References

Relevant publications by our group:

  1. Lengauer T, Sander O, Sierra S, Thielen A, Kaiser R. Bioinformatics prediction of HIV coreceptor usage.. Nat Biotechnol., 2007.
    Please use this reference when citing geno2pheno[coreceptor].

  2. Daeumer M, Kaiser R, Klein R, Lengauer T, Thiele B, Thielen A. Genotypic tropism testing by massively parallel sequencing: qualitative and quantitative analysis.. BMC Medical Informatics and Decision Making, (accepted).

  3. Thielen A, Lengauer T, Swenson LC, Dong W, McGovern RA, Lewis M, James I, Heera J, Valdez H, Harrigan PR Mutations in gp41 are correlated with coreceptor tropism but do not improve prediction methods substantially.. Antiviral Therapy, 2011.

  4. Swenson LC, Mo T, Dong WW, Zhong X, Woods CK, Jensen MA, Thielen A, Chapman D, Lewis M, James I, Heera J, Valdez H, Harrigan PR Deep sequencing to infer HIV-1 co-receptor usage: application to three clinical trials of maraviroc in treatment-experienced patients.. J Infect Dis., 2011.

  5. Thielen A, Sichtig N, Kaiser R, Lam J, Harrigan PR, Lengauer T Improved prediction of HIV-1 coreceptor usage with sequence information from the second hypervariable loop of gp120.. J Infect Dis, 2010.

  6. McGovern RA, Thielen A, Mo T, Dong W, Woods CK, Chapman D, Lewis M, James I, Heera J, Valdez H, Harrigan PR Population-based V3 genotypic tropism assay: a retrospective analysis using screening samples from the A4001029 and MOTIVATE studies.. AIDS, 2010.

  7. Swenson LC, Moores A, Low AJ, Thielen A, Dong W, Woods C, Jensen MA, Wynhoven B, Chan D, Glascock C, Harrigan PR Improved detection of CXCR4-using HIV by V3 genotyping: application of population-based and "deep" sequencing to plasma RNA and proviral DNA.. J Acquir Immune Defic Syndr, 2010.

  8. Bozek K, Thielen A, Sierra S, Kaiser R, Lengauer T V3 loop sequence space analysis suggests different evolutionary patterns of CCR5- and CXCR4-tropic HIV.. PLoS One, 2009.

  9. Sing T, Low AJ, Beerenwinkel N, Sander O, Cheung PK, Domingues F, Büch J, Däumer M, Kaiser R, Lengauer T, Harrigan PR. Predicting HIV co-receptor usage based on genetic and clinical covariates.. Antiviral Therapy, 2007

  10. Sander O, Sing T, Sommer I, Low AJ, Cheung PK, Harrigan PR, Lengauer T. Structural Descriptors of gp120 V3 Loop for the Prediction of HIV-1 Coreceptor Usage. PLoS Comput Biol, 2007.

  11. Sierra S, Kaiser R, Thielen A, Lengauer T. Genotypic coreceptor analysis.. Eur J Med Res., 2007.

  12. Lehmann CJ, Däumer M, , Boussaad I, Sing T, Schmeisser N, Wyen C, Fätkenheuer G, Kaiser R. Stable coreceptor usage of HIV-1 in patients with ongoing treatment failure on HAART. J Clin Virol, 2006.

  13. Sing T, Beerenwinkel N, Kaiser R, Hoffmann D, Däumer M, Lengauer T. Geno2pheno[coreceptor]: A tool for predicting coreceptor usage from genotype and for monitoring coreceptor-associated sequence alterations. 3rd European HIV Drug Resistance Workshop, 2005.

  14. Sirois S, Sing T, Chou KC. HIV-1 V3 loop for structure-based design. Current Protein and Peptide Science, 2005.

  15. Sing T, Beerenwinkel N, Lengauer T. Learning mixtures of localized rules by maximizing the area under the ROC curve. 16th European Conference on Artificial Intelligence (ECAI), Workshop on ROC Analysis in AI, 2004.

  16. Sing T. Learning mixtures of localized rules by maximizing the area under the ROC curve, with an application to the prediction of HIV coreceptor usage. Diploma Thesis, Max Planck Institute for Informatics, Saarbrücken, Germany.

  17. Beerenwinkel N, Nolden T, Kupfer B, Selbig J, Däumer M, Hoffmann D, Rockstroh J, Kaiser R. Predicting HIV-1 cytopathogenicity and co-receptor usage from V3 envelope sequences by machine learning.. Proc. 1st IAS Conf. on HIV Pathogenesis and Treatment, 2001.

  18. Beerenwinkel N, Schmidt B, Walter H, Kaiser R, Lengauer T, Hoffmann D, Korn K, Selbig J. Geno2pheno: Interpreting Genotypic HIV Drug Resistance Tests. IEEE Intelligent Systems in Biology 2001; 16(6):35-41.

Relevant publications by other groups working on HIV coreceptor usage:

  1. Skrabal K, Low AJ, Dong W, Cheung PK, Mammano F, Harrigan PR. Determining human immunodeficiency virus coreceptor use in a clinical setting: degree of correlation between two phenotypic assays and a bioinformatic model.. J Clin Microbiol, 2007.

  2. Jensen MA, Coetzer M, van 't Wout AB, Morris L, Mullins JI. A reliable phenotype predictor for human immunodeficiency virus type 1 subtype C based on envelope V3 sequences.. J Virol. 2006 May;80(10):4698-704.

  3. Jensen MA, Li FS, van 't Wout AB, Nickle DC, Shriner D, He HX, McLaughlin S, Shankarappa R, Margolick JB, Mullins JI. Improved coreceptor usage prediction and genotypic monitoring of R5-to-X4 transition by motif analysis of human immunodeficiency virus type 1 env V3 loop sequences. J Virol. 2003 Dec;77(24):13376-88

  4. Jensen MA, van 't Wout AB. Predicting HIV-1 coreceptor usage with sequence analysis. AIDS Rev. 2003 Apr-Jun;5(2):104-12

  5. Pillai S, Good B, Richman D, Corbeil J. A new perspective on V3 phenotype prediction. AIDS Res Hum Retroviruses. 2003 Feb;19(2):145-9

  6. Resch W, Hoffman N, Swanstrom R. Improved success of phenotype prediction of the human immunodeficiency virus type 1 from envelope variable loop 3 sequence using neural networks. Virology. 2001 Sep 15;288(1):51-62