HIV-1 CRF01_AE coreceptor usage prediction using kernel methods based logistic model trees

Feng, 1996, HIV-1 entry cofactor: functional cDNA cloning of a seven-transmembrane, G-protein-coupled receptor, Science, 272, 872, 10.1126/science.272.5263.872 Berger, 1998, A new classification for HIV-1, Nature, 391, 240, 10.1038/34571 Koot, 1993, Progmosis value of HIV-1 syncytium-inducing phenotype for rate of CD4+ cell depletion and progression to AIDs, Ann. Intern. Med., 118, 681, 10.7326/0003-4819-118-9-199305010-00004 Richman, 1994, The impact of the syncytium-inducing phenotype of HIV on disease progression, J. Infect. Dis., 169, 968, 10.1093/infdis/169.5.968 Weber, 2006, HIV type 1 tropism and inhibitors of viral entry: clinical implications, AIDS Rev., 8, 60 Hwang, 1991, Identification of the envelope V3 loop as the primary determinant of cell tropism in HIV-1, Science, 253, 71, 10.1126/science.1905842 Pillai, 2003, A new perspective on V3 phenotype prediction, AIDS Res. Hum. Retrov., 19, 145, 10.1089/088922203762688658 Resch, 2001, Improved success of phenotype prediction of the human immunodeficiency virus type 1 from envelop variable loop 3 sequence using neural networks, Virology, 288, 51, 10.1006/viro.2001.1087 Jensen, 2003, 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., 77, 13376, 10.1128/JVI.77.24.13376-13388.2003 Fouchier, 1992, Phenotype-associated sequence variation in the third variable of the human immunodeficiency virus type1 gp120 molecule, J. Virol., 66, 3183, 10.1128/JVI.66.5.3183-3187.1992 Delobel, 2007, Population-based sequencing of the V3 region of env for predicting the coreceptor usage of human immunodeficiency virus type 1 quasispecies, J. Clin. Microbiol., 45, 1572, 10.1128/JCM.02090-06 Vandekerckhove, 2011, European consensus group on clinical management of tropism testing. European guidelines on clinical management of HIV-1 tropism testing, Lancet Infect. Dis, 11, 394, 10.1016/S1473-3099(10)70319-4 Garrido, 2008, Evaluation of eight different bioinformatics tools to predict viral tropism in different human immunodeficiency virus type1 subtypes, J. Clin. Microbiol., 46, 887, 10.1128/JCM.01611-07 Vapnik, 1995 Xia, 2009, Two-stage gene selection for support vector machine classification of microarray data, Int. J. Model. Ident. Control, 8, 164, 10.1504/IJMIC.2009.029029 Park, 2008, Classification of gene functions using support vector machine for time-course gene expression data, Comput. Stat. Data Anal., 52, 2578, 10.1016/j.csda.2007.09.002 Sing, 2007, Predicting HIV co-receptor usage based on genetic and clinical covariates, Antivir. Ther., 12, 1097, 10.1177/135965350701200709 To, 2006, A combination of kernel methods and genetic programming for gene expression pattern classification, Res. Innov. Vision Future, 214 Cortes, 1995, Support-vector networks, Mach. Learn., 20, 273, 10.1007/BF00994018 Vapnik, 1998 Cristianini, 2000 T. Gärtner, A Survey of Kernels for Structured Data, SIGKDD Explorations, 2003. Han, 2001 N. Landwehr, Logistic Model Trees, Master's Thesis, Institute for Computer Science, University of Freiburg, Germany, 2003. Friedman, 1998, Additive logistic regression: a statistical view of boosting, Ann. Stat., 28, 1 Landwehr, 2005, Logistic model trees, Mach. Learn., 59, 161, 10.1007/s10994-005-0466-3 A. Karatzoglou, A. Smolo, K. Hornik, kernlab (kernel-based machine learning lab), software, 2009, Available from: 〈http://cran.r-project.org/web/packages/kernlab/index.html〉. K. Hornik, C. Buchta, T. Hothorn, A. Karatzoglou, D. Meyer, A. Zeileis, LMT (logistic model trees implement), software, 2011, Available from: 〈http://cran.r-project.org/web/packages/RWeka/index.html〉. B. Ripley, K. Hornik, A. Gebhardt, nnet (feed-forward neural networks and multinomial log-linear models), software, 2009, Available from: 〈http://cran.r-project.org/web/packages/nnet/index.html〉.