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MPI-INF D3 Publications

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Your search returned the following 37 documents:

  1. 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
  2. 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
  3. 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
  4. 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
  5. Added value of deep sequencing relative to population sequencing in heavily pre-treated HIV-1-infected subjects
    Francisco Codoner, Christian Pou, Alexander Thielen, Federico García, Rafael Delgado, David Dalmau, Miguel Álvarez-Tejado, Lidia Ruiz, Bonaventura Clotet, and Roger Paredes
    PLoS One 6 (5): e19461,1-e19461,5, 2011
  6. 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
  7. Deep Sequencing to Infer HIV-1 Co-Receptor Usage: Application to Three Clinical Trials of Maraviroc in Treatment-Experienced Patients
    Luke C. Swenson, Theresa Mo, Winnie W. Y. Dong, Xiaoyin Zhong, Conan K. Woods, Mark A. Jensen, Alexander Thielen, Douglass Chapman, Marilyn Lewis, Ian James, Jayvant Heera, Hernan Valdez, and P. Richard Harrigan
    The Journal of Infectious Diseases 203 (3): 237-245, 2011
  8. Deep V3 sequencing for HIV type 1 tropism in treatment-naive patients: a reanalysis of the MERIT trial of maraviroc.
    Luke C Swenson, Theresa Mo, Winnie WY Dong, Xiaoyin Zhong, Conan K Woods, Alexander Thielen, Mark A Jensen, David JHF Knapp, Douglass Chapman, Marilyn Lewis, Ian James, Jayvant Heera, Hernan Valdez, and P Richard Harrigan
    Clinical Infectious Diseases 53 (7): 732-742, 2011
  9. Genotypic Analysis of HIV-1 Coreceptor Usage
    Alexander Thielen
    Doctoral dissertation, Universität des Saarlandes, 2011
  10. 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
  11. High Concordance between the Position-Specific Scoring Matrix and Geno2pheno Algorithms for Genotypic Interpretation of HIV-1 Tropism: V3 Length as the Major Cause of Disagreement
    Eduardo Seclen, Vincente Soriano, Maria M González, Sagrario Gómez, Alexander Thielen, and Eva Poveda
    Journal of Clinical Microbiology 49: 3380-3382, 2011
  12. In-depth analysis of G-to-A hypermutation rate in HIV-1 env DNA induced by endogenous APOBEC3 proteins using massively parallel sequencing
    Stefanie Knoepfel, Francesca Di Giallonardoc, Martin Däumer, Alexander Thielen, and Karin J Metzner
    Journal of Virological Methods 71 (2): 329-338, 2011
  13. 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
  14. 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
  15. Chasing the AIDS Virus
    Thomas Lengauer, André Altmann, Alexander Thielen, and Rolf Kaiser
    Communications of the ACM 53 (3): 66-74, 2010
  16. Decreased HIV diversity after allogeneic stem cell transplantation of an HIV-1 infected patient: a case report.
    Christel Kamp, Timo Wolf, Ignacio G Bravo, Benjamin Kraus, Birgit Krause, Britta Neumann, Gudrun Winskowsky, Alexander Thielen, Albrecht Werner, and Barbara S Schnierle
    Virology Journal 7 (1): 55,1-55,9, 2010
  17. Dynamic escape of pre-existing raltegravir-resistant HIV-1 from raltegravir selection pressure
    Francisco M Codoñer, Christian Pou, Alexander Thielen, Federico García, Rafael Delgado, David Dalmau, José Ramon Santos, Maria José Buzón, Javier Alvarez-Tejado, Miguel Martínez-Picado, Bonaventura Clotet, Lidia Ruiz, and Roger Paredes
    Antiviral Research 88 (3): 281-286, 2010
  18. Genotypic determination of HIV-1 tropism in the clinical setting
    Luke C. Swenson, Richard Boehme, Alexander Thielen, Rachel A. McGovern, and P. Richard Harrigan
    HIV Therapy 4 (3): 293-303, 2010
  19. Improved detection of CXCR4-using HIV by V3 genotyping: application of population-based and "deep" sequencing to plasma RNA and proviral DNA
    Luke C. Swenson, Andrew Moores, Andrew J. Low, Alexander Thielen, Winnie Dong, Conan Woods, Mark A. Jensen, Brian Wynhoven, Dennison Chan, Christopher Glascock, and P. Richard Harrigan
    Journal of Acquired Immune Deficiency Syndromes 54 (5): 506-510, 2010
  20. 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
  21. 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
  22. Population-based V3 genotypic tropism assay: a retrospective analysis using screening samples from the A4001029 and MOTIVATE studies
    Rachel A McGovern, Alexander Thielen, Theresa Mo, Winnie Dong, Conan K Woods, Douglass Chapman, Marilyn Lewis, Ian James, Jayvant Heera, Hernan Valdez, and P Richard Harrigan
    AIDS 24 (16): 2517-2525, 2010
  23. Bioinformatische Unterstützung der Auswahl von HIV Therapien
    Thomas Lengauer, André Altmann, and Alexander Thielen
    Informatik Spektrum 32 (2): 320-331, 2009
  24. 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.
  25. 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
  26. Screening for HIV tropism using population-based V3 genotypic analysis: a retrospective outcome analysis using stored plasma screening samples from MOTIVATE-1
    P Richard Harrigan, Rachel McGovern, Winnie Dong, Alexander Thielen, Mark Jensen, Theresa Mo, Douglas Chapman, Marilyn Lewis, Ian James, and Hernan Valdez
    In: Abstracts presented at the XVIII International HIV Drug Resistance Workshop : Basic Principles & Clinical Implications, Fort Myers, USA, 2009, A17-A17, paper no. Abstract 15.
  27. 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
  28. 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.
  29. 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.
  30. 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
  31. Improved detection of X4 virus by V3 genotyping: application to plasma RNA and proviral DNA
    Andrew Moores, Alexander Thielen, Winnie Dong, Andrew J. Low, Conan Woods, Mark Jensen, Brian Wynhoven, Dennison Chan, Christopher Glascock, and P Richard Harrigan
    In: Antiviral Therapy, Sitges, Spain, 2008, A99 p.
  32. 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.
  33. 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
  34. 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.
  35. Prediction of linear B-cell epitopes and MHC class II binding peptides
    Alexander Thielen
    Master's thesis, Eberhardt-Karls-Universität Tübingen, 2006
  36. Bioinformatics prediction of HIV coreceptor usage
    Thomas Lengauer, Oliver Sander, Saleta Sierra, Alexander Thielen, and Rolf Kaiser
    Nature Biotechnology 25 (12): 1407-1410, 2007
  37. Genotypic coreceptor analysis.
    Saleta Sierra, Rolf Kaiser, Alexander Thielen, and Thomas Lengauer
    European Journal of Medical Research 12 (9): 453-462, 2007