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MPI-INF D3 Publications

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Your search returned the following 291 documents:

  1. Accurate prediction of drug-exposure without using established drug-resistance mutations
    Alejandro Pironti, Nico Pfeifer, and Thomas Lengauer
    In: Antiviral Therapy, Berlin, Germany, 2014, A75 p.
  2. Accurate prediction of drug-exposure without using established drug-resistance mutations
    Alejandro Pironti, Nico Pfeifer, Rolf Kaiser, Hauke Walter, and Thomas Lengauer
    In: Antiviral Therapy, Berlin, Germany, 2014, A75 p.
  3. Improved HIV-1 drug-exposure reconstruction with linear support vector machines
    Alejandro Pironti, Nico Pfeifer, and Thomas Lengauer
    In: Reviews in Antiviral Therapy & Infectious Diseases, Barcelona, Spain, 2014, 67 p.
  4. Improved HIV-1 drug-exposure reconstruction with linear support vector machines
    Alejandro Pironti, Nico Pfeifer, Rolf Kaiser, Hauke Walter, and Thomas Lengauer
    In: Reviews in Antiviral Therapy & Infectious Diseases, Barcelona, Spain, 2014, 67 p.
  5. Improved therapy-success prediction with GSS estimated from clinical HIV-1 sequences
    Alejandro Pironti, Nico Pfeifer, Rolf Kaiser, Hauke Walter, and Thomas Lengauer
    In: Abstract Supplement of the HIV Drug Therapy Glasgow Congress 2014, Glasgow, UK, 2014, 155 p.
  6. Simulation of Sanger-sequencing errors in the context of genotypic tropism determination
    Alejandro Pironti, Thomas Lengauer, and Nico Pfeifer
    In: Antiviral Therapy, Berlin, Germany, 2014, A81 p.
  7. Simulation of Sanger-sequencing errors in the context of genotypic tropism determination
    Alejandro Pironti, Saleta Sierra, Rolf Kaiser, Thomas Lengauer, and Nico Pfeifer
    In: Antiviral Therapy, Berlin, Germany, 2014, A81 p.
  8. A method for finding consensus breakpoints in the cancer genome from copy number data
    Laura Tolosi, J. Theißen, Konstantin Halachev, B. Hero, F. Berthold, and Thomas Lengauer
    Bioinformatics 29 (14): 1793-1800, 2013
  9. Analysis of physicochemical and structural properties determining HIV-1 coreceptor usage
    K. Bozek, Thomas Lengauer, S. Sierra, Rolf Kaiser, and F.S. Domingues
    PLoS Computational Biology x, 2013
  10. Association Between HIV-1 Coreceptor Usage and Resistance to Some Broadly Neutralizing Antibodies
    Nico Pfeifer and Thomas Lengauer
    In: Proceedings of the AIDS Vaccine Conference 2013, Barcelona, Spain, 2013, A-1-A-208
  11. Comparative genome-wide DNA methylation analysis of colorectal tumor and matched human tissue
    F. Simmer, A.B. Brinkmann, Yassen Assenov, F. Matarese, A. Kaan, Thomas Lengauer, Christoph Bock, V. Colantuoni, L. Altucci, and H.G. Stunnenberg
    Epigenetics 7 (12): 1355-1367, 2013
  12. Deep sequencing reveals mutagenic effects of ribavirin during monotherapy of HCV genotype 1-infected patients
    J. Dietz, Sven-Eric Schelhorn, D. Fitting, U. Mihm, S. Susser, M.-W. Welker, C. Füller, M. Däumer, G. Teuber, H. Wedemeyer, T. Berg, Thomas Lengauer, Stefan Z., E. Herrmann, and C. Sarrazin
    Journal of Virology 87 (11): 6172-6181, 2013
  13. DNA Methylation Patterns Facilitate the Identification of Transcription Start Sites: A Brain-specofoc Study
    T. Bhadra, M. Battacharya, L. Feuerbach, Thomas Lengauer, and S. Bandyopadhyay
    PLOSONE 8 (6), 2013
  14. Effects of sequencing errors on geno2pheno[coreceptor] predictions
    Alejandro Pironti, Thomas Lengauer, and Nico Pfeifer
    In: Abstract Book 11th European Meeting on HIV & Hepatitis, Rome, Italy, 2013, 23-24
  15. Full genome ultra-deep pyrosequencing associates G-to-A-hypermutation of the hepatitis B virus genome with the natural progression of hepatitis B
    Bastian Beggel, C. Münk, M. Däumer, K. Hauck, D. Häussinger, Thomas Lengauer, and A. Ehrhardt
    Journal of Viral Hepatitis 12: 882-889, 2013
  16. In silico analysis of the effects of sequencing errors on geno2pheno[coreceptor]
    Alejandro Pironti, Thomas Lengauer, and Nico Pfeifer
    In: Abstract Book of the International Workshop on HIV&Hepatitis Virus, Toronto, Canada, 2013, A142 p.
  17. Inferring short-range linkage information from sequencing chromatograms
    Bastian Beggel and Thomas Lengauer
    PLoS One , 2013
  18. Interactive exploration of large genome and epigenome datasets in real time
    Konstantin Halachev, H. Bast, Thomas Lengauer, and Christoph Bock
    Genome Biology 13 (10), 2013
  19. 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
    Olga Kalinina, Nico Pfeifer, and Thomas Lengauer
    Retrovirology 10: 130 p., 2013
  20. Sensitive detection of viral transcripts in human tumor transcriptomes
    Sven-Eric Schelhorn, M. Fischer, Laura Tolosi, J. Altmüller, P. Nürnberg, H. Pfister, Thomas Lengauer, and F. Berthold
    PLOS Computational Biology 9 (10), 2013
  21. A DNA methylation fingerprint of 1628 human samples
    Agustin F. Fernandez, Yassen Assenov, Jose Ignacio Martin-Subero, Balazs Balint, Reiner Siebert, Hiroaki Taniguchi, Hiroyuki Yamamoto, Manuel Hidalgo, Aik-Choon Tan, Oliver Galm, Isidre Ferrer, Montse Sanchez-Cespedes, Alberto Villanueva, Javier Carmona, Jose V. Sanchez-Mut, Maria Berdasco, Victor Moreno, Gabriel Capella, David Monk, Esteban Ballestar, Santiago Ropero, Ramon Martinez, Marta Sanchez-Carbayo, Felipe Prosper, Xabier Agirre, Mario F. Fraga, Osvaldo Gran˜a, Luis Perez-Jurado, Jaume Mora, Susana Puig, Jaime Prat, Lina Badimon, Annibale A. Puca, Stephen J. Meltzer, Thomas Lengauer, John Bridgewater, Christoph Bock, and Manel Esteller
    Genome Research 22 (2): 407-419, 2012. Note: PMID: 21613409
  22. An expanded model of HIV cell entry phenotype based on multi-parameter single-cell data
    Katarzyna Bozek, Manon Eckhardt, Saleta Sierra, Rolf Kaiser, Hans-Georg Kräusslich, Barbara Müller, and Thomas Lengauer
    Retrovirology 9 (1): 60.1-60.15, 2012
  23. Analyzing epigenome data in context of genome evolution and human diseases
    Lars Feuerbach, Konstantin Halachev, Yassen Assenov, Fabian Mueller, Christoph Bock, and Thomas Lengauer
    In: Evolutionary Genomics : Statistical and Computational Methods, Volume 2, 2012, 431-467
  24. Bioinformatical Assistance of Selecting Anti-HIV Therapies: Where Do We Stand?
    Thomas Lengauer
    Intervirology 55 (2): 108-112, 2012
  25. Characterization of HIV-1 Gag Subtype C
    Alejandro Pironti, Thomas Lengauer, Rolf Kaiser, Eugen Schülter, and Jens Verheyen
    In: Abstract Book. 9th Workshop on HIV \& Hepatitis Treatment Strategies \& Antiviral Drug Resistance, Barcelona, Spain, 2012, 40-41
  26. Comparative genome-wide DNA methylation analysis of colorectal tumor and matched normal tissues
    Femke Simmer, Arie B. Brinkman, Yassen Assenov, Filomena Matarese, Anita Kaan, Lina Sabatino, Alberto Villanueva, Dori Huertas, Manel Esteller, Thomas Lengauer, Christoph Bock, Vittorio Colantuoni, Lucia Altucci, and Henk G. Stunnenberg
    Epigenetics 7 (12): 1355-1367, 2012
  27. Computational Biology
    Thomas Lengauer, Mario Albrecht, and Francisco S. Domingues
    In: Encyclopedia of Molecular Cell Biology and Molecular Medicine, 2012, 1-71
  28. Endogenous or exogenous spreading of HIV-1 in Nordrhein-Westfalen, Germany, investigated by phylodynamic analysis of the RESINA Study cohort
    Glenn Lawyer, Eugen Schülter, Rolf Kaiser, Stefan Reuter, Mark Oette, and Thomas Lengauer
    Medical Microbiology and Immunology 201 (3): 259-269, 2012
    [PDF: Download: RESINA_publication.pdf]
  29. EpiExplorer: live exploration and global analysis of large epigenomic datasets
    K. Halachev, H. Bast, F. Albrecht, Thomas Lengauer, and Christoph Bock
    Genome Biology 13: R96,1-R96,14, 2012
  30. EpiExplorer: live exploration and global analysis of large epigenomic datasets
    Konstantin Halachev, Hannah Bast, Felipe Albrecht, Thomas Lengauer, and Christoph Bock
    Genome Biology 13 (10): R96,1-R96,14, 2012

  31. Epigenom-Karten erstellen und nutzen
    Christoph Bock and Thomas Lengauer
    BIOspektrum 18 (2): 138-141, 2012
  32. Etravirine in protease inhibitor-free antiretroviral combination therapies
    Eugen Schuelter, Nadine Lübcke, Björn Jensen, Maurizio Zazzi, Anders Sönnerborg, Thomas Lengauer, Francesca Incardona, Richardo Camacho, J Schmit, Bonaventura Clotet, Rolf Kaiser, and Alejandro Pironti
    In: Journal of the International AIDS Society, Glasgow, UK, 2012, 155-156
  33. Geno2pheno[454]: A Web Server for the Prediction of HIV-1 Coreceptor Usage from Next-Generation Sequencing Data
    Alexander Thielen and Thomas Lengauer
    Intervirology 55: 113-117, 2012
  34. Genotyping hepatitis B virus dual infections using population-based sequence data
    Bastian Beggel, Maria Neumann-Fraune, Matthias Doering, Glenn Lawyer, Rolf Kaiser, Jens Verheyen, and Thomas Lengauer
    Journal of General Virology 9 (93): 1899-1907, 2012
  35. Hierarchical Bayes Model for Predicting Effectiveness of HIV Combination Therapies
    Jasmina Bogojeska and Thomas Lengauer
    Statistical Applications in Genetics and Molecular Biology 11 (3): 11.1-11.19, 2012
  36. History-alignment models for bias-aware prediction of virological response to HIV combination therapy
    Jasmina Bogojeska, Daniel Stöckel, Maurizio Zazzi, Rolf Kaiser, Francesca Incardona, Michal Rosen-Zvi, and Thomas Lengauer
    In: Proceedings of the Fifteenth International Conference on Artificial Intelligence and Statistics (AISTATS 2012), La Palma, Canary Islands, Spain, 2012, 118-126
  37. Improving coreceptor usage prediction in the clinic using hints from next generation sequencing data
    Nico Pfeifer and Thomas Lengauer
    Bioinformatics 28 (18): i589-i595, 2012
  38. Improving HIV coreceptor usage prediction in the clinic using hints from next-generation sequencing data
    Nico Pfeifer and Thomas Lengauer
    Bioinformatics 28 (18): i589-i595, 2012

  39. Managing drug resistance in cancer: lessons from HIV therapy
    Thomas Lengauer and Christoph Bock
    Nature Reviews Cancer 12 (7): 494-501, 2012
  40. Managing drug resistance in cancer: lessons from HIV therapy
    Christoph Bock and Thomas Lengauer
    Nature Reviews Cancer 12 (7): 494-501, 2012
  41. On the Applicability of Elastic Network Normal Modes in Small-Molecule Docking
    Matthias Dietzen, Elena Zotenko, Andreas Hildebrandt, and Thomas Lengauer
    Journal of Chemical Information and Modeling 52 (3): 844-856, 2012
  42. Optimisation of baseline genotypic testing for safe and efficient maraviroc administration
    Saleta Sierra, Jan Nikolaj Dzbowski, Alejandro Pironti, L Gueney, Alexander Thielen, Stefan Reuter, Stefan Esser, Gerd Fätkenheuer, Thomas Lengauer, Dominik Hider, Daniel Hoffmann, Holger Pfister, Björn Jensen, and Rolf Kaiser
    In: Journal of the International AIDS Society, Glasgow, UK, 2012, 101-102
  43. Paving the future: finding suitable ISMB venues
    Burkhard Rost, Terry Gaasterland, Thomas Lengauer, Michal Linial, Scott Markel, B. J. Morrison McKay, Reinhard Schneider, Paul Horton, and Janet Kelso
    Bioinformatics 28 (19): 2556-2559, 2012
  44. Peptidomimetic Escape Mechanisms Arise via Genetic Diversity in the Ligand-Binding Site of the Hepatitis C Virus NS3/4A Serine Protease
    Christoph Welsch, Tetsuro Shimakami, Christoph Hartmann, Yan Yang, Francisco S. Domingues, Thomas Lengauer, Stefan Zeuzem, and Stanley M. Lemon
    Gastroenterology 142 (3): 654-663, 2012
  45. Predicting Response to Antiretroviral Treatment by Machine Learning: The EuResist Project
    Maurizio Zazzi, Francesca Incardona, Michal Rosen-Zvi, Mattia Prosperi, Thomas Lengauer, Andre Altmann, Anders Sonnerborg, Tamar Lavee, Eugen Schülter, and Rolf Kaiser
    Intervirology 55 (2): 123-127, 2012
  46. Risk factors associated with older age in treatment-naive HIV-positive patients
    Stefan Reuter, Mark Oette, Rolf Kaiser, Thomas Lengauer, Gerd Fätkenheuer, Jürgen Rockstroh, Heribert Knechten, and Dieter Häussinger
    Intervirology 55 (2): 147-153, 2012
  47. APOBEC3G/F a one possible driving source for co-receptor switch of the human immunodeficiency virus-1
    Eva Heger, Alexander Thielen, Ramona Gilles, Martin Obermeier, Thomas Lengauer, Rolf Kaiser, and Susanna Trapp
    Medical Microbiology and Immunology 201 (1): 7-16, 2012
  48. BLUEPRINT to decode the epigenetic signature written in blood
    David Adams, Lucia Altucci, Stylianos E Antonarakis, Juan Ballesteros, Stephan Beck, Adrian Bird, Christoph Bock, Bernhard Boehm, Elias Campo, Andrea Caricasole, Fredrik Dahl, Emmanouil T Dermitzakis, Tariq Enver, Manel Esteller, Xavier Estivill, Anne Ferguson-Smith, Jude Fitzgibbon, Paul Flicek, Claudia Giehl, Thomas Graf, Frank Grosveld, Roderic Guigó, Ivo Gut, Kristian Helin, Jonas Jarvius, Ralf Küppers, Hans Lehrach, Thomas Lengauer, Åke Lernmark, David Leslie, Markus Loeffler, Elizabeth Macintyre, Antonello Mai, Joost H A Martens, Saverio Minucci, Willem H Ouwehand, Pier Giuseppe Pelicci, Hèléne Pendeville, Bo Porse, Vardhman Rakyan, Wolf Reik, Martin Schrappe, Dirk Schübeler, Martin Seifert, Reiner Siebert, David Simmons, Nicole Soranzo, Salvatore Spicuglia, Michael Stratton, Hendrik G Stunnenberg, Amos Tanay, David Torrents, Alfonso Valencia, Edo Vellenga, Martin Vingron, Jörn Walter, and Spike Willcocks
    Nature Biotechnology 30 (3): 224-226, 2012
  49. A Computational Method for Predicting First-Line Antiretroviral Therapy Success
    Alejandro Pironti, André Altmann, Joachim Büch, and Thomas Lengauer
    In: Abstract Book. 9th Workshop on HIV & Hepatitis Treatment Strategies & Antiviral Drug Resistance, Paphos, Cyprus, 2011, 94 p.
  50. APOBEC3G/F as one possible driving force for co-receptor switch of the human immunodeficiency virus-1
    Eva Heger, Alexander Thielen, Ramona Gilles, Martin Obermeier, Thomas Lengauer, Rolf Kaiser, and Susanna Trapp
    Medical Microbiology and Immunology 201 (1): 7-16, 2011
  51. BiQ Analyzer HT: locus-specific analysis of DNA methylation by high-throughput bisulfite sequencing
    Pavlo Lutsik, Lars Feuerbach, Julia Arand, Thomas Lengauer, Jörn Walter, and Christoph Bock
    Nucleic Acids Research 39 (Suppl. 2): W551-W556, 2011
  52. Classification with correlated features: unreliability of feature ranking and solutions
    Laura Tolosi and Thomas Lengauer
    Bioinformatics 27 (14): 1986-1994, 2011
  53. Erratum to: Prevalence and characteristics of hepatitis B and C virus infections in treatment-naïve HIV-infected patients.
    Stefan Reuter, Mark Oette, Frank Clemens Wilhelm, Bastian Beggel, Rolf Kaiser, Melanie Balduin, Finja Schweitzer, Jens Verheyen, Ortwin Adams, Thomas Lengauer, Gerd Faetkenheuer, Herbert Pfister, and Dieter Haeussinger
    Medical Microbiology and Immunology 200 (1): 51-51, 2011

  54. Genomic distribution and inter-sample variation of non-CpG methylation across human cell types
    Michael J. Ziller, Fabian Müller, Jing Liao, Yingying Zhang, Hongcang Gu, Christoph Bock, Patrick Boyle, Charles B. Epstein, Bradley E. Bernstein, Thomas Lengauer, Andreas Gnirke, and Alexander Meissner
    PLoS Genetics 17 (12): e1002389,1-e1002389,15, 2011
  55. Genotypic tropism testing by massively parallel sequencing: qualitative and quantitative analysis
    Martin Däumer, Rolf Kaiser, Rolf Klein, Thomas Lengauer, Bernhard Thiele, and Alexander Thielen
    BMC Medical Informatics and Decision Making 11 (1): 30,1-30,8, 2011
  56. HIV prevalence and route of transmission in Turkish immigrants living in North-Rhine Westphalia, Germany
    Eugen Schülter, Mark Oette, Melanie Balduin, Stefan Reuter, Jürgen Rockstroh, Gerd Fätkenheuer, Stefan Esser, Thomas Lengauer, Ali Agacfidan, Herbert Pfister, Rolf Kaiser, and Baki Akgul
    Medical Microbiology and Immunology 200 (4): 219-223, 2011
  57. Learning from past treatments and their outcome improves prediction of In Vivo response to anti-HIV therapy
    Hiroto Saigo, André Altmann, Jasmina Bogojeska, Fabian Müller, Sebastian Nowozin, and Thomas Lengauer
    Statistical Applications in Genetics and Molecular Biology 10 (1): 1-32, 2011

  58. Mutations in gp41 are correlated with coreceptor tropism but do not improve prediction methods substantially
    Alexander Thielen, Thomas Lengauer, Luke C Swenson, Winnie W.Y. Dong, Rachel A McGovern, Marilyn Lewis, Ian James, Jayvant Heera, Hernan Valdez, and P Richard Harrigan
    Antiviral Therapy 16 (3): 319-328, 2011
  59. Prediction of Response to Antiretroviral Therapy by Human Experts and by the EuResist Data-Driven Expert System (the EVE study)
    M. Zazzi, R. Kaiser, A. Sönnerborg, D Struck, Andre Altmann, M. Prosperi, M. Rosen-Zvi, A. Petroczi, Y. Peres, E. Schülter, C.A. Boucher, F. Brun-Vezinet, R. Harrigan, L. Morris, M. Obermeier, C.-F. Perno, P. Phanuphak, D Pillay, R.W. Shafer, A.-M. Vandamme, K. Van Laethem, A. Wensing, Thomas Lengauer, and F. Incardona
    HIV Medicine 12 (4): 211-218, 2011
  60. Prediction of HIV-1 coreceptor usage (tropism) by sequence analysis using a genotypic approach
    Saleta Sierra, Rolf Kaiser, Nadine Lübke, Alexander Thielen, Eugen Schuelter, Eva Heger, Martin Däumer, Stefan Reuter, Stefan Esser, Gerd Fätkenheuer, Herbert Pfister, Mark Oette, and Thomas Lengauer
    Journal of Visualized Experiments 58: e3264,1-e3264,9, 2011
  61. Prevalence and characteristics of hepatitis B and C virus infections in treatment-naïve HIV-infected patients
    Stefan Reuter, Mark Oette, Frank Clemens Wilhelm, Bastian Beggel, Rolf Kaiser, Melanie Balduin, Finja Schweitzer, Jens Verheyen, Ortwin Adams, Thomas Lengauer, Gerd Faetkenheuer, Herbert Pfister, and Dieter Haeussinger
    Medical Microbiology and Immunology 200 (1): 39-49, 2011
  62. Reconstructing the ancestral germline methylation state of young repeats
    Lars Feuerbach, Rune B. Lyngso, Thomas Lengauer, and Jotun Hein
    Molecular Biology and Evolution 28 (6): 1777-1784, 2011
  63. Recruitment and activation of a lipid kinase by hepatitis C virus NS5A is essential for integrity of the membranous replication compartment
    Simon Reiss, Ilka Rebhan, Perdita Backes, Ines Romero-Brey, Holger Erfle, Petr Matula, Lars Kaderali, Marion Poenisch, Hagen Blankenburg, Marie-Sophie Hiet, Thomas Longerich, Sarah Diehl, Fidel Ramírez, Tamas Balla, Karl Rohr, Artur Kaul, Sandra Bühler, Rainer Pepperkok, Thomas Lengauer, Mario Albrecht, Roland Eils, Peter Schirmacher, Volker Lohmann, and Ralf Bartenschlager
    Cell Host & Microbe 9 (1): 32-45, 2011
  64. HIV-1 mutational pathways under multidrug therapy
    Glenn Lawyer, André Altmann, Alex Thielen, Maurizio Zazzi, Anders Sönnerborg, and Thomas Lengauer
    AIDS Research and Therapy 8 (1): 1-13, 2011
  65. Ancestral germline methylation reconstruction of young repeats
    Lars Feuerbach and Thomas Lengauer
    In: Transcription, chromatin structure and DNA repair in development and differentiation, Zeche Zollverein, Essen, Germany, 2010, 81 p.
  66. Chasing the AIDS Virus
    Thomas Lengauer, André Altmann, Alexander Thielen, and Rolf Kaiser
    Communications of the ACM 53 (3): 66-74, 2010
  67. Comparative Epigenomiocs - Towards Ancestral Germline Methylome Reconstruction
    Lars Feuerbach, Rune Lyngsoe, Thomas Lengauer, and Jotun Hein
    In: Abstracts of papers presented at the 2010 meeting on The Biology of genomes, Cold Spring Harbor,New York ,USA, 2010, 87 p.
  68. Dealing with sparse data in predicting outcomes of HIV combination therapies
    Jasmina Bogojeska, Steffen Bickel, André Altmann, and Thomas Lengauer
    Bioinformatics 26 (17): 2085-2092, 2010

  69. Determination of clinically relevant cutoffs for HIV-1 phenotypic resistance estimates through a combined analysis of clinical trial and cohort data
    Andre Altmann, Alejandro Pironti, Juliane Perner, Joachim Büch, and Thomas Lengauer
    In: Abstract Book. 8th European Drug Resistance Workshop, Sorrento, Italy, 2010, 46 p.
  70. Dimerization of the hepatitis C virus nonstructural protein 4B depends on the integrity of an aminoterminal basic leucine zipper
    Martin-Walter Welker, Christoph Welsch, Aline Meyer, Iris Antes, Mario Albrecht, Nicole Forestier, Bernd Kronenberger, Thomas Lengauer, Albrecht Piiper, Stefan Zeuzem, and Christoph Sarrazin
    Protein Science 19 (7): 1327-1336, 2010
  71. Effect of ribavirin on the frequency of RNAse L cleavage sites within the hepatitis C viral genome
    Ulrike Mihm, W.P. Hofmann, Christoph Welsch, A. Polta, Thomas Lengauer, Stefan Zeuzem, Christoph Sarrazin, and E. Herrmann
    Journal of Viral Hepatitis 17 (3): 217-221, 2010
  72. Improved prediction of HIV-1 coreceptor usage with sequence information from the second hypervariable loop of gp120
    Alexander Thielen, Nadine Sichtig, Rolf Kaiser, Jeffrey Lam, P. Richard Harrigan, and Thomas Lengauer
    Journal of Infectious Diseases 202 (9): 1435-1443, 2010
  73. Improving disease gene prioritization using the semantic similarity of Gene Ontology terms
    Andreas Schlicker, Thomas Lengauer, and Mario Albrecht
    Bioinformatics 26 (18): i561-i567, 2010
  74. Mutations within GP41 are correlated with coreceptor tropism but do not substantially improve coreceptor usage prediction
    Alexander Thielen, Thomas Lengauer, P Richard Harrigan, Luke Swenson, Winnie WY Dong, Rachel A McGovern, Marilyn Lewis, Ian James, Jayvant Heera, and Hernan Valdez
    In: Reviews in Antiviral Therapy & Infectious Diseases, Sorrento, Italy, 2010, 47-47
  75. Only Slight Impact of Predicted Replicative Capacity for Therapy Response Prediction
    Hendrik Weisser, André Altmann, Saleta Sierra, Francesca Incardona, Daniel Struck, Anders Sönnerborg, Rolf Kaiser, Maurizio Zazzi, Monika Tschochner, Hauke Walter, and Thomas Lengauer
    PLoSOne 5 (2): e9044,1-e9044,10, 2010
  76. Permutation importance: an unbiased feature importance measure
    André Altmann, Laura Tolosi, Oliver Sander, and Thomas Lengauer
    Bioinformatics 26 (10): 1340-1347, 2010
  77. Positive selection of HIV host factors and the evolution of lentivirus genes
    Katarzyna Bozek and Thomas Lengauer
    BMC Evolutionary Biology 10 (1): 186,1-186,15, 2010
  78. Predicting MHC class I epitopes in large datasets
    Kirsten Roomp, Iris Antes, and Thomas Lengauer
    BMC Bioinformatics 11 (1): 90,1-90,11, 2010
  79. Prediction of Response to Antiretroviral Therapy by Human Experts and by the EuResist Data-Driven Expert System (the EVE Study)
    Maurizio Zazzi, Rolf Kaiser, Anders Sönnerborg, Daniel Struck, Andre Altmann, Mattia C. F. Prosperi, Michal Rosen-Zvi, Andrea Petroczi, Yardena Peres, Eugen Schülter, Charles Boucher, Francoise Brun-Vezinet, Richard Harigan, Lynn Morris, Martin Obermeier, Federico Perno, Robert Shafer, Anne-Mieke Vandamme, Kristel van Laethem, Annemarie Wensing, Thomas Lengauer, and Francesca Incardona
    HIV Medicine Early View: 1-8, 2010
  80. Short Communication: Selection of Thymidine Analogue Resitance Mutational Patterns in Children from a Common HIV Type 1 Subtype G Source
    Martin Däumer, Sabine Awerkiew, Saleto Sierra Aragon, Vladimir Kartashev, Tatjana Poplavskaja, Rolf Klein, Nadine Sichtig, Bernhard Thielen, Thomas Lengauer, Kirsten Roomp, Herbert Pfister, and Rolf Kaiser
    AIDS Research and Human Retroviruses 26 (3): 275-278, 2010
  81. Web-based analysis of (epi-) genome data using EpiGRAPH and Galaxy.
    Christoph Bock, Greg Von Kuster, Konstantin Halachev, James Taylor, Anton Nekrutenko, and Thomas Lengauer
    In: Genetic Variation : Methods and Protocols, 2010, 275-296
  82. AltAnalyze and DomainGraph: analyzing and visualizing exon expression data
    Dorothea Emig, Nathan Salomonis, Jan Baumbach, Thomas Lengauer, Bruce R. Conklin, and Mario Albrecht
    Nucleic Acids Research 38 (Suppl. 2): W755-W762, 2010
  83. HLA class I allele associations with HCV genetic variants in patients with chronic HCV genotypes 1a or 1b infection
    Christian Markus Lange, Kirsten Roomp, Anette Dragan, Jacob Nattermann, Monika Michalk, Ulrich Spengler, Viola Weich, Thomas Lengauer, Stefan Zeuzem, Thoma Berg, and Christoph Sarrazin
    Journal of Hepatology 53 (6): 1022-1028, 2010
  84. Advantages of Predicted Phenotypes and Statistical Learning Models in Inferring Virological Response to Antiretroviral Therapy from HIV Genotype
    André Altmann, Tobias Sing, Hans Vermeiren, Bart Winters, Elke Van Craenenbroeck, Koen Van der Borght, Soo-Yon Rhee, Robert W. Shafer, Eugen Schülter, Rolf Kaiser, Yardena Peres, Anders Sönnerborg, W. Jeffrey Fessel, Francesca Incardona, Maurizio Zazzi, Lee Bacheler, Hermann Van Vlijmen, and Thomas Lengauer
    Antiviral Therapy 14 (2): 273-283, 2009
  85. An exhaustive methode for CpG island annotation
    Lars Feuerbach, Konstantin Halachev, Thomas Lengauer, and Christoph Bock
    In: Special Issue: Abstracts of the 3rd MC-GARD Meeting, Pollock Halls of Residence, 18 Holyrood Park Road, Edinburgh, Scotland, 2009, 146-146, paper no. P77.
  86. Bioinformatische Unterstützung der Auswahl von HIV Therapien
    Thomas Lengauer, André Altmann, and Alexander Thielen
    Informatik Spektrum 32 (2): 320-331, 2009
  87. Clinical relevance of the 2'-5'-oligoadenylate synthetase/RNase L system for treatment response in chronic hepatitis C
    Ulrike Mihm, Oliver Ackermann, Christoph Welsch, Eva Herrmann, Wolf Peter Hofmann, Natalia Grigorian, Martin Walter Welker, Thomas Lengauer, Stefan Zeuzem, and Christoph Sarrazin
    Journal of Hepatology 50 (1): 49-58, 2009
  88. Computerjagd auf das AIDSVIRUS
    Thomas Lengauer and Rolf Kaiser
    Spektrum der Wissenschaft 08: 62-67, 2009
  89. Docking and scoring with alternative side-chain conformations
    Christoph Hartmann, Iris Antes, and Thomas Lengauer
    Proteins: Structure, Function, and Bioinformatics 74 (3): 712-726, 2009
  90. Dynamics of NRTI resistance mutations during therapy interruption
    Maria Trignetti, Tobias Sing, Valentina Svicher, Maria Mercedes Santoro, Federica Forbici, Roberta D'Arrigo, Maria Concetta Bellocchi, Mario Santoro, Patrizia Marconi, Mauro Zaccarelli, Maria Paola Trotta, Rita Bellagamba, Pasquale Narciso, Andrea Antinori, Thomas Lengauer, Carlo Federico Perno, and Francesca Ceccherini-Silberstein
    AIDS Research and Human Retroviruses 25 (1): 57-64, 2009
  91. Estimating evolutionary pathways to 7CXCR4 usage from cross-sectional data
    Alexander Thielen, André Altmann, Jasmina Bogojeska, Rolf Kaiser, and Thomas Lengauer
    In: Abstracts presented at the XVIII International HIV Drug Resistance Workshop : Basic Principles & Clinical Implications, Fort Myers, USA, 2009, A16-A16, paper no. Abstract 14.
  92. MethMarker: User-friendly design and optimization of gene-specific DNA methylation assays
    Peter Schüffler, Thomas Mikeska, Andreas Waha, Thomas Lengauer, and Christoph Bock
    Genome Biology 10 (10): R105:1-R105:10, 2009
    [PDF: Download: MethMarker - user-friendly design and optimization of gene-specific DNA methylation assays.pdf]
  93. 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
    Alexander Thielen, Nadine Sichtig, Patrick Braun, Martin Däumer, Hauke Walter, Christian Noah, Eva Wolf, Harm Müller, Martin Stürmer, Thomas Lengauer, Rolf Kaiser, and Martin Obermeier
    In: Reviews in Antiviral Therapy, Stockholm, Sweden, 2009, 99-99
  94. Predicting the Response to Combination Antiretroviral Therapy: Retrospective Validation of geno2pheno-THEO on a Large Clinical Database
    André Altmann, Martin Däumer, Niko Beerenwinkel, Yardena Peres, Eugen Schülter, Joachim Büch, Soo-Yon Rhee, Anders Sönnerborg, W. Jeffrey Fessel, Robert W. Shafer, Maurizio Zazzi, Rolf Kaiser, and Thomas Lengauer
    The Journal of Infectious Diseases 199 (7): 999-1006, 2009
  95. Protein-protein interactions: analysis and prediction
    Dmitrij Frishman, Mario Albrecht, Hagen Blankenburg, Peer Bork, Eoghan D. Harrington, Henning Hermjakob, Lars J. Jensen, David A. Juan, Thomas Lengauer, Philipp Pagel, Vincent Schachter, and Alfonso Valencia
    In: Modern Genome Annotation - The Biosapiens Network, 2009, 353-410
  96. Resistenzbestimmung
    Thomas Lengauer, S. Sierra, and Rolf Kaiser
    MMW Fortschritte in der Medizin 151 (18): 74-75, 2009
  97. V3 loop sequence space analysis suggests different evolutionary patterns of CCR5- and CXCR4-tropic HIV.
    Kasia Bozek, Alexander Thielen, Saleta Sierra, Rolf Kaiser, and Thomas Lengauer
    PLoS One 4 (11): e7387:1-e.7387:14, 2009
  98. Viral Bioinformatics
    Ben Adams, Alice McHardy, C. Lundegaard, and Thomas Lengauer
    In: Modern Genome Annotation - The BioSapiens Network, 2009, 429-452
  99. DASMI: exchanging, annotating and assessing molecular interaction data
    Hagen Blankenburg, Robert D. Finn, Andreas Prlić, Andrew M. Jenkinson, Fidel Ramírez, Dorothea Emig, Sven-Eric Schelhorn, Joachim Büch, Thomas Lengauer, and Mario Albrecht
    Bioinformatics 25 (10): 1321-1328, 2009
  100. EpiGRAPH: user-friendly software for statistical analysis and prediction of (epi)genomic data
    Christoph Bock, Konstantin Halachev, Joachim Büch, and Thomas Lengauer
    Genome Biology 10: R14.1-R14.14, 2009
    [PDF: Download: EpiGRAPH - User-friendly software for statistical analysis and prediction of (epi-) genomic data.pdf]
  101. Alignment of Non-Covalent Interactions at Protein-Protein Interfaces
    Hongbo Zhu, Ingolf Sommer, Thomas Lengauer, and Francisco S. Domingues
    PLoS ONE 3 (4): e1926 p., 2008
    [PDF: Download: Zhu2008.pdf]
  102. An integrative approach for predicting interactions of protein regions
    Sven-Eric Schelhorn, Thomas Lengauer, and Mario Albrecht
    Bioinformatics 24 (16): i35-i41, 2008
  103. Comparison of Classifier Fusion Methods for Predicting Response to Anti HIV-1 Therapy
    Andre Altmann, Michal Rosen-Zvi, Mattia Prosperi, Ehud Aharoni, Hani Neuvirth, Anders Sönnerborg, Eugen Schülter, Joachim Büch, Daniel Struck, Yardena Peres, Francesca Incardona, Rolf Kaiser, Maurizio Zazzi, and Thomas Lengauer
    PLoS ONE 3 (10): e3470 p., 2008
  104. Computational analysis of covariation and interactions between HIV-1 reverse transcriptase and Integrase
    Oliver Sander, Andre Altmann, and Thomas Lengauer
    In: Reviews in Antiviral Therapy, Budapest, Hungary, 2008, 113-114
  105. Computational epigenetics
    Christoph Bock and Thomas Lengauer
    Bioinformatics 24 (1): 1-10, 2008
    [PDF: Download: Review on Computational Epigenetics - Advanced Access.pdf]
  106. Computing topological parameters of biological networks
    Yassen Assenov, Fidel Ramírez, Sven-Eric Schelhorn, Thomas Lengauer, and Mario Albrecht
    Bioinformatics 24 (2): 282-284, 2008
  107. Genotypic Analysis of HIV Co-Receptor Usage
    Saleta Sierra, Rolf Kaiser, Alexander Thielen, Oliver Sander, and Thomas Lengauer
    In: Entry Inhibitoren - Neue Formen der HIV-Therapie, 2008, 31-39
  108. Improved genotypic prediction of HIV-1 coreceptor usage by incorporating V2 loop sequence variation
    Alexander Thielen, P Richard Harrigan, Andrew J. Low, A Moores, Andre Altmann, Kasia Bozek, Eva Heger, Nadine Sichtig, Rolf Kaiser, and Thomas Lengauer
    In: Antiviral Therapy, Sitges, Spain, 2008, A100 p.
  109. Improving HIV-1 coreceptor usage prediction from genotype with regions outside of V3
    Alexander Thielen, Rolf Kaiser, and Thomas Lengauer
    In: Reviews in Antiviral Therapy, Washington, US, 2008, 81-82
  110. Inferring viral tropism from genotype with massively parallel sequencing; qualitative and quantitative analysis
    Martin Däumer, Rolf Kaiser, Rolf Klein, Thomas Lengauer, Bernhard Thiele, and Alexander Thielen
    In: Antiviral Therapy, Sitges, Spain, 2008, A101 p.
  111. Integrating expression data with domain interaction networks
    Dorothea Emig, Melissa S. Cline, Thomas Lengauer, and Mario Albrecht
    Bioinformatics 24 (21): 2546-2548, 2008
  112. Integrative visual analysis of the effects of alternative splicing on protein domain interaction networks
    Dorothea Emig, Melissa S. Cline, Karsten Klein, Anne Kunert, Petra Mutzel, Thomas Lengauer, and Mario Albrecht
    Journal of Integrative Bioinformatics 5 (2): 101-115, 2008
  113. Inter-individual variation of DNA methylation and its implications for large-scale epigenome mapping
    Christoph Bock, Jörn Walter, Martina Paulsen, and Thomas Lengauer
    Nucleic Acids Research 36 (10): e55 p., 2008
    [PDF: Download: Bock et al. (2008) Inter-individual variation of DNA methylation and its implications for large-scale epigenome mapping.pdf]
  114. Local function conservation in sequence and structure space
    Nils Weinhold, Oliver Sander, Francisco S. Domingues, Thomas Lengauer, and Ingolf Sommer
    PLoS Computational Biology 4: e1000105 p., 2008
    [PDF: Download: Weinhold2008.pdf]
  115. Molecular basis of telaprevir resistance due to V36 and T54 mutations in the NS3-4A protease of HCV
    Christoph Welsch, Francisco S. Domingues, Simone Susser, Iris Antes, Christoph Hartmann, Gabriele Mayr, Andreas Schlicker, Christoph Sarrazin, Mario Albrecht, Stefan Zeuzem, and Thomas Lengauer
    Genome Biology 9 (1): R16 p., 2008
    [PDF: Download: Welsch2008.pdf]
  116. Multi-Task Learning for HIV Therapy Screening
    Steffen Bickel, Jasmina Bogojeska, Thomas Lengauer, and Tobias Sheffer
    In: Proceedings, Twenty-Fifth International Conference on Machine Learning, Helsinki, Finland, 2008, 56-63

  117. Rtreemix: an R package for estimating evolutionary pathways and genetic progression scores
    Jasmina Bogojeska, Adrian Alexa, André Altmann, Thomas Lengauer, and Jörg Rahnenführer
    Bioinformatics 24 (20): 2391-2392, 2008

  118. Selecting anti-HIV therapies based on a variety of genomic and clinical factors
    Michal Rosen-Zvi, Andre Altmann, Mattia Prosperi, Ehud Aharoni, Hani Neuvirth, Anders Sönnerborg, Eugen Schülter, Daniel Struck, Yardena Peres, Francesca Incardona, Rolf Kaiser, Maurizio Zazzi, and Thomas Lengauer
    In: Proceedings of the 16th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB 2008), Toronto, Canada, 2008, i399-406
  119. Stability analysis of mixtures of mutagenetic trees
    Jasmina Bogojeska, Thomas Lengauer, and Jörg Rahnenführer
    BMC Bioinformatics 9 (1): 165-181, 2008
  120. Structural descriptors of protein-protein binding sites
    Oliver Sander, Francisco S. Domingues, Hongbo Zhu, Thomas Lengauer, and Ingolf Sommer
    In: Proceedings of 6th Asia-Pacific Bioinformatics Conference, Kyoto, Japan, 2008, 79-88
  121. Sustaining lamivudine/emtricitabine, abacavir, zidovudine or atazanavir from a previous treatment shows a clinical benefit
    Michal Rosen-Zvi, Eugen Schülter, Andre Altmann, Saleta Sierra-Aragon, Maurizio Zazzi, Anders Sönnerborg, Mark Oette, Thomas Lengauer, and Rolf Kaiser
    In: Antiviral Therapy, Sitges, Spain, 2008, A86 p.
  122. The EuResist approach for predicting response to anti HIV-1 therapy
    Andre Altmann, Michal Rosen-Zvi, Mattia Prosperi, Ehud Aharoni, Hani Neuvirth, Eugen Schülter, Joachim Büch, Yardena Peres, Incardona Incardona, Anders Sönnerborg, Rolf Kaiser, Maurizio Zazzi, and Thomas Lengauer
    In: Reviews in Antiviral Therapy, Budapest, Hungary, 2008, 107 p.
  123. Towards Comparative Epigenomics: A Software Toolkit For Cross-Species Epigenome Data Analysis
    Lars Feuerbach, Bock Christopher, Konstantin Halachev, Joachim Büch, and Thomas Lengauer
    In: Abstracts of the 2nd MC-GARD Meeting, Madrid, Spain, 2008, 230 p.
  124. A genome-wide association scan of nonsynonymous SNPs identifies a susceptibility variant for Crohn disease in ATG16L1
    Jochen Hampe, Andre Franke, Philip Rosenstiel, Andreas Till, Markus Teuber, Klaus Huse, Mario Albrecht, Gabriele Mayr, Francisco M. De La Vega, Jason Briggs, Simone Günther, Natalie J. Prescott, Clive M. Onnie, Robert Häsler, Bence Sipos, Ulrich R. Fölsch, Thomas Lengauer, Matthias Platzer, Christopher G. Mathew, Michael Krawczak, and Stefan Schreiber
    Nature Genetics 39 (2): 207-211, 2007
  125. Analysis of Expression Data: Classification of genes
    Jörg Rahnenführer and Thomas Lengauer
    In: Bioinformatics - From Genomes to Therapies 2. Getting at the Inner Workings: Molecular Interactions, 2007, 993-1021
  126. Application of oncogenetic trees mixtures as a biostatistical model of the clonal cytogenetic evolution of meningiomas
    Ralf Ketter, Steffi Urbschat, Wolfram Henn, Wolfgang Feiden, Niko Beerenwinkel, Thomas Lengauer, Wolf-Ingo Steudel, Klaus D. Zang, and Jörg Rahnenführer
    International Journal of Cancer 121 (7): 1473-1480, 2007
  127. Bioinformatics prediction of HIV coreceptor usage
    Thomas Lengauer, Oliver Sander, Saleta Sierra, Alexander Thielen, and Rolf Kaiser
    Nature Biotechnology 25 (12): 1407-1410, 2007
  128. Bioinformatik
    Thomas Lengauer
    In: Technologiefüher - Grundlagen, Anwendungen, Trends, 2007, 4 p.
  129. Characterization and structural analysis of novel mutations in human immunodeficiency virus type 1 reverse transcriptase involved in the regulation of restistance to nonnucleoside inhibitors
    Francesca Ceccherini-Silberstein, Valentina Svicher, Tobias Sing, Anna Artese, Maria Mercedes Santoro, Federica Forbici, Ada Bertoli, Stefano Alcaro, Guido Palamara, Antonella d'Arminio Monforte, Jan Balzarini, Andrea Antinori, Thomas Lengauer, and Carlo Federico Perno
    Journal of Virology 81 (20): 11507-11519, 2007

  130. Combined similarity and QSPR virtual screening for guest molecules of $\beta$-cyclodextrin
    Andreas Steffen, Maximilian Karasz, Carolin Thiele, Thomas Lengauer, Andreas Kämper, Gerhard Wenz, and Joannis Apostolakis
    New Journal of Chemistry 31 (11): 1941-1949, 2007
  131. Computational analysis of human protein interaction networks
    Fidel Ramírez, Andreas Schlicker, Yassen Assenov, Thomas Lengauer, and Mario Albrecht
    Proteomics 7 (15): 2541-2552, 2007
  132. Computational Epigenetics: Bioinformatik für neue Wege in der Krebsforschung
    Christoph Bock and Thomas Lengauer
    In: Jahrbuch 2007, 2007, 271-277
    [PDF: Download: Reprint - Computational Epigenetics - Bioinformatik für neue Wege in der Krebsforschung.pdf]
  133. Conformational analysis of alternative protein structures
    Francisco S. Domingues, Jörg Rahnenführer, and Thomas Lengauer
    Bioinformatics 23 (23): 3131-3138, 2007
  134. Correlation nonstructural (NS)4B amino acid variations with initial viral kinetics during interferon-alpha-based therapy in HCV-1b-infected patients
    Martin W. Welker, Wolf-Peter Hofmann, Christoph Welsch, Michael von Wagner, Eva Herrmann, Thomas Lengauer, Stefan Zeuzem, and Christoph Sarrazin
    Journal of Viral Hepatitis 14 (5): 338-349, 2007
  135. Expression pattern analysis of transcribed HERV sequences is complicated by ex vitvo recombination
    Aline Flockerzi, Jochen Maydt, Oliver Frank, Alessia Ruggieri, Esther Maldener, Wolfgang Seifarth, Patrik Medstrand, Thomas Lengauer, Andreas Meyerhans, Christine Leib-Mosch, Eckart Meese, and Jens Mayer
    Retrovirology 4 (1): 39 p., 2007
    [PDF: Download: Flockerzi.pdf]
  136. Factor interaction analysis for chromosome 8 and DNA methylation alterations highlights innate immune response suppression and cytoskeletal changes in prostate cancer
    Wolfgang A. Schulz, Adrian Alexa, Volker Jung, Christiane Hader, Michele J. Hoffmann, Masanori Yamanaka, Sandy Fritzsche, Agnes Wlazlinski, Mirko Müller, Thomas Lengauer, Rainer Engers, Andrea R. Florl, Bernd Wullich, and Jörg Rahnenführer
    Molecular Cancer 6: 1-16, 2007
    [PDF: Download: Rahnenfuehrer2007c.pdf]
  137. Fifteen years of env C2V3C3 evolution in six individuals clonally infected with human immunodeficiency virus type 1
    Bernd Kupfer, Tobias Sing, Peter Schüffler, Rabea Hall, Ralf Kurz, Astrid McKeown, Karl-Eduard Schneweis, Wolfgang Eberl, Johannes Oldenburg, Hans H. Brackmann, Jürgen K. Rockstroh, Ulrich Spengler, Martin Däumer, Rolf Kaiser, Thomas Lengauer, and Bertfried Matz
    Journal of Medical Virology 79 (11): 1629-1639, 2007
  138. Functional evaluation of domain-domain interactions and human protein interaction networks
    Andreas Schlicker, Carola Huthmacher, Fidel Ramírez, Thomas Lengauer, and Mario Albrecht
    Bioinformatics 23 (7): 859-865, 2007

  139. Future Trends
    Thomas Lengauer
    In: Bioinformatics - From Genomes to Therapies 3. The Holy Grail: Molecular Function, 2007, 1651-1687
  140. Genotypic coreceptor analysis.
    Saleta Sierra, Rolf Kaiser, Alexander Thielen, and Thomas Lengauer
    European Journal of Medical Research 12 (9): 453-462, 2007

  141. Identification of PatL1, a human homolog to yeast P body component Pat1
    Nicoletta Scheller, Patricia Resa-Infante, Susana de la Luna, Rui Pedro Galao, Mario Albrecht, Lars Kaestner, Peter Lipp, Thomas Lengauer, Andreas Meyerhans, and Juana Díez
    Biochimica et Biophysica Acta - Molecular Cell Research 1773 (12): 1786-1792, 2007
  142. Improved cyclodextrin-based receptors for camptothecin by inverse virtual screening
    Andreas Steffen, Carolin Thiele, Simon Tietze, Christian Strassnig, Andreas Kämper, Thomas Lengauer, Gerhard Wenz, and Joannis Apostolakis
    Chemistry 13 (24): 6801-6809, 2007
  143. Improved prediction of response to antiretroviral combination therapy using the genetic barrier to drug resistance
    Andre Altmann, Niko Beerenwinkel, Tobias Sing, Igor Savenkov, Martin Däumer, Rolf Kaiser, Soo-Yon Rhee, W Jeffrey Fessel, Robert W Shafer, and Thomas Lengauer
    Antiviral Therapy 12 (2): 169-178, 2007
  144. Inferring Protein Function from Protein Structure
    Francisco S. Domingues and Thomas Lengauer
    In: Bioinformatics - From Genomes to Therapies 3. The Holy Grail: Molecular Function, 2007, 1211-1252
  145. Inferring virological response from genotype: with or without predicted phenotypes?
    Andre Altmann, Tobias Sing, Hans Vermeiren, Bart Winters, Elke Van Craenenbroeck, Koen Van der Borght, Soo-Yon Rhee, Robert W Shafer, Eugen Schülter, Rolf Kaiser, Yardena Peres, Anders Sonnerborg, W Jeffrey Fessel, Francesca Incardona, Maurizio Zazzi, Lee Bacheler, Hermann Van Vlijmen, and Thomas Lengauer
    In: Proceedings of the 16th International HIV Drug Resistance Workshop, Barbados, Barbados, 2007, S169 p.
  146. Introduction
    Thomas Lengauer
    In: Bioinformatics - From Genomes to Therapies 1. The Building Blocks: Molecular Sequences and Structures, 2007, 1-24
  147. Lead Identification by Virtual Screening
    Andreas Kämper, Didier Rognan, and Thomas Lengauer
    In: Bioinformatics - From Genomes to Therapies 2. Getting at the Inner Workings: Molecular Interactions, 2007, 651-704
  148. Moment invariants as shape recognition technique for comparing protein binding sites
    Ingolf Sommer, Oliver Müller, Francisco S. Domingues, Oliver Sander, Joachim Weickert, and Thomas Lengauer
    Bioinformatics 23 (23): 3139-3146, 2007
  149. Predicting HIV coreceptor usage on the basis of genetic and clinical covariates
    Tobias Sing, Andrew J. Low, Niko Beerenwinkel, Oliver Sander, Peter K. Cheung, Francisco S. Domingues, Joachim Büch, Martin Däumer, Rolf Kaiser, Thomas Lengauer, and P. Richard Harrigan
    Antiviral Therapy 12 (7): 1097-1106, 2007
  150. Selective pressures of HLA genotypes and antiviral therapy on human immunodeficiency virus type 1 sequence mutation at a population level
    G. Ahlenstiel, Kirsten Roomp, Martin Däumer, T. Nattermann, M. Vogel, J.K. Rockstroh, Niko Beerenwinkel, R. Kaiser, H.-D. Nischalke, T. Sauerbruch, Thomas Lengauer, and U. Spengler
    Clinical and Vaccine Immunology 14 (10): 1266-1273, 2007

  151. Strategiekonzept "Molekulare Bioinformatik"
    Thomas Lengauer
    In: Informatikforschung in Deutschland, 2007, 9 p.
  152. Structural and functional comparison of the non-structural protein 4B of flaviviridae
    Christoph Welsch, Mario Albrecht, Jochen Maydt, E. Herrmann, M.W. Welker, C. Sarrazin, A. Scheidig, Thomas Lengauer, and S. Zeuzem
    Journal of Molecular Graphics and Modeling 26 (2): 546-557, 2007
  153. Structural Descriptors of gp120 V3 Loop for the Prediction of HIV-1 Coreceptor Usage
    Oliver Sander, Tobias Sing, Ingolf Sommer, Andrew J. Low, Peter K. Cheung, P. Richard Harrigan, Thomas Lengauer, and Francisco S. Domingues
    PLoS Computational Biology 3 (3): 555-564, 2007
    [PDF: Download: Sander.pdf]
  154. The implications of alternative splicing in the ENCODE protein complement
    Michael L. Tress, Pier L. Martelli, Adam Frankish, Gabrielle A. Reeves, Jan J. Wesselink, Corin Yeats, Páll Í. Ólason, Mario Albrecht, Hedi Hegyi, Alejandro Giorgetti, Domenico Raimondo, Julien Lagarde, Roman A. Laskowski, Gonzalo López, Michael I. Sadowski, James D. Watson, Piero Fariselli, Ivan Rossi, Alinda Nagy, Wang Kai, Zenia Størling, Massimiliano Orsini, Yassen Assenov, Hagen Blankenburg, Carola Huthmacher, Fidel Ramírez, Andreas Schlicker, France Denoued, Phil Jones, Samuel Kerrien, Sandra Orchard, Stylianos E. Antonarakis, Alexandre Reymond, Ewan Birney, Søren Brunak, Rita Casadio, Roderic Guigo, Jennifer Harrow, Henning Hermjakob, David T. Jones, Thomas Lengauer, Christine A. Orengo, László Patthy, Janet M. Thornton, Anna Tramontano, and Alfonso Valencia
    Proceedings of the National Academy of Sciences 104 (13): 5495-5500, 2007

  155. Validation of geno2pheno and THEO on a large independent clinical dataset
    Andre Altmann, Martin Däumer, Tobias Sing, Niko Beerenwinkel, Hauke Walter, Rolf Kaiser, and Thomas Lengauer
    In: Proceedings of the 5th European HIV Drug Resistance Workshop, Cascais, Portugal, 2007
  156. CpG Island Mapping by Epigenome Prediction
    Christoph Bock, Jörn Walter, Martina Paulsen, and Thomas Lengauer
    PLoS Computational Biology 3 (6): 1055-1070, 2007
    [PDF: Download: C. Bock et al. (2007) CpG island mapping by epigenome prediction.pdf] [PDF: Download: BockWalter.pdf]
  157. EuResist: exploration of multiple modeling techniques for prediction of response to treatment
    Maurizio Zazzi, Ehud Aharoni, Andre Altmann, Fulop Baszó, Penny Bidgood, Gabór Borgulya, J Denholm-Prince, M Fielder, Rolf Kaiser, Carmel Kent, Thomas Lengauer, T Nepusz, Hanni Neuvirth, Yardena Peres, Andrea Petroczi, Mattia Prosperi, L Romano, Michal Rosen-Zvi, Eugen Schülter, Tobias Sing, Andras Sonnerborg, R Thompson, G Ulivi, L Zalány, and Francesca Incardona
    In: Proceedings of the 5th European HIV Drug Resistance Workshop, Cascais, Portugal, 2007
  158. GOTax: investigating biological processes and biochemical activities along the taxonomic tree
    Andreas Schlicker, Jörg Rahnenführer, Mario Albrecht, Thomas Lengauer, and Francisco S. Domingues
    Genome Biology 8 (3): R33.1-10, 2007
    [PDF: Download: Schlicker2007.pdf]
  159. IRECS: A new algorithm for the selection of most probable ensembles of side-chain conformations in protein models.
    Christoph Hartmann, Iris Antes, and Thomas Lengauer
    Protein Science 16: 1294-1307, 2007

  160. A Fully Computational Model for Predicting Percutaneous Drug Absorption
    Dirk Neumann, Oliver Kohlbacher, Christian Merkwirth, and Thomas Lengauer
    Journal of Chemical Information and Modeling 1 (46): 424-429, 2006
  161. A new measure for functional similarity of gene products based on Gene Ontology
    Andreas Schlicker, Francisco S. Domingues, Jörg Rahnenführer, and Thomas Lengauer
    BMC Bioinformatics 7: 1-16, 2006
    [PDF: Download: Schlicker_BMCBioinformatics_2006.pdf]
  162. Amino acid variations in hepatitis C virus p7 and sensitivity to antiviral combination therapy with amantadine in chronic hepatitis C
    Ulrike Mihm, Natalia Grigorian, Christoph Welsch, Eva Herrmann, Bernd Kronenberger, Gerlinde Teuber, Michael von Wagner, Wolf-Peter Hofmann, Mario Albrecht, Thomas Lengauer, Stefan Zeuzem, and Christoph Sarrazin
    Antiviral Therapy 11 (4): 507-519, 2006
  163. Analysis and prediction of protein-protein-interaction types
    Thomas Lengauer, F.S. Domingues, Ingolf Sommer, and Hongbo Zhu
    BMC Bioinformatics 7 (1), 2006
  164. Arevir: A Secure Platform for Designing Personalized Antiretroviral Therapies Against HIV
    Kirsten Roomp, Niko Beerenwinkel, Tobias Sing, Eugen Schülter, Joachim Büch, Saleta Sierra-Aragon, Martin Däumer, Daniel Hoffmann, Rolf Kaiser, Thomas Lengauer, and Joachim Selbig
    Lecture Notes in Computer Science 4075: 185-194, 2006
  165. Bioinformatics-assisted anti-HIV therapy
    Thomas Lengauer and Tobias Sing
    Nature Reviews Microbiology 4: 790-797, 2006
  166. Bioinformatisches Data Mining erschließt neue Strategien gegen Krebs
    Christoph Bock, Konstantin Halachev, and Thomas Lengauer
    In: Aktuelle Trends in der Softwareforschung, 2006, 91-99
  167. Computational recognition of potassium channel sequences
    Burkhard Heil, Jost Ludwig, Hella Lichtenberg-Fraté, and Thomas Lengauer
    Bioinformatics 13 (22): 1562-1568, 2006
  168. Development of Computational Methods for Analysis of Metabolic Profiling Data
    Priti Talwar, Thomas Lengauer, Christoph Wittmann, V. R. Velagapudi, and Elmar Heinzle
    In: Proceedings of International Conference on Systems Biology (ICSB 2006), Japan, Yokohama, Japan, 2006, 42-42
  169. Editorial: Selection of papers of the German Conference of Bioinformatics (GCB) 2005
    Andrew E. Torda and Thomas Lengauer
    Bioinformatics 22 (10): 1 p., 2006

  170. Flexible Docking of Ligands into Synthetic Receptors Using a Two-Sided Incremental Construction Algorithm
    Andreas Steffen, Andreas Kämper, and Thomas Lengauer
    Journal of Chemical Information and Modeling 46 (4): 1695-1703, 2006
  171. Fully Automated Flexible Docking of Ligands into Flexible Synthetic Receptors Using Forward and Inverse Docking Strategies
    Andreas Kämper, Joannis Apostolakis, Matthias Rarey, Christel Maria Marian, and Thomas Lengauer
    Journal of Chemical Information and Modeling 46 (2): 903-911, 2006
  172. Functional evaluation of domain-domain interactions and human protein interaction networks
    Andreas Schlicker, Carola Huthmacher, Fidel Ramírez, Thomas Lengauer, and Mario Albrecht
    In: German Conference on Bioinformatics (GCB 2006), Tübingen, Germany, 2006, 115-126
  173. Improved Scoring of Functional Groups from Gene Expression Data by Decorrelating GO Graph Structure
    Adrian Alexa, Jörg Rahnenführer, and Thomas Lengauer
    Bioinformatics 22 (13): 1600-1607, 2006

  174. Improving the quality of protein structure models by selecting from alignment alternatives
    Ingolf Sommer, Stefano Toppo, Oliver Sander, Thomas Lengauer, and Silvio C. E. Tosatto
    BMC Bioinformatics 7: 1-11, 2006
  175. Involvement of novel HIV-1 reverse transcriptase mutations in the regulation of resistance to nucleoside inhibitors
    Valentina Svicher, Tobias Sing, Maria Mercedes Santoro, Federica Forbici, Fátima Rodriguez- Barrios, Ada Bertoli, Niko Beerenwinkel, Maria Concetta Bellocchi, Federigo Gago, Antonella d´Arminio Monforte, Andrea Antinori, Thomas Lengauer, Francesca Ceccherini-Silberstein, and Carlo-Federico Perno
    Journal of Virology 80 (14): 7186-7198, 2006
  176. Local protein structure prediction using discriminative models
    Oliver Sander, Ingolf Sommer, and Thomas Lengauer
    BMC Bioinformatics 7 (14): 1-13, 2006
  177. Metabolic high- content screening of Saccharomyces cerevisiae reveals superior performance of single gene deletion strains
    Vidya R. Velagapudi, Christoph Wittmann, Thomas Lengauer, Priti Talwar, and Elmar Heinzle
    Process Biochemistry 41 (10): 2170-2179, 2006
  178. Model Selection for Mixtures of Mutagenetic Trees
    Junming Yin, Niko Beerenwinkel, Jörg Rahnenführer, and Thomas Lengauer
    Statistical Applications in Genetics and Molecular Biology 5 (1): Article 17 p., 2006

  179. Mutations in the MutSalpha interaction interface of MLH1 can abolish DNA mismatch repair
    Guido Plotz, Christoph Welsch, Luis Giron-Monzon, Peter Friedhoff, Mario Albrecht, Albrecht Piiper, Ricardo M. Biondi, Thomas Lengauer, Stefan Zeuzem, and Jochen Raedle
    Nucleic Acids Research 34 (22): 6574-6586, 2006
    [PDF: Download: Plotz.pdf]
  180. Mutations in the NB-ARC domain of I-2 that impair ATP hydrolysis cause autoactivation
    Wladimir I. Tameling, Jack H. Vossen, Mario Albrecht, Thomas Lengauer, Jan A. Berden, Michel A. Haring, Ben J.C. Cornelissen, and Frank L. W. Takken
    Plant Physiology 140 (4): 1233-1245, 2006
  181. Prediction of percutaneous drug absorption
    Dirk Neumann, Oliver Kohlbacher, Christian Merkwirth, and Thomas Lengauer
    Journal of Chemical Information and Modeling 1 (46): 424-429, 2006
  182. Refinement of homology modeled protein structures for molecular docking
    Iris Antes and Thomas Lengauer
    In: Proceedings of the 367. WE-Heraeus Seminar on Biomolecular Simulations, Bad Honnef, 2006, 1 p.
  183. Stable coreceptor usage of HIV in patients with ongoing treatment failure on HAART
    Clara Lehmann, Martin Däumer, Ibrahim Bousaad, Tobias Sing, Niko Beerenwinkel, Thomas Lengauer, Norbert Schmeisser, Christoph Wyen, Gerd Fätkenheuer, and Rolf Kaiser
    Journal of Clinical Virology 37 (4): 300-304, 2006
  184. Virtual screening for guest molecules of a biosensor
    Andreas Steffen, Andreas Kämper, and Thomas Lengauer
    In: Biosensors 2006: The ninth world congress on biosensors, Toronto, Canada, 2006, O66 p.
  185. CpG Island Methylation in Human Lymphocytes Is Highly Correlated with DNA Sequence, Repeats, and Predicted DNA Structure
    Christoph Bock, Martina Paulsen, Sascha Tierling, Thomas Mikeska, Thomas Lengauer, and Jörn Walter
    PLoS Genetics 2 (3): 0243-0252, 2006
    [PDF: Download: Bock et al. (2006) - CpG Island Methylation in Human Lymphocytes.pdf]
  186. DynaPred: A structure and sequence based method for the prediction of MHC class I binding peptide sequence and conformations
    Iris Antes, Shirley Weng-In Siu, and Thomas Lengauer
    Bioinformatics 22 (14): 16-24, 2006
    [PDF: Download: AntesSiuLengauer.pdf]
  187. NOXclass: prediction of protein-protein interaction types
    Hongbo Zhu, Francisco S. Domingues, Ingolf Sommer, and Thomas Lengauer
    BMC Bioinformatics 7 (27): 1-15, 2006
  188. ROCR: Visualizing classifier performance in R
    Tobias Sing, Oliver Sander, Niko Beerenwinkel, and Thomas Lengauer
    Bioinformatics 21 (20): 3940-3941, 2006
  189. Recco: recombination analysis using cost optimization
    Jochen Maydt and Thomas Lengauer
    Bioinformatics 22 (9): 1064-1071, 2006
  190. A new CARD15 mutation in Blau syndrome
    Marjan M. Van Duist, Mario Albrecht, Marta Podswiadek, Daniela Giachino, Thomas Lengauer, Leonardo Punzi, and Mario De Marchi
    European Journal of Human Genetics 13 (6): 742-747, 2005
  191. An integrative approach to gain insights into the cellular function of human ataxin-2
    Markus Ralser, Mario Albrecht, Ute Nonhoff, Thomas Lengauer, Hans Lehrach, and Sylvia Krobitsch
    Journal of Molecular Biology 346 (1): 203-214, 2005
  192. Analysis and prediction of protein-protein interaction types
    Hongbo Zhu, Francisco S. Domingues, Ingolf Sommer, and Thomas Lengauer
    In: 4th European Conference on Computational Biology (ECCB05), Madrid, Spain, 2005, 1 p.
  193. Ataxin-2 and huntingtin interact with endophilin-A complexes to function in plastin-associated pathways
    Markus Ralser, Ute Nonhoff, Mario Albrecht, Thomas Lengauer, Erich E. Wanker, Hans Lehrach, and Sylvia Krobitsch
    Human Molecular Genetics 14 (19): 2893-2909, 2005
  194. Automatic Generation of complementary descriptors with molecular graph networks
    Thomas Lengauer and Christian Merkwirth
    Journal of Chemical Information and Modeling 45 (5): 1159-1168, 2005
  195. Characterization of novel HIV Drug Resistance Mutations using clustering, multidimensional scaling and SVM-based feature ranking
    Tobias Sing, Valentina Svicher, Niko Beerenwinkel, Francesca Ceccherini-Silberstein, Martin Däumer, Rolf Kaiser, Hauke Walter, Klaus Korn, Daniel Hoffmann, Mark Oette, Jürgen K. Rockstroh, Gerd Fätkenheuer, Carlo-Federico Perno, and Thomas Lengauer
    In: Knowledge Discovery in Databases: PKDD 2005., Porto, Portugal, 2005, 285-296
  196. Clinical significance of in vitro replication-enhancing mutations of the hepatitis C virus (HCV) replicon in patients with chronic HCV infection
    Christoph Sarrazin, Ulrike Mihm, Eva Herrmann, Christoph Welsch, Mario Albrecht, Ulrike Sarrazin, Stella Traver, Thomas Lengauer, and Stefan Zeuzem
    The Journal of Infectious Diseases 192 (10): 1710-1719, 2005
  197. Clinical significance of in vitro replication-enhancing mutations of the hepatitis C virus (HCV) replicon in patients with chronic HCV infection.
    Thomas Lengauer, Mario Albrecht, C. Sarrazin, U. Mihm, E. Herrmann, Christoph Welsch, U. Sarrazin, S. Traver, and S. Zeuzem
    Journal of Infectious Diseases 192 (10): 1710-1719, 2005
  198. Computational methods for the design of effective therapies against drug resistant HIV strains
    Niko Beerenwinkel, Tobias Sing, Thomas Lengauer, Jörg Rahnenführer, Kirsten Roomp, Igor Savenkov, Roman Fischer, Daniel Hoffmann, Joachim Selbig, Klaus Korn, Hauke Walter, Thomas Berg, Patrick Braun, Gerd Fätkenheuer, Mark Oette, Jürgen Rockstroh, Bernd Kupfer, Rolf Kaiser, and Martin Däumer
    Bioinformatics 21 (21): 3943-3950, 2005
  199. Computational Methods for Protein Function Prediction using Metabolomics Data
    Priti Talwar, Thomas Lengauer, Jörg Rahnenführer, Christoph Wittmann, VR Velagapudi, and Elmar Heinzle
    In: Proceedings of International Workshop on Systems Biology 2005, Milan, Italy., 2005, 1 p.
  200. Confirmation of human protein interaction data by human expression data
    Andreas Hahn, Jörg Rahnenführer, Priti Talwar, and Thomas Lengauer
    BMC Bioinformatics 6 (112): 1-11, 2005
  201. Decomposing protein networks into domain-domain interactions
    Mario Albrecht, Carola Huthmacher, Silvio C.E. Tosatto, and Thomas Lengauer
    Bioinformatics 21 (Suppl. 2): ii220-ii221, 2005
  202. Dissection of the inflammatory bowel disease transcriptome using genome-wide cDNA microarrays identifies novel candidate disease genes
    Christine M. Costello, Nancy Mah, Robert Häsler, Philip Rosenstiel, Georg H. Waetzig, Andreas Hahn, Tim Lu, Yesim Gurbuz, Susanna Nikolaus, Mario Albrecht, Jochen Hampe, Ralph Lucius, Günther Klöppel, Holger Eickhoff, Hans Lehrach, Thomas Lengauer, and Stefan Schreiber
    PLoS Medicine 2 (8): 771-787, 2005
  203. Diversity and functional plasticity of eukaryotic selenoproteins: Identification and characterization of the SelJ family
    Sergi Castellano, Alexey V. Lobanov, Charles Chapple, Sergey V. Novoselov, Mario Albrecht, Deame Hua, Alain Lescure, Thomas Lengauer, Alain Krol, Vadim N. Gladyshev, and Roderic Guigó
    Proceedings of the National Academy of Sciences 102 (45): 16188-16193, 2005
  204. Efficient conformational analysis of synthetic receptors with macrocyclic and fused ring systems
    Andreas Kämper, Melanie Kaspar, and Thomas Lengauer
    In: Synthetic Receptors 2005: Second World Congress on Synthetic Receptors, Salzburg, Austria, 2005, O4 p.. Note: Abstract for an oral presentation at the conference
  205. Estimating cancer survival and clinical outcome based on genetic tumor progression scores
    Jörg Rahnenführer, Niko Beerenwinkel, Wolfgang A. Schulz, Christian Hartmann, Andreas von Deimling, Bernd Wullich, and Thomas Lengauer
    Bioinformatics 21 (10): 2438-2446, 2005
  206. Estimating HIV evolutionary pathways and the genetic barrier to drug resistance
    Niko Beerenwinkel, Martin Däumer, Tobias Sing, Jörg Rahnenführer, Thomas Lengauer, Joachim Selbig, Daniel Hoffmann, and Rolf Kaiser
    The Journal of Infectious Diseases 191 (11): 1953-1960, 2005
  207. Geno2pheno[coreceptor]: a tool for predicting coreceptor usage from genotype and for monitoring coreceptor-associated sequence alterations
    Tobias Sing, Niko Beerenwinkel, Rolf Kaiser, Daniel Hoffmann, Martin Däumer, and Thomas Lengauer
    In: Proceedings of the 3rd European HIV Drug Resistance Workshop, Athens, Greece, 2005
  208. Informatics (Computational Biology)
    Thomas Lengauer
    In: Growth Factors and Oncogenes in Gastrointestinal Cancers to Informatics (Computational Biology), 2005, 567-626
    [PDF: Download: E000476803.pdf]
  209. Learning multiple evolutionary pathways from cross-sectional data
    Niko Beerenwinkel, Jörg Rahnenführer, Martin Däumer, Daniel Hoffmann, Rolf Kaiser, Joachim Selbig, and Thomas Lengauer
    Journal of Computational Biology 12 (6): 584-598, 2005
  210. Mtreemix: a software package for learning and using mixture models of mutagenetic trees
    Niko Beerenwinkel, Jörg Rahnenführer, Rolf Kaiser, Daniel Hoffmann, Joachim Selbig, and Thomas Lengauer
    Bioinformatics 21 (9): 2106-2107, 2005
  211. Multiple-Ligand-Based Virtual Screening: Methods and Applications of the MTree Approach
    G. Hessler, M. Zimmermann, H. Matter, A. Evers, T. Naumann, Thomas Lengauer, and M. Rarey
    Journal of Medicinal Chemistry 48 (21): 6575-6584, 2005
  212. Patients with high grade gliomas harboring delections of chromosomes 9p and 10q benefit from temozolomide treatment
    Silke Wemmert, Ralf Ketter, Jörg Rahnenführer, Niko Beerenwinkel, Martin Strowitzki, Wolfgang Feiden, Christian Hartmann, Thomas Lengauer, Florian Stockhammer, Klaus D. Zang, Eckart Meese, Wolf-Ingo Steudel, Andreas von Deimling, and Steffi Urbschat
    Neoplasia 7 (10): 883-893, 2005

  213. Sarcoidosis is associated with a truncating splice site mutation in BTNL2
    Ruta Valentonyte, Jochen Hampe, Klaus Huse, Philip Rosenstiel, Mario Albrecht, Annette Stenzel, Marion Nagy, Karoline I. Gaede, Andre Franke, Robert Haesler, Andreas Koch, Thomas Lengauer, Dirk Seegert, Norbert Reiling, Stefan Ehlers, Eberhard Schwinger, Mathias Platzer, Michael Krawczak, Joachim Müller-Quernheim, Manfred Schürmann, and Stefan Schreiber
    Nature Genetics 37 (4): 357-364, 2005
  214. Structural and functional analysis of a novel mutation of CYP21B in a heterozygote carrier of 21-hydroxylase deficiency
    Jörg Bojunga, Christoph Welsch, Iris Antes, Mario Albrecht, Thomas Lengauer, and Stefan Zeuzem
    Human Genetics 117 (6): 558-564, 2005
  215. Synthesis and Evaluation of Imidazolylmethylenetetrahydronaphthalenes and Imidazolylmethyleneindanes: Potent Inhibitors of Aldosterone Synthase
    Sarah Ulmschneider, Ursula Mueller-Vieira, Markus Mitrenga, Rolf W. Hartmann, S Oberwinkler-Marchais, Christian D. Klein, M. Bureik, R. Bernhardt, Iris Antes, and Thomas Lengauer
    Journal of Medicinal Chemistry 48 (6): 1796-1805, 2005
  216. Synthesis and Evaluation of Pyridylmethylene-tetrahydronaphthalenes and -indanes: Potent and Selective Inhibitors of Aldosterone Synthase (CYP11B2)
    Sarah Ulmschneider, Ursula Mueller-Vieira, Christian D. Klein, Iris Antes, Thomas Lengauer, and Rolf W. Hartmann
    Journal of Medicinal Chemistry 48 (13): 4489-4490, 2005
  217. The HIN domain of IFI-200 proteins consists of two OB folds
    Mario Albrecht, Divaker Choubey, and Thomas Lengauer
    Biochemical and Biophysical Research Communications 327 (3): 679-687, 2005
  218. Towards computational analysis of metabolic profiling data for protein function prediction.
    Priti Talwar, Thomas Lengauer, Jörg Rahnenführer, Elmar Heinzle, VR Velagapudi, and Christoph Wittmann
    In: Proceedings of the Yeast Systems Biology, 6th International Conference on Systems Biology (ICSB 2005), Boston, USA., 2005, 1 p.
  219. BiQ Analyzer: visualization and quality control for DNA methylation data from bisulfite sequencing
    Christoph Bock, Thomas Lengauer, Sabine Reither, Thomas Mikeska, Martina Paulsen, and Jörn Walter
    Bioinformatics 21 (21): 4067-4068, 2005

  220. FlexR - A new tool for predicting the structure of synthetic host-guest complexes
    Andreas Steffen, Andreas Kämper, and Thomas Lengauer
    In: Synthetic Receptors 2005: Second World Congress on Synthetic Receptors, Salzburg, Austria, 2005, O7 p., paper no. O7.. Note: Abstract for an oral presentation at the conference
  221. POEM: Parameter Optimization using Ensemble Methods: Application to target specific scoring functions
    Iris Antes, Christian Merkwirth, and Thomas Lengauer
    Journal of Chemical Information and Modeling 45 (5): 1291-1302, 2005
  222. Arby: Automatic protein structure prediction using profile-profile alignment and confidence measures
    Niklas Öhsen von, Ingolf Sommer, Ralf Zimmer, and Thomas Lengauer
    Bioinformatics 20 (14): 2228-2235, 2004
  223. Association of HCV-related mixed cryoglobulinemia with specific mutational patterns of the HCV E2 protein and CD81 expression on peripheral B lymphocytes
    W.P. Hofmann, E. Herrmann, B. Kronenberger, Christian Merkwirth, Christoph Welsch, Thomas Lengauer, S. Zeuzem, and C. Sarrazin
    Blood 104 (4): 1228-1229, 2004
  224. Automated clustering of ensembles of alternative models in protein structure databases
    Francisco S. Domingues, Jörg Rahnenführer, and Thomas Lengauer
    Protein Engineering Design and Selection 17 (6): 537-543, 2004
  225. Calculating the statistical significance of changes in pathway activity from gene expression data
    Jörg Rahnenführer, Francisco S. Domingues, Jochen Maydt, and Thomas Lengauer
    Statistical Applications in Genetics and Molecular Biology 3 (1): Article 16 p., 2004
  226. Computational Methods For Metabolite Screening
    Priti Talwar, Thomas Lengauer, Jörg Rahnenführer, VR Velagapudi, Christoph Wittmann, and Elmar Heinzle
    In: Proceedings of the 12th International Conference on Intelligent Systems for Molecular Biology + 3rd European Conference on Computational Biology (ISMB/ECCB 2004), Glasgow, UK., 2004, 1 p.
  227. Computational Methods For Metabolite Screening
    Priti Talwar, Thomas Lengauer, Jörg Rahnenführer, VR Velagapudi, Christoph Wittmann, and Elmar Heinzle
    In: Proceedings of the 5th International Conference on Systems Biology (ICSB 2004), Heidelberg, Germany, 2004, 1 p.
  228. Computing the genetic barrier
    Niko Beerenwinkel, Tobias Sing, Martin Däumer, Rolf Kaiser, and Thomas Lengauer
    In: XII International HIV Drug resistance Workshop, Tenerife, Spain, 2004, S125-S125
  229. Development of a new tool for predicting the structure of host-guest complexes
    Andreas Steffen, Andreas Kämper, and Thomas Lengauer
    In: Proceedings of the 2nd Summer School Medicinal Chemistry Regensburg 2004, Regensburg, Germany, 2004, 83 p.
  230. Ensemble methods for classification in cheminformatics
    Christian Merkwirth, H. Mauser, T. Schulz-Gasch, O. Roche, M. Stahl, and Thomas Lengauer
    Journal of Chemical Information and Modeling 44 (6): 1971-1978, 2004
  231. Expression analysis for inflammatory bowel disease
    Andreas Hahn, Christine M. Costello, Tim Lu, Thomas Lengauer, and Stefan Schreiber
    In: Workshop Poster Competition, Saarbrücken, 2004
  232. Genetic variation in DLG5 is associated with inflammatory bowel disease
    Monika Stoll, Brit Corneliussen, Christine M. Costello, Georg H. Waetzig, Bjorn Mellgard, W. Andreas Koch, Philip Rosenstiel, Mario Albrecht, Peter J.P. Croucher, Dirk Seegert, Susanna Nikolaus, Jochen Hampe, Thomas Lengauer, Stefan Pierrou, Ulrich R. Foelsch, Christopher G. Mathew, Maria Lagerstrom-Fermer, and Stefan Schreiber
    Nature Genetics 36 (5): 376-380, 2004
  233. Learning mixtures of localized rules by maximizing the area under the ROC curve
    Tobias Sing, Niko Beerenwinkel, and Thomas Lengauer
    In: ROCAI-2004: 1st International Workshop on ROC Analysis in Artificial Intelligence, Valencia, Spain, 2004, 89-96
  234. Learning multiple evolutionary pathways from cross-sectional data
    Niko Beerenwinkel, Jörg Rahnenführer, Martin Däumer, Daniel Hoffmann, Rolf Kaiser, Joachim Selbig, and Thomas Lengauer
    In: RECOMB 2004 : proceedings of the Eighth Annual International Conference on Research in Computational Molecular Biology, San Diego, USA, March, 27-31, 2004, 36-44
  235. Modelling amorphous Si3B3N7: Structure and elastic properties
    A. Hannemann, J.C. Schön, M. Jansen, H. Putz, and Thomas Lengauer
    Physical Review B 70 (14): 144201-144201, 2004
  236. Novel technologies for virtual screening
    Thomas Lengauer, Christian Lemmen, Matthias Rarey, and M. Zimmermann
    Drug Discovery Today 9 (1): 27-34, 2004
  237. Novel Sm-like proteins with long C-terminal tails and associated methyltransferases
    Mario Albrecht and Thomas Lengauer
    FEBS Letters 569 (1-3): 18-26, 2004
  238. Predicting Protein Structure Classes from Function Predictions
    Ingolf Sommer, Jörg Rahnenführer, Francisco S. Domingues, Ulrik de Lichtenberg, and Thomas Lengauer
    Bioinformatics 20 (5): 770-776, 2004
  239. Protein Structure Prediction and Databases
    Francisco S. Domingues, Thomas Lengauer, and Ingolf Sommer
    In: Nature Encyclopedia of the Human Genome, 2004, 864-867
  240. Structural and functional analysis of ataxin-2 and ataxin-3
    Mario Albrecht, Michael Golatta, Ullrich Wüllner, and Thomas Lengauer
    European Journal of Biochemistry 271 (15): 3155-3170, 2004
  241. Survey on the PABC recognition motif PAM2
    Mario Albrecht and Thomas Lengauer
    Biochemical and Biophysical Research Communications 316 (1): 129-138, 2004
  242. The Helmholtz Network for Bioinformatics: an integrative web portal for bioinformatics resources
    T. Crass, Iris Antes, R. Basekow, P. Bork, Christian Buning, M. Christensen, H. Claußen, C. Ebeling, P. Ernst, V. Gailus-Durner, K.-H. Glatting, R. Gohla, F. Gößling, K. Grote, K. Heidtke, A. Herrmann, S. O Keefe, O. Kießlich, S. Kolibal, J.O. Korbel, Thomas Lengauer, I. Liebich, M. van der Linden, H. Luz, K. Meissner, C. von Mering, T. Mevissen, H.-W. Mewes, H. Michael, M. Mokrejs, T. Müller, H. Pospisil, Matthias Rarey, J.G. Reich, R. Schneider, D. Schomburg, S. Schulze-Kremer, K. Schwarzer, Ingolf Sommer, S. Springstubbe, S. Suhai, G. Thoppae, M. Vingron, J. Warfsmann, T. Werner, D. Wetzler, E. Wingender, and Ralf Zimmer
    Bioinformatics 20: 268-270, 2004
  243. FlexR - Predicting the structure of host-guest complexes
    Andreas Steffen, Andreas Kämper, and Thomas Lengauer
    In: Proceedings of the Annual Meeting of the German Pharmaceutical Society - Joint Meeting 2004 (DPhG 2004), Regensburg, Germany, 2004, 130 p.
  244. Analyzing resistance phenomena in HIV with bioinformatics methods
    Thomas Lengauer
    Bioinformatics 19: 92i p., 2003
  245. Bioinformatikmethoden für die Optimierung antiviraler Kombinationstherapien
    Niko Beerenwinkel, Martin Däumer, Daniel Hoffmann, Rolf Kaiser, Joachim Selbig, and Thomas Lengauer
    In: MPG Jahrbuch, 2003, 481-486
  246. Combinatorial Optimization Techniques for Three-Dimensional Arrangement Problems
    Thomas Lengauer and M. Schäfer
    In: Mathematics - Key Technology for the Future, 2003, 63-73
  247. Disease-associated variants in PYPAF1 and NOD2 result in similar alterations of conserved sequence
    Mario Albrecht, Thomas Lengauer, and Stefan Schreiber
    Bioinformatics 19: 2171-2175, 2003. Note: In press.
  248. Docking into the homology models of CYP11B1 and CYP11B2
    Iris Antes, Thomas Lengauer, Ursula Mueller, Sarah Ulmschneider, and Rolf Hartmann
    In: Proceedings of the German Conference on Bioinformatics 2003, Munich, Germany, October12-14, 2003, 13 p.
  249. Estimating effective drug combinations against drug-resistant mutants from genotypes
    Niko Beerenwinkel, Martin Däumer, Rolf Kaiser, Hauke Walter, Klaus Korn, Daniel Hoffmann, Joachim Selbig, and Thomas Lengauer
    In: Proceedings of the 1st European HIV Drug Resistamce Workshop, Luxembourg, March 6-8, 2003, 2003, 18-18
  250. Geno2pheno: estimating phenotypic drug resistance from HIV-1 genotypes
    Niko Beerenwinkel, Martin Däumer, Mark Oette, Klaus Korn, Daniel Hoffmann, Rolf Kaiser, Thomas Lengauer, Joachim Selbig, and Hauke Walter
    Nucleic Acids Research 31 (13): 3850-3855, 2003
  251. Identification of mammalian orthologs associates PYPAF5 with distinct functional roles
    Mario Albrecht, Francisco S. Domingues, Stefan Schreiber, and Thomas Lengauer
    FEBS Letters 538 (1-3): 173-177, 2003
  252. Methods for optimizing antiviral combination therapies
    Niko Beerenwinkel, Thomas Lengauer, Martin Däumer, Rolf Kaiser, Hauke Walter, Klaus Korn, Daniel Hoffmann, and Joachim Selbig
    Bioinformatics 19 (Supplement): i16-i25, 2003
  253. Microarrays: How many do you need?
    Alexander Zien, Juliane Fluck, Ralf Zimmer, and Thomas Lengauer
    Journal of Computational Biology 10 (3-4): 653-667, 2003
  254. New inhibitors of human cathepsin G identified by surface display library screening and peptide-protein docking
    Joachim Jose, Dirk Betschieder, Somak Ray, Thomas Lengauer, and D Zangen
    In: 7th International Symposium on Pharmaceutical Sciences (ISOPS-7), Ankara, Turkey, June, 24 - June, 27, 2003, 46-49
  255. Parallel "go with the winners algorithms" in Distributed Memory Models
    M. Peinado and Thomas Lengauer
    Journal of Parallel and Distributed Processing 63 (9): 801-814, 2003
  256. Protein Function from Sequence and Structure Data
    Francisco S. Domingues and Thomas Lengauer
    Applied Bioinformatics 2 (1): 3-12, 2003
  257. Pyranose oxidase identified as a member of the GMC oxidoreductase family
    Mario Albrecht and Thomas Lengauer
    Bioinformatics 19 (10): 1216-1220, 2003
  258. Simple consensus procedures are effective and sufficient in secondary structure prediction
    Mario Albrecht, Silvio C.E. Tosatto, Thomas Lengauer, and Giorgio Valle
    Protein Engineering 16 (7): 459-462, 2003
  259. Software tool for automated processing of 13C labeling data from mass spectrometry data
    Priti Talwar, Christoph Wittmann, Thomas Lengauer, and Elmar Heinzle
    BioTechniques 35: 1214-1215, 2003
  260. Structural localization of disease-associated sequence variations in the NACHT and LRR domains of PYPAF1 and NOD2
    Mario Albrecht, Francisco S. Domingues, Stefan Schreiber, and Thomas Lengauer
    FEBS Letters 554 (3): 520-528, 2003
  261. Structural modeling of ataxin-3 reveals distant homology to adaptins
    Mario Albrecht, Daniel Hoffmann, Bernd O. Evert, Ina Schmitt, Ullrich Wüllner, and Thomas Lengauer
    Proteins: Structure, Function, and Genetics 50 (2): 355-370, 2003
  262. Tenofovir resistance and resensitization
    Katharina Wolf, Hauke Walter, Niko Beerenwinkel, Wilco Keulen, Rolf Kaiser, Daniel Hoffmann, Thomas Lengauer, Joachim Selbig, Anne-Mieke Vandamme, Klaus Korn, and Barbara Schmidt
    Antimicrobial Agents and Chemotherapy 47 (11): 3478-3484, 2003
  263. Towards cellular function through metabolite screening
    Priti Talwar, Thomas Lengauer, Christoph Wittmann, Vidya Mangadu, and Elmar Heinzle
    In: Proceedings of the 3rd Annual Conference on Metabolic Profiling: Pathways in Discovery, Princeton, New Jersey, 2003, 7 p., paper no. 7.
  264. Tree models for the evolution of drug resistance
    Niko Beerenwinkel, Rolf Kaiser, Jörg Rahnenführer, Martin Däumer, Daniel Hoffmann, Joachim Selbig, and Thomas Lengauer
    In: XII International HIV Drug resistance Workshop, Los Cabos, Mexico, June 10 - June 14, 2003, S107-S107
  265. Virtual Screening for novel Urease Inhibitors
    Andreas Kämper and Thomas Lengauer
    In: Proceedings of the International Workshop on New Approaches in Drug Design & Discovery, Marburg, Germany, 2003, 39 p.
  266. ECLIPPSE: Environment for Chemical Library Inspection, Pre- and Postprocessing, and Screening Evaluation. User Guide
    Andreas Kämper and Thomas Lengauer

  267. A hypergraph-based method for unification of existing protein structure- and sequence-families
    Jan Freudenberg, Ralf Zimmer, Daniel Hanisch, and Thomas Lengauer
    In Silico Biology 2 (3): 339 - 349, 2002
  268. Ausbildung im Bereich Bioinformatik
    Thomas Lengauer
    Ernst & Young Report Biotechnologie, Segmentreport Bioinformatik 1: 57-58, 2002
  269. Co-clustering of biological networks and gene expression data
    Daniel Hanisch, Alexander Zien, Ralf Zimmer, and Thomas Lengauer
    In: Proceedings of the Tenth Conference on Intelligent Systems for Molecular Biology (ISMB 2002), Alberta, Canada, 2002, 145-154
  270. Confidence measures for protein fold recognition
    Ingolf Sommer, Alexander Zien, Niklas Öhsen von, Ralf Zimmer, and Thomas Lengauer
    Bioinformatics 18 (6): 802-812, 2002
  271. Diversity and complexity of HIV-1drug resistance: A bioinformatics approach to predicting phenotype from genotype
    Niko Beerenwinkel, Barbara Schmidt, Hauke Walter, Rolf Kaiser, Thomas Lengauer, Daniel Hoffmann, Klaus Korn, and Joachim Selbig
    Proceedings of the National Academy of Sciences 99 (12): 8271-8276, 2002
  272. Docking of Bacterial Cell-Wall Fragments into Glycopeptide Antibiotics
    Andreas Kämper, Joannis Apostolakis, and Thomas Lengauer
    In: From Genes to Drugs via Crystallography: 33rd crytallographic course at the E. Majorana Center, Erice, Italy, 2002, 49 p.
  273. Docking of Ligands into Molecular Tweezers and Molecular Clips
    Andreas Kämper and Thomas Lengauer
    In: Workshop of the SFB 624 'Templates', Walberberg, Germany, 2002
  274. Expression analysis for inflammatory bowel disease
    Andreas Hahn, Christine M. Costello, Tim Lu, Thomas Lengauer, and Stefan Schreiber
    In: Proceedings of the n?th Conference on, 2002

  275. Flexible docking under pharmacophore type constraints
    Sally A. Hindle, Matthias Rarey, Christian Buning, and Thomas Lengauer
    Journal of Computer-Aided Molecular Design 16: 129-149, 2002
  276. Geno2pheno is predictive of short-term virological response
    Niko Beerenwinkel, Thomas Lengauer, Martin Däumer, S. Sierra, Barbara Schmidt, Hauke Walter, Klaus Korn, Mark Oette, Gerd Fätkenheuer, J. Rockstroh, Daniel Hoffmann, Rolf Kaiser, and Joachim Selbig
    In: Proceedings from the 5th International Workshop on HIV Drug Resistance & Treatment Strategies, Scotsdale, Arizona, 2002, 74-74, paper no. 89.
  277. Improving fold recognition of protein threading by experimental distance constraints
    Mario Albrecht, Daniel Hanisch, Ralf Zimmer, and Thomas Lengauer
    In Silico Biology 2 (3): 325-337, 2002
    [PDF: Download: mario albrecht.pdf]
  278. Microarrays: How Many Do You Need?
    Alexander Zien, Juliane Fluck, Ralf Zimmer, and Thomas Lengauer
    In: Proceedings of the Sixth Annual Conference on Research in Computational Molecular Biology (RECOMB2002), Washington, USA, 2002, 321-330
  279. Preface: Special RECOMB 2001 Issue
    Thomas Lengauer
    Journal of Computational Biology 9 (2): 147-148, 2002
  280. ProML - the Protein Markup Language for specification of protein sequences, structures and families
    Daniel Hanisch, Ralf Zimmer, and Thomas Lengauer
    In Silico Biology 2 (3): 313 - 324, 2002
  281. Quantitative phenotype prediction by support vector machines
    Niko Beerenwinkel, Thomas Lengauer, Barbara Schmidt, Hauke Walter, Rolf Kaiser, Daniel Hoffmann, Klaus Korn, and Joachim Selbig
    In: Proceedings from the 5th International Workshop on HIV Drug resistance & Treatment Strategies, Scotsdale, Arizona, 2002, 97 p.
  282. Automated Layout Generation and Wiring Area Estimation for 3D Electronic Modules
    M. Schäfer and Thomas Lengauer
    ASME Journal of Machanical Design 123 (3): 330-336, 2001
  283. Bioinformatik an der Schwelle zur postgenomischen Ära
    Thomas Lengauer
    In: Was wissen wir, wenn wir das menschliche Genom kennen, 2001, 56-62
  284. Centralization: A biologically sensible method for the normalization of gene expression data
    Alexander Zien, T. Aigner, Ralf Zimmer, and Thomas Lengauer
    Bioinformatics 17: 323S-331S, 2001. Note: Proceedings published as special journal issue: Proceedings of the 9th International Conference on Intelligent Systems for Molecular Biology (ISMB2001)
  285. Derivation of a scoring function for crystal structure prediction
    Joannis Apostolakis, D. Hofmann, and Thomas Lengauer
    Acta Crystallographica A57: 442-450, 2001
  286. Docking of Ligands into Artificial Receptors
    Andreas Kämper, Joannis Apostolakis, Matthias Rarey, Christel Maria Marian, and Thomas Lengauer
    Poster at the Annual Meeting of the German CHemical Society, Würzburg, Germany
  287. Docking of Ligands into Artificial Receptors
    Andreas Kämper, Joannis Apostolakis, Matthias Rarey, Christel Maria Marian, and Thomas Lengauer
    In: Electronically Excited Molecules: Structure and Dynamics, 37th Symposium for Theoretical Chemistry, Bad Herrenalb, Germany, Sep. 23-29, 2001, 2001, P76 p.
  288. FlexE: Efficient Molecular Docking Considering Protein Structure Variations
    C. Claussen, Christian Buning, Matthias Rarey, and Thomas Lengauer
    Journal of Molecular Biology 308 (2): 377-395, 2001
  289. Geno2pheno: a new machine learning approach to predicting phenotypic drug resistance from genotype
    Thomas Lengauer, Niko Beerenwinkel, B. Schmidt, H. Walter, R. Kaiser, D. Hoffmann, K. Korn, and J. Selbig
    Antiviral Therapy 6 (Supp. 1): 104 p., 2001
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