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List of works by Mary Kearney

A robust measure of HIV-1 population turnover within chronically infected individuals.

scientific article

Acquisition of tenofovir-susceptible, emtricitabine-resistant HIV despite high adherence to daily pre-exposure prophylaxis: a case report

scientific article published on 29 November 2018

Administration of vorinostat disrupts HIV-1 latency in patients on antiretroviral therapy

scientific article

Amplifying and quantifying HIV-1 RNA in HIV infected individuals with viral loads below the limit of detection by standard clinical assays

scientific article published on 26 September 2011

Analysis of 454 sequencing error rate, error sources, and artifact recombination for detection of Low-frequency drug resistance mutations in HIV-1 DNA.

scientific article published on 13 February 2013

Baseline natural killer and T cell populations correlation with virologic outcome after regimen simplification to atazanavir/ritonavir alone (ACTG 5201).

scientific article

Blinded, multicenter comparison of methods to detect a drug-resistant mutant of human immunodeficiency virus type 1 at low frequency

scientific article

Clonally expanded CD4+ T cells can produce infectious HIV-1 in vivo

scientific article published on 8 February 2016

Clones of infected cells arise early in HIV-infected individuals

scientific article published on 20 June 2019

Combined HIV-1 sequence and integration site analysis informs viral dynamics and allows reconstruction of replicating viral ancestors

scientific article published on 27 November 2019

Comparison of standard PCR/cloning to single genome sequencing for analysis of HIV-1 populations

scientific article published on 06 May 2010

Connection subdomain mutations in HIV-1 subtype-C treatment-experienced patients enhance NRTI and NNRTI drug resistance

scientific article published on 13 October 2012

Correction: The Effect of Raltegravir Intensification on Low-level Residual Viremia in HIV-Infected Patients on Antiretroviral Therapy: A Randomized Controlled Trial.

scientific article published on 4 August 2011

Current status of xenotropic murine leukemia virus-related retrovirus in chronic fatigue syndrome and prostate cancer: reach for a scorecard, not a prescription pad.

scientific article published on 11 October 2010

Effector memory differentiation increases detection of replication-competent HIV-l in resting CD4+ T cells from virally suppressed individuals

scientific article published on 14 October 2019

Estimate of effective recombination rate and average selection coefficient for HIV in chronic infection

scientific article

Ex vivo activation of CD4+ T-cells from donors on suppressive ART can lead to sustained production of infectious HIV-1 from a subset of infected cells

scientific article

Failure to confirm XMRV/MLVs in the blood of patients with chronic fatigue syndrome: a multi-laboratory study

scientific article

False-positive HIV PCR test following ex vivo lentiviral gene transfer treatment of X-linked severe combined immunodeficiency vector

scientific article published on February 2014

Frequent polymorphism at drug resistance sites in HIV-1 protease and reverse transcriptase

scientific article

Genetic diversity of simian immunodeficiency virus encoding HIV-1 reverse transcriptase persists in macaques despite antiretroviral therapy

scientific article

HIV Infected T Cells Can Proliferate in vivo Without Inducing Expression of the Integrated Provirus

scientific article published on 01 October 2019

HIV Proviral Sequence Database: A New Public Database for Near Full-Length HIV Proviral Sequences and Their Meta-Analyses

scientific article published on 29 October 2019

HIV evolution and diversity in ART-treated patients

scientific article published on 30 January 2018

HIV latency. Specific HIV integration sites are linked to clonal expansion and persistence of infected cells

scientific article

HIV populations are large and accumulate high genetic diversity in a nonlinear fashion

scientific article published on 15 May 2013

HIV-1 continues to replicate and evolve in patients with natural control of HIV infection

scientific article

HIV-1 expression within resting CD4+ T cells after multiple doses of vorinostat

scientific article

HIV-1 in lymph nodes is maintained by cellular proliferation during antiretroviral therapy

scientific article published on 30 July 2019

HIV-1 persistence following extremely early initiation of antiretroviral therapy (ART) during acute HIV-1 infection: An observational study.

scientific article published on 7 November 2017

Histone deacetylase inhibitor romidepsin induces HIV expression in CD4 T cells from patients on suppressive antiretroviral therapy at concentrations achieved by clinical dosing

scientific article

Human immunodeficiency virus type 1 population genetics and adaptation in newly infected individuals.

scientific article published on 30 December 2008

Immediate antiviral therapy appears to restrict resting CD4+ cell HIV-1 infection without accelerating the decay of latent infection

scientific article

Immunogenicity of AGS-004 Dendritic Cell Therapy in Patients Treated During Acute HIV Infection

scientific article published on 21 June 2017

Improved single-copy assays for quantification of persistent HIV-1 viremia in patients on suppressive antiretroviral therapy

scientific article

Intact HIV Proviruses Persist in Children Seven to Nine Years after Initiation of Antiretroviral Therapy in the First Year of Life

scientific article published on 31 January 2020

Lack of detectable HIV-1 molecular evolution during suppressive antiretroviral therapy

scientific article

Limited nucleotide changes in the Rev response element (RRE) during HIV-1 infection alter overall Rev-RRE activity and Rev multimerization

scientific article

Linked dual-class HIV resistance mutations are associated with treatment failure

scientific article published on 03 October 2019

Low frequency nonnucleoside reverse-transcriptase inhibitor-resistant variants contribute to failure of efavirenz-containing regimens in treatment- experienced patients

scientific article

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.

scientific article published on 16 January 2014

Lower pre-ART intra-participant HIV-1 pol diversity may not be associated with virologic failure in adults

scientific article

Majority of CD4+ T cells from peripheral blood of HIV-1-infected individuals contain only one HIV DNA molecule

scientific article

Multiple sources of contamination in samples from patients reported to have XMRV infection

scientific article (publication date: 2012)

Multiple, linked human immunodeficiency virus type 1 drug resistance mutations in treatment-experienced patients are missed by standard genotype analysis

scientific article

No effect of raltegravir intensification on viral replication markers in the blood of HIV-1-infected patients receiving antiretroviral therapy

scientific article

No evidence of HIV replication in children on antiretroviral therapy.

scientific article published on 11 September 2017

No evidence of ongoing HIV replication or compartmentalization in tissues during combination antiretroviral therapy: Implications for HIV eradication

scientific article published on 25 September 2019

Nucleic Acid, Antibody, and Virus Culture Methods to Detect Xenotropic MLV-Related Virus in Human Blood Samples.

scientific article published on 17 November 2011

Ongoing HIV Replication During ART Reconsidered

article

Origin of Rebound Plasma HIV Includes Cells with Identical Proviruses That Are Transcriptionally Active before Stopping of Antiretroviral Therapy

scientific article

PAPNC, a novel method to calculate nucleotide diversity from large scale next generation sequencing data

scientific article

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.

scientific article

Phylogenetic inference for the study of within-host HIV-1 dynamics and persistence on antiretroviral therapy

scientific article published on 05 April 2019

Predictors of residual viraemia in patients on long-term suppressive antiretroviral therapy

scientific article published on 22 August 2012

Prevalence of XMRV nucleic acid and antibody in HIV-1-Infected men and in men at risk for HIV-1 Infection.

scientific article published on 21 November 2011

Proviruses with identical sequences comprise a large fraction of the replication-competent HIV reservoir

scientific article

RT-SHIV subpopulation dynamics in infected macaques during anti-HIV therapy

scientific article

Restricted replication of xenotropic murine leukemia virus-related virus in pigtailed macaques

scientific article published on 11 January 2012

Retrovirus Integration Database (RID): a public database for retroviral insertion sites into host genomes

scientific article published on 04 July 2016

Review: HIV-1 phylogeny during suppressive antiretroviral therapy

scientific article published on 01 May 2019

Review: Influence of ART on HIV genetics

scientific article

Selection and persistence of non-nucleoside reverse transcriptase inhibitor-resistant HIV-1 in patients starting and stopping non-nucleoside therapy.

scientific article

Short-course raltegravir intensification does not reduce persistent low-level viremia in patients with HIV-1 suppression during receipt of combination antiretroviral therapy

scientific article

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

scientific article

Single-cell analysis of HIV-1 transcriptional activity reveals expression of proviruses in expanded clones during ART.

scientific article published on 17 April 2017

Single-strand specificity of APOBEC3G accounts for minus-strand deamination of the HIV genome

scientific article (publication date: May 2004)

Suppression of viremia and evolution of human immunodeficiency virus type 1 drug resistance in a macaque model for antiretroviral therapy

scientific article

The effect of raltegravir intensification on low-level residual viremia in HIV-infected patients on antiretroviral therapy: a randomized controlled trial

scientific article

Therapeutic Vaccination With Dendritic Cells Loaded With Autologous HIV Type 1-Infected Apoptotic Cells

scientific article published on 8 December 2015

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

scientific article

Ultrasensitive single-genome sequencing: accurate, targeted, next generation sequencing of HIV-1 RNA.

scientific article

Well-mixed plasma and tissue viral populations in RT-SHIV-infected macaques implies a lack of viral replication in the tissues during antiretroviral therapy

scientific article

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