Reading+List


 * __ COMPREHENSIVE READING LIST: __**
 * BELE, R., and R. TAMPE, 1999 Function of the transport complex TAP in cellular immune recognition. Biochim. Biophys. Acta 1461: 405–419.[Medline]
 * ADDO, M., M. ALTFELD, E. S. ROSENBERG, R. L. ELDRIDGE, M. N. PHILIPS et al., 2001 The HIV-1 regulatory proteins Tat and Rev are frequently targeted by cytotoxic T lymphocytes derived from HIV-1-infected individuals. Proc. Natl. Acad. Sci. USA 98: 1783–1796.
 * ALLEN, T. M., D. H. O'CONNOR, P. JING, J. L. DZURIS, B. R. MOTHE etal., 2000 Tat-specific cytotoxic T lymphocytes select for SIV escape variants during resolution of primary viraemia. Nature 407:386–390.[CrossRef][Medline]
 * ANISIMOVA, M., J. P. BIELAWSKI and Z. YANG, 2001 Accuracy and power ofthe likelihood ratio test in detecting adaptive molecular evolution.Mol. Biol. Evol. 18: 1585–1592.[Abstract/Free Full Text]
 * ANISIMOVA, M., R. NIELSEN and Z. YANG, 2003 Effect of recombination on the accuracy of the likelihood method for detecting positive selection at amino acid sites. Genetics 164: 1229–1236.[Abstract/Free Full Text]
 * BAROUCH, D. H., J. KUNSTMAN, M. J. KURODA, J. E. SCHMITZ, S. SANTRA et al., 2002 AIDS vaccine failure in a rhesus monkey by viral escape from cytotoxic T lymphocytes. Nature 415: 335–339.[CrossRef][Medline]
 * BOCHTLER, M., L. DITZEL, M. GROLL, C. HARTMANN and R. HUBER, 1999 The proteasome. Annu. Rev. Biophys. Biomol. Struct. 28: 295–317.[CrossRef][Medline]
 * BORROW, P., H. LEWICKI, X. WEI, M. S. HORWITZ, N. PEFFER et al., 1997 Antiviral pressure exerted by HIV-1 specific cytotoxic T lymphocytes (CTLs) during primary infection demonstrated by rapid selection of CTL escape virus. Nat. Med. 3: 205–211.[CrossRef][Medline]
 * BRANDER, C., and P. J. R. GOULDER, 1999 Recent advances in HIV-1 CTL epitope characterization, pp. IV-1–17 in HIV Molecular Immunology Database, edited by T. M. KORBER, C. BRANDER, B. F. HAYNES, R. KOUP,
 * C. KUIKEN et al. Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM.
 * CHECK, E., 2003 AIDS vaccines: back to ‘plan A.’ Nature 424: 912–914.[CrossRef][Medline]
 * CHUN, R. F., O. J. SEMMES, C. NEUVEUT and K. T. JEANG, 1998 Modulation of Sp1 phosphorylation by human immunodeficiency virus type 1 Tat. J. Virol. 72: 2615–2629.[Abstract/Free Full Text]
 * DANIEL, M. D., F. KIRCHHOFF, S. C. CZAJAK, P. K. SEHGAL and R. C. DESROSIERS, 1992 Protective effects of a live attenuated SIV vaccine with a deletion in the nef gene. Science 258: 1938–1941.[Abstract/Free Full Text]
 * DA SILVA, J., and A. L. HUGHES, 1998 Conservation of cytotoxic T lymphocyte (CTL) epitopes as a host strategy to constrain parasite adaptation: evidence from the nef gene of human immunodeficiency virus 1 (HIV-1). Mol. Biol. Evol. 15: 1259–1268.[Abstract]
 * DELWART, E. L., J. I. MULLINS, P. GUPTA, G. H. LEARN and M. HOLODINY, 1998 Human immunodeficiency virus type 1 populations in blood and semen. J. Virol. 72: 617–623.[Abstract/Free Full Text]
 * DE OLIVEIRA, T., S. ENGELBRECHT, E. J. VAN RENSBURG, M. GORDON, K. BISHOP et al., 2003a Variability at HIV-1 subtype C protease cleavage sites: An indication of viral fitness? J. Virol. 77: 9422–9430.[Abstract/Free Full Text]
 * DE OLIVEIRA, T., R. MILLER, M. TARIN and S. CASSOL, 2003b An integrated genetic data environment (GDE)-based LINUX interface for analysis of HIV-1 and other microbial sequences. Bioinformatics 19: 153–154.[Abstract/Free Full Text]
 * DUNN, C. S., B. HURTREL, C. BEYER, L. GLOECKLER, T. N. LEDGER et al., 1997 Protection of SIV mac-infected macaque monkeys against superinfection by a simian immunodeficiency virus expressing envelope glycoproteins of HIV type 1. AIDS Res. Hum. Retroviruses 13: 913–922.[Medline]
 * FOUTS, D. E., H. L. TRUE, K. A. CENGEL and D. CELANDER, 1997 Site-specific phosphorylation of the human immunodeficiency virus type-1 Rev protein accelerates formation of an efficient RNA-binding conformation. Biochemistry 36: 13256–13263.[CrossRef][ Medline]
 * GASCHEN, B., J. TAYLOR, K. YUSIM, B. FOLEY, F. GAO et al., 2002 Diversity considerations in HIV-1 vaccine selection. Science 296: 2354–2360.[Abstract/Free Full Text]
 * GOULDER, P. J., R. E. PHILLIPS, R. A. COLBERT, S. MCADAM, G. OGG et al., 1997 Late escape from an immunodominant cytotoxic T-lymphocyte response associated with progression to AIDS. Nat. Med. 3: 212–217.[CrossRef][Medline]
 * HIRSCH, V. M., S. GOLDSTEIN, N. A. HYNES, W. R. ELKINS, W. T. LONDON et al., 1994 Prolonged clinical latency and survival of macaques given a whole inactivated simian immunodeficiency virus vaccine. J. Infect. Dis. 170: 51–59.[Medline]
 * HOLMES, A. M., 1996 In vitro phosphorylation of human immunodeficiency virus type 1 Tat protein by protein kinase C: evidence for the phosphorylation of amino acid residue serine-46. Arch. Biochem. Biophys. 335: 8–12.[CrossRef][Medline]
 * HOOVER, E. A., N. A. PERIGO, S. L. QUACKENBUSH, C. K. MATHIASON-DUBARD, J. M. OVERBAUGH et al., 1991 Protection against feline leukemia virus infection by use of an inactivated virus vaccine. J. Am. Vet. Med. Assoc. 199: 1392–1401.[Medline]
 * HUELSENBECK, J. P., and F. RONQUIST, 2001 MRBayes: Bayesian inference of phylogenetic trees. Bioinformatics 17: 754–755.[Abstract/Free Full Text]
 * JEANG, K-T., H. XIAO and E. A. RICH, 1999 Multifaceted activities of the HIV-1 transactivator of transcription, Tat. J. Biol. Chem. 274: 28837–28840.[Free Full Text]
 * KARLSSON, A. C., S. LINDBACK, H. GAINES and A. SONNERBORG, 1998 Characterization of the viral population during primary HIV-1 infection. AIDS 12: 839–847.[CrossRef][Medline]
 * KLAUSNER, R. D., A. S. FAUCI, L. COREY, G. J. NABEL, H. GAYLE et al., 2003 The need for a global HIV vaccine enterprise. Science 300(5628): 2036–2039.[Abstract/Free Full Text]
 * KORBER, B., and G. MYERS, 1992 Signature pattern analysis: a method for assessing viral sequence relatedness. AIDS Res. Hum. Retroviruses 8: 1549–1560.[Medline]
 * MARIN, O., S. SARNO, M. BOSCHETTI, M. A. PAGANO, F. MEGGIO et al., 2000 Unique features of HIV-1 Rev protein phosphorylation by protein kinase CK2. FEBS Lett. 481: 63–67.[CrossRef][Medline]
 * MCMICHAEL, A. T., 1998 Cell responses and viral escape. Cell 93: 673–676.[CrossRef][Medline]
 * MCMICHAEL, A. J., and R. E. PHILLIPS, 1997 Escape of human immunodeficiency virus from immune control. Annu. Rev. Immunol. 15: 271–296.[CrossRef][Medline]
 * MEGGIO, F., D. M. D'AGOSTINO, V. CIMINALE, L. CHIEVO-BIANCHI and L. A. PINNA, 1996 Phosphorylation of HIV-1 Rev protein: implication of protein kinase CK2 and pro-directed kinases. Biochem. Biophys. Res. Commun. 226: 547–554.[CrossRef][Medline]
 * MELLORS, J. W., C. R. RINALDO, JR., P. GUPTA, R. M. WHITE, J. A. TODD et al., 1996 Prognosis in HIV-1 infection predicted by the quantity of virus in plasma. Science 272: 1167–1170.[Abstract]
 * MELLORS, J. W., A. MUNOZ, J. V. GIORGI, J. B. MARGOLICK, C. J. TASSONI et al., 1997 Plasma viral load and CD4+ lymphocytes as prognostic makers of HIV-1 infection. Ann. Intern. Med. 126: 946–954.[Abstract/Free Full Text]
 * NIELSEN, R., and Z. YANG, 1998 Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene. Genetics 148: 929–936.[Abstract/Free Full Text]
 * NOVITSKY, V., N. RYBAK, M. F. MCLANE, P. GILBERT, P. CHIGWEDERE et al., 2001 Identification of human immunodeficiency virus type I subtype C Gag-, Tat-, Rev-, and Nef-specific Elispot-based cytotoxic T-lymphocyte responses for AIDS vaccine design. J. Virol. 75: 9210–9228.[Abstract/Free Full Text]
 * O'CONNOR, D., T. ALLEN and D. I. WATKINS, 2001 Vaccination with CTL epitopes that escape: An alternative approach to HIV vaccine development? Immunol. Lett. 79: 71–84.
 * OVERBAUGH, J., and C. R. M. BANGHAM, 2001 Selection forces and constraints on retroviral sequence variation. Science 292: 1106–1109.[Abstract/Free Full Text]
 * PAMER, E., and P. CRESSWELL, 1998 Mechanisms of MHC class I-restricted antigen processing. Annu. Rev. Immunol. 16: 323–358.[CrossRef][Medline]
 * PARADA, C. A., and R. G. ROEDER, 1996 Enhanced processivity of RNA polymerase II triggered by Tat-induced phosphorylation of its carboxy-terminal domain. Nature 384: 375–378.[CrossRef][Medline]
 * POLLARD, V. W., and M. H. MALIM, 1998 The HIV-1 Rev protein. Annu. Rev. Microbiol. 52: 491–532.[CrossRef][Medline]
 * POSADA, D., and K. A. CRANDALL, 1998 MODELTEST: testing the model of DNA substitution. Bioinformatics 14: 817–818.[Abstract/Free Full Text]
 * PRICE, D. A., P. J. GOULDER, P. KLENERMAN, A. K. SEWELL, P. J. EASTERBROOK et al., 1997 Positive selection of HIV-1 cytotoxic T lymphocytes escape variants during primary infection. Proc. Natl. Acad. Sci. USA 94: 1890–1895.[Abstract/Free Full Text]
 * RAMBAUT, A., D. POSADA, K. A. CRANDALL and E. C. HOLMES, 2004 The causes and consequences of HIV evolution. Nat. Rev. Genet. 5: 52–61.[CrossRef][Medline]
 * RAMMENSEE, H. G., J. BACHMANN, N. P. EMMERICH, O. A. BACHOR, S. STEVANOVIC et al., 1999 SYFPEITHI: database for MHC ligands and peptide motifs. Immunogenetics 50: 213–219.[CrossRef][Medline]
 * ROSENBERG, E. S., J. M. BILLINGSLEY, A. M. CALIENDO, S. L. BOSWELL, P. E. SAX et al., 1997 Vigorous HIV-1-specific CD4+ T cell responses associated with control of viremia. Science 278: 1447–1450.[Abstract/Free Full Text]
 * SWOFFORD, D. L., 2002 PAUP* 4.0: Phylogenetic Analysis Using Parsimony (and Other Methods), Version 4.0b2a. Sinauer Associates, Sunderland, MA.
 * WILSON, C., R. C. BROWN, B. T. KORBER, B. M. WILKES, D. J. RUHL et al., 1999 Frequent detection of escape from cytotoxic T-lymphocyte recognition in perinatal human immunodeficiency virus (HIV) type 1 transmission: the Ariel project for the prevention of transmission of HIV from mother to infant. J. Virol. 73: 3975–3985.[Abstract/Free Full Text]
 * XIA, X., and Z. XIE, 2001 DAMBE: software package for data analysis in molecular biology and evolution. J. Hered. 92(4): 371–373.[Abstract/Free Full Text]
 * YANG, W., J. P. BIELAWSKI and Z. YANG, 2003 Widespread adaptive evolution in the human immunodeficiency virus type 1 genome. J. Mol. Evol. 57(2): 212–221.[CrossRef][Medline]
 * YANG, X., C. H. HERRMAN and A. P. RICE, 1996 The human immunodeficiency virus Tat proteins specifically associated with TAK in vivo and require the carboxyl-terminal domain of RNA polymerase II for function. J. Virol. 70: 4576–4584.[Abstract/Free Full Text]
 * YANG, Z. 1997 PAML: a program package for phylogenetic analysis by maximum likelihood. Comput. Appl. Biosci. 13: 555–556.[Free Full Text]
 * YANG, Z., 2001 Maximum likelihood analysis of adaptive evolution in HIV-1 gp120 env gene. Pac. Symp. Biocomput. 2001: 226–237.
 * YANG, Z., R. NIELSEN, N. GOLDMAN and A. M. PEDERSEN, 2000 Codon-substitution models for heterogeneous selection pressure at amino acid sites. Genetics 155: 431–449.[Abstract/Free Full Text]
 * YUSIM, K., C. KESMIR, B. GASCHEN, M. M. ADDO, M. ALTFELD et al., 2002 Clustering patterns of cytotoxic T-lymphocyte epitopes in human immunodeficiency virus type 1 (HIV-1) proteins reveal imprints of immune evasion on HIV-1 global variation. J. Virol. 76: 8757–8768.[Abstract/Free Full Text]
 * ZANOTTO, P. M., E. G. KALLAS, R. F. DE SOUZA and E. C. HOLMES, 1999 Genealogical evidence for positive selection in the nef gene of HIV-1. Genetics 153: 1077–1089.[Abstract/Free Full Text]