Global analysis of shared T cell specificities in human non-small cell lung cancer enables HLA inference and antigen discovery

Circulating tumor DNA analysis to assess risk of progression after long-term response to PD-(L)1 blockade in NSCLC

(2020) Matthew D. Hellmann et al.   CLINICAL CANCER RESEARCH

Comprehensive T cell repertoire characterization of non-small cell lung cancer

(2020) Alexandre Reuben et al.   Nature Communications

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

NetMHCpan-4.1 and NetMHCIIpan-4.0: improved predictions of MHC antigen presentation by concurrent motif deconvolution and integration of MS MHC eluted ligand data

(2020) Birkir Reynisson et al.   NUCLEIC ACIDS RESEARCH

Single-cell atlas of colonic CD8+ T cells in ulcerative colitis

(2020) Daniele Corridoni et al.   NATURE MEDICINE

Commensal bacteria stimulate antitumor responses via T cell cross-reactivity

(2020) Catherine A. Bessell et al.   JCI Insight

Mechanism of EBV inducing anti-tumour immunity and its therapeutic use

(2020) Il-Kyu Choi et al.   NATURE

Virus-specific memory T cells populate tumors and can be repurposed for tumor immunotherapy

(2019) Pamela C. Rosato et al.   Nature Communications

T cell antigen discovery via trogocytosis

(2019) Guideng Li et al.   NATURE METHODS

T cell antigen discovery via signaling and antigen-presenting bifunctional receptors

(2019) Alok V. Joglekar et al.   NATURE METHODS

Detection of Epstein-Barr Virus Infection in Non-Small Cell Lung Cancer

(2019) Fayez Kheir et al.   Cancers

T-Scan: A Genome-wide Method for the Systematic Discovery of T Cell Epitopes

(2019) Tomasz Kula et al.   CELL

Tumor Microbiome Diversity and Composition Influence Pancreatic Cancer Outcomes

(2019) Erick Riquelme et al.   CELL

Spatial heterogeneity of the T cell receptor repertoire reflects the mutational landscape in lung cancer

(2019) Kroopa Joshi et al.   NATURE MEDICINE

Intratumoral injection of the seasonal flu shot converts immunologically cold tumors to hot and serves as an immunotherapy for cancer

(2019) Jenna H. Newman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Antigen Identification for Orphan T Cell Receptors Expressed on Tumor-Infiltrating Lymphocytes

(2018) Marvin H. Gee et al.   CELL

Global characterization of T cells in non-small-cell lung cancer by single-cell sequencing

(2018) Xinyi Guo et al.   NATURE MEDICINE

The commensal microbiome is associated with anti–PD-1 efficacy in metastatic melanoma patients

(2018) Vyara Matson et al.   SCIENCE

Isolation of a Structural Mechanism for Uncoupling T Cell Receptor Signaling from Peptide-MHC Binding

(2018) Leah V. Sibener et al.   CELL

Bystander CD8+ T cells are abundant and phenotypically distinct in human tumour infiltrates

(2018) Yannick Simoni et al.   NATURE

Dynamics of tumor and immune responses during immune checkpoint blockade in non-small cell lung cancer

(2018) Valsamo Anagnostou et al.   CANCER RESEARCH

Low and variable tumor reactivity of the intratumoral TCR repertoire in human cancers

(2018) Wouter Scheper et al.   NATURE MEDICINE

UniProt: a worldwide hub of protein knowledge

(2018)   NUCLEIC ACIDS RESEARCH

NetMHCpan-4.0: Improved Peptide–MHC Class I Interaction Predictions Integrating Eluted Ligand and Peptide Binding Affinity Data

(2017) Vanessa Jurtz et al.   JOURNAL OF IMMUNOLOGY

Identifying specificity groups in the T cell receptor repertoire

(2017) Jacob Glanville et al.   NATURE

Immunosequencing identifies signatures of cytomegalovirus exposure history and HLA-mediated effects on the T cell repertoire

(2017) Ryan O Emerson et al.   NATURE GENETICS

Broad TCR repertoire and diverse structural solutions for recognition of an immunodominant CD8+ T cell epitope

(2017) InYoung Song et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

VDJdb: a curated database of T-cell receptor sequences with known antigen specificity

(2017) Mikhail Shugay et al.   NUCLEIC ACIDS RESEARCH

A pilot study using metagenomic sequencing of the sputum microbiome suggests potential bacterial biomarkers for lung cancer

(2017) Simon J. S. Cameron et al.   PLoS One

Gut microbiome modulates response to anti–PD-1 immunotherapy in melanoma patients

(2017) V. Gopalakrishnan et al.   SCIENCE

Gut microbiome influences efficacy of PD-1–based immunotherapy against epithelial tumors

(2017) Bertrand Routy et al.   SCIENCE

Broad TCR repertoire and diverse structural solutions for recognition of an immunodominant CD8+ T cell epitope

(2017) InYoung Song et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Quantitative Characterization of the T Cell Receptor Repertoire of Naïve and Memory Subsets Using an Integrated Experimental and Computational Pipeline Which Is Robust, Economical, and Versatile

(2017) Theres Oakes et al.   Frontiers in Immunology

The Microbiome and the Respiratory Tract

(2016) Robert P. Dickson et al.   Annual Review of Physiology

Analysis of protein-coding genetic variation in 60,706 humans

(2016) Monkol Lek et al.   NATURE

T cell fate and clonality inference from single-cell transcriptomes

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

Clonal Deletion Prunes but Does Not Eliminate Self-Specific αβ CD8+ T Lymphocytes

(2015) Wong Yu et al.   IMMUNITY

Commensal Bifidobacterium promotes antitumor immunity and facilitates anti-PD-L1 efficacy

(2015) A. Sivan et al.   SCIENCE

Anticancer immunotherapy by CTLA-4 blockade relies on the gut microbiota

(2015) M. Vetizou et al.   SCIENCE

Studies of OC-STAMP in Osteoclast Fusion: A New Knockout Mouse Model, Rescue of Cell Fusion, and Transmembrane Topology

(2015) Hanna Witwicka et al.   PLoS One

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

An ultrasensitive method for quantitating circulating tumor DNA with broad patient coverage

(2014) Aaron M Newman et al.   NATURE MEDICINE

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

(2014) Simone Picelli et al.   Nature Protocols

Clustering HLA Class I Superfamilies Using Structural Interaction Patterns

(2014) Sumitro Harjanto et al.   PLoS One

GSVA: gene set variation analysis for microarray and RNA-Seq data

(2013) Sonja Hänzelmann et al.   BMC BIOINFORMATICS

Virus-Specific CD4+ Memory-Phenotype T Cells Are Abundant in Unexposed Adults

(2013) Laura F. Su et al.   IMMUNITY

Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples

(2013) Kristian Cibulskis et al.   NATURE BIOTECHNOLOGY

Strelka: accurate somatic small-variant calling from sequenced tumor–normal sample pairs

(2012) Christopher T. Saunders et al.   BIOINFORMATICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Dissection of T-cell Antigen Specificity in Human Melanoma

(2012) R. S. Andersen et al.   CANCER RESEARCH

VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing

(2012) D. C. Koboldt et al.   GENOME RESEARCH

Fiji: an open-source platform for biological-image analysis

(2012) Johannes Schindelin et al.   NATURE METHODS

Overlap and Effective Size of the Human CD8+ T Cell Receptor Repertoire

(2010) H. S. Robins et al.   Science Translational Medicine

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

HLA class I supertypes: a revised and updated classification

(2008) John Sidney et al.   BMC IMMUNOLOGY

NCBI BLAST: a better web interface

(2008) M. Johnson et al.   NUCLEIC ACIDS RESEARCH

Recognition of a Ubiquitous Self Antigen by Prostate Cancer-Infiltrating CD8+ T Lymphocytes

(2008) P. A. Savage et al.   SCIENCE