Clonal CD4+ T cells in the HIV-1 latent reservoir display a distinct gene profile upon reactivation

Clonal expansion of genome-intact HIV-1 in functionally polarized Th1 CD4+ T cells

(2017) Guinevere Q. Lee et al.   JOURNAL OF CLINICAL INVESTIGATION

Proliferation of latently infected CD4+T cells carrying replication-competent HIV-1: Potential role in latent reservoir dynamics

(2017) Nina N. Hosmane et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Measuring the Size of the Latent Human Immunodeficiency Virus Reservoir: The Present and Future of Evaluating Eradication Strategies

(2017) Timothy J. Henrich et al.   JOURNAL OF INFECTIOUS DISEASES

Clonal Expansion of Human Immunodeficiency Virus–Infected Cells and Human Immunodeficiency Virus Persistence During Antiretroviral Therapy

(2017) James I. Mullins et al.   JOURNAL OF INFECTIOUS DISEASES

CD32a is a marker of a CD4 T-cell HIV reservoir harbouring replication-competent proviruses

(2017) Benjamin Descours et al.   NATURE

SC3: consensus clustering of single-cell RNA-seq data

(2017) Vladimir Yu Kiselev et al.   NATURE METHODS

Dissecting How CD4 T Cells Are Lost During HIV Infection

(2016) Gilad Doitsh et al.   Cell Host & Microbe

Single-Cell Characterization of Viral Translation-Competent Reservoirs in HIV-Infected Individuals

(2016) Amy E. Baxter et al.   Cell Host & Microbe

The Latent Reservoir for HIV-1: How Immunologic Memory and Clonal Expansion Contribute to HIV-1 Persistence

(2016) Alexandra J. Murray et al.   JOURNAL OF IMMUNOLOGY

Defective proviruses rapidly accumulate during acute HIV-1 infection

(2016) Katherine M Bruner et al.   NATURE MEDICINE

T cell fate and clonality inference from single-cell transcriptomes

(2016) Michael J T Stubbington et al.   NATURE METHODS

Paired quantitative and qualitative assessment of the replication-competent HIV-1 reservoir and comparison with integrated proviral DNA

(2016) Julio C. C. Lorenzi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2016) Francesco R. Simonetti et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Visualizing antibody affinity maturation in germinal centers

(2016) J. M. J. Tas et al.   SCIENCE

Enhanced clearance of HIV-1-infected cells by broadly neutralizing antibodies against HIV-1 in vivo

(2016) C.-L. Lu et al.   SCIENCE

CD4+ T Cells Expressing PD-1, TIGIT and LAG-3 Contribute to HIV Persistence during ART

(2016) Rémi Fromentin et al.   PLoS Pathogens

IVA: accuratede novoassembly of RNA virus genomes

(2015) Martin Hunt et al.   BIOINFORMATICS

Single-Cell Genomics Unveils Critical Regulators of Th17 Cell Pathogenicity

(2015) Jellert T. Gaublomme et al.   CELL

HIV-1 Integration Landscape during Latent and Active Infection

(2015) Lillian B. Cohn et al.   CELL

MicroRNA-155 Reinforces HIV Latency

(2015) Debbie S. Ruelas et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Blimp-1, an Intrinsic Factor that Represses HIV-1 Proviral Transcription in Memory CD4+T Cells

(2015) Katarzyna Kaczmarek Michaels et al.   JOURNAL OF IMMUNOLOGY

Precise Quantitation of the Latent HIV-1 Reservoir: Implications for Eradication Strategies

(2015) Amanda M. Crooks et al.   JOURNAL OF INFECTIOUS DISEASES

Spatial reconstruction of single-cell gene expression data

(2015) Rahul Satija et al.   NATURE BIOTECHNOLOGY

Gene activity in primary T cells infected with HIV89.6: intron retention and induction of genomic repeats

(2015) Scott Sherrill-Mix et al.   Retrovirology

Blimp-1 overexpression is associated with low HIV-1 reservoir and transcription levels in central memory CD4+ T cells from elite controllers

(2014) Adèle de Masson et al.   AIDS

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

Linking T-cell receptor sequence to functional phenotype at the single-cell level

(2014) Arnold Han et al.   NATURE BIOTECHNOLOGY

CD4+ and CD8+ T Cell Activation Are Associated with HIV DNA in Resting CD4+ T Cells

(2014) Leslie R. Cockerham et al.   PLoS One

Proliferation of cells with HIV integrated into cancer genes contributes to persistent infection

(2014) T. A. Wagner et al.   SCIENCE

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

(2014) F. Maldarelli et al.   SCIENCE

Replication-Competent Noninduced Proviruses in the Latent Reservoir Increase Barrier to HIV-1 Cure

(2013) Ya-Chi Ho et al.   CELL

Quantitative single-cell RNA-seq with unique molecular identifiers

(2013) Saiful Islam et al.   NATURE METHODS

HIV Latency

(2013) R. F. Siliciano et al.   Cold Spring Harbor Perspectives in Medicine

An In-Depth Comparison of Latent HIV-1 Reactivation in Multiple Cell Model Systems and Resting CD4+ T Cells from Aviremic Patients

(2013) Celsa A. Spina et al.   PLoS Pathogens

Rapid Quantification of the Latent Reservoir for HIV-1 Using a Viral Outgrowth Assay

(2013) Gregory M. Laird et al.   PLoS Pathogens

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Engagement of NKp30 on V 1 T cells induces the production of CCL3, CCL4, and CCL5 and suppresses HIV-1 replication

(2012) K. Hudspeth et al.   BLOOD

Complex-type N-glycan recognition by potent broadly neutralizing HIV antibodies

(2012) H. Mouquet et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Different B Cell Populations Mediate Early and Late Memory During an Endogenous Immune Response

(2011) K. A. Pape et al.   SCIENCE

Sequence and Structural Convergence of Broad and Potent HIV Antibodies That Mimic CD4 Binding

(2011) J. F. Scheid et al.   SCIENCE

Broad and Potent Neutralizing Antibodies from an African Donor Reveal a New HIV-1 Vaccine Target

(2009) L. M. Walker et al.   SCIENCE