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MPI-INF D3 Publications

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Your search returned the following 83 documents:

  1. 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.
  2. 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.
  3. 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.
  4. 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.
  5. 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
  6. High frequency of complex mutational patterns in lamivudine resistant hepatitis B virus isolates
    Maria Neumann-Fraune, Bastian Beggel, Herbert Pfister, Rolf Kaiser, and Jens Verheyen
    Journal of Medical Virology 200 (1): 39-49, 2013
  7. 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
  8. 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
  9. Efficacy of antiretroviral therapy switch in HIV-infected patients: A 10-year analysis of the EuResist cohort
    Mark Oette, Eugen Schulter, Michal Rosen-Zvi, Yardena Peres, Maurizio Zazzi, Anders Sonnerborg, Daniel Struck, Andre Altmann, and Rolf Kaiser
    Intervirology 55 (2): 160-166, 2012
  10. 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]
  11. 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
  12. 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
  13. 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
  14. HIV-GRADE: A Publicly Available, Rules-Based Drug Resistance Interpretation Algorithm Integrating Bioinformatic Knowledge
    Martin Obermeier, Alejandro Pironti, Thomas Berg, Patrick Braun, Martin Däumer, Josef Eberle, Robert Ehret, Rolf Kaiser, Niels Kleinkauf, Klaus Korn, Claudia Kücherer, Harm Müller, Christian Noah, Martin Stürmer, Alexander Thielen, Eva Wolf, and Hauke Walter
    Intervirology 55: 102-107, 2012
  15. HIV2EU: supporting standardized HIV-2 drug resistance interpretation in Europe
    Martin Obermeier, Ricardo Camacho, Charlotte Charpentier, Diane Deschamps, Joseph Eberle, Lutz Gürtler, Jean Ruelle, Alejandro Pironti, Francoise Brun-Veziet, Martin Stürmer, and Rolf Kaiser
    In: Journal of the International AIDS Society, Glasgow, UK, 2012, 135 p.
  16. 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
  17. 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
  18. 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
  19. 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
  20. 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
  21. 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

  22. 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
  23. 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
  24. 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
  25. 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
  26. Antiretroviral Therapy Optimisation without Genotype Resistance Testing: A Perspective on Treatment History Based Models
    Mattia C. F. Prosperi, Michal Rosen-Zvi, Andre Altmann, Maurizio Zazzi, Simona Di Giambenedetto, Rolf Kaiser, Eugen Schülter, Daniel Struck, Peter Sloot, David A. van de Vijver, Anne-Mieke Vandamme, and Anders Sönnerborg
    PLoS ONE 5 (10): e13753,1-e13753,8, 2010
  27. Chasing the AIDS Virus
    Thomas Lengauer, André Altmann, Alexander Thielen, and Rolf Kaiser
    Communications of the ACM 53 (3): 66-74, 2010
  28. Hepatitis B virus reverse transcriptase sequence variant database for sequence analysis and mutation discovery
    Soo-Yon Rhee, Severin Margeridon-Thermet, Mindie Nguyen, Tommy Liu, Ron Kagan, Bastian Beggel, Jens Verheyen, Rolf Kaiser, and Robert Shafer
    Antiviral Research 88 (3): 269-275, 2010

  29. 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
  30. 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
  31. 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
  32. 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
  33. 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
  34. Computerjagd auf das AIDSVIRUS
    Thomas Lengauer and Rolf Kaiser
    Spektrum der Wissenschaft 08: 62-67, 2009
  35. 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.
  36. Evolution of raltegravir resistance during therapy
    Nadine Sichtig, Saleta Sierra, Rolf Kaiser, Martin Däumer, Stefan Reuter, Eugen Schülter, André Altmann, Gerd Fätkenheuer, Ulf Dittmer, Herbert Pfister, and Stefan Esser
    Journal of antimicrobial chemotherapy 64 (1): 25-32, 2009
  37. 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
  38. 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
  39. Resistenzbestimmung
    Thomas Lengauer, S. Sierra, and Rolf Kaiser
    MMW Fortschritte in der Medizin 151 (18): 74-75, 2009
  40. 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
  41. 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
  42. Determination of HIV-1 co-receptor usage in German patients – comparison of genotypic methods with the TROFILE® phenotypic assay
    Martin Obermeier, Thomas Berg, Nadine Sichtig, Patrick Braun, Martin Däumer, Hauke Walter, Christian Noah, Eva Wolf, Harm Müller, Martin Stürmer, Alexander Thielen, and Rolf Kaiser
    In: Abstracts of the Ninth International Congress on Drug Therapy in HIV Infection, Glasgow, UK, 2008, 123 p.
  43. Determination of HIV-1 coreceptor usage in German patients - comparison of genotypic methods with the TROFILE phenotypic assay
    Martin Obermeier, Nadine Sichtig, Patrick Braun, Martin Däumer, Hauke Walter, Christian Noah, Eva Wolf, Harm Müller, Martin Stürmer, Rolf Kaiser, and Alexander Thielen
    In: Antiviral Therapy, Sitges, Spain, 2008, A112 p.
  44. 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
  45. 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.
  46. 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
  47. 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.
  48. Relevance of HIV gag cleavage site mutations in failures of protease inhibitor therapies
    Jens Verheyen, Andre Altmann, Elena Knops, Eugen Schülter, Nadine Sichtig, Stefan Reuter, Gerd Fätkenheuer, Herbert Pfister, and Rolf Kaiser
    In: Antiviral Therapy, Sitges, Spain, 2008, A53 p.
  49. 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
  50. 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.
  51. 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.
  52. Bioinformatics prediction of HIV coreceptor usage
    Thomas Lengauer, Oliver Sander, Saleta Sierra, Alexander Thielen, and Rolf Kaiser
    Nature Biotechnology 25 (12): 1407-1410, 2007
  53. 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
  54. Genotypic coreceptor analysis.
    Saleta Sierra, Rolf Kaiser, Alexander Thielen, and Thomas Lengauer
    European Journal of Medical Research 12 (9): 453-462, 2007

  55. 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
  56. 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.
  57. 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
  58. 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
  59. 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
  60. 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
  61. Compensatory mutations at the HIV cleavage sites p7/p1 and p1/p6-gag in therapy-naive and therapy-experienced patients
    Jens Verheyen, Elena Litau, Tobias Sing, Martin Däumer, Melanie Balduin, Mark Oette, Gerd Fätkenheuer, Jürgen K. Rockstroh, Ulrike Schuldenzucker, Daniel Hoffmann, Herbert Pfister, and Rolf Kaiser
    Antiviral Therapy 11 (7): 879-887, 2006
  62. 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
  63. 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
  64. 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
  65. 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
  66. Evolution of HIV resistance during treatment interruption in experienced patients and after restarting a new therapy
    Melanie Balduin, Niko Beerenwinkel, Saleta Sierra, Martin Däumer, Jürgen Rockstroh, Mark Oette, Gerd Fätkenheuer, Bernd Kupfer, Daniel Hoffmann, Joachim Selbig, Herbert Pfister, and Rolf Kaiser
    J Clin Virol 34 (4): 277-287, 2005
  67. 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
  68. 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
  69. 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
  70. Stable coreceptor usage of HIV-1 in patients with ongoing treatment failure on HAART
    Rolf Kaiser, Ibo Boussaad, C. Lehmann, Martin Däumer, Tobias Sing, N. Schmeisser, C. Wyen, and Gerd Fätkenheuer
    In: Proceedings of the 3rd European HIV Drug Resistance Workshop, Athens, Greece, 2005
  71. 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
  72. 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
  73. 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
  74. 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
  75. 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
  76. 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
  77. 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
  78. 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
  79. 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
  80. 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.
  81. 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.
  82. Geno2pheno: A system for the interpretation of genotypic HIV Drug resistance tests
    Niko Beerenwinkel, Barbara Schmidt, Hauke Walter, Rolf Kaiser, Thomas Lengauer, Daniel Hoffmann, Klaus Korn, and Joachim Selbig
    IEEE Intelligent Systems 16 (6): 35-41, 2001
  83. Neue Wege zur Optimierung von Anti-HIV Therapien
    Niko Beerenwinkel, Martin Däumer, Daniel Hoffmann, Rolf Kaiser, Klaus Korn, Thomas Lengauer, Barbara Schmidt, Hauke Walter, and Joachim Selbig
    BIOforum 24 (12): 912-914, 2001