Lineage tracking reveals dynamic relationships of T cells in colorectal cancer

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

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

A transcriptionally and functionally distinct PD-1+ CD8+ T cell pool with predictive potential in non-small-cell lung cancer treated with PD-1 blockade

(2018) Daniela S. Thommen et al.   NATURE MEDICINE

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

(2018) Xinyi Guo et al.   NATURE MEDICINE

Induction and transcriptional regulation of the co-inhibitory gene module in T cells

(2018) Norio Chihara et al.   NATURE

Identifying specificity groups in the T cell receptor repertoire

(2017) Jacob Glanville et al.   NATURE

Elements of cancer immunity and the cancer–immune set point

(2017) Daniel S. Chen et al.   NATURE

Single-cell mRNA quantification and differential analysis with Census

(2017) Xiaojie Qiu et al.   NATURE METHODS

SC3: consensus clustering of single-cell RNA-seq data

(2017) Vladimir Yu Kiselev et al.   NATURE METHODS

Mismatch repair deficiency predicts response of solid tumors to PD-1 blockade

(2017) Dung T. Le et al.   SCIENCE

A Distinct Gene Module for Dysfunction Uncoupled from Activation in Tumor-Infiltrating T Cells

(2016) Meromit Singer et al.   CELL

Tumor-Specific T Cell Dysfunction Is a Dynamic Antigen-Driven Differentiation Program Initiated Early during Tumorigenesis

(2016) Andrea Schietinger et al.   IMMUNITY

Integrative Analyses of Colorectal Cancer Show Immunoscore Is a Stronger Predictor of Patient Survival Than Microsatellite Instability

(2016) Bernhard Mlecnik et al.   IMMUNITY

T cell fate and clonality inference from single-cell transcriptomes

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

Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq

(2016) I. Tirosh et al.   SCIENCE

MAIT cells are activated during human viral infections

(2016) Bonnie van Wilgenburg et al.   Nature Communications

T-cell receptor profiling in cancer

(2015) Ilan Kirsch et al.   Molecular Oncology

PD-1 Blockade in Tumors with Mismatch-Repair Deficiency

(2015) Dung T. Le et al.   NEW ENGLAND JOURNAL OF MEDICINE

Individual intestinal symbionts induce a distinct population of ROR + regulatory T cells

(2015) E. Sefik et al.   SCIENCE

The Molecular Signatures Database Hallmark Gene Set Collection

(2015) Arthur Liberzon et al.   Cell Systems

Chemokines and Chemokine Receptors: Positioning Cells for Host Defense and Immunity

(2014) Jason W. Griffith et al.   Annual Review of Immunology

Inferring copy number and genotype in tumour exome data

(2014) Kaushalya C Amarasinghe et al.   BMC GENOMICS

Tissue-Resident Memory T Cells

(2014) Jason M. Schenkel et al.   IMMUNITY

Triggering Through Toll-like Receptor 2 Limits Chronically Stimulated T-helper Type 1 Cells From Undergoing Exhaustion

(2014) Sathi Babu Chodisetti et al.   JOURNAL OF INFECTIOUS DISEASES

Linking T-cell receptor sequence to functional phenotype at the single-cell level

(2014) Arnold Han et al.   NATURE BIOTECHNOLOGY

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

(2014) Simone Picelli et al.   Nature Protocols

Clustering by fast search and find of density peaks

(2014) A. Rodriguez et al.   SCIENCE

The Vigorous Immune Microenvironment of Microsatellite Instable Colon Cancer Is Balanced by Multiple Counter-Inhibitory Checkpoints

(2014) Nicolas J. Llosa et al.   Cancer Discovery

Genome-wide DNA methylation analysis identifies hypomethylated genes regulated by FOXP3 in human regulatory T cells

(2013) Y. Zhang et al.   BLOOD

BACH2 represses effector programs to stabilize Treg-mediated immune homeostasis

(2013) Rahul Roychoudhuri et al.   NATURE

Natural and Induced T Regulatory Cells in Cancer

(2013) Dennis O. Adeegbe et al.   Frontiers in Immunology

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

(2012) Christopher T. Saunders et al.   BIOINFORMATICS

Comprehensive molecular characterization of human colon and rectal cancer

(2012)   NATURE

Progenitor and Terminal Subsets of CD8+ T Cells Cooperate to Contain Chronic Viral Infection

(2012) M. A. Paley et al.   SCIENCE

Murine Insulin Growth Factor-like (IGFL) and Human IGFL1 Proteins Are Induced in Inflammatory Skin Conditions and Bind to a Novel Tumor Necrosis Factor Receptor Family Member, IGFLR1

(2011) Adrian A. Lobito et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

Repression of the genome organizer SATB1 in regulatory T cells is required for suppressive function and inhibition of effector differentiation

(2011) Marc Beyer et al.   NATURE IMMUNOLOGY

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

Fast and SNP-tolerant detection of complex variants and splicing in short reads

(2010) T. D. Wu et al.   BIOINFORMATICS

Raising the NKT cell family

(2010) Dale I Godfrey et al.   NATURE IMMUNOLOGY

Second-Generation Anti-Carcinoembryonic Antigen Designer T Cells Resist Activation-Induced Cell Death, Proliferate on Tumor Contact, Secrete Cytokines, and Exhibit Superior Antitumor Activity In vivo: A Preclinical Evaluation

(2008) P. C.R. Emtage et al.   CLINICAL CANCER RESEARCH