M. Kearney

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

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

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

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 drug resistance in various body compartments

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

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

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

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

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

Proceedings of the Frontiers of Retrovirology Conference 2016

R. König, D. Elleder, R. Sachidanandam, 2016, Retrovirology.

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.

HIV Populations Are Large and Accumulate High Genetic Diversity in a Nonlinear Fashion

R. Stephens, J. Metcalf, R. Davey, 2013, Journal of Virology.

1 HIV Populations are Large and Accumulate High Genetic Diversity in Nonlinear

R. Stephens, J. Metcalf, R. Davey, 2013 .

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.

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.

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.

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

Claudia Stewart, Natalia Volfovsky, Wei Shao, 2013, Retrovirology.

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.

Limited Nucleotide Changes in the Rev Response Element (RRE) during HIV-1 Infection Alter Overall Rev-RRE Activity and Rev Multimerization

J. Margolick, K. Anastos, E. Daar, 2013, Journal of Virology.

Integration in 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, 2021, PLoS pathogens.

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.

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

R. Siliciano, D. Richman, D. Kuritzkes, 2017, PLoS medicine.

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

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

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

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

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

John W. Mellors, John M. Coffin, Wei Shao, 2016, Retrovirology.

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.

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.

Clones of infected cells arise early in HIV-infected individuals.

S. Hughes, J. Mellors, B. Luke, 2019, JCI insight.

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

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

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.

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

S. Hughes, J. Mellors, J. Coffin, 2014, Science.

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

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

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.

HIV Population Dynamics

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

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.

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.

1 Title : Improved Single Copy Assays for Quantification of Persistent HIV-1 Viremia in 1 Patients on Suppressive Antiretroviral Therapy 2 3

J. Mellors, J. Coffin, M. Piatak, 2014 .

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.

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

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

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.

Low genetic diversity may be an Achilles heel of SARS-CoV-2

M. Kearney, Mary F. Kearney, J. Rausch, 2020, Proceedings of the National Academy of Sciences.

HIV evolution and diversity in ART-treated patients

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

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.

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.

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

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

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.

Review: influence of ART on HIV genetics

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

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

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

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.

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.

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

J. Mellors, J. Coffin, F. Maldarelli, 2016, Retrovirology.

HIV-1 Persistence in Children during Suppressive ART

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

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.

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

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

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

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

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.

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.

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.

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

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

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.

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.

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.

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.

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.

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

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

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

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

Intact HIV Proviruses Persist in Children 7-9 Years after Initiation of ART in the First Year of Life

Wei-Shau Hu, J. Mellors, Imogen A. Wright, 2019, SSRN Electronic Journal.

Ongoing HIV Replication During ART Reconsidered

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

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.

Therapeutic implications of ongoing alveolar viral replication in COVID-19

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

Use of Drug-level Testing and Single-genome Sequencing to Unravel a Case of Human Immunodeficiency Virus Seroconversion on Pre-exposure Prophylaxis

R. Grant, P. Defechereux, M. Gandhi, 2020, Clinical Infectious Diseases.

Acquisition of tenofovir-susceptible HIV despite consistently high level adherence to daily PrEP as measured by plasma, dried blood spot (DBS) and segmental hair analysis: a case report

R. Grant, D. Sachdev, S. Scheer, 2019 .

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

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

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

S. Hughes, J. Coffin, J. Gray, 2014, Molecular therapy : the journal of the American Society of Gene Therapy.

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.

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.

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.

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

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

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.

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.

HIV evolution and diversity in ART-treated patients

M. Kearney, M. Bale, G. V. van Zyl, 2018, Retrovirology.

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

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

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.

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

R. Stephens, J. Mellors, N. Volfovsky, 2013, Retrovirology.

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.

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 (cid:1) †

O. Nikolaitchik, V. Pathak, Wei-Shau Hu, 2010 .

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.

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

S. Hughes, J. Mellors, B. Luke, 2016, Retrovirology.

Proceedings of the Frontiers of Retrovirology Conference 2016

Sebastian A. Wagner, R. König, D. Elleder, 2016, Retrovirology.

Application of ultrasensitive digital ELISA for p24 enables improved evaluation of HIV-1 reservoir diversity and growth kinetics in viral outgrowth assays

R. Ptak, C. Lackman-Smith, S. Bakkour, 2023, Scientific reports.