estimation and Classification, 323-332
			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
			von Öhsen, Niklas Sommer, Ingolf Zimmer, Ralf		Profile-Profile Alignment: A Powerful Tool For Protein Structure Prediction In: Pacific Symposium on Biocomputing, PSB 2003, 252-263
3		Poster
			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
			Kämper, Andreas Lengauer, Thomas		Virtual Screening for novel Urease Inhibitors In: Proceedings of the International Workshop on New Approaches in Drug Design & Discovery, 39
			Rahnenführer, Jörg Bozinov, Daniel		Comparative quality analyses for hybrid clustering of microarray images In: Proceedings of the Sventh Annual International Conference on Computational Biology, -
19		Journal Article
			Albrecht, Mario Domingues, Francisco S. Schreiber, Stefan Lengauer, Thomas		Identification of mammalian orthologs associates PYPAF5 with distinct functional roles In: FEBS Letters [538], 173-177
			Albrecht, Mario Domingues, Francisco S. Schreiber, Stefan Lengauer, Thomas		Structural localization of disease-associated sequence variations in the NACHT and LRR domains of PYPAF1 and NOD2 In: FEBS Letters [554], 520-528
			Albrecht, Mario Hoffmann, Daniel Evert, Bernd O. Schmitt, Ina Wüllner, Ullrich Lengauer, Thomas		Structural modeling of ataxin-3 reveals distant homology to adaptins In: Proteins: Structure, Function, and Genetics [50], 355-370
			Albrecht, Mario Lengauer, Thomas		Pyranose oxidase identified as a member of the GMC oxidoreductase family In: Bioinformatics [19], 1216-1220
			Albrecht, Mario Lengauer, Thomas Schreiber, Stefan		Disease-associated variants in PYPAF1 and NOD2 result in similar alterations of conserved sequence In: Bioinformatics [19], 2171-2175
			Albrecht, Mario Tosatto, Silvio C.E. Lengauer, Thomas Valle, Giorgio		Simple consensus procedures are effective and sufficient in secondary structure prediction In: Protein Engineering [16], 459-462
			Antes, Iris Wang, Hongyun Chandler, David Oster, George		The unbinding of ATP from F1-ATPase In: Biophysical Journal [85], 695-706
			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
			Beerenwinkel, Niko Lengauer, Thomas Däumer, Martin Kaiser, Rolf Walter, Hauke Korn, Klaus Hoffmann, Daniel Selbig, Joachim		Methods for optimizing antiviral combination therapies In: Bioinformatics [19], i16-i25
			Domingues, Francisco S. Lengauer, Thomas		Protein Function from Sequence and Structure Data In: Applied Bioinformatics [2], 3-12
			Janssen, A. Rahnenführer, Jörg		A hazard based approach to dependence tests for bivariate censored models In: Mathematical Methods in Statistics [11], 297-322
			Lengauer, Thomas		Analyzing resistance phenomena in HIV with bioinformatics methods In: Bioinformatics [19], 92i
			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
			Peinado, M. Lengauer, Thomas		Parallel "go with the winners algorithms" in Distributed Memory Models In: Journal of Parallel and Distributed Processing [63], 801-814
			Rahnenführer, Jörg		On preferences of general two-sided tests with applications to Kolmogorov-Smirnov-type tests In: Statistics & Decisions [21], 115-136
			Rahnenführer, Jörg Futschik, Andreas		Cost-effective screening for differentially expressed genes in microarray experiments based on normal mixtures In: Austrian Journal of Statistics [32], 225-238
			Talwar, Priti Wittmann, Christoph Lengauer, Thomas Heinzle, Elmar		Software tool for automated processing of 13C labeling data from mass spectrometry data In: BioTechniques [35], 1214-1215
			Wolf, Katharina Walter, Hauke Beerenwinkel, Niko Keulen, Wilco Kaiser, Rolf Hoffmann, Daniel Lengauer, Thomas Selbig, Joachim Vandamme, Anne-Mieke Korn, Klaus Schmidt, Barbara		Tenofovir resistance and resensitization In: Antimicrobial Agents and Chemotherapy [47], 3478-3484
			Zien, Alexander Fluck, Juliane Zimmer, Ralf Lengauer, Thomas		Microarrays: How many do you need? In: Journal of Computational Biology [10], 653-667
1		Thesis - PhD thesis
			Beerenwinkel, Niko		Computational Analysis of HIV Drug Resistance Data Universität des Saarlandes
1		Manual
			Kämper, Andreas Lengauer, Thomas		ECLIPPSE: Environment for Chemical Library Inspection, Pre- and Postprocessing, and Screening Evaluation. User Guide
1		Miscellaneous
			James, Jackson Das, Ani V. Rahnenführer, Jörg Leon, FAS Ahmad, Iqbal		Identification of rat brahma (rBRM), a subunit of SWI/SNF chromatin remodeling complex: Involvement in the differentiation of retinal stem cells/progenitors
28	2002
1		Proceedings
			Lengauer, Lenhof (ed.)		Proceedings of the European Conference on Computational Biology (ECCB 2002)
8		Proceedings Article
			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
			Beerenwinkel, Niko Lengauer, Thomas Schmidt, Barbara Walter, Hauke Kaiser, Rolf Hoffmann, Daniel Korn, Klaus Selbig, Joachim		Quantitative phenotype prediction by support vector machines In: Proceedings from the 5th International Workshop on HIV Drug resistance & Treatment Strategies, 97
			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
			Hanisch, Daniel Zien, Alexander Zimmer, Ralf Lengauer, Thomas		Co-clustering of biological networks and gene expression data In: Proceedings of the Tenth Conference on Intelligent Systems for Molecular Biology (ISMB 2002), 145-154
			Hoffmann, Daniel Schnaible, Volker Wefing, Stephan, Albrecht, Mario Hanisch, Daniel Zimmer, Ralf		A new method for the fast solution of protein-3D-structures, combining experiments and bioinformatics In: Coupling of Biological and Electronic Systems: Proceedings of the 2nd Caesarium, Bonn, 1-3 November 2000, 59-78
			Lienhart, Rainer Maydt, Jochen		An Extended Set of Haar-like Features for Rapid Object Detection In: Proceedings of the International Conference on Image Processing, 900-903
			Maydt, Jochen Lienhart, Rainer		A Fast Method for Training Support Vector Machines With a Very Large Set of Linear Features In: Proceedings of the International Conference on Multimedia and Expo, 309-312
			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
5		Poster
			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, -
			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, ?
			Kämper, Andreas Apostolakis, Joannis Lengauer, Thomas		Docking of Bacterial Cell-Wall Fragments into Glycopeptide Antibiotics In: From Genes to Drugs via Crystallography: 33rd crytallographic course at the E. Majorana Center, 49
			Kämper, Andreas Lengauer, Thomas		Docking of Ligands into Molecular Tweezers and Molecular Clips In: Workshop of the SFB 624 'Templates', ?-?
			Rahnenführer, Jörg		Hybrid clustering for microarray analysis combining intensity and shape features In: Poster book of the European Conference on Computational Biology, Saarbrücken, Germany 2002, -
14		Journal Article
			Albrecht, Mario Hanisch, Daniel Zimmer, Ralf Lengauer, Thomas		Improving fold recognition of protein threading by experimental distance constraints In: In Silico Biology [2], 325-337
			Antes, Iris Thiel, Walter Gunsteren van, Wilfred F.		Molecular dynamics simulations of photoactive yellow protein (PYP) in three states of its photocycle: a comparison with X-ray and NMR data and analysis of the effects of Glu46 deprotonation and mutation In: European Biophysics Jounal [31], 504-520
			Beerenwinkel, Niko Schmidt, Barbara Walter, Hauke Kaiser, Rolf Lengauer, Thomas Hoffmann, Daniel Korn, Klaus Selbig, Joachim		Diversity and complexity of HIV-1drug resistance: A bioinformatics approach to predicting phenotype from genotype In: Proceedings of the National Academy of Sciences [99], 8271-8276
			Freudenberg, Jan Zimmer, Ralf Hanisch, Daniel Lengauer, Thomas		A hypergraph-based method for unification of existing protein structure- and sequence-families In: In Silico Biology [2], 339 - 349
			Hanisch, Daniel Zimmer, Ralf Lengauer, Thomas		ProML - the Protein Markup Language for specification of protein sequences, structures and families In: In Silico Biology [2], 313 - 324
			Hindle, Sally A. Rarey, Matthias Buning, Christian Lengauer, Thomas		Flexible docking under pharmacophore type constraints In: Journal of Computer-Aided Molecular Design [16], 129-149
			Lengauer, Thomas		Ausbildung im Bereich Bioinformatik In: Ernst & Young Report Biotechnologie, Segmentreport Bioinformatik [1], 57-58
			Lengauer, Thomas		Preface: Special RECOMB 2001 Issue In: Journal of Computational Biology [9], 147-148
			Nishida, Yoshiharu Hirano, Kenichi Tsukamoto, Kosuke Nagano, Makoto Ikegami, Chiaki Roomp, Kirsten Ishihara, Mitsuaki Sakane, Naoki Zhang, Zhongyan Tsujii, Ken-ichi Matsuyama, Akifumi Ohama, Tohru Matsuura, Fumihiko Ishigami, Masato Sakai, Naohiko Hiraoka, Hisatoyo Hattori, Hiroaki Wellington, Cheryl L. Yoshida, Yoshihide Misugi, Susumu Hayden, Michael R. Egashira, Toru Yamashita, Shizuya Matsuzawa, Yuji		Expression and Functional Analyses of Novel Mutations ot ATP-Binding Cassette Transporter-1 in Japanese Patients with High-Density Lipoprotein Deficiency In: Biochemical and Biophysical Research Communications [290], 713-721
			Rahnenführer, Jörg		Multivariate permutation tests for the k-sample problem with clustered data In: Computational Statistics [17], 165-184
			Rahnenführer, Jörg Bozinov, Daniel		Unsupervised technique for robust target separation and analysis of DNA microarray spots through adaptive pixel clustering In: Bioinformatics [18], 747-756
			Sommer, Ingolf Zien, Alexander Öhsen von, Niklas Zimmer, Ralf Lengauer, Thomas		Confidence measures for protein fold recognition In: Bioinformatics [18], 802-812
			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
			Zwarts, K.Y. Clee, Susanne M. Zwinderman, A.H. Engert, J.C. Singaraja, Roshni Loubser, O James, E Roomp, Kirsten Hudson, T.J. Jukema, J.W. Kastelein, J.J.P. Hayden, Michael R.		ABCA1 regulatory variants influence coronary artery disease independent of effects on plasma lipid levels In: Clinical Genetics [61], 115-125
14	2001
2		Book
			Lengauer (ed.)		From Genomes to Drugs
			Lengauer, Sankoff, Istrail, Pevzner, Waterman (ed.)		Proceedings of the 5th Annual Conference on Research in Computational Molecular Biology (RECOMB2001)
1		Part of a Book
			Lengauer, Thomas		Bioinformatik an der Schwelle zur postgenomischen Ära In: Was wissen wir, wenn wir das menschliche Genom kennen, 56-62
1		Proceedings Article
			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
8		Journal Article
			Apostolakis, Joannis Hofmann, D. Lengauer, Thomas		Derivation of a scoring function for crystal structure prediction In: Acta Crystallographica [A57], 442-450
			Beerenwinkel, Niko Däumer, Martin Hoffmann, Daniel Kaiser, Rolf Korn, Klaus Lengauer, Thomas Schmidt, Barbara Walter, Hauke Selbig, Joachim		Neue Wege zur Optimierung von Anti-HIV Therapien In: BIOforum [24], 912-914
			Beerenwinkel, Niko Schmidt, Barbara Walter, Hauke Kaiser, Rolf Lengauer, Thomas Hoffmann, Daniel Korn, Klaus Selbig, Joachim		Geno2pheno: A system for the interpretation of genotypic HIV Drug resistance tests In: IEEE Intelligent Systems [16], 35-41
			Claussen, C. Buning, Christian Rarey, Matthias Lengauer, Thomas		FlexE: Efficient Molecular Docking Considering Protein Structure Variations In: Journal of Molecular Biology [308], 377-395
			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
			Lengauer, Thomas Beerenwinkel, Niko Schmidt, B. Walter, H. Kaiser, R. Hoffmann, D. Korn, K. Selbig, J.		Geno2pheno: a new machine learning approach to predicting phenotypic drug resistance from genotype In: Antiviral Therapy [6], 104
			Schäfer, M. Lengauer, Thomas		Automated Layout Generation and Wiring Area Estimation for 3D Electronic Modules In: ASME Journal of Machanical Design [123], 330-336
			Zien, Alexander Aigner, T. Zimmer, Ralf Lengauer, Thomas		Centralization: A biologically sensible method for the normalization of gene expression data In: Bioinformatics [17], 323S-331S
2		Miscellaneous
			Antes, Iris Klein, Michael L.		The formation of a β-Peptide/DPC-micelle complex studied by MD simulations
			Kämper, Andreas Apostolakis, Joannis Rarey, Matthias Marian, Christel Maria Lengauer, Thomas		Docking of Ligands into Artificial Receptors
2	2000
2		Journal Article
			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
			Ramírez, Fidel Garcia, Sergio		GenLab: Laboratorio virtual de genetica In: Acta Biologica Colombiana [5], 45-48
2	1999
2		Journal Article
			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
			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
1	1995
1		Journal Article
			Stohr, H. Roomp, Kirsten Felbor, U. Weber, B. H.		Genomic organization of the human tissue inhibitor of metalloproteinases-3 (TIMP3) In: Genome Research [5], 483-7
639