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Mary Kearney, Ph.D.

Selected Publications

1)  Maldarelli F, Wu X, Su L, Simonetti FR, Shao W, Hill S, Spindler J, Ferris AL, Mellors JW, Kearney MF, Coffin JM, Hughes SH.
Specific HIV integration sites are linked to clonal expansion and persistence of infected cells.
Science. 2014.
Full Text Article. In Press. [Journal]
2)  Kearney MF, Spindler J, Shao W, Yu S, Anderson EM, O'Shea A, Rehm C, Poethke C, Kovacs N, Mellors JW, Coffin JM, Maldarelli F.
Lack of Detectable HIV-1 Molecular Evolution during Suppressive Antiretroviral Therapy.
PLoS Pathog. 10: e1004010, 2014.
[Journal]
3)  Kearney M, Spindler J, Wiegand A, Shao W, Anderson E, Maldarelli F, Ruscetti F, Mellors J, Hughes S, Le Grice S, Coffin J.
Multiple sources of contamination in samples from patients reported to have XMRV infection.
PLoS ONE. 7(2): e30889, 2012.
Full Text Article. [Journal]
4)  Kearney M, Spindler J, Shao W, Maldarelli F, Palmer S, Hu SL, Lifson JD, Kewalramani VN, Mellors JW, Coffin JM, Ambrose Z.
Genetic Diversity of Simian Immunodeficiency Virus Encoding HIV-1 Reverse Transcriptase Persists in Macaques despite Antiretroviral Therapy.
J. Virol. 85: 1067-76, 2011.
[Journal]
5)  Kearney M, Maldarelli F, Shao W, Margolick JB, Daar ES, Mellors JW, Rao V, Coffin JM, Palmer S.
Human immunodeficiency virus type 1 population genetics and adaptation in newly infected individuals.
J. Virol. 83: 2715-27, 2009.
[Journal]
6)  Wei D, Chiang V, Fyne E, Balakrishnan M, Barnes T, Graupe M, Hesselgesser J, Irrinki I, Murry J, Stepan G, Stray K, Tsai A, Yu H, Spindler J, Kearney M, Spina C, McMahon D, Lalezari J, Sloan D, Mellors J, Geleziunas R, Cihlar T.
Histone deacetylase inhibitor romidepsin induces HIV expression in CD4 T cells from patients on suppressive antiretroviral therapy at concentrations achieved by clinical dosing.
PLoS Pathog. 10(4): e1004071, 2014.
Full Text Article. [Journal]
7)  Shao W, Kearney MF, Boltz VF, Spindler JE, Mellors JW, Maldarelli F, Coffin JM.
PAPNC, a novel method to calculate nucleotide diversity from large scale next generation sequencing data.
J. Virol. Methods. 203C: 73-80, 2014.
[Journal]
8)  De Ravin SS, Gray JT, Throm RE, Spindler J, Kearney M, Wu X, Coffin JM, Hughes SH, Malderelli F, Sorrentino BP, Malech HL.
False-Positive HIV PCR Test Following Ex Vivo Lentiviral Gene Transfer Treatment of X-linked Severe Combined Immunodeficiency Vector.
Mol. Ther. 22: 244-5, 2014.
[Journal]
9)  Archin NM, Bateson R, Tripathy M, Crooks AM, Yang KH, Dahl NP, Kearney MF, Anderson EM, Coffin JM, Strain MC, Richman DD, Robertson KR, Kashuba AD, Bosch RJ, Hazuda DJ, Kuruc JD, Eron JJ, Margolis DM.
HIV-1 Expression within Resting CD4 T-Cells Following Multiple Doses of Vorinostat.
J. Infect. Dis. 2014.
[Journal]
10)  Boltz VF, Bao Y, Lockman S, Halvas EK, Kearney MF, McIntyre JA, Schooley RT, Hughes MD, Coffin JM, Mellors JW.
Low-Frequency Nevirapine (NVP)-Resistant HIV-1 Variants Are Not Associated With Failure of Antiretroviral Therapy in Women Without Prior Exposure to Single-Dose NVP.
J. Infect. Dis. 209: 703-10, 2014.
[Journal]
11)  Shao W, Boltz VF, Spindler JE, Kearney MF, Maldarelli F, Mellors JW, Stewart C, Volfovsky N, Levitsky A, Stephens RM, Coffin JM.
Analysis of 454 sequencing error rate, error sources, and artifact recombination for detection of Low-frequency drug resistance mutations in HIV-1 DNA.
Retrovirology. 10: 18, 2013.
[Journal]
12)  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.
[Journal]
13)  Maldarelli F, Kearney M, Palmer S, Stephens R, Mican J, Polis MA, Davey RT, Kovacs J, Shao W, Rock-Kress D, Metcalf JA, Rehm C, Greer SE, Lucey DL, Danley K, Alter H, Mellors JW, Coffin JM.
HIV Populations Are Large and Accumulate High Genetic Diversity in a Nonlinear Fashion.
J. Virol. 87: 10313-23, 2013.
[Journal]
14)  Sloan EA, Kearney MF, Gray LR, Anastos K, Daar ES, Margolick J, Maldarelli F, Hammarskjold ML, Rekosh D.
Limited Nucleotide Changes in the Rev Response Element (RRE) during HIV-1 Infection Alter Overall Rev-RRE Activity and Rev Multimerization.
J. Virol. 87: 11173-86, 2013.
[Journal]
15)  Zheng L, Bosch RJ, Chan ES, Read S, Kearney M, Margolis DM, Mellors JW, Eron JJ, Gandhi RT.
Predictors of residual viraemia in patients on long-term suppressive antiretroviral therapy.
Antivir. Ther. (Lond.). 18: 39-43, 2013.
[Journal]
16)  Josefsson L, Palmer S, Faria NR, Lemey P, Casazza J, Ambrozak D, Kearney M, Shao W, Kottilil S, Sneller M, Mellors J, Coffin JM, Maldarelli F.
Single Cell Analysis of Lymph Node Tissue from HIV-1 Infected Patients Reveals that the Majority of CD4(+) T-cells Contain One HIV-1 DNA Molecule.
PLoS Pathog. 9: e1003432, 2013.
[Journal]
17)  Casazza JP, Bowman KA, Adzaku S, Smith EC, Enama ME, Bailer RT, Price DA, Gostick E, Gordon IJ, Ambrozak DR, Nason MC, Roederer M, Andrews CA, Maldarelli FM, Wiegand A, Kearney MF, Persaud D, Ziemniak C, Gottardo R, Ledgerwood JE, Graham BS, Koup RA.
Therapeutic Vaccination Expands and Improves the Function of the HIV-Specific Memory T-Cell Repertoire.
J. Infect. Dis. 207: 1829-40, 2013.
[Journal]
18)  Archin NM, Liberty AL, Kashuba AD, Choudhary SK, Kuruc JD, Crooks AM, Parker DC, Anderson EM, Kearney MF, Strain MC, Richman DD, Hudgens MG, Bosch RJ, Coffin JM, Eron JJ, Hazuda DJ, Margolis DM.
Administration of vorinostat disrupts HIV-1 latency in patients on antiretroviral therapy.
Nature. 487: 482-5, 2012.
[Journal]
19)  Archin NM, Vaidya NK, Kuruc JD, Liberty AL, Wiegand A, Kearney MF, Cohen MS, Coffin JM, Bosch RJ, Gay CL, Eron JJ, Margolis DM, Perelson AS.
Immediate antiviral therapy appears to restrict resting CD4+ cell HIV-1 infection without accelerating the decay of latent infection.
Proc. Natl. Acad. Sci. U.S.A. 109: 9523-8, 2012.
[Journal]
20)  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.
[Journal]
21)  Boltz VF, Ambrose Z, Kearney MF, Shao W, Kewalramani VN, Maldarelli F, Mellors JW, Coffin JM.
Ultrasensitive allele-specific PCR reveals rare preexisting drug-resistant variants and a large replicating virus population in macaques infected with a simian immunodeficiency virus containing human immunodeficiency virus reverse transcriptase.
J. Virol. 86: 12525-30, 2012.
[Journal]
22)  Mens H, Kearney M, Wiegand A, Spindler J, Maldarelli F, Mellors JW, Coffin JM.
Amplifying and quantifying HIV-1 RNA in HIV infected individuals with viral loads below the limit of detection by standard clinical assays.
J Vis Exp. 2011.
[Journal]
23)  Batorsky R, Kearney MF, Palmer SE, Maldarelli F, Rouzine IM, Coffin JM.
Estimate of effective recombination rate and average selection coefficient for HIV in chronic infection.
Proc. Natl. Acad. Sci. U.S.A. 108: 5661-6, 2011.
[Journal]
24)  Simmons G, Glynn SA, Komaroff AL, Mikovits JA, Tobler LH, Hackett J, Tang N, Switzer WM, Heneine W, Hewlett IK, Zhao J, Lo SC, Alter HJ, Linnen JM, Gao K, Coffin JM, Kearney MF, Ruscetti FW, Pfost MA, Bethel J, Kleinman S, Holmberg JA, Busch MP.
Failure to Confirm XMRV/MLVs in the Blood of Patients with Chronic Fatigue Syndrome: A Multi-Laboratory Study.
Science (New York, N.Y.). 334: 814-817, 2011.
[Journal]
25)  Josefsson L, King MS, Makitalo B, Brännström J, Shao W, Maldarelli F, Kearney MF, Hu W, Chen J, Gaines H, Mellors JW, Albert J, Coffin JM, Palmer SE.
Majority of CD4+ T cells from peripheral blood of HIV-1-infected individuals contain only one HIV DNA molecule.
Proc Natl Acad Sci U S A. 108: 11199-11204, 2011.
[Journal]
26)  Spindler J, Hackett J, Qiu X, Wiegand A, Boltz VF, Swanson P, Bream JH, Jacobson LP, Li X, Rinaldo CR, Wolinsky SM, Coffin JM, Mellors JW.
Prevalence of XMRV Nucleic Acid and Antibody in HIV-1-Infected Men and in Men at Risk for HIV-1 Infection.
Adv Virol. 2011: 268214, 2011.
Full Text Article. [Journal]
27)  Kearney MF, Lee K, Bagni RK, Wiegand A, Spindler J, Maldarelli F, Pinto PA, Linehan WM, Vocke CD, Delviks-Frankenberry KA, Devere White RW, Del Prete GQ, Mellors JW, Lifson JD, Kewalramani VN, Pathak VK, Coffin JM, Le Grice SF.
Nucleic Acid, Antibody, and Virus Culture Methods to Detect Xenotropic MLV-Related Virus in Human Blood Samples.
Adv Virol. 2011: 272193, 2011.
[Journal]
28)  Jordan MR, Kearney M, Palmer S, Shao W, Maldarelli F, Coakley EP, Chappey C, Wanke C, Coffin JM.
Comparison of standard PCR/cloning to single genome sequencing for analysis of HIV-1 populations.
J. Virol. Methods. 168: 114-20, 2010.
[Journal]
29)  Kearney M, Maldarelli F.
Current status of xenotropic murine leukemia virus-related retrovirus in chronic fatigue syndrome and prostate cancer: reach for a scorecard, not a prescription pad.
J. Infect. Dis. 202: 1463-6, 2010.
[Journal]
30)  Mens H, Kearney M, Wiegand A, Shao W, Schønning K, Gerstoft J, Obel N, Maldarelli F, Mellors JW, Benfield T, Coffin JM.
HIV-1 continues to replicate and evolve in patients with natural control of HIV infection.
J. Virol. 84: 12971-81, 2010.
[Journal]
31)  Halvas EK, Wiegand A, Boltz VF, Kearney M, Nissley D, Wantman M, Hammer SM, Palmer S, Vaida F, Coffin JM, Mellors JW.
Low Frequency Nonnucleoside Reverse-Transcriptase Inhibitor-Resistant Variants Contribute to Failure of Efavirenz-Containing Regimens in Treatment-Experienced Patients.
J Infect Dis. 201: 672-680, 2010.
[Journal]
32)  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.
[Journal]
33)  McMahon D, Jones J, Wiegand A, Gange SJ, Kearney M, Palmer S, McNulty S, Metcalf JA, Acosta E, Rehm C, Coffin JM, Mellors JW, Maldarelli F.
Short-Course Raltegravir Intensification Does Not Reduce Persistent Low-Level Viremia in Patients with HIV-1 Suppression during Receipt of Combination Antiretroviral Therapy.
Clin Infect Dis. 50: 912-919, 2010.
[Journal]
34)  Gandhi RT, Zheng L, Bosch RJ, Chan ES, Margolis DM, Read S, Kallungal B, Palmer S, Medvik K, Lederman MM, Alatrakchi N, Jacobson JM, Wiegand A, Kearney M, Coffin JM, Mellors JW, Eron JJ.
The effect of raltegravir intensification on low-level residual viremia in HIV-infected patients on antiretroviral therapy: a randomized controlled trial.
PLoS Med. 7, 2010.
[Journal]
35)  Shao W, Kearney M, Maldarelli F, Mellors JW, Stephens RM, Lifson JD, KewalRamani VN, Ambrose Z, Coffin JM, Palmer SE.
RT-SHIV subpopulation dynamics in infected macaques during anti-HIV therapy.
Retrovirology. 6: 101, 2009.
[Journal]
36)  Dinoso JB, Kim SY, Wiegand AM, Palmer SE, Gange SJ, Cranmer L, O'Shea A, Callender M, Spivak A, Brennan T, Kearney MF, Proschan MA, Mican JM, Rehm CA, Coffin JM, Mellors JW, Siliciano RF, Maldarelli F.
Treatment intensification does not reduce residual HIV-1 viremia in patients on highly active antiretroviral therapy.
Proc. Natl. Acad. Sci. U.S.A. 106: 9403-8, 2009.
[Journal]
37)  Kearney M, Palmer S, Maldarelli F, Shao W, Polis MA, Mican J, Rock-Kress D, Margolick JB, Coffin JM, Mellors JW.
Frequent polymorphism at drug resistance sites in HIV-1 protease and reverse transcriptase.
AIDS. 22: 497-501, 2008.
[Journal]
38)  Ambrose Z, Palmer S, Boltz VF, Kearney M, Larsen K, Polacino P, Flanary L, Oswald K, Piatak M, Smedley J, Shao W, Bischofberger N, Maldarelli F, Kimata JT, Mellors JW, Hu SL, Coffin JM, Lifson JD, KewalRamani VN.
Suppression of viremia and evolution of human immunodeficiency virus type 1 drug resistance in a macaque model for antiretroviral therapy.
J. Virol. 81: 12145-55, 2007.
[Journal]
39)  Halvas EK, Aldrovandi GM, Balfe P, Beck IA, Boltz VF, Coffin JM, Frenkel LM, Hazelwood JD, Johnson VA, Kearney M, Kovacs A, Kuritzkes DR, Metzner KJ, Nissley DV, Nowicki M, Palmer S, Ziermann R, Zhao RY, Jennings CL, Bremer J, Brambilla D, Mellors JW.
Blinded, multicenter comparison of methods to detect a drug-resistant mutant of human immunodeficiency virus type 1 at low frequency.
J. Clin. Microbiol. 44: 2612-4, 2006.
[Journal]
40)  Palmer S, Boltz V, Maldarelli F, Kearney M, Halvas EK, Rock D, Falloon J, Davey RT, Dewar RL, Metcalf JA, Mellors JW, Coffin JM.
Selection and persistence of non-nucleoside reverse transcriptase inhibitor-resistant HIV-1 in patients starting and stopping non-nucleoside therapy.
AIDS. 20: 701-10, 2006.
[Journal]
41)  Palmer S, Kearney M, Maldarelli F, Halvas EK, Bixby CJ, Bazmi H, Rock D, Falloon J, Davey RT, Dewar RL, Metcalf JA, Hammer S, Mellors JW, Coffin JM.
Multiple, linked human immunodeficiency virus type 1 drug resistance mutations in treatment-experienced patients are missed by standard genotype analysis.
J. Clin. Microbiol. 43: 406-13, 2005.
[Journal]
42)  Achaz G, Palmer S, Kearney M, Maldarelli F, Mellors JW, Coffin JM, Wakeley J.
A robust measure of HIV-1 population turnover within chronically infected individuals.
Mol. Biol. Evol. 21: 1902-12, 2004.
[Journal]
43)  Yu Q, König R, Pillai S, Chiles K, Kearney M, Palmer S, Richman D, Coffin JM, Landau NR.
Single-strand specificity of APOBEC3G accounts for minus-strand deamination of the HIV genome.
Nat. Struct. Mol. Biol. 11: 435-42, 2004.
[Journal]
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This page was last updated on 6/28/2014.