Research Topics
| Tobias SingSummaryAffiliation: Max-Planck-Institute for Informatics Country: Germany Publications
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Detail Information
Publications
ROCR: visualizing classifier performance in RTobias Sing
Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarbrucken, Germany
Bioinformatics 21:3940-1. 2005..AVAILABILITY: http://rocr.bioinf.mpi-sb.mpg.de. ROCR can be used under the terms of the GNU General Public License. Running within R, it is platform-independent. CONTACT: tobias.sing@mpi-sb.mpg.de...- Predicting HIV coreceptor usage on the basis of genetic and clinical covariatesTobias 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... - Improved prediction of response to antiretroviral combination therapy using the genetic barrier to drug resistanceAndre 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... - Advantages of predicted phenotypes and statistical learning models in inferring virological response to antiretroviral therapy from HIV genotypeAndre 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... - Bioinformatics-assisted anti-HIV therapyThomas 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... 
Structural descriptors of gp120 V3 loop for the prediction of HIV-1 coreceptor usageOliver 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...- Estimating HIV evolutionary pathways and the genetic barrier to drug resistanceNiko 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... - Determining human immunodeficiency virus coreceptor use in a clinical setting: degree of correlation between two phenotypic assays and a bioinformatic modelKatharina 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... 
CD4-dependent characteristics of coreceptor use and HIV type 1 V3 sequence in a large population of therapy-naive individualsAndrew 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...- Fifteen years of env C2V3C3 evolution in six individuals infected clonally with human immunodeficiency virus type 1Bernd 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... - Current V3 genotyping algorithms are inadequate for predicting X4 co-receptor usage in clinical isolatesAndrew 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... - HIV-1 gp120 V3 loop for structure-based drug designSuzanne 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... - Involvement of novel human immunodeficiency virus type 1 reverse transcriptase mutations in the regulation of resistance to nucleoside inhibitorsValentina Svicher
Department of Experimental Medicine, University of Rome Tor Vergata, Via Montpellier 1, 00133 Rome, Italy
J Virol 80:7186-98. 2006.... - Stable coreceptor usage of HIV in patients with ongoing treatment failure on HAARTClara 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... - Compensatory mutations at the HIV cleavage sites p7/p1 and p1/p6-gag in therapy-naive and therapy-experienced patientsJens 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... - Characterization and structural analysis of novel mutations in human immunodeficiency virus type 1 reverse transcriptase involved in the regulation of resistance to nonnucleoside inhibitorsFrancesca 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... - Computational methods for the design of effective therapies against drug resistant HIV strainsNiko 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...