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Our Science – Pathak Website

Vinay K. Pathak, Ph.D.

Selected Publications

1)  Desimmie BA, Delviks-Frankenberrry KA, Burdick RC, Qi D, Izumi T, Pathak VK.
Multiple APOBEC3 Restriction Factors for HIV-1 and One Vif to Rule Them All.
J. Mol. Biol. 426: 1220-1245, 2014.
2)  Burdick R, Hu W, Pathak V.
Nuclear import of APOBEC3F-labeled HIV-1 preintegration complexes.
Proc Natl Acad Sci USA Plus. 110: E4780-9, 2013.
3)  Paprotka T, Delviks-Frankenberry K, Cingoz O, Martinez A, Kung H, Tepper C, Hu W, Fivash M, Coffin J, Pathak V.
Recombinant origin of the retrovirus XMRV.
Science. 333: 97-101, 2011.
Full Text Article. [Journal]
4)  Delviks-Frankenberry KA, Nikolenko GN, Boyer PL, Hughes SH, Coffin JM, Jere A, Pathak VK.
HIV-1 reverse transcriptase connection subdomain mutations reduce template RNA degradation and enhance AZT excision.
Proc. Natl. Acad. Sci. U.S.A. 105: 10943-10948, 2008.
5)  Nikolenko GN, Palmer S, Maldarelli F, Mellors JW, Coffin JM, Pathak VK.
Mechanism for nucleoside analog-mediated abrogation of HIV-1 replication: balance between RNase H activity and nucleotide excision.
Proc Natl Acad Sci U S A. 102: 2093-8, 2005.
6)  Xu H, Svarovskaia ES, Barr R, Zhang Y, Khan MA, Strebel K, Pathak VK.
A single amino acid substitution in human APOBEC3G antiretroviral enzyme confers resistance to HIV-1 virion infectivity factor-induced depletion.
Proc Natl Acad Sci U S A. 101: 5652-7, 2004.
7)  Chaipan C, Smith JL, Hu WS, Pathak VK.
APOBEC3G Restricts HIV-1 to a Greater Extent than APOBEC3F and APOBEC3DE in Human Primary CD4+ T Cells and Macrophages.
J. Virol. 87: 444-53, 2013.
8)  Delviks-Frankenberry KA, Lengruber RB, Santos AF, Silveira JM, Soares MA, Kearney MF, Maldarelli F, Pathak VK.
Connection subdomain mutations in HIV-1 subtype-C treatment-experienced patients enhance NRTI and NNRTI drug resistance.
Virology. 435: 433-41, 2013.
9)  Nikolaitchik O, Dilley K, Fu W, Gorelick R, Tai S, Soheilian F, Ptak R, Nagashima K, Pathak V, Hu W.
Dimeric RNA recognition regulates HIV-1 genome packaging.
PLoS Pathog. 9(3): e1003249: e1003249, 2013.
Full Text Article. [Journal]
10)  Hatch SC, Sardo L, Chen J, Burdick R, Gorelick R, Fivash MJ, Pathak VK, Hu WS.
Gag-Dependent Enrichment of HIV-1 RNA near the Uropod Membrane of Polarized T Cells.
J. Virol. 87: 11912-11915, 2013.
11)  Delviks-Frankenberry K, Paprotka T, Cingöz O, Wildt S, Hu WS, Coffin JM, Pathak VK.
Generation of Multiple Replication-Competent Retroviruses through Recombination between PreXMRV-1 and PreXMRV-2.
J. Virol. 87: 11525-11537, 2013.
12)  Izumi T, Burdick R, Shigemi M, Plisov S, Hu WS, Pathak VK.
Mov10 and APOBEC3G Localization to Processing Bodies Is Not Required for Virion Incorporation and Antiviral Activity.
J. Virol. 87: 11047-62, 2013.
13)  Murgai M, Thomas J, Cherepanova O, Delviks-Frankenberry K, Deeble P, Pathak V, Rekosh D, Owens G.
Xenotropic MLV envelope proteins induce tumor cells to secrete factors that promote the formation of immature blood vessels.
Retrovirology. 10: 34, 2013.
Full Text Article. [Journal]
14)  Ndongwe TP, Adedeji AO, Michailidis E, Ong YT, Hachiya A, Marchand B, Ryan EM, Rai DK, Kirby KA, Whatley AS, Burke DH, Johnson M, Ding S, Zheng Y, Liu S, Kodama E, Delviks-Frankenberry KA, Pathak VK, Mitsuya H, Parniak MA, Singh K, Sarafianos SG.
Biochemical, inhibition and inhibitor resistance studies of xenotropic murine leukemia virus-related virus reverse transcriptase.
Nucleic Acids Res. 40: 345-359, 2012.
15)  Cingöz O, Paprotka T, Delviks-Frankenberry KA, Wildt S, Hu WS, Pathak VK, Coffin JM.
Characterization, Mapping, and Distribution of the Two XMRV Parental Proviruses.
J. Virol. 86: 328-38, 2012.
16)  Delviks-Frankenberry K, Cingöz O, Coffin JM, Pathak VK.
Recombinant origin, contamination, and de-discovery of XMRV.
Curr Opin Virol. 2: 499-507, 2012.
17)  Del Prete GQ, Kearney MF, Spindler J, Wiegand A, Chertova E, Roser JD, Estes JD, Hao XP, Trubey CM, Lara A, Lee K, Chaipan C, Bess JW, Nagashima K, Keele BF, Macallister R, Smedley J, Pathak VK, Kewalramani VN, Coffin JM, Lifson JD.
Restricted replication of xenotropic murine leukemia virus-related virus in pigtailed macaques.
J. Virol. 86: 3152-66, 2012.
18)  Delviks-Frankenberry K, Chaipan C, Bagni R, Wyvill K, Yarchoan R, Pathak V.
Lack of detection of xenotropic murine leukemia virus-related virus in HIV-1 lymphoma patients.
Adv Virol. 2011: article ID 797820, 4 pages: ., 2011.
Full Text Article. [Journal]
19)  Delviks-Frankenberry K, Galli A, Nikolaitchik O, Mens H, Pathak VK, Hu WS.
Mechanisms and Factors that Influence High Frequency Retroviral Recombination.
Viruses. 3: 1650-80, 2011.
20)  Ni N, Nikolaitchik OA, Dilley KA, Chen J, Galli A, Fu W, Prasad VV, Ptak RG, Pathak VK, Hu WS.
Mechanisms of human immunodeficiency virus type 2 RNA packaging: efficient trans packaging and selection of RNA copackaging partners.
J. Virol. 85: 7603-12, 2011.
21)  Nikolaitchik OA, Galli A, Moore MD, Pathak VK, Hu WS.
Multiple Barriers to Recombination between Divergent HIV-1 Variants Revealed by a Dual-Marker Recombination Assay.
J. Mol. Biol. 407: 521-31, 2011.
22)  Kearney M, Lee K, Bagni R, Wiegand A, Spindler J, Maldarelli F, Pinto P, Linehan W, Vocke C, Delviks-Frankenberry K, deVere White R, Del Prete G, Mellors J, Lifson J, KewalRamani V, Pathak V, Coffin J, Le Grice S.
Nucleic acid, antibody, and virus culture methods to detect xenotropic MLV-related virus (XMRV) in macaque and human blood samples.
Adv Virol. 2011: article ID 272193, 12 pages: ., 2011.
Full Text Article. [Journal]
23)  Lengruber R, Delviks-Frankenberry K, Nikolenko G, Baumann J, Santos A, Pathak V, Soares M.
Phenotypic characterization of drug resistance-associated mutations in HIV-1 RT connection and RNase H domains and their correlation with thymidine analogue mutations.
J Antimicrob Chemother. 66: 702-708, 2011.
24)  Chaipan C, Dilley KA, Paprotka T, Delviks-Frankenberry KA, Venkatachari NJ, Hu W, Pathak VK.
Severe Restriction of Xenotropic Murine Leukemia Virus-Related Virus Replication and Spread in Cultured Human Peripheral Blood Mononuclear Cells.
J Virol. 85: 4888-4897, 2011.
25)  Pak V, Heidecker G, Pathak VK, Derse D.
The Role of Amino-Terminal Sequences in Cellular Localization and Antiviral Activity of APOBEC3B.
J. Virol. 85: 8538-47, 2011.
26)  Nikolenko GN, Delviks-Frankenberry KA, Pathak VK.
A novel molecular mechanism of dual resistance to nucleoside and nonnucleoside reverse transcriptase inhibitors.
J. Virol. 84: 5238-49, 2010.
27)  Mbisa JL, Bu W, Pathak VK.
APOBEC3F and APOBEC3G inhibit HIV-1 DNA integration by different mechanisms.
J. Virol. 84: 5250-9, 2010.
28)  Smith JL, Pathak VK.
Identification of Specific Determinants of Human APOBEC3F, APOBEC3C, and APOBEC3DE and African Green Monkey APOBEC3F That Interact with HIV-1 Vif.
J. Virol. 84: 12599-608, 2010.
29)  Paprotka T, Venkatachari NJ, Chaipan C, Burdick R, Delviks-Frankenberry KA, Hu WS, Pathak VK.
Inhibition of xenotropic murine leukemia virus-related virus by APOBEC3 proteins and antiviral drugs.
J. Virol. 84: 5719-29, 2010.
30)  Burdick R, Smith JL, Chaipan C, Friew Y, Chen J, Venkatachari NJ, Delviks-Frankenberry KA, Hu WS, Pathak VK.
P body-associated protein Mov10 inhibits HIV-1 replication at multiple stages.
J. Virol. 84: 10241-53, 2010.
31)  Galli A, Kearney M, Nikolaitchik OA, Yu S, Chin MP, Maldarelli F, Coffin JM, Pathak VK, Hu WS.
Patterns of Human Immunodeficiency Virus type 1 recombination ex vivo provide evidence for coadaptation of distant sites, resulting in purifying selection for intersubtype recombinants during replication.
J. Virol. 84: 7651-61, 2010.
32)  Delviks-Frankenberry KA, Nikolenko GN, Pathak VK.
The 'connection' between HIV drug resistance and RNase H.
Viruses. 2: 1476-1503, 2010.
33)  Russell R, Moore M, Hu W, Pathak V.
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, 2009.
Full Text Article. [Journal]
34)  Russell RA, Smith J, Barr R, Bhattacharyya D, Pathak VK.
Distinct Domains within APOBEC3G and APOBEC3F Interact with Separate Regions of Human Immunodeficiency Virus Type 1 Vif.
J. Virol. 83: 1992-2003, 2009.
35)  Chen J, Nikolaitchik O, Singh J, Wright A, Bencsics CE, Coffin JM, Ni N, Lockett S, Pathak VK, Hu WS.
High efficiency of HIV-1 genomic RNA packaging and heterozygote formation revealed by single virion analysis.
Proc. Natl. Acad. Sci. U.S.A. 106: 13535-40, 2009.
36)  Friew YN, Boyko V, Hu WS, Pathak VK.
Intracellular interactions between APOBEC3G, RNA, and HIV-1 Gag: APOBEC3G multimerization is dependent on its association with RNA.
Retrovirology. 6: 56, 2009.
37)  Jern P, Russell RA, Pathak VK, Coffin JM.
Likely role of APOBEC3G-mediated G-to-A mutations in HIV-1 evolution and drug resistance.
PLoS Pathog. 5: e1000367, 2009.
38)  Smith JL, Bu W, Burdick RC, Pathak VK.
Multiple ways of targeting APOBEC3-virion infectivity factor interactions for anti-HIV-1 drug development.
Trends Pharmacol. Sci. 30: 638-46, 2009.
39)  Mbisa JL, Delviks-Frankenberry KA, Thomas JA, Gorelick RJ, Pathak VK.
Real-Time PCR Analysis of HIV-1 Replication Post-entry Events.
Methods Mol. Biol. 485: 55-72, 2009.
40)  Perkovic M, Schmidt S, Marino D, Russell RA, Stauch B, Hofmann H, Kopietz F, Kloke B, Zielonka J, Strover H, Hermle J, Lindemann D, Pathak VK, Schneider G, Lochelt M, Cichutek K, Munk C.
Species-specific inhibition of APOBEC3C by the prototype foamy virus protein Bet.
J. Biol. Chem. 284: 5819-5826, 2009.
Full Text Article. [Journal]
41)  Delviks-Frankenberry KA, Nikolenko GN, Maldarelli F, Hase S, Takebe Y, Pathak VK.
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: 8502-13, 2009.
42)  Chen J, Pathak VK, Peng W, Hu W.
Capsid proteins from human immunodeficiency virus type 1 and simian immunodeficiency virus SIVmac can coassemble into mature cores of infectious viruses.
J. Virol. 82: 8253-61, 2008.
43)  Larue RS, Andrésdóttir V, Blanchard Y, Conticello SG, Derse D, Emerman M, Greene WC, Jónsson SR, Landau NR, Löchelt M, Malik HS, Malim MH, Münk C, O'Brien SJ, Pathak VK, Strebel K, Wain-Hobson S, Yu X, Yuhki N, Harris RS.
Guidelines for Naming Non-Primate APOBEC3 Genes and Proteins.
J. Virol. 83: 494-7, 2008.
44)  Moore MD, Fu W, Soheilian F, Nagashima K, Ptak RG, Pathak VK, Hu W.
Suboptimal inhibition of protease activity in human immunodeficiency virus type 1: Effects on virion morphogenesis and RNA maturation.
Virology. 379: 152-60, 2008.
45)  Santos AF, Lengruber RB, Soares EA, Jere A, Sprinz E, Martinez AM, Silveira J, Sion FS, Pathak VK, Soares MA.
Conservation patterns of HIV-1 RT connection and RNase H domains: identification of new mutations in NRTI-treated patients.
PLoS ONE. 3: e1781, 2008.
46)  Nikolaitchik OA, Gorelick RJ, Leavitt MG, Pathak VK, Hu W.
Functional complementation of nucleocapsid and late domain PTAP mutants of human immunodeficiency virus type 1 during replication.
Virology. 375: 539-49, 2008.
47)  Thomas DC, Voronin YA, Nikolenko GN, Chen J, Hu WS, Pathak VK.
Determination of the ex vivo rates of human immunodeficiency virus type 1 reverse transcription by using novel strand-specific amplification analysis.
J. Virol. 81: 4798-807, 2007.
48)  Mbisa JL, Barr R, Thomas JA, Vandegraaff N, Dorweiler IJ, Svarovskaia ES, Brown WL, Mansky LM, Gorelick RJ, Harris RS, Engelman A, Pathak VK.
Human Immunodeficiency Virus Type 1 cDNAs Produced in the Presence of APOBEC3G Exhibit Defects in Plus-Strand DNA Transfer and Integration.
J. Virol. 81: 7099-110, 2007.
49)  Russell RA, Pathak VK.
Identification of Two Distinct Human Immunodeficiency Virus Type 1 Vif Determinants Critical for Interactions with Human APOBEC3G and APOBEC3F.
J. Virol. 81: 8201-10, 2007.
50)  Delviks-Frankenberry KA, Nikolenko GN, Barr R, Pathak VK.
Mutations in Human Immunodeficiency Virus Type 1 RNase H Primer Grip Enhance 3'-Azido-3'-Deoxythymidine Resistance.
J. Virol. 81: 6837-45, 2007.
51)  Nikolenko GN, Delviks-Frankenberry KA, Palmer S, Maldarelli F, Fivash MJ, Coffin JM, Pathak VK.
Mutations in the connection domain of HIV-1 reverse transcriptase increase 3'-azido-3'-deoxythymidine resistance.
Proc. Natl. Acad. Sci. U.S.A. 104: 317-22, 2007.
52)  Brehm JH, Koontz D, Meteer JD, Pathak V, Sluis-Cremer N, Mellors JW.
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: 7852-9, 2007.
53)  Xu H, Chertova E, Chen J, Ott DE, Roser JD, Hu WS, Pathak VK.
Stoichiometry of the antiviral protein APOBEC3G in HIV-1 virions.
Virology. 360: 247-56, 2007.
54)  Voronin YA, Sidorov IA, Pathak VK.
A probability model predicting initiation efficiency of retroviral vectors with two primer-binding sites.
J. Theor. Biol. 242: 347-55, 2006.
55)  Boyko V, Leavitt M, Gorelick R, Fu W, Nikolaitchik O, Pathak VK, Nagashima K, Hu WS.
Coassembly and Complementation of Gag Proteins from HIV-1 and HIV-2, Two Distinct Human Pathogens.
Mol. Cell. 23: 281-7, 2006.
56)  Fu W, Dang Q, Nagashima K, Freed EO, Pathak VK, Hu WS.
Effects of Gag mutation and processing on retroviral dimeric RNA maturation.
J Virol. 80: 1242-9, 2006.
57)  Krajewski K, Zhang Y, Parrish D, Deschamps J, Roller PP, Pathak VK.
New HIV-1 reverse transcriptase inhibitors based on a tricyclic benzothiophene scaffold: Synthesis, resolution, and inhibitory activity.
Bioorg Med Chem Lett. 16: 3034-8, 2006.
58)  Williams KL, Zhang Y, Shkriabai N, Karki RG, Nicklaus MC, Kotrikadze N, Hess S, Le Grice SF, Craigie R, Pathak VK, Kvaratskhelia M.
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: 7949-55, 2005.
59)  Chen J, Dang Q, Unutmaz D, Pathak VK, Maldarelli F, Powell D, Hu WS.
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: 4140-9, 2005.
60)  Mbisa JL, Nikolenko GN, Pathak VK.
Mutations in the RNase H primer grip domain of murine leukemia virus reverse transcriptase decrease efficiency and accuracy of plus-strand DNA transfer.
J Virol. 79: 419-27, 2005.
61)  Nikolenko GN, Svarovskaia ES, Delviks KA, Pathak VK.
Antiretroviral drug resistance mutations in human immunodeficiency virus type 1 reverse transcriptase increase template-switching frequency.
J. Virol. 78: 8761-70, 2004.
62)  Svarovskaia ES, Barr R, Zhang X, Pais GC, Marchand C, Pommier Y, Burke TR, Pathak VK.
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: 3210-22, 2004.
63)  Voronin YA, Pathak VK.
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: 5402-13, 2004.
64)  Svarovskaia ES, Xu H, Mbisa JL, Barr R, Gorelick RJ, Ono A, Freed EO, Hu WS, Pathak VK.
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: 35822-8, 2004.
65)  Dang Q, Chen J, Unutmaz D, Coffin JM, Pathak VK, Powell D, KewalRamani VN, Maldarelli F, Hu WS.
Nonrandom HIV-1 infection and double infection via direct and cell-mediated pathways.
Proc Natl Acad Sci U S A. 101: 632-7, 2004.
66)  Zhang X, Pais GC, Svarovskaia ES, Marchand C, Johnson AA, Karki RG, Nicklaus MC, Pathak VK, Pommier Y, Burke TR.
Azido-Containing aryl beta-Diketo acid HIV-1 integrase inhibitors.
Bioorg Med Chem Lett. 13: 1215-9, 2003.
67)  Voronin YA, Pathak VK.
Frequent dual initiation of reverse transcription in murine leukemia virus-based vectors containing two primer-binding sites.
Virology. 312: 281-94, 2003.
68)  Svarovskaia ES, Cheslock SR, Zhang WH, Hu WS, Pathak VK.
Retroviral mutation rates and reverse transcriptase fidelity.
Front Biosci. 8: D117-34, 2003.
69)  Hu WS, Rhodes T, Dang Q, Pathak V.
Retroviral recombination: review of genetic analyses.
Front Biosci. 8: d143-55, 2003.
70)  Pais GC, Zhang X, Marchand C, Neamati N, Cowansage K, Svarovskaia ES, Pathak VK, Tang Y, Nicklaus M, Pommier Y, Burke TR.
Structure activity of 3-aryl-1,3-diketo-containing compounds as HIV-1 integrase inhibitors.
J Med Chem. 45: 3184-94, 2002.
71)  Zhang WH, Svarovskaia ES, Barr R, Pathak VK.
Y586F mutation in murine leukemia virus reverse transcriptase decreases fidelity of DNA synthesis in regions associated with adenine-thymine tracts.
Proc Natl Acad Sci U S A. 99: 10090-5, 2002.
72)  Zhang WH, Hwang CK, Hu WS, Gorelick RJ, Pathak VK.
Zinc finger domain of murine leukemia virus nucleocapsid protein enhances the rate of viral DNA synthesis in vivo.
J Virol. 76: 7473-84, 2002.
73)  Hwang CK, Svarovskaia ES, Pathak VK.
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 U S A. 98: 12209-14, 2001.
74)  Hu WS, Pathak VK.
Design of retroviral vectors and helper cells for gene therapy.
Pharmacol Rev. 52: 493-511, 2000.
75)  Halvas EK, Svarovskaia ES, Pathak VK.
Development of an in vivo assay to identify structural determinants in murine leukemia virus reverse transcriptase important for fidelity.
J Virol. 74: 312-9, 2000.
76)  Anderson JA, Pathak VK, Hu WS.
Effect of the murine leukemia virus extended packaging signal on the rates and locations of retroviral recombination.
J Virol. 74: 6953-63, 2000.
77)  Halvas EK, Svarovskaia ES, Pathak VK.
Role of murine leukemia virus reverse transcriptase deoxyribonucleoside triphosphate-binding site in retroviral replication and in vivo fidelity.
J Virol. 74: 10349-58, 2000.
78)  Svarovskaia ES, Delviks KA, Hwang CK, Pathak VK.
Structural determinants of murine leukemia virus reverse transcriptase that affect the frequency of template switching.
J Virol. 74: 7171-8, 2000.
79)  Cheslock SR, Anderson JA, Hwang CK, Pathak VK, Hu WS.
Utilization of nonviral sequences for minus-strand DNA transfer and gene reconstitution during retroviral replication.
J Virol. 74: 9571-9, 2000.
80)  Halvas EK, Svarovskaia ES, Freed EO, Pathak VK.
Wild-type and YMDD mutant murine leukemia virus reverse transcriptases are resistant to 2',3'-dideoxy-3'-thiacytidine.
J Virol. 74: 6669-74, 2000.
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This page was last updated on 2/27/2014.