Tobias Sing

Summary

Affiliation: Max-Planck-Institute for Informatics
Country: Germany

Publications

  1. ncbi request reprint ROCR: visualizing classifier performance in R
    Tobias Sing
    Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarbrucken, Germany
    Bioinformatics 21:3940-1. 2005
  2. ncbi request reprint Predicting HIV coreceptor usage on the basis of genetic and clinical covariates
    Tobias Sing
    Max Planck Institute for Informatics, Saarbrucken, Germany
    Antivir Ther 12:1097-106. 2007
  3. ncbi request reprint Improved prediction of response to antiretroviral combination therapy using the genetic barrier to drug resistance
    Andre Altmann
    Max Planck Institute for Informatics, Saarbrucken, Germany
    Antivir Ther 12:169-78. 2007
  4. ncbi request reprint Advantages of predicted phenotypes and statistical learning models in inferring virological response to antiretroviral therapy from HIV genotype
    Andre Altmann
    Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarbr product operatorcken, Germany
    Antivir Ther 14:273-83. 2009
  5. ncbi request reprint Bioinformatics-assisted anti-HIV therapy
    Thomas Lengauer
    Max Planck Institute for Informatics, Stuhlsatzenhausweg 85, 66123 Saarbrucken, Germany
    Nat Rev Microbiol 4:790-7. 2006
  6. pmc Structural descriptors of gp120 V3 loop for the prediction of HIV-1 coreceptor usage
    Oliver Sander
    Max Planck Institute for Informatics, Saarbrucken, Germany
    PLoS Comput Biol 3:e58. 2007
  7. ncbi request reprint Estimating HIV evolutionary pathways and the genetic barrier to drug resistance
    Niko Beerenwinkel
    Max Planck Institute for Informatics, Saarbrucken, Germany
    J Infect Dis 191:1953-60. 2005
  8. pmc Determining human immunodeficiency virus coreceptor use in a clinical setting: degree of correlation between two phenotypic assays and a bioinformatic model
    Katharina Skrabal
    INSERM U552 Recherche Antivirale, Paris, France
    J Clin Microbiol 45:279-84. 2007
  9. doi request reprint CD4-dependent characteristics of coreceptor use and HIV type 1 V3 sequence in a large population of therapy-naive individuals
    Andrew J Low
    B C Centre for Excellence in HIV AIDS, St Paul s Hospital, Vancouver, British Columbia, Canada
    AIDS Res Hum Retroviruses 24:219-28. 2008
  10. ncbi request reprint Fifteen years of env C2V3C3 evolution in six individuals infected clonally with human immunodeficiency virus type 1
    Bernd Kupfer
    Institute for Medical Microbiology, Immunology, and Parasitology, University of Bonn, Bonn, Germany
    J Med Virol 79:1629-39. 2007

Detail Information

Publications17

  1. ncbi request reprint ROCR: visualizing classifier performance in R
    Tobias Sing
    Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarbrucken, Germany
    Bioinformatics 21:3940-1. 2005
    ..Being equipped with only three commands and reasonable default values for optional parameters, ROCR combines flexibility with ease of usage...
  2. ncbi request reprint Predicting HIV coreceptor usage on the basis of genetic and clinical covariates
    Tobias Sing
    Max Planck Institute for Informatics, Saarbrucken, Germany
    Antivir Ther 12:1097-106. 2007
    ..We compared several statistical learning methods for the prediction of HIV coreceptor use from clonal HIV third hypervariable (V3) loop sequences, and evaluated and improved their effectiveness on clinical samples...
  3. ncbi request reprint Improved prediction of response to antiretroviral combination therapy using the genetic barrier to drug resistance
    Andre Altmann
    Max Planck Institute for Informatics, Saarbrucken, Germany
    Antivir Ther 12:169-78. 2007
    ..The virus's evolutionary potential for escaping from drug pressure is explored as an additional predictor...
  4. ncbi request reprint Advantages of predicted phenotypes and statistical learning models in inferring virological response to antiretroviral therapy from HIV genotype
    Andre Altmann
    Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarbr product operatorcken, Germany
    Antivir Ther 14:273-83. 2009
    ..The utility of an intermediate step of predicting in vitro drug susceptibility is currently controversial. Here, we provide a retrospective comparison of approaches using either genotype or predicted phenotypes alone, or in combination...
  5. ncbi request reprint Bioinformatics-assisted anti-HIV therapy
    Thomas Lengauer
    Max Planck Institute for Informatics, Stuhlsatzenhausweg 85, 66123 Saarbrucken, Germany
    Nat Rev Microbiol 4:790-7. 2006
    ..With several free and commercial software services available, computational advice is rapidly gaining acceptance as an important element of rational decision-making in the treatment of HIV infection...
  6. pmc Structural descriptors of gp120 V3 loop for the prediction of HIV-1 coreceptor usage
    Oliver Sander
    Max Planck Institute for Informatics, Saarbrucken, Germany
    PLoS Comput Biol 3:e58. 2007
    ..The proposed method constitutes the first approach to an improved prediction of coreceptor usage based on an original integration of structural bioinformatics methods with statistical learning...
  7. ncbi request reprint Estimating HIV evolutionary pathways and the genetic barrier to drug resistance
    Niko Beerenwinkel
    Max Planck Institute for Informatics, Saarbrucken, Germany
    J Infect Dis 191:1953-60. 2005
    ..The evolution of drug-resistant viruses challenges the management of human immunodeficiency virus (HIV) infections. Understanding this evolutionary process is important for the design of effective therapeutic strategies...
  8. pmc Determining human immunodeficiency virus coreceptor use in a clinical setting: degree of correlation between two phenotypic assays and a bioinformatic model
    Katharina Skrabal
    INSERM U552 Recherche Antivirale, Paris, France
    J Clin Microbiol 45:279-84. 2007
    ..quot; X4 (CXCR4-using) minority species in clinically derived samples likely complicate the interpretation of both phenotypic and genotypic assessments of HIV tropism...
  9. doi request reprint CD4-dependent characteristics of coreceptor use and HIV type 1 V3 sequence in a large population of therapy-naive individuals
    Andrew J Low
    B C Centre for Excellence in HIV AIDS, St Paul s Hospital, Vancouver, British Columbia, Canada
    AIDS Res Hum Retroviruses 24:219-28. 2008
    ..The ability to predict X4 virus using genotypic determinants at positions 25 and 6-8 of the V3 loop is CD4 dependent, while position 11 appears to be CD4 independent...
  10. ncbi request reprint Fifteen years of env C2V3C3 evolution in six individuals infected clonally with human immunodeficiency virus type 1
    Bernd Kupfer
    Institute for Medical Microbiology, Immunology, and Parasitology, University of Bonn, Bonn, Germany
    J Med Virol 79:1629-39. 2007
    ..These common changes within the V3 loop are likely to be enforced by HIV-1 specific immune response...
  11. ncbi request reprint Current V3 genotyping algorithms are inadequate for predicting X4 co-receptor usage in clinical isolates
    Andrew J Low
    B C Centre for Excellence in HIV AIDS St Paul s Hospital, Vancouver, British Columbia, Canada
    AIDS 21:F17-24. 2007
    ..Integrating CCR5 antagonists into clinical practice would benefit from accurate assays of co-receptor usage (CCR5 versus CXCR4) with fast turnaround and low cost...
  12. ncbi request reprint HIV-1 gp120 V3 loop for structure-based drug design
    Suzanne Sirois
    Universite du Quebec a Montreal, Chemistry Department, Montreal, Quebec, Canada H3C 3P8
    Curr Protein Pept Sci 6:413-22. 2005
    ..The third variable (V3) loop of gp120, crucially involved in all these aspects, will be a major focus of this review...
  13. pmc Involvement of novel human immunodeficiency virus type 1 reverse transcriptase mutations in the regulation of resistance to nucleoside inhibitors
    Valentina Svicher
    Department of Experimental Medicine, University of Rome Tor Vergata, Via Montpellier 1, 00133 Rome, Italy
    J Virol 80:7186-98. 2006
    ....
  14. ncbi request reprint Stable coreceptor usage of HIV in patients with ongoing treatment failure on HAART
    Clara Lehmann
    Department of Internal Medicine, University of Cologne, Germany
    J Clin Virol 37:300-4. 2006
    ..Disease progression in HIV infection has been associated with switch of viral coreceptor usage from CCR5 to CXCR4...
  15. ncbi request reprint Compensatory mutations at the HIV cleavage sites p7/p1 and p1/p6-gag in therapy-naive and therapy-experienced patients
    Jens Verheyen
    Institute of Virology, University of Cologne, Cologne, Germany
    Antivir Ther 11:879-87. 2006
    ..Protease (PR) cleavage site (CS) mutations could compensate for impaired replication capacity of drug-resistant viruses...
  16. pmc Characterization and structural analysis of novel mutations in human immunodeficiency virus type 1 reverse transcriptase involved in the regulation of resistance to nonnucleoside inhibitors
    Francesca Ceccherini-Silberstein
    Department of Experimental Medicine, University of Rome Tor Vergata, Via Montpellier 1, 00133 Rome, Italy
    J Virol 81:11507-19. 2007
    ..Mutations beyond those currently known to confer resistance should be considered for a better prediction of clinical response to reverse transcriptase inhibitors and for the development of more efficient new-generation NNRTIs...
  17. ncbi request reprint Computational methods for the design of effective therapies against drug resistant HIV strains
    Niko Beerenwinkel
    Department of Mathematics, University of California, Berkeley, CA, USA
    Bioinformatics 21:3943-50. 2005
    ..We have developed several computational methods whose combined use can support the design of optimal antiretroviral therapies based on viral genomic data...