Pan-cancer single-cell landscape of tumor-infiltrating T cells

Peripheral T cell expansion predicts tumour infiltration and clinical response

(2020) Thomas D. Wu et al.   NATURE

Dysfunctional CD8 T Cells Form a Proliferative, Dynamically Regulated Compartment within Human Melanoma

(2020) Hanjie Li et al.   CELL

The TGF‐b/SOX4 axis and ROS‐driven autophagy co‐mediate CD39 expression in regulatory T‐cells

(2020) Marlene C. Gerner et al.   FASEB JOURNAL

A pan-cancer blueprint of the heterogeneous tumor microenvironment revealed by single-cell profiling

(2020) Junbin Qian et al.   CELL RESEARCH

Generalizing RNA velocity to transient cell states through dynamical modeling

(2020) Volker Bergen et al.   NATURE BIOTECHNOLOGY

The Roles of CD8+ T Cell Subsets in Antitumor Immunity

(2020) Michael St. Paul et al.   TRENDS IN CELL BIOLOGY

Defining T Cell States Associated with Response to Checkpoint Immunotherapy in Melanoma

(2019) Moshe Sade-Feldman et al.   CELL

Intratumoral Tcf1+PD-1+CD8+ T Cells with Stem-like Properties Promote Tumor Control in Response to Vaccination and Checkpoint Blockade Immunotherapy

(2019) Imran Siddiqui et al.   IMMUNITY

Subsets of exhausted CD8+ T cells differentially mediate tumor control and respond to checkpoint blockade

(2019) Brian C. Miller et al.   NATURE IMMUNOLOGY

The single-cell transcriptional landscape of mammalian organogenesis

(2019) Junyue Cao et al.   NATURE

A comparison of single-cell trajectory inference methods

(2019) Wouter Saelens et al.   NATURE BIOTECHNOLOGY

Scrublet: Computational Identification of Cell Doublets in Single-Cell Transcriptomic Data

(2019) Samuel L. Wolock et al.   Cell Systems

TOX is a critical regulator of tumour-specific T cell differentiation

(2019) Andrew C. Scott et al.   NATURE

TOX transcriptionally and epigenetically programs CD8+ T cell exhaustion

(2019) Omar Khan et al.   NATURE

Massively parallel single-cell chromatin landscapes of human immune cell development and intratumoral T cell exhaustion

(2019) Ansuman T. Satpathy et al.   NATURE BIOTECHNOLOGY

TCF-1-Centered Transcriptional Network Drives an Effector versus Exhausted CD8 T Cell-Fate Decision

(2019) Zeyu Chen et al.   IMMUNITY

Fast, sensitive and accurate integration of single-cell data with Harmony

(2019) Ilya Korsunsky et al.   NATURE METHODS

Single-cell transcriptomics of human T cells reveals tissue and activation signatures in health and disease

(2019) Peter A. Szabo et al.   Nature Communications

NicheNet: modeling intercellular communication by linking ligands to target genes

(2019) Robin Browaeys et al.   NATURE METHODS

Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics

(2018) Kelly Street et al.   BMC GENOMICS

T Cell Dysfunction in Cancer

(2018) Daniela S. Thommen et al.   CANCER CELL

A time for YAP1: Tumorigenesis, immunosuppression and targeted therapy

(2018) Masahiro Shibata et al.   INTERNATIONAL JOURNAL OF CANCER

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

(2018) Xinyi Guo et al.   NATURE MEDICINE

Assembly and activation of the Hippo signalome by FAT1 tumor suppressor

(2018) Daniel Martin et al.   Nature Communications

Human Sox4 facilitates the development of CXCL13-producing helper T cells in inflammatory environments

(2018) Hiroyuki Yoshitomi et al.   Nature Communications

Development of tumor mutation burden as an immunotherapy biomarker: utility for the oncology clinic

(2018) T A Chan et al.   ANNALS OF ONCOLOGY

Lineage tracking reveals dynamic relationships of T cells in colorectal cancer

(2018) Lei Zhang et al.   NATURE

Dimensionality reduction for visualizing single-cell data using UMAP

(2018) Etienne Becht et al.   NATURE BIOTECHNOLOGY

Paradoxical effects of obesity on T cell function during tumor progression and PD-1 checkpoint blockade

(2018) Ziming Wang et al.   NATURE MEDICINE

SCENIC: single-cell regulatory network inference and clustering

(2017) Sara Aibar et al.   NATURE METHODS

Single-cell sequencing reveals dissociation-induced gene expression in tissue subpopulations

(2017) Susanne C van den Brink et al.   NATURE METHODS

Massively parallel digital transcriptional profiling of single cells

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

T Cell Factor 1-Expressing Memory-like CD8 + T Cells Sustain the Immune Response to Chronic Viral Infections

(2016) Daniel T. Utzschneider et al.   IMMUNITY

Transcriptional Landscape of Human Tissue Lymphocytes Unveils Uniqueness of Tumor-Infiltrating T Regulatory Cells

(2016) Marco De Simone et al.   IMMUNITY

Regulatory T Cells Exhibit Distinct Features in Human Breast Cancer

(2016) George Plitas et al.   IMMUNITY

Defining CD8+ T cells that provide the proliferative burst after PD-1 therapy

(2016) Se Jin Im et al.   NATURE

Diffusion pseudotime robustly reconstructs lineage branching

(2016) Laleh Haghverdi et al.   NATURE METHODS

The epigenetic landscape of T cell exhaustion

(2016) D. R. Sen et al.   SCIENCE

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

(2016) I. Tirosh et al.   SCIENCE

Diffusion maps for high-dimensional single-cell analysis of differentiation data

(2015) Laleh Haghverdi et al.   BIOINFORMATICS

T-cell receptor profiling in cancer

(2015) Ilan Kirsch et al.   Molecular Oncology

Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells

(2015) Florian Buettner et al.   NATURE BIOTECHNOLOGY

CD39 Expression Identifies Terminally Exhausted CD8+ T Cells

(2015) Prakash K. Gupta et al.   PLoS Pathogens

Bystander Chronic Infection Negatively Impacts Development of CD8+ T Cell Memory

(2014) Erietta Stelekati et al.   IMMUNITY

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

(2014) Simone Picelli et al.   Nature Protocols

CD4 CTL: Living up to the challenge

(2013) Hilde Cheroutre et al.   SEMINARS IN IMMUNOLOGY

Human MAIT cells are xenobiotic-resistant, tissue-targeted, CD161hi IL-17-secreting T cells

(2010) M. Dusseaux et al.   BLOOD

Moderated effect size and P-value combinations for microarray meta-analyses

(2009) G. Marot et al.   BIOINFORMATICS

PD-L1 regulates the development, maintenance, and function of induced regulatory T cells

(2009) Loise M. Francisco et al.   JOURNAL OF EXPERIMENTAL MEDICINE