Single-Cell Sequencing Facilitates Elucidation of HIV Immunopathogenesis: A Review of Current Literature

Population Impact and Efficiency of Improvements to HIV PrEP Under Conditions of High ART Coverage among San Francisco Men Who Have Sex with Men

(2021) Adrien Le Guillou et al.   JAIDS-JOURNAL OF ACQUIRED IMMUNE DEFICIENCY SYNDROMES

Leveraging Novel Integrated Single-Cell Analyses to Define HIV-1 Latency Reversal

(2021) Suhui Zhao et al.   Viruses-Basel

Combined single-cell transcriptional, translational, and genomic profiling reveals HIV-1 reservoir diversity

(2021) Gérémy Sannier et al.   Cell Reports

Selective elimination of host cells harboring replication-competent human immunodeficiency virus reservoirs: a promising therapeutic strategy for HIV cure

(2021) Silvere D. Zaongo et al.   CHINESE MEDICAL JOURNAL

Preclinical and clinical studies on bryostatins, a class of marine-derived protein kinase C modulators: A mini-review

(2020) Rinky Raghuvanshi et al.   CURRENT TOPICS IN MEDICINAL CHEMISTRY

Integrated single-cell analysis of multicellular immune dynamics during hyperacute HIV-1 infection

(2020) Samuel W. Kazer et al.   NATURE MEDICINE

Single-cell transcriptional landscapes reveal HIV-1–driven aberrant host gene transcription as a potential therapeutic target

(2020) Runxia Liu et al.   Science Translational Medicine

Identification of pathogenic TRAIL-expressing innate immune cells during HIV-1 infection in humanized mice by scRNA-seq

(2020) Liang Cheng et al.   JCI Insight

Single-cell sequencing techniques from individual to multiomics analyses

(2020) Yukie Kashima et al.   EXPERIMENTAL AND MOLECULAR MEDICINE

Recommendations for measuring HIV reservoir size in cure-directed clinical trials

(2020) Mohamed Abdel-Mohsen et al.   NATURE MEDICINE

An Atlas of Immune Cell Exhaustion in HIV-Infected Individuals Revealed by Single-Cell Transcriptomics

(2020) Shaobo Wang et al.   Emerging Microbes & Infections

Distinct gut microbiota profile in ART-treated perinatally HIV-infected patients associated with cardiac and inflammatory biomarkers

(2019) Libera Sessa et al.   AIDS

The single-cell transcriptional landscape of mammalian organogenesis

(2019) Junyue Cao et al.   NATURE

A quantitative approach for measuring the reservoir of latent HIV-1 proviruses

(2019) Katherine M. Bruner et al.   NATURE

Evolution of the gut microbiome following acute HIV-1 infection

(2019) Muntsa Rocafort et al.   Microbiome

Immunology Driven by Large-Scale Single-Cell Sequencing

(2019) Tomás Gomes et al.   TRENDS IN IMMUNOLOGY

Elite control of HIV is associated with distinct functional and transcriptional signatures in lymphoid tissue CD8+ T cells

(2019) Son Nguyen et al.   Science Translational Medicine

Single-Cell Genomics: A Stepping Stone for Future Immunology Discoveries

(2018) Amir Giladi et al.   CELL

Mapping the Mouse Cell Atlas by Microwell-Seq

(2018) Xiaoping Han et al.   CELL

Single-cell RNA sequencing: Technical advancements and biological applications

(2018) Eva Hedlund et al.   MOLECULAR ASPECTS OF MEDICINE

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

(2018) Lillian B. Cohn et al.   NATURE MEDICINE

Single-Cell RNA-Seq Reveals Transcriptional Heterogeneity in Latent and Reactivated HIV-Infected Cells

(2018) Monica Golumbeanu et al.   Cell Reports

Association Between Gut Microbiota and CD4 Recovery in HIV-1 Infected Patients

(2018) Wei Lu et al.   Frontiers in Microbiology

Relationship between intact HIV-1 proviruses in circulating CD4+ T cells and rebound viruses emerging during treatment interruption

(2018) Ching-Lan Lu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Single-Cell Analysis of Quiescent HIV Infection Reveals Host Transcriptional Profiles that Regulate Proviral Latency

(2018) Todd Bradley et al.   Cell Reports

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

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

Ultrasensitive HIV-1 p24 Assay Detects Single Infected Cells and Differences in Reservoir Induction by Latency Reversal Agents

(2017) Caroline Pereira Bittencourt Passaes et al.   JOURNAL OF VIROLOGY

Massively parallel single-nucleus RNA-seq with DroNc-seq

(2017) Naomi Habib et al.   NATURE METHODS

Seq-Well: portable, low-cost RNA sequencing of single cells at high throughput

(2017) Todd M Gierahn et al.   NATURE METHODS

Comprehensive single-cell transcriptional profiling of a multicellular organism

(2017) Junyue Cao et al.   SCIENCE

Mapping the human DC lineage through the integration of high-dimensional techniques

(2017) Peter See et al.   SCIENCE

Single-cell RNA-seq reveals new types of human blood dendritic cells, monocytes, and progenitors

(2017) Alexandra-Chloé Villani et al.   SCIENCE

Single-cell analyses to tailor treatments

(2017) Alex K. Shalek et al.   Science Translational Medicine

Massively parallel digital transcriptional profiling of single cells

(2017) Grace X. Y. Zheng et al.   Nature Communications

Perturbed CD8+ T cell TIGIT/CD226/PVR axis despite early initiation of antiretroviral treatment in HIV infected individuals

(2017) Johanna Tauriainen et al.   Scientific Reports

Identification of Genetically Intact HIV-1 Proviruses in Specific CD4 + T Cells from Effectively Treated Participants

(2017) Bonnie Hiener et al.   Cell Reports

The Human Cell Atlas

(2017) Aviv Regev et al.   eLife

High-throughput Characterization of HIV-1 Reservoir Reactivation Using a Single-Cell-in-Droplet PCR Assay

(2017) Robert W. Yucha et al.   EBioMedicine

Richer gut microbiota with distinct metabolic profile in HIV infected Elite Controllers

(2017) Jan Vesterbacka et al.   Scientific Reports

Dissecting Immune Circuits by Linking CRISPR-Pooled Screens with Single-Cell RNA-Seq

(2016) Diego Adhemar Jaitin et al.   CELL

Perturb-Seq: Dissecting Molecular Circuits with Scalable Single-Cell RNA Profiling of Pooled Genetic Screens

(2016) Atray Dixit et al.   CELL

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

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

Incidence and Prevalence of Opportunistic and Other Infections and the Impact of Antiretroviral Therapy Among HIV-infected Children in Low- and Middle-income Countries: A Systematic Review and Meta-analysis

(2016) Marie-Renée B-Lajoie et al.   CLINICAL INFECTIOUS DISEASES

Incidence of Opportunistic Infections and the Impact of Antiretroviral Therapy Among HIV-Infected Adults in Low- and Middle-Income Countries: A Systematic Review and Meta-analysis

(2016) Andrea Low et al.   CLINICAL INFECTIOUS DISEASES

Interleukin 32: a novel player in the control of infectious diseases

(2016) Fátima Ribeiro-Dias et al.   JOURNAL OF LEUKOCYTE BIOLOGY

Identification of innate immune antiretroviral factors during in vivo and in vitro exposure to HIV-1

(2016) Wildeman Zapata et al.   MICROBES AND INFECTION

The heterogeneity of human CD127+ innate lymphoid cells revealed by single-cell RNA sequencing

(2016) Åsa K Björklund et al.   NATURE IMMUNOLOGY

Defective proviruses rapidly accumulate during acute HIV-1 infection

(2016) Katherine M Bruner et al.   NATURE MEDICINE

The STRING database in 2017: quality-controlled protein–protein association networks, made broadly accessible

(2016) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

Specification of tissue-resident macrophages during organogenesis

(2016) E. Mass et al.   SCIENCE

Lessons from acute HIV infection

(2016) Merlin L. Robb et al.   Current Opinion in HIV and AIDS

Gut microbiota diversity predicts immune status in HIV-1 infection

(2015) Piotr Nowak et al.   AIDS

Droplet Barcoding for Single-Cell Transcriptomics Applied to Embryonic Stem Cells

(2015) Allon M. Klein et al.   CELL

Transcriptional Heterogeneity and Lineage Commitment in Myeloid Progenitors

(2015) Franziska Paul et al.   CELL

Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets

(2015) Evan Z. Macosko et al.   CELL

Identification of cDC1- and cDC2-committed DC progenitors reveals early lineage priming at the common DC progenitor stage in the bone marrow

(2015) Andreas Schlitzer et al.   NATURE IMMUNOLOGY

Single-Cell and Single-Cycle Analysis of HIV-1 Replication

(2015) Mowgli Holmes et al.   PLoS Pathogens

Interleukin-32 isoforms: expression, interaction with interferon-regulated genes and clinical significance in chronically HIV-1-infected patients

(2014) Katia Monteleone et al.   MEDICAL MICROBIOLOGY AND IMMUNOLOGY

Full-length RNA-seq from single cells using Smart-seq2

(2014) Simone Picelli et al.   Nature Protocols

Impact of Antiretroviral Therapy on Opportunistic Infections of HIV-infected Children in the Therapeutic Research, Education and AIDS Training Asia Pediatric HIV Observational Database

(2014) Wasana Prasitsuebsai et al.   PEDIATRIC INFECTIOUS DISEASE JOURNAL

Immunologic strategies for HIV-1 remission and eradication

(2014) D. H. Barouch et al.   SCIENCE

Massively Parallel Single-Cell RNA-Seq for Marker-Free Decomposition of Tissues into Cell Types

(2014) D. A. Jaitin et al.   SCIENCE

T-bet and Eomes Are Differentially Linked to the Exhausted Phenotype of CD8+ T Cells in HIV Infection

(2014) Marcus Buggert et al.   PLoS Pathogens

Dynamics of HIV Latency and Reactivation in a Primary CD4+ T Cell Model

(2014) Pejman Mohammadi et al.   PLoS Pathogens

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

(2013) Ya-Chi Ho et al.   CELL

Immune restoration after antiretroviral therapy: the pitfalls of hasty or incomplete repairs

(2013) Eleanor M. P. Wilson et al.   IMMUNOLOGICAL REVIEWS

Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells

(2013) Alex K. Shalek et al.   NATURE

Quantitative single-cell RNA-seq with unique molecular identifiers

(2013) Saiful Islam et al.   NATURE METHODS

Smart-seq2 for sensitive full-length transcriptome profiling in single cells

(2013) Simone Picelli et al.   NATURE METHODS

Reduced Inflammation and Lymphoid Tissue Immunopathology in Rhesus Macaques Receiving Anti–Tumor Necrosis Factor Treatment During Primary Simian Immunodeficiency Virus Infection

(2012) Brian Tabb et al.   JOURNAL OF INFECTIOUS DISEASES

Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells

(2012) Daniel Ramsköld et al.   NATURE BIOTECHNOLOGY

IL-7 signaling and CD127 receptor regulation in the control of T cell homeostasis

(2012) Florent Carrette et al.   SEMINARS IN IMMUNOLOGY

Microbial translocation, immune activation, and HIV disease

(2012) Nichole R. Klatt et al.   TRENDS IN MICROBIOLOGY

CEL-Seq: Single-Cell RNA-Seq by Multiplexed Linear Amplification

(2012) Tamar Hashimshony et al.   Cell Reports

Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq

(2011) S. Islam et al.   GENOME RESEARCH

A human memory T cell subset with stem cell–like properties

(2011) Luca Gattinoni et al.   NATURE MEDICINE

Prevention of HIV-1 Infection with Early Antiretroviral Therapy

(2011) Myron S. Cohen et al.   NEW ENGLAND JOURNAL OF MEDICINE

Adherence to Antiretroviral Therapy and HIV Transmission Risks: Implications for Test-and-Treat Approaches to HIV Prevention

(2010) Seth C. Kalichman et al.   AIDS PATIENT CARE AND STDS

Antiretroviral therapy and management of HIV infection

(2010) Paul A Volberding et al.   LANCET

Incomplete Peripheral CD4+Cell Count Restoration in HIV‐Infected Patients Receiving Long‐Term Antiretroviral Treatment

(2009) Colleen F. Kelley et al.   CLINICAL INFECTIOUS DISEASES

The TRAIL to Viral Pathogenesis: The Good, the Bad and the Ugly

(2009) Nathan Cummins et al.   CURRENT MOLECULAR MEDICINE

HIV reservoir size and persistence are driven by T cell survival and homeostatic proliferation

(2009) Nicolas Chomont et al.   NATURE MEDICINE

mRNA-Seq whole-transcriptome analysis of a single cell

(2009) Fuchou Tang et al.   NATURE METHODS

Immune dysregulation in human immunodeficiency virus infection: know it, fix it, prevent it?

(2008) A. Boasso et al.   JOURNAL OF INTERNAL MEDICINE