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

Lymphocyte innateness defined by transcriptional states reflects a balance between proliferation and effector functions

(2019) Maria Gutierrez-Arcelus et al.   Nature Communications

Fast interpolation-based t-SNE for improved visualization of single-cell RNA-seq data

(2019) George C. Linderman et al.   NATURE METHODS

A comparison of single-cell trajectory inference methods

(2019) Wouter Saelens et al.   NATURE BIOTECHNOLOGY

TCR sequencing paired with massively parallel 3′ RNA-seq reveals clonotypic T cell signatures

(2019) Ang A. Tu et al.   NATURE IMMUNOLOGY

Immunology Driven by Large-Scale Single-Cell Sequencing

(2019) Tomás Gomes et al.   TRENDS IN IMMUNOLOGY

Integrating single-cell transcriptomic data across different conditions, technologies, and species

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

Single-cell transcriptional profiling: a window into embryonic cell-type specification

(2018) Blanca Pijuan-Sala et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Detection and treatment of Fiebig stage I HIV-1 infection in young at-risk women in South Africa: a prospective cohort study

(2018) Krista L Dong et al.   Lancet HIV

Allergic inflammatory memory in human respiratory epithelial progenitor cells

(2018) Jose Ordovas-Montanes et al.   NATURE

Multiplexed droplet single-cell RNA-sequencing using natural genetic variation

(2017) Hyun Min Kang et al.   NATURE BIOTECHNOLOGY

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

(2017) Todd M Gierahn et al.   NATURE METHODS

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

Single-cell RNA-sequencing uncovers transcriptional states and fate decisions in haematopoiesis

(2017) Emmanouil I. Athanasiadis et al.   Nature Communications

The Human Cell Atlas

(2017) Aviv Regev et al.   eLife

Early type I Interferon response induces upregulation of human β-defensin 1 during acute HIV-1 infection

(2017) Björn Corleis et al.   PLoS One

Antiviral CD8 + T Cells Restricted by Human Leukocyte Antigen Class II Exist during Natural HIV Infection and Exhibit Clonal Expansion

(2016) Srinika Ranasinghe et al.   IMMUNITY

Low-Grade Inflammation Is Associated with Susceptibility to Infection in Healthy Men: Results from the Danish Blood Donor Study (DBDS)

(2016) Kathrine Agergård Kaspersen et al.   PLoS One

Lessons from acute HIV infection

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

Exhaustion of Activated CD8 T Cells Predicts Disease Progression in Primary HIV-1 Infection

(2016) Matthias Hoffmann et al.   PLoS Pathogens

NK Cells in HIV Disease

(2016) Eileen Scully et al.   Current HIV/AIDS Reports

Soluble CD14 is a nonspecific marker of monocyte activation

(2015) Carey L. Shive et al.   AIDS

Magnitude and Kinetics of CD8 + T Cell Activation during Hyperacute HIV Infection Impact Viral Set Point

(2015) Zaza M. Ndhlovu et al.   IMMUNITY

TIGIT predominantly regulates the immune response via regulatory T cells

(2015) Sema Kurtulus et al.   JOURNAL OF CLINICAL INVESTIGATION

Antigen-specific NK cell memory in rhesus macaques

(2015) R Keith Reeves et al.   NATURE IMMUNOLOGY

Interleukin-6 (IL-6) and IL-17 Synergistically Promote Viral Persistence by Inhibiting Cellular Apoptosis and Cytotoxic T Cell Function

(2014) W. Hou et al.   JOURNAL OF VIROLOGY

NK Cell Subset Redistribution during the Course of Viral Infections

(2014) Enrico Lugli et al.   Frontiers in Immunology

Causal analysis approaches in Ingenuity Pathway Analysis

(2013) Andreas Krämer et al.   BIOINFORMATICS

CD52 as both a marker and an effector molecule of T cells with regulatory action: Identification of novel regulatory T cells

(2013) Buka Samten   Cellular & Molecular Immunology

Productive Entry of HIV-1 during Cell-to-Cell Transmission via Dynamin-Dependent Endocytosis

(2013) R. D. Sloan et al.   JOURNAL OF VIROLOGY

Intact Type I Interferon Production and IRF7 Function in Sooty Mangabeys

(2013) Steven E. Bosinger et al.   PLoS Pathogens

Innate Immune Sensing of HIV-1 by Dendritic Cells

(2012) Jeremy Luban   Cell Host & Microbe

Plasma IP-10 Is Associated with Rapid Disease Progression in Early HIV-1 Infection

(2012) Yanmei Jiao et al.   VIRAL IMMUNOLOGY

Interferon-stimulated genes and their antiviral effector functions

(2011) John W Schoggins et al.   Current Opinion in Virology

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

CXCL10 Production by Human Monocytes in Response to Leishmania braziliensis Infection

(2009) D. A. Vargas-Inchaustegui et al.   INFECTION AND IMMUNITY

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

Virus-Specific Interleukin-17-Producing CD4+ T Cells Are Detectable in Early Human Immunodeficiency Virus Type 1 Infection

(2008) F. Y. Yue et al.   JOURNAL OF VIROLOGY