Selected Publications

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., in press (Dec 12 Epub ahead of print).
[Abstract]     [Full-text PDF article - 881 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.  (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 January 2009