Profiling SARS-CoV-2 HLA-I peptidome reveals T cell epitopes from out-of-frame ORFs

SARS-CoV-2–specific CD8+ T cell responses in convalescent COVID-19 individuals

(2021) Hassen Kared et al.   JOURNAL OF CLINICAL INVESTIGATION

How ‘killer’ T cells could boost COVID immunity in face of new variants

(2021) Heidi Ledford   NATURE

Resistance of SARS-CoV-2 variants to neutralization by monoclonal and serum-derived polyclonal antibodies

(2021) Rita E. Chen et al.   NATURE MEDICINE

Serum Neutralizing Activity Elicited by mRNA-1273 Vaccine — Preliminary Report

(2021) Kai Wu et al.   NEW ENGLAND JOURNAL OF MEDICINE

Most non-canonical proteins uniquely populate the proteome or immunopeptidome

(2021) Maria Virginia Ruiz Cuevas et al.   Cell Reports

SARS-CoV-2 genome-wide T cell epitope mapping reveals immunodominance and substantial CD8+ T cell activation in COVID-19 patients

(2021) Sunil Kumar Saini et al.   Science Immunology

Conflicting and ambiguous names of overlapping ORFs in the SARS-CoV-2 genome: A homology-based resolution

(2021) Irwin Jungreis et al.   VIROLOGY

Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding

(2020) Roujian Lu et al.   LANCET

A new coronavirus associated with human respiratory disease in China

(2020) Fan Wu et al.   NATURE

Pervasive functional translation of noncanonical human open reading frames

(2020) Jin Chen et al.   SCIENCE

Comprehensive annotations of human herpesvirus 6A and 6B genomes reveal novel and conserved genomic features

(2020) Yaara Finkel et al.   eLife

The Architecture of SARS-CoV-2 Transcriptome

(2020) Dongwan Kim et al.   CELL

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

A Sequence Homology and Bioinformatic Approach Can Predict Candidate Targets for Immune Responses to SARS-CoV-2

(2020) Alba Grifoni et al.   Cell Host & Microbe

Human leukocyte antigen susceptibility map for SARS-CoV-2

(2020) Austin Nguyen et al.   JOURNAL OF VIROLOGY

The race for coronavirus vaccines: a graphical guide

(2020) Ewen Callaway   NATURE

A SARS-CoV-2 protein interaction map reveals targets for drug repurposing

(2020) David E. Gordon et al.   NATURE

The Nucleocapsid Protein of SARS–CoV-2: a Target for Vaccine Development

(2020) Noton K. Dutta et al.   JOURNAL OF VIROLOGY

Phase 1/2 study of COVID-19 RNA vaccine BNT162b1 in adults

(2020) Mark J. Mulligan et al.   NATURE

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

(2020) Nina Le Bert et al.   NATURE

An mRNA Vaccine against SARS-CoV-2 — Preliminary Report

(2020) Lisa A. Jackson et al.   NEW ENGLAND JOURNAL OF MEDICINE

Sequence-based prediction of SARS-CoV-2 vaccine targets using a mass spectrometry-based bioinformatics predictor identifies immunogenic T cell epitopes

(2020) Asaf Poran et al.   Genome Medicine

A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology

(2020) Andrew Rambaut et al.   Nature Microbiology

SARS-CoV-2 T cell immunity: Specificity, function, durability, and role in protection

(2020) Daniel M. Altmann et al.   Science Immunology

Phenotype and kinetics of SARS-CoV-2-specific T cells in COVID-19 patients with acute respiratory distress syndrome

(2020) Daniela Weiskopf et al.   Science Immunology

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

(2020) Takuya Sekine et al.   CELL

Antigen-Specific Adaptive Immunity to SARS-CoV-2 in Acute COVID-19 and Associations with Age and Disease Severity

(2020) Carolyn Rydyznski Moderbacher 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

The coding capacity of SARS-CoV-2

(2020) Yaara Finkel et al.   NATURE

SARS-CoV-2 Nsp1 binds the ribosomal mRNA channel to inhibit translation

(2020) Katharina Schubert et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

Multi-Omics Resolves a Sharp Disease-State Shift between Mild and Moderate COVID-19

(2020) Yapeng Su et al.   CELL

SARS-CoV-2 Epitopes Are Recognized by a Public and Diverse Repertoire of Human T Cell Receptors

(2020) Alina S. Shomuradova et al.   IMMUNITY

The SARS-CoV-2 RNA–protein interactome in infected human cells

(2020) Nora Schmidt et al.   Nature Microbiology

Reference-based analysis of lung single-cell sequencing reveals a transitional profibrotic macrophage

(2019) Dvir Aran et al.   NATURE IMMUNOLOGY

Pre-fractionation Extends but also Creates a Bias in the Detectable HLA Class Ι Ligandome

(2019) Laura C. Demmers et al.   JOURNAL OF PROTEOME RESEARCH

Efficient integration of heterogeneous single-cell transcriptomes using Scanorama

(2019) Brian Hie et al.   NATURE BIOTECHNOLOGY

Quantification of epitope abundance reveals the effect of direct and cross-presentation on influenza CTL responses

(2019) Ting Wu et al.   Nature Communications

A large peptidome dataset improves HLA class I epitope prediction across most of the human population

(2019) Siranush Sarkizova et al.   NATURE BIOTECHNOLOGY

Recovering Gene Interactions from Single-Cell Data Using Data Diffusion

(2018) David van Dijk et al.   CELL

Interactions Between KIR3DS1 and HLA-F Activate Natural Killer Cells to Control HCV Replication in Cell Culture

(2018) Sebastian Lunemann et al.   GASTROENTEROLOGY

Influenza A Virus Negative Strand RNA Is Translated for CD8+T Cell Immunosurveillance

(2018) Heather D. Hickman et al.   JOURNAL OF IMMUNOLOGY

Improved Ribo-seq enables identification of cryptic translation events

(2018) Florian Erhard et al.   NATURE METHODS

Mass Spectrometry Profiling of HLA-Associated Peptidomes in Mono-allelic Cells Enables More Accurate Epitope Prediction

(2017) Jennifer G. Abelin et al.   IMMUNITY

High-throughput and Sensitive Immunopeptidomics Platform Reveals Profound Interferonγ-Mediated Remodeling of the Human Leukocyte Antigen (HLA) Ligandome

(2017) Chloe Chong et al.   MOLECULAR & CELLULAR PROTEOMICS

Nowhere to hide: unconventional translation yields cryptic peptides for immune surveillance

(2016) Shelley R. Starck et al.   IMMUNOLOGICAL REVIEWS

Defining Viral Defective Ribosomal Products: Standard and Alternative Translation Initiation Events Generate a Common Peptide from Influenza A Virus M2 and M1 mRNAs

(2016) Ning Yang et al.   JOURNAL OF IMMUNOLOGY

Unsupervised HLA Peptidome Deconvolution Improves Ligand Prediction Accuracy and Predicts Cooperative Effects in Peptide–HLA Interactions

(2016) Michal Bassani-Sternberg et al.   JOURNAL OF IMMUNOLOGY

Analysis of Major Histocompatibility Complex-Bound HIV Peptides Identified from Various Cell Types Reveals Common Nested Peptides and Novel T Cell Responses

(2016) Marijana Rucevic et al.   JOURNAL OF VIROLOGY

The Perseus computational platform for comprehensive analysis of (prote)omics data

(2016) Stefka Tyanova et al.   NATURE METHODS

Defining the HLA class I-associated viral antigen repertoire from HIV-1-infected human cells

(2015) Nicola Ternette et al.   EUROPEAN JOURNAL OF IMMUNOLOGY

Physical detection of influenza A epitopes identifies a stealth subset on human lung epithelium evading natural CD8 immunity

(2015) Derin B. Keskin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Measles Virus Epitope Presentation by HLA: Novel Insights into Epitope Selection, Dominance, and Microvariation

(2015) Ingrid M. Schellens et al.   Frontiers in Immunology

Ribosome Profiling Reveals Pervasive Translation Outside of Annotated Protein-Coding Genes

(2014) Nicholas T. Ingolia et al.   Cell Reports

Kinetics of Antigen Expression and Epitope Presentation during Virus Infection

(2013) Nathan P. Croft et al.   PLoS Pathogens

Decoding Human Cytomegalovirus

(2012) N. Stern-Ginossar et al.   SCIENCE

On programmed ribosomal frameshifting: the alternative proteomes

(2012) Robin Ketteler   Frontiers in Genetics

Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity and Dynamics of Mammalian Proteomes

(2011) Nicholas T. Ingolia et al.   CELL

Global quantification of mammalian gene expression control

(2011) Björn Schwanhäusser et al.   NATURE

CD8+ T Cell Recognition of Cryptic Epitopes Is a Ubiquitous Feature of AIDS Virus Infection

(2010) N. J. Maness et al.   JOURNAL OF VIROLOGY

Regulation of Translation Initiation in Eukaryotes: Mechanisms and Biological Targets

(2009) Nahum Sonenberg et al.   CELL

Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling

(2009) N. T. Ingolia et al.   SCIENCE

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Balancing selection and heterogeneity across the classical human leukocyte antigen loci: A meta-analytic review of 497 population studies

(2008) Owen D. Solberg et al.   HUMAN IMMUNOLOGY

Epitope discovery in West Nile virus infection: Identification and immune recognition of viral epitopes

(2008) C. P. McMurtrey et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA