Selected Publications

Smith, J.L., Bu, W., Burdick, R.C., and Pathak, V.K.  (2009)  Multiple ways of targeting APOBEC3-virion infectivity factor interactions for anti-HIV-1 drug development. Trends Pharmacol. Sci., in press (Oct 16 Epub ahead of print).
[Abstract]     [Full-text PDF article - 762 K]

Chen, J., Nikolaitchik, O., Singh, J., Wright, A., Bencsics, C.E., Coffin, J.M., Ni, N., Lockett, S., Pathak, V.K., and Hu, W.-S.  (2009)  High efficiency of HIV-1 genomic RNA packaging and heterozygote formation revealed by single virion analysis.  Proc. Natl. Acad. Sci. USA 106: 13535-13540.     [Abstract]     [Full-text PDF article - 574 K]

Delviks-Frankenberry, K.A., Nikolenko, G.N., Maldarelli, F., Hase, S., Takebe, Y., and Pathak, V.K.  (2009)  Subtype-specific differences in the human immunodeficiency virus type 1 reverse transcriptase connection subdomain of CRF01_AE are associated with higher levels of resistance to 3'-azido-3'-deoxythymidine.  J. Virol. 83: 8502-8513.
[Abstract]     [Full-text PDF article - 1260 K]

Friew, Y.N., Boyko, V., Hu, W.-S., and Pathak, V.K.  (2009)  Intracellular interactions between APOBEC3G, RNA, and HIV-1 Gag: APOBEC3G multimerization is dependent on its association with RNA.  Retrovirology 6: 56.     [Abstract]     [Full-text PDF article - 2125 K]

Jern, J., Russell, R.A., Pathak, V.K., and Coffin, J.M.  (2009)  Likely role of APOBEC3G-mediated G-to-A mutations in HIV-1 evolution and drug resistance.  PLoS Pathog. 5: e1000367.     [Abstract]     [Full-text PDF article - 928 K]

Russell, R.A., Moore, M.D., Hu, W.-S., and Pathak, V.K.  (2009)  APOBEC3G induces a hypermutation gradient: Purifying selection at multiple steps during HIV-1 replication results in levels of G-to-A mutations that are high in DNA, intermediate in cellular viral RNA, and low in virion RNA.  Retrovirology 6: 16.
[Abstract]     [Full-text PDF article - 369 K]

Perkovic, M., Schmidt, S., Marino, D., Russell, R.A., Stauch, B., Hofmann, H., Kopietz, F., Kloke, B.P., Zielonka, J., Ströver, H., Hermle, J., Lindemann, D., Pathak, V.K., Schneider, G., Löchelt, M., Cichutek, K., and Münk, C.  (2009)  Species-specific inhibition of APOBEC3C by the prototype foamy virus protein Bet.  J. Biol. Chem. 284: 5819-5826.
[Abstract]     [Full-text PDF article - 525 K]

Russell, R.A., Smith, J., Barr, R., Bhattacharyya, D., and Pathak, V.K.  (2009)  Distinct domains within APOBEC3G and APOBEC3F interact with separate regions of human immunodeficiency virus type 1 Vif.  J. Virol. 83: 1992-2003.
[Abstract]     [Full-text PDF article - 1351 K]

LaRue, R.S., Andrésdóttir, V., Blanchard, Y., Conticello, S.G., Derse, D., Emerman, M., Greene, W.C., Jónsson, S.R., Landau, N.R., Löchelt, M., Malik, H.S., Malim, M.H., Münk, C., O'Brien, S.J., Pathak, V.K., Strebel, K., Wain-Hobson, S., Yu, X.F., Yuhki, N., and Harris, R.S.  (2009)  Guidelines for naming non-primate APOBEC3 genes and proteins.  J. Virol. 83: 494-497.     [PubMed citation]     [Full-text PDF article - 148 K]

Mbisa, J., K.A. Delviks-Frankenberry, J.A. Thomas, R.J. Gorelick, and Pathak, V.K.  (2009)  Real-time PCR analysis of HIV-1 replication post-entry events.  In Prasad, V.R., and Kalpana, G.V. (eds.), HIV Protocols, 2nd Ed., Methods in Molecular Biology, Vol. 485, Humana Press, pp. 55-72.     [Abstract]

Moore, M.D., Fu, W., Soheilian, F., Nagashima, K., Ptak, R.G., Pathak, V.K., and Hu, W.-S.  (2008)  Suboptimal inhibition of protease activity in human immunodeficiency virus type 1: Effects on virion morphogenesis and RNA maturation.  Virology 379: 152-160.
[Abstract]      [Full-text PDF article - 1204 K]

Chen, J., Pathak, V.K., Peng, W., and Hu, W.-S.  (2008)  Capsid proteins from human immunodeficiency virus type 1 and simian immunodeficiency virus SIV_mac can coassemble into mature cores of infectious viruses.  J. Virol. 82: 8253-8261.
[Abstract]     [Full-text PDF article - 472 K]

Delviks-Frankenberry, K.A., Nikolenko, G.N., Boyer, P.L., Hughes, S.H., Coffin, J.M., Jere, A., and Pathak, V.K.  (2008)  HIV-1 reverse transcriptase connection subdomain mutations reduce template RNA degradation and enhance AZT excision.  Proc. Natl. Acad. Sci. USA 105: 10943-10948.     [Abstract]     [Full-text PDF article - 536 K]

Nikolaitchik, O.A., Gorelick, R.J., Leavitt, M.G., Pathak, V.K., and Hu, W.-S.  (2008)  Functional complementation of nucleocapsid and late domain PTAP mutants of human immunodeficiency virus type 1 during replication.  Virology 375: 539-549.
[Abstract]     [Full-text PDF article]

Santos, A.F., Lengruber, R.B., Soares, E.A., Jere, A., Sprinz, E., Martinez, A.M., Silveira, J., Sion, F.S., Pathak, V.K., and Soares, M.A.  (2008)  Conservation patterns of HIV-1 RT connection and RNase H domains: Identification of new mutations in NRTI-treated patients.  PLoS ONE 3: e1781.     [Abstract]     [Full-text PDF article]

Brehm, J.H., Koontz, D., Meteer, J.D., Pathak, V., Sluis-Cremer, N., and Mellors, J.W.  (2007)  Selection of mutations in the connection and RNase H domains of human immunodeficiency virus type 1 reverse transcriptase that increase resistance to 3'-azido-3'-dideoxythymidine.  J. Virol. 81: 7852-7859.     [Abstract]     [Full-text PDF article]

Russell, R.A., and Pathak, V.K.  (2007)  Identification of two distinct human immunodeficiency virus type 1 Vif determinants critical for interactions with human APOBEC3G and APOBEC3F.  J. Virol. 81: 8201-8210.     [Abstract]     [Full-text PDF article]

Mbisa, J.L., Barr, R., Thomas, J.A., Vandergraaff, N., Dorweiler, I.J., Svarovskaia, E.S., Brown, W.L., Mansky, L.M., Gorelick, R.J., Harris, R.S., Engelman, A., and Pathak, V.K.  (2007)  Human immunodeficiency virus type 1 cDNAs produced in the presence of APOBEC3G exhibit defects in plus-strand DNA transfer and integration.  J. Virol. 81: 7099-7110.
[Abstract]     [Full-text PDF article]

Delviks-Frankenberry, K.A., Nikolenko, G.N., Barr, R., and Pathak, V.K.  (2007)  Mutations in human immunodeficiency virus type 1 RNase H primer grip enhance 3'-azido-3'-deoxythymidine resistance.  J. Virol. 81: 6837-6845.     [Abstract]     [Full-text PDF article]

Thomas, D.C., Voronin, Y.A., Nikolenko, G.N., Chen, J., Hu, W.-S., and Pathak, V.K.  (2007)  Determination of the ex vivo rates of human immunodeficiency virus type 1 reverse transcription by using novel strand-specific amplification analysis.  J. Virol. 81: 4798-4807.
[Abstract]     [Full-text PDF article]

Xu, H., Chertova, E., Chen, J., Ott, D.E., Roser, J.D., Hu, W.-S., and Pathak, V.K.  (2007)  Stoichiometry of the antiviral protein APOBEC3G in HIV-1 virions.  Virology 360: 247-256.
[Abstract]     [Full-text PDF article]

Nikolenko, G.N., Delviks-Frankenberry, K.A., Palmer, S., Maldarelli, F., Fivash, M.J., Jr., Coffin, J.M., and Pathak, V.K.  (2007)  Mutations in the connection domain of HIV-1 reverse transcriptase increase 3'-azido-3'-deoxythymidine resistance.  Proc. Natl. Acad. Sci. USA 104: 317-322.      [Abstract]     [Full-text PDF article]

Voronin, Y.A., Sidorov, I.A., and Pathak, V.K.  (2006)  A probability model predicting initiation efficiency of retroviral vectors with two primer-binding sites.  J. Theoret. Biol. 242: 347-355.
[Abstract]     [Full-text PDF article]

Boyko, V., Leavitt, M., Gorelick, R., Fu, W., Nikolaitchik, O., Pathak, V., Nagashima, K., and Hu, W.-S.  (2006)  Coassembly and complementation of Gag proteins from HIV-1 and HIV-2, two distinct human pathogens.  Mol. Cell 23: 281-287.
[Abstract]     [Full-text PDF article]

Krajewski, K., Zhang, Y., Parrish, D., Deschamps, J., Roller, P.P., and Pathak, V.K.  (2006)  New HIV-1 reverse transcriptase inhibitors based on a tricyclic benzothiophene scaffold: Synthesis, resolution, and inhibitory activity.  Bioorg. Med. Chem. Lett. 16: 3034-3038.
[Abstract]     [Full-text PDF article]

Fu, W., Dang, Q., Nagashima, K., Freed, E.O., Pathak, V.K., and Hu, W.-S.  (2006)  Effects of Gag mutation and processing on retroviral dimeric RNA maturation.  J. Virol. 80: 1242-1249.
[Abstract]     [Full-text PDF article]

Chen, J., Dang, Q., Unutmaz, D., Pathak, V.K., Maldarelli, F., Powell, D., and Hu, W.-S.  (2005)  Mechanisms of nonrandom human immunodeficiency virus type 1 infection and double infection: Preference in virus entry is important but is not the sole factor.  J. Virol. 79: 4140-4149.     [Abstract]     [Full-text PDF article]

Nikolenko, G.N., Palmer, S., Maldarelli, F., Mellors, J.W., Coffin, J.M., and Pathak, V.K.  (2005)  Mechanism for nucleoside analog-mediated abrogation of HIV-1 replication: Balance between RNase H activity and nucleotide excision.  Proc. Natl. Acad. Sci. USA 102: 2093-2098.     [Abstract]     [Full-text PDF article]

Mbisa, J.L., Nikolenko, G.N., and Pathak, V.K.  (2005)  Mutations in RNase H primer grip domain of murine leukemia virus reverse transcriptase decrease efficiency and accuracy of plus-strand DNA transfer.  J. Virol. 79: 419-427.
[Abstract]     [Full-text PDF article]

Williams, K.L., Zhang, Y., Shkriabai, N., Karki, R.G., Nicklaus, M.C., Kotrikadze, N., Hess, S., Le Grice, S.F.J., Craigie, R., Pathak, V.K., and Kvaratskhelia, M.  (2005)  Mass spectrometric analysis of the HIV-1 integrase:pyridoxal-5'-phosphate complex reveals a new binding site for a nucleotide inhibitor.  J. Biol. Chem. 280: 7949-7955.
[Abstract]     [Full-text PDF article]

Nikolenko, G.N., Svarovskaia, E.S., Delviks, K.A., and Pathak, V.K.  (2004)  Antiretroviral drug resistance mutations in human immunodeficiency virus type 1 reverse transcriptase increase template switching frequency.  J. Virol. 78:8761-8770.
[Abstract]     [Full-text PDF article]

Svarovskaia, E.S., Xu, H., Mbisa, J.L., Barr, R., Gorelick, R.J., Ono, A., Freed, E.O., Hu, W.-S., and Pathak, V.K.  (2004)  Human apolipoprotein B mRNA-editing enzyme-catalytic polypeptide-like 3G (APOBEC3G) is incorporated into HIV-1 virions through interactions with viral and nonviral RNAs.  J. Biol. Chem. 279: 35822-35828.
[Abstract]     [Full-text PDF article]

Voronin, Y.A., and Pathak, V.K.  (2004)  Frequent dual initiation in human immunodeficiency virus-based vectors containing two primer-binding sites: A quantitative in vivo assay for function of initiation complexes.  J. Virol. 78: 5402-5413.     [Abstract]     [Full-text PDF article]

Xu, H., Svarovskaia, E.S., Barr, R., Zhang, Y., Khan, M.A., Strebel, K., and Pathak, V.K.  (2004)  A single amino acid substitution in human APOBEC3G antiretroviral enzyme confers resistance to HIV-1 virion infectivity factor-induced depletion.  Proc. Natl. Acad. Sci. USA 101: 5652-5657.     [Abstract]     [Full-text PDF article]

Svarovskaia, E.S., Barr, R., Zhang, X., Pais, G., Marchand, C., Pommier, Y., Burke, T.R., Jr., and Pathak, V.K.  (2004)  Azido-containing diketo acid derivatives inhibit human immunodeficiency virus type 1 integrase in vivo and influence the frequency of deletions at two-long-terminal-repeat-circle junctions.  J. Virol. 78: 3210-3222.
[Abstract]     [Full-text PDF article]

Dang, Q., Chen, J., Unutmaz, D., Coffin, J.M., Pathak, V.K., Powell, D., KewalRamani, V.N., Maldarelli, F., and Hu, W.-S.  (2004)  Nonrandom HIV-1 infection and double infection via direct and cell-mediated pathways.  Proc. Natl. Acad. Sci. USA 101: 632-637.
[Abstract]     [Full-text PDF article]     [Supporting text]

Voronin, Y.A., and Pathak, V.K..  (2003)  Frequent dual initiation of reverse transcription in murine leukemia virus-based vectors containing two primer-binding sites.  Virology 312: 281-294.     [Abstract]     [Full-text PDF article]

Zhang, X., Pais, G.C., Svarovskaia, E.S., Marchand, C., Johnson, A.A., Karki, R.G., Nicklaus, M.C., Pathak, V.K., Pommier, Y., and Burke, T.R.  (2003)  Azido-containing aryl beta-diketo acid HIV-1 integrase inhibitors.  Bioorg. Med. Chem. Lett. 13: 1215-1219.
[Abstract]     [Full-text PDF article]

Hu, W.-S., Rhodes, T., Dang, Q., and Pathak, V.K.  (2003)  Retroviral recombination:  Review of genetic analyses.   Front. Biosci. 8: D143-D155.     [Abstract]     [Full-text HTML article]

Svarovskaia, E.S., Cheslock, S.R., Zhang, W.-H., Hu, W.-S., and Pathak, V.K.  (2003)  Retroviral mutation rates and reverse transcriptase fidelity.   Front. Biosci. 8: D117-D134.      [Abstract]     [Full-text HTML article]

Zhang, W.-H., Svarovskaia, E.S., Barr, R., and Pathak, V.K.  (2002)  Y586F mutation in murine leukemia virus reverse transcriptase decreases fidelity of DNA synthesis in regions associated with adenine--thymine tracts.  Proc. Natl. Acad. Sci. USA 99: 10090-10095.
[Abstract]     [Full-text PDF article]

Pais, G.C.G., Zhang, X., Marchand, C., Neamati, N., Cowansage, K., Svarovskaia, E.S., Pathak, V.K., Tang, Y., Nicklaus, M., Pommier, Y., and Burke, T.R., Jr.  (2002)  Structure activity of 3-aryl-1,3-diketo-containing compounds as HIV-1 integrase inhibitors.  J. Med. Chem. 45: 3184-3194.     [Abstract]     [Full-text PDF article]

Zhang, W.-H., Hwang, C.K., Hu, W.-S., Gorelick, R.J., and Pathak, V.K.  (2002)  Zinc finger domain of murine leukemia virus nucleocapsid protein enhances the rate of viral DNA synthesis in vivo.  J. Virol. 76: 7473-7484.     [Abstract]     [Full-text PDF article]

Hwang, C.K., Svarovskaia, E.S., and Pathak, V.K. (2001) Dynamic copy choice: Steady state between murine leukemia virus polymerase and polymerase-dependent RNase H activity determines frequency of in vivo template switching. Proc. Natl. Acad. Sci. USA 98:12209-12214.      [Abstract]     [Full-text PDF article]

Hu, W.-S., and Pathak, V.K. (2000) Design of retroviral vectors and helper cells for gene therapy. Pharmacol. Rev. 52: 493-511.      [Abstract]     [Full-text PDF article]

Halvas, E.K., Svarovskaia, E.S., and Pathak, V.K. (2000) Role of murine leukemia virus reverse transcriptase deoxyribonucleoside triphosphate-binding site in retroviral replication and in vivo fidelity. J. Virol. 74: 10349-10358.      [Abstract]     [Full-text PDF article]

Svarovskaia, E.S., Delviks, K.A., Hwang, C.K., and Pathak, V.K. (2000) Structural determinants of murine leukemia virus reverse transcriptase that affect the frequency of template switching. J. Virol. 74: 7171-7178.      [Abstract]     [Full-text PDF article]

Halvas, E.K., Svarovskaia, E.S., Freed, E.O., and Pathak, V.K. (2000) Wild-type and YMDD mutant murine leukemia virus reverse transcriptases are resistant to 2’,3’-dideoxy-3’-thiacytidine. J. Virol. 74: 6669-6674.      [Abstract]     [Full-text PDF article]

Halvas, E.K., Svarovskaia, E.S., and Pathak, V.K. (2000) Development of an in vivo assay to identify structural determinants in murine leukemia virus reverse transcriptase important for fidelity. J. Virol. 74: 312-319.      [Abstract]     [Full-text PDF article]

Delviks, K.D., and Pathak, V.K. (1999) Development of murine leukemia virus-based self-activating vectors that efficiently delete the selectable drug resistance gene during reverse transcription. J. Virol. 73: 8837-8842.      [Abstract]     [Full-text PDF article]

Delviks, K.D., and Pathak, V.K. (1999) Effect of distance between homologous sequences and 3' homology on the frequency of retroviral reverse transcriptase template switching. J. Virol. 73: 7923-7932.      [Abstract]     [Full-text PDF article]

Pathak, V.K., and Hu, W.-S. (1998) Mutation, recombination, and dynamics of HIV-1 in vivo. In: Human Immunodeficiency Viruses: Biology, Immunology, and Molecular Biology (Nitin Saksena, Ed.), Medical Systems SpA, pp. 299-330.

Julias, J.G., and Pathak, V.K. (1998) Deoxyribonucleoside triphosphate pool imbalances in vivo are associated with an increased retroviral mutation rate. J. Virol. 72: 7941-7949.
[Abstract]     [Full-text PDF article]

Hu, W.-S., Bowman, E.H., Delviks, K.A., and Pathak, V.K. (1997) Homologous recombination occurs in a distinct retroviral subpopulation and exhibits high negative interference. J. Virol. 71: 6028-6036.      [Abstract]     [Full-text PDF article]

Last modified: 30 October 2009