Mary F. Kearney

Simon C Watkins, Janet S. Lee, J. Mellors, 2021, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.

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

S. Hughes, J. Mellors, J. Coffin, 2019, The Journal of clinical investigation.

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

M. Lederman, J. Mellors, J. Coffin, 2015, Journal of Virology.

HIV evolution and diversity in ART-treated patients

G. V. Van Zyl, M. Kearney, Mary F. Kearney, 2018, Retrovirology.

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

P. Lemey, J. Casazza, J. Mellors, 2013, PLoS pathogens.

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

Wei Shao, Jan Albert, Jianbo Chen, 2011, Proceedings of the National Academy of Sciences.

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.

M. Hughes, R. Schooley, J. Mellors, 2014, The Journal of infectious diseases.

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

R. Ptak, M. Busch, S. Deeks, 2019, PLoS pathogens.

No Effect of Raltegravir Intensification on Viral Replication Markers in the Blood of HIV-1–Infected Patients Receiving Antiretroviral Therapy

John W. Mellors, Robert W. Coombs, Michael M. Lederman, 2012, Journal of acquired immune deficiency syndromes.

Failure to Confirm XMRV/MLVs in the Blood of Patients with Chronic Fatigue Syndrome: A Multi-Laboratory Study

W. Heneine, A. Komaroff, S. Glynn, 2011, Science.

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

S. Hughes, J. Mellors, B. Luke, 2017, PLoS pathogens.

Multiple, Linked Human Immunodeficiency Virus Type 1 Drug Resistance Mutations in Treatment-Experienced Patients Are Missed by Standard Genotype Analysis

John W. Mellors, John M. Coffin, Sarah Palmer, 2005, Journal of Clinical Microbiology.

Predictors of Residual Viraemia in Patients on Long-Term Suppressive Antiretroviral Therapy

J. Mellors, R. Bosch, D. Margolis, 2012, Antiviral therapy.

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

M. Lederman, J. Mellors, J. Coffin, 2010, PLoS medicine.

Treatment intensification does not reduce residual HIV-1 viremia in patients on highly active antiretroviral therapy

S J Gange, M A Proschan, R. Siliciano, 2009, Proceedings of the National Academy of Sciences.

Predictors of Residual Viremia in Patients on Long-term Suppressive Antiretroviral Therapy

J. Mellors, R. Bosch, J. Eron, 2013 .

New Approaches to Multi-Parametric HIV-1 Genetics Using Multiple Displacement Amplification: Determining the What, How, and Where of the HIV-1 Reservoir

F. Maldarelli, M. Kearney, Mary F. Kearney, 2021, Viruses.

CpG Methylation Profiles of HIV-1 Proviral DNA in Individuals on ART

J. Coffin, B. Keele, S. Deeks, 2021, Viruses.

Early Emergence and Long-Term Persistence of HIV-Infected T-Cell Clones in Children

S. Hughes, J. Mellors, J. Coffin, 2021, mBio.

Integration in or Near Oncogenes Plays Only a Minor Role in Determining the in Vivo Distribution of HIV Integration Sites Before or During Suppressive Antiretroviral Therapy

S. Hughes, J. Mellors, B. Luke, 2020, bioRxiv.

Early Emergence and Long-Term Persistence of HIV-Infected T Cell Clones in Children

S. Hughes, J. Mellors, J. Coffin, 2020, bioRxiv.

HIV-1 Viremia Not Suppressible By Antiretroviral Therapy Can Originate from Large T-Cell Clones Producing Infectious Virus

S. Hughes, J. Mellors, J. Coffin, 2020, bioRxiv.

No evidence of HIV replication in children on antiretroviral therapy.

J. Mellors, B. Luke, J. Coffin, 2017, The Journal of clinical investigation.

Ongoing HIV Replication During ART Reconsidered

J. Mellors, B. Luke, J. Coffin, 2017, Open forum infectious diseases.

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

S. Hughes, J. Kovacs, M. Polis, 2016, Proceedings of the National Academy of Sciences.

Lack of Detectable HIV-1 Molecular Evolution during Suppressive Antiretroviral Therapy

J. Mellors, J. Coffin, Nicholas A. Kovacs, 2014, PLoS pathogens.

NanoHIV: A Bioinformatics Pipeline for Producing Accurate, Near Full-Length HIV Proviral Genomes Sequenced Using the Oxford Nanopore Technology

Imogen A. Wright, M. Kearney, S. Engelbrecht, 2021, Cells.

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

Wei-Shau Hu, J. Mellors, J. Coffin, 2020, AIDS research and human retroviruses.

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

J. Mellors, J. Coffin, F. Maldarelli, 2011, Journal of visualized experiments : JoVE.

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

D. Hazuda, D. Richman, J. Coffin, 2014, The Journal of infectious diseases.

B-108 Specific HIV integration sites are linked to clonal expansion and persistence of infected cells

S. Hughes, J. Mellors, J. Coffin, 2016 .

The largest HIV-1-infected T cell clones in children on long-term combination antiretroviral therapy contain solo LTRs

S. Hughes, J. Mellors, G. V. Van Zyl, 2023, mBio.

Deep Sequencing Analysis of Individual HIV-1 Proviruses Reveals Frequent Asymmetric Long Terminal Repeats

S. Mallal, J. Mellors, J. Coffin, 2022, Journal of virology.

Engineered Bacteriophage T4 Nanoparticle as a Potential Targeted Activator of HIV-1 Latency in CD4+ Human T-cells

V. Rao, F. Maldarelli, Jingen Zhu, 2021, bioRxiv.

Tracking HIV-1-Infected Cell Clones Using Integration Site-Specific qPCR

S. Hughes, J. Mellors, J. Coffin, 2021, Viruses.

HIV-1 Persistence in Children during Suppressive ART

G. V. Van Zyl, M. Cotton, M. Kearney, 2021, Viruses.

Dynamic Shifts in the HIV Proviral Landscape During Long Term Combination Antiretroviral Therapy: Implications for Persistence and Control of HIV Infections

S. Hughes, E. Boritz, J. Coffin, 2020, Viruses.

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

S. Hughes, E. Boritz, J. Mellors, 2019, Front. Microbiol..

Review: HIV-1 phylogeny during suppressive antiretroviral therapy

M. Kearney, Mary F. Kearney, M. Bale, 2019, Current opinion in HIV and AIDS.

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

M. Kearney, Mary F. Kearney, M. Bale, 2019, The lancet. HIV.

Review

M. Kearney, Mary F. Kearney, M. Bale, 2019, Current Opinion in HIV and AIDS.

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

J. Mellors, B. Luke, W. Shao, 2017, PLoS pathogens.

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

J. Mellors, J. Coffin, Z. Ambrose, 2015, Retrovirology.

Review: influence of ART on HIV genetics

M. Kearney, Mary F. Kearney, F. Simonetti, 2015, Current opinion in HIV and AIDS.

HIV-1 in Lymph Nodes is Maintained by Cellular Proliferation During Antiretroviral 1 Therapy 2 3

Patro, S. Hughes, J. Mellors, 2019 .

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

S. Hammer, F. Vaida, J. Mellors, 2010, The Journal of infectious diseases.

Blinded, Multicenter Comparison of Methods To Detect a Drug-Resistant Mutant of Human Immunodeficiency Virus Type 1 at Low Frequency

Ingrid A. Beck, K. Metzner, V. Johnson, 2006, Journal of Clinical Microbiology.

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

Sarah Palmer, R. Dewar, J. Metcalf, 2006, AIDS.

Low Frequency NNRTI-Resistant Variants Contribute to Failure of Efavirenz-Containing Regimens in Treatment-Experienced Patients

S. Hammer, F. Vaida, J. Coffin, 2010 .

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

A. Perelson, J. Coffin, R. Bosch, 2012, Proceedings of the National Academy of Sciences.

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

M. Hughes, R. Haubrich, J. Mellors, 2018, PloS one.

Plasma SARS-CoV-2 RNA levels as a biomarker of lower respiratory tract SARS-CoV-2 infection in critically ill patients with COVID-19.

Janet S. Lee, J. Mellors, A. Naqvi, 2022, medRxiv.

Therapeutic implications of ongoing alveolar viral replication in COVID-19

L. Quartuccio, D. McGonagle, A. O’Regan, 2021, The Lancet Rheumatology.

Mechanistic Analysis of the Broad Antiretroviral Resistance Conferred by HIV-1 Envelope Glycoprotein Mutations

J. Mellors, E. Freed, Y. Hikichi, 2020, mBio.

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

Wei-Shau Hu, J. Mellors, Imogen A. Wright, 2019, Journal of Virology.

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

Rebecca Batorsky, Igor M Rouzine, J. Coffin, 2011, Proceedings of the National Academy of Sciences.

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

J. Coffin, C. Chappey, F. Maldarelli, 2010, Journal of virological methods.

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

Wei Shao, Sarah Palmer, J. Margolick, 2008, AIDS.

Highlights from the Tenth International Workshop on HIV Persistence during Therapy, December 13-16, 2022, Miami, Florida-USA

D. Kuritzkes, J. Martinez-Picado, T. Burdo, 2023, Journal of virus eradication.

A Pre-Vaccination Baseline of SARS-CoV-2 Genetic Surveillance and Diversity in the United States

J. Coffin, M. Kearney, Mary F. Kearney, 2022, Viruses.

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

M. Soares, V. Pathak, K. Delviks-Frankenberry, 2013, Virology.

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

S J Gange, S. Gange, J. Metcalf, 2010, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.

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

Z. Grossman, D. Kleiner, R. Gorelick, 2019, Science Advances.

Histone Deacetylase Inhibitor Romidepsin Induces HIV Expression in CD4 T Cells from Patients on Suppressive Antiretroviral Therapy at Concentrations Achieved by Clinical Dosing

C. Spina, J. Mellors, Helen Yu, 2014, PLoS pathogens.

2020 SARS-CoV-2 diversification in the United States: Establishing a pre-vaccination baseline

J. Coffin, W. Shao, M. Kearney, 2021, medRxiv.

Multiple Sources of Contamination in Samples from Patients Reported to Have XMRV Infection

S. Hughes, J. Mellors, J. Coffin, 2012, PloS one.

Restricted Replication of Xenotropic Murine Leukemia Virus-Related Virus in Pigtailed Macaques

K. Nagashima, V. Pathak, J. Lifson, 2012, Journal of Virology.

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

O. Nikolaitchik, V. Pathak, Wei-Shau Hu, 2010, Journal of Virology.

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

F. Maldarelli, M. Kearney, Mary F. Kearney, 2010, The Journal of infectious diseases.

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

M. Soares, V. Pathak, K. Delviks-Frankenberry, 2013, Virology.

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

R. Stephens, J. Lifson, J. Mellors, 2009, Retrovirology.

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

M. Hughes, R. Schooley, J. Mellors, 2019, JCI insight.

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.

M. Hughes, R. Schooley, J. Mellors, 2014, Journal of Infectious Diseases.

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. Mellors, J. Coffin, V. KewalRamani, 2012, Journal of Virology.

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

J. Coffin, D. Margolis, N. Archin, 2017, AIDS research and human retroviruses.

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

J. Mellors, C. Rinaldo, T. Whiteside, 2016, The Journal of infectious diseases.

HIV Population Dynamics

J. Coffin, M. Kearney, Mary F. Kearney, 2013 .

Baseline Natural Killer and T Cell Populations Correlation with Virologic Outcome after Regimen Simplification to Atazanavir/Ritonavir Alone (ACTG 5201)

J. Mellors, C. Rinaldo, S. Swindells, 2014, PloS one.

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

G Achaz, J. Mellors, J. Coffin, 2004, Molecular biology and evolution.

Suppression of Viremia and Evolution of Human Immunodeficiency Virus Type 1 Drug Resistance in a Macaque Model for Antiretroviral Therapy

J. Lifson, J. Mellors, J. Coffin, 2007, Journal of Virology.

HIV drug resistance in various body compartments

J. Dorfman, G. V. Van Zyl, M. Kearney, 2022, Current opinion in HIV and AIDS.

No evidence of HIV replication in children on antiretroviral therapy.

J. Mellors, B. Luke, J. Coffin, 2017, The Journal of clinical investigation.

Genetic Diversity of Simian Immunodeficiency Virus Encoding HIV-1 Reverse Transcriptase Persists in Macaques despite Antiretroviral Therapy

J. Lifson, J. Mellors, J. Coffin, 2010, Journal of Virology.

Therapeutic vaccination expands and improves the function of the HIV-specific memory T-cell repertoire.

R. Gottardo, R. Koup, C. Andrews, 2013, The Journal of infectious diseases.

HIV Expression in Infected T Cell Clones

Mary F. Kearney, J. Rausch, A. Capoferri, 2024, Viruses.

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

J. Mellors, B. Luke, J. Coffin, 2016, Retrovirology.

Current HIV/SIV Reservoir Assays for Preclinical and Clinical Applications: Recommendations from the Experts 2022 NIAID Workshop Summary.

Brigitte E. Sanders-Beer, R. Siliciano, J. Karn, 2023, AIDS research and human retroviruses.

HIVIntact: a python-based tool for HIV-1 genome intactness inference

Wei-Shau Hu, J. Coffin, Imogen A. Wright, 2021, Retrovirology.

HIV-1 Continues To Replicate and Evolve in Patients with Natural Control of HIV Infection

J. Mellors, J. Coffin, F. Maldarelli, 2010, Journal of Virology.

Human Immunodeficiency Virus Type 1 Population Genetics and Adaptation in Newly Infected Individuals

J. Margolick, J. Mellors, J. Coffin, 2008, Journal of Virology.

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

Wei Shao, R. Stephens, J. Lifson, 2009, Retrovirology.

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

J. Margolick, M. Polis, J. Mellors, 2008, AIDS.

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

D. Havlir, R. Grant, Stephanie E Cohen, 2018, The lancet. HIV.