Programme of self-reactive innate-like T cell-mediated cancer immunity

Classical MHC expression by DP thymocytes impairs the selection of non-classical MHC restricted innate-like T cells

(2021) Hristo Georgiev et al.   Nature Communications

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

(2021) Liangtao Zheng et al.   SCIENCE

Intestinal CD8αα IELs derived from two distinct thymic precursors have staggered ontogeny

(2020) Roland Ruscher et al.   JOURNAL OF EXPERIMENTAL MEDICINE

CD8 T Cell Exhaustion During Chronic Viral Infection and Cancer

(2019) Laura M. McLane et al.   Annual Review of Immunology

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

TOX reinforces the phenotype and longevity of exhausted T cells in chronic viral infection

(2019) Francesca Alfei et al.   NATURE

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

Clonal replacement of tumor-specific T cells following PD-1 blockade

(2019) Kathryn E. Yost et al.   NATURE MEDICINE

Single-Cell Map of Diverse Immune Phenotypes in the Breast Tumor Microenvironment

(2018) Elham Azizi et al.   CELL

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

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

Distinct human circulating NKp30+FcεRIγ+CD8+T cell population exhibiting high natural killer-like antitumor potential

(2018) Margareta P. Correia et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2018) Yannick Simoni et al.   NATURE

Lineage tracking reveals dynamic relationships of T cells in colorectal cancer

(2018) Lei Zhang 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

Reversed graph embedding resolves complex single-cell trajectories

(2017) Xiaojie Qiu et al.   NATURE METHODS

Tumor Mutational Burden and Response Rate to PD-1 Inhibition

(2017) Mark Yarchoan et al.   NEW ENGLAND JOURNAL OF MEDICINE

Coinhibitory Pathways in Immunotherapy for Cancer

(2016) Susanne H. Baumeister et al.   Annual Review of Immunology

Cancer Immunosurveillance by Tissue-Resident Innate Lymphoid Cells and Innate-like T Cells

(2016) Saïda Dadi et al.   CELL

An essential role for the IL-2 receptor in Treg cell function

(2016) Takatoshi Chinen et al.   NATURE IMMUNOLOGY

destiny: diffusion maps for large-scale single-cell data in R

(2015) Philipp Angerer et al.   BIOINFORMATICS

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

(2015) Laleh Haghverdi et al.   BIOINFORMATICS

Creating reference gene annotation for the mouse C57BL6/J genome assembly

(2015) Jonathan M. Mudge et al.   MAMMALIAN GENOME

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

Tissue residency of innate lymphoid cells in lymphoid and nonlymphoid organs

(2015) G. Gasteiger et al.   SCIENCE

Neoantigens in cancer immunotherapy

(2015) T. N. Schumacher et al.   SCIENCE

The future of immune checkpoint therapy

(2015) P. Sharma et al.   SCIENCE

Distinct mechanisms define murine B cell lineage immunoglobulin heavy chain (IgH) repertoires

(2015) Yang Yang et al.   eLife

Interferon-Stimulated Genes: A Complex Web of Host Defenses

(2014) William M. Schneider et al.   Annual Review of Immunology

Elevated T Cell Receptor Signaling Identifies a Thymic Precursor to the TCRαβ+CD4−CD8β− Intraepithelial Lymphocyte Lineage

(2014) Benjamin D. McDonald et al.   IMMUNITY

αβT Cell Receptors Expressed by CD4−CD8αβ− Intraepithelial T Cells Drive Their Fate into a Unique Lineage with Unusual MHC Reactivities

(2014) Sofia Mayans et al.   IMMUNITY

Fgd5identifies hematopoietic stem cells in the murine bone marrow

(2014) Roi Gazit et al.   JOURNAL OF EXPERIMENTAL MEDICINE

A committed precursor to innate lymphoid cells

(2014) Michael G. Constantinides et al.   NATURE

The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells

(2014) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Improved vectors and genome-wide libraries for CRISPR screening

(2014) Neville E Sanjana et al.   NATURE METHODS

The cellular and molecular origin of tumor-associated macrophages

(2014) R. A. Franklin et al.   SCIENCE

CD8 + Dendritic Cell Trans Presentation of IL-15 to Naive CD8+ T Cells Produces Antigen-Inexperienced T Cells in the Periphery with Memory Phenotype and Function

(2013) T. Sosinowski et al.   JOURNAL OF IMMUNOLOGY

The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote

(2013) Yang Liao et al.   NUCLEIC ACIDS RESEARCH

Selection of Self-Reactive T Cells in the Thymus

(2012) Gretta L. Stritesky et al.   Annual Review of Immunology

Cancer exome analysis reveals a T-cell-dependent mechanism of cancer immunoediting

(2012) Hirokazu Matsushita et al.   NATURE

Expression of tumour-specific antigens underlies cancer immunoediting

(2012) Michel DuPage et al.   NATURE

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

(2012) Guangchuang Yu et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

High-throughput, high-fidelity HLA genotyping with deep sequencing

(2012) C. Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

CTLA-4 suppresses the pathogenicity of self antigen–specific T cells by cell-intrinsic and cell-extrinsic mechanisms

(2009) Wataru Ise et al.   NATURE IMMUNOLOGY

Batf3 Deficiency Reveals a Critical Role for CD8 + Dendritic Cells in Cytotoxic T Cell Immunity

(2008) K. Hildner et al.   SCIENCE

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

(2008) P. A. Savage et al.   SCIENCE