An immunodominant NP105–113-B*07:02 cytotoxic T cell response controls viral replication and is associated with less severe COVID-19 disease

Evidence of escape of SARS-CoV-2 variant B.1.351 from natural and vaccine induced sera

(2021) Daming Zhou et al.   CELL

Cellsnp-lite: an efficient tool for genotyping single cells

(2021) Xianjie Huang et al.   BIOINFORMATICS

Antibody evasion by the P.1 strain of SARS-CoV-2

(2021) Wanwisa Dejnirattisai et al.   CELL

CD8+ T cells specific for an immunodominant SARS-CoV-2 nucleocapsid epitope cross-react with selective seasonal coronaviruses

(2021) Katie E. Lineburg et al.   IMMUNITY

CD8+ T cells specific for an immunodominant SARS-CoV-2 nucleocapsid epitope display high naive precursor frequency and TCR promiscuity

(2021) Thi H.O. Nguyen et al.   IMMUNITY

Neutrophils in respiratory viral infections

(2021) Cecilia Johansson et al.   Mucosal Immunology

Hypoxic and pharmacological activation of HIF inhibits SARS-CoV-2 infection of lung epithelial cells

(2021) Peter A.C. Wing et al.   Cell Reports

Reduced neutralization of SARS-CoV-2 B.1.617 by vaccine and convalescent serum

(2021) Chang Liu et al.   CELL

The impact of viral mutations on recognition by SARS-CoV-2 specific T cells

(2021) Thushan I. de Silva et al.   iScience

Targets of T Cell Responses to SARS-CoV-2 Coronavirus in Humans with COVID-19 Disease and Unexposed Individuals

(2020) Alba Grifoni et al.   CELL

Analyzing the Mycobacterium tuberculosis immune response by T-cell receptor clustering with GLIPH2 and genome-wide antigen screening

(2020) Huang Huang et al.   NATURE BIOTECHNOLOGY

SARS-CoV-2-specific T cell immunity in cases of COVID-19 and SARS, and uninfected controls

(2020) Nina Le Bert et al.   NATURE

Robust T Cell Immunity in Convalescent Individuals with Asymptomatic or Mild COVID-19

(2020) Takuya Sekine et al.   CELL

Unbiased screens show CD8+ T cells of COVID-19 patients recognize shared epitopes in SARS-CoV-2, most of which are not located in the Spike protein

(2020) Andrew P. Ferretti et al.   IMMUNITY

Broad and strong memory CD4+ and CD8+ T cells induced by SARS-CoV-2 in UK convalescent individuals following COVID-19

(2020) Yanchun Peng et al.   NATURE IMMUNOLOGY

Suboptimal SARS-CoV-2−specific CD8+ T cell response associated with the prominent HLA-A*02:01 phenotype

(2020) Jennifer R. Habel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

Enriched HLA-E and CD94/NKG2A Interaction Limits Antitumor CD8+ Tumor-Infiltrating T Lymphocyte Responses

(2019) Megat Abd Hamid et al.   Cancer Immunology Research

Self-maintaining CD103+ cancer-specific T cells are highly energetic with rapid cytotoxic and effector responses

(2019) Megat Abd Hamid et al.   Cancer Immunology Research

Orchestrating single-cell analysis with Bioconductor

(2019) Robert A. Amezquita et al.   NATURE METHODS

Interleukin-10 Directly Inhibits CD8 + T Cell Function by Enhancing N-Glycan Branching to Decrease Antigen Sensitivity

(2018) Logan K. Smith et al.   IMMUNITY

Antigen receptor repertoire profiling from RNA-seq data

(2017) Dmitriy A Bolotin et al.   NATURE BIOTECHNOLOGY

Massively parallel digital transcriptional profiling of single cells

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

MiXCR: software for comprehensive adaptive immunity profiling

(2015) Dmitriy A Bolotin et al.   NATURE METHODS

Matrikines are key regulators in modulating the amplitude of lung inflammation in acute pulmonary infection

(2015) Samia Akthar et al.   Nature Communications

Differential effect of DJ-1/PARK7 on development of natural and induced regulatory T cells

(2015) Yogesh Singh et al.   Scientific Reports

Boosted Influenza-Specific T Cell Responses after H5N1 Pandemic Live Attenuated Influenza Virus Vaccination

(2015) YanChun Peng et al.   Frontiers in Immunology

circlize implements and enhances circular visualization in R

(2014) Zuguang Gu et al.   BIOINFORMATICS

Parkinsonism-associated Protein DJ-1/Park7 Is a Major Protein Deglycase That Repairs Methylglyoxal- and Glyoxal-glycated Cysteine, Arginine, and Lysine Residues

(2014) Gilbert Richarme et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

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

(2014) Simone Picelli et al.   Nature Protocols

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

HLA-B may be more protective against HIV-1 than HLA-A because it resists negative regulatory factor (Nef) mediated down-regulation

(2012) U. S. Rajapaksa et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Antiviral Efficacy of HIV-Specific CD8+ T-Cells to a Conserved Epitope Is Heavily Dependent on the Infecting HIV-1 Isolate

(2011) Srinika R. F. Ranasinghe et al.   PLoS Pathogens