Discovering dominant tumor immune archetypes in a pan-cancer census

Global absence and targeting of protective immune states in severe COVID-19

(2021) Alexis J. Combes et al.   NATURE

Distinct metabolic programs established in the thymus control effector functions of γδ T cell subsets in tumor microenvironments

(2021) Noella Lopes et al.   NATURE IMMUNOLOGY

Developmental cell programs are co-opted in inflammatory skin disease

(2021) Gary Reynolds et al.   SCIENCE

Mutant p53 suppresses innate immune signaling to promote tumorigenesis

(2021) Monisankar Ghosh et al.   CANCER CELL

Tumor and immune reprogramming during immunotherapy in advanced renal cell carcinoma

(2021) Kevin Bi et al.   CANCER CELL

A pan-cancer single-cell transcriptional atlas of tumor infiltrating myeloid cells

(2021) Sijin Cheng et al.   CELL

Contribution of resident and circulating precursors to tumor-infiltrating CD8+ T cell populations in lung cancer

(2021) Paul Gueguen et al.   Science Immunology

Conserved pan-cancer microenvironment subtypes predict response to immunotherapy

(2021) Alexander Bagaev et al.   CANCER CELL

Cross-tissue single-cell landscape of human monocytes and macrophages in health and disease

(2021) Kevin Mulder et al.   IMMUNITY

Phenotype, specificity and avidity of antitumour CD8+ T cells in melanoma

(2021) Giacomo Oliveira et al.   NATURE

Spatially confined sub-tumor microenvironments in pancreatic cancer

(2021) Barbara T. Grünwald et al.   CELL

Tissue-resident macrophages in omentum promote metastatic spread of ovarian cancer

(2020) Anders Etzerodt et al.   JOURNAL OF EXPERIMENTAL MEDICINE

B cells are associated with survival and immunotherapy response in sarcoma

(2020) Florent Petitprez et al.   NATURE

SciPy 1.0: fundamental algorithms for scientific computing in Python

(2020) Pauli Virtanen et al.   NATURE METHODS

Single-Cell Analyses Inform Mechanisms of Myeloid-Targeted Therapies in Colon Cancer

(2020) Lei Zhang et al.   CELL

Inflammatory Type 2 cDCs Acquire Features of cDC1s and Macrophages to Orchestrate Immunity to Respiratory Virus Infection

(2020) Cedric Bosteels et al.   IMMUNITY

Developmental Relationships of Four Exhausted CD8+ T Cell Subsets Reveals Underlying Transcriptional and Epigenetic Landscape Control Mechanisms

(2020) Jean-Christophe Beltra et al.   IMMUNITY

A conserved dendritic-cell regulatory program limits antitumour immunity

(2020) Barbara Maier et al.   NATURE

Visualizing and interpreting cancer genomics data via the Xena platform

(2020) Mary J. Goldman et al.   NATURE BIOTECHNOLOGY

A single-cell and single-nucleus RNA-Seq toolbox for fresh and frozen human tumors

(2020) Michal Slyper et al.   NATURE MEDICINE

Intratumoral CD4+ T Cells Mediate Anti-tumor Cytotoxicity in Human Bladder Cancer

(2020) David Y. Oh et al.   CELL

TREM2 Modulation Remodels the Tumor Myeloid Landscape Enhancing Anti-PD-1 Immunotherapy

(2020) Martina Molgora et al.   CELL

ZipSeq: barcoding for real-time mapping of single cell transcriptomes

(2020) Kenneth H. Hu et al.   NATURE METHODS

Therapy-Induced Evolution of Human Lung Cancer Revealed by Single-Cell RNA Sequencing

(2020) Ashley Maynard et al.   CELL

SCENITH: A Flow Cytometry-Based Method to Functionally Profile Energy Metabolism with Single-Cell Resolution

(2020) Rafael J. Argüello et al.   Cell Metabolism

Approaches to treat immune hot, altered and cold tumours with combination immunotherapies

(2019) Jérôme Galon et al.   NATURE REVIEWS DRUG DISCOVERY

CCR2-Dependent Recruitment of Tregs and Monocytes Following Radiotherapy Is Associated with TNFα-Mediated Resistance

(2019) Michele Mondini et al.   Cancer Immunology Research

Single-Cell RNA-Seq Reveals AML Hierarchies Relevant to Disease Progression and Immunity

(2019) Peter van Galen et al.   CELL

Human Tumor-Associated Macrophage and Monocyte Transcriptional Landscapes Reveal Cancer-Specific Reprogramming, Biomarkers, and Therapeutic Targets

(2019) Luca Cassetta et al.   CANCER CELL

Unleashing Type-2 Dendritic Cells to Drive Protective Antitumor CD4+ T Cell Immunity

(2019) Mikhail Binnewies et al.   CELL

Single-Cell Transcriptomics of Human and Mouse Lung Cancers Reveals Conserved Myeloid Populations across Individuals and Species

(2019) Rapolas Zilionis et al.   IMMUNITY

Immunity as a continuum of archetypes

(2019) Adriana M. Mujal et al.   SCIENCE

DoubletFinder: Doublet Detection in Single-Cell RNA Sequencing Data Using Artificial Nearest Neighbors

(2019) Christopher S. McGinnis et al.   Cell Systems

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

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

(2019) Andrew C. Scott et al.   NATURE

Loss of p53 triggers WNT-dependent systemic inflammation to drive breast cancer metastasis

(2019) Max D. Wellenstein et al.   NATURE

TOX transcriptionally and epigenetically programs CD8+ T cell exhaustion

(2019) Omar Khan et al.   NATURE

Landscape and Dynamics of Single Immune Cells in Hepatocellular Carcinoma

(2019) Qiming Zhang et al.   CELL

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

(2019) Ilya Korsunsky et al.   NATURE METHODS

A Spatiotemporal Organ-Wide Gene Expression and Cell Atlas of the Developing Human Heart

(2019) Michaela Asp et al.   CELL

Immune profiling of human tumors identifies CD73 as a combinatorial target in glioblastoma

(2019) Sangeeta Goswami et al.   NATURE MEDICINE

A Comprehensive Pan-Cancer Molecular Study of Gynecologic and Breast Cancers

(2018) Ashton C. Berger et al.   CANCER CELL

Fc Effector Function Contributes to the Activity of Human Anti-CTLA-4 Antibodies

(2018) Frederick Arce Vargas et al.   CANCER CELL

NK Cells Stimulate Recruitment of cDC1 into the Tumor Microenvironment Promoting Cancer Immune Control

(2018) Jan P. Böttcher et al.   CELL

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

(2018) Elham Azizi et al.   CELL

Genomic Hallmarks and Structural Variation in Metastatic Prostate Cancer

(2018) David A. Quigley et al.   CELL

Epigenomic-Guided Mass Cytometry Profiling Reveals Disease-Specific Features of Exhausted CD8 T Cells

(2018) Bertram Bengsch et al.   IMMUNITY

The Immune Landscape of Cancer

(2018) Vésteinn Thorsson et al.   IMMUNITY

Adjustment of dendritic cells to the breast-cancer microenvironment is subset specific

(2018) Paula Michea et al.   NATURE IMMUNOLOGY

Single-cell gene expression reveals a landscape of regulatory T cell phenotypes shaped by the TCR

(2018) David Zemmour et al.   NATURE IMMUNOLOGY

Single-cell profiling of breast cancer T cells reveals a tissue-resident memory subset associated with improved prognosis

(2018) Peter Savas et al.   NATURE MEDICINE

Understanding the tumor immune microenvironment (TIME) for effective therapy

(2018) Mikhail Binnewies et al.   NATURE MEDICINE

A natural killer–dendritic cell axis defines checkpoint therapy–responsive tumor microenvironments

(2018) Kevin C. Barry et al.   NATURE MEDICINE

Overview of the Mechanisms that May Contribute to the Non-Redundant Activities of Interferon-Inducible CXC Chemokine Receptor 3 Ligands

(2018) Mieke Metzemaekers et al.   Frontiers in Immunology

A Structured Tumor-Immune Microenvironment in Triple Negative Breast Cancer Revealed by Multiplexed Ion Beam Imaging

(2018) Leeat Keren et al.   CELL

Macrophages of distinct origins contribute to tumor development in the lung

(2018) Pierre-Louis Loyher et al.   JOURNAL OF EXPERIMENTAL MEDICINE

TGFβ attenuates tumour response to PD-L1 blockade by contributing to exclusion of T cells

(2018) Sanjeev Mariathasan et al.   NATURE

High-Dimensional Analysis Delineates Myeloid and Lymphoid Compartment Remodeling during Successful Immune-Checkpoint Cancer Therapy

(2018) Matthew M. Gubin et al.   CELL

Tumor Mutational Burden as an Independent Predictor of Response to Immunotherapy in Diverse Cancers

(2017) Aaron M. Goodman et al.   MOLECULAR CANCER THERAPEUTICS

Elements of cancer immunity and the cancer–immune set point

(2017) Daniel S. Chen et al.   NATURE

Toil enables reproducible, open source, big biomedical data analyses

(2017) John Vivian et al.   NATURE BIOTECHNOLOGY

BAD-LAMP controls TLR9 trafficking and signalling in human plasmacytoid dendritic cells

(2017) Alexis Combes et al.   Nature Communications

T Regulatory Cells Support Plasma Cell Populations in the Bone Marrow

(2017) Arielle Glatman Zaretsky et al.   Cell Reports

Human Tissue-Resident Memory T Cells Are Defined by Core Transcriptional and Functional Signatures in Lymphoid and Mucosal Sites

(2017) Brahma V. Kumar et al.   Cell Reports

Critical Role for CD103 + /CD141 + Dendritic Cells Bearing CCR7 for Tumor Antigen Trafficking and Priming of T Cell Immunity in Melanoma

(2016) Edward W. Roberts et al.   CANCER CELL

Genomic and Transcriptomic Features of Response to Anti-PD-1 Therapy in Metastatic Melanoma

(2016) Willy Hugo et al.   CELL

A high-resolution transcriptome map of cell cycle reveals novel connections between periodic genes and cancer

(2016) Daniel Dominguez et al.   CELL RESEARCH

The Where, the When, and the How of Immune Monitoring for Cancer Immunotherapies in the Era of Checkpoint Inhibition

(2016) P. S. Hegde et al.   CLINICAL CANCER RESEARCH

The Chemokine Receptor CX3CR1 Defines Three Antigen-Experienced CD8 T Cell Subsets with Distinct Roles in Immune Surveillance and Homeostasis

(2016) Carmen Gerlach et al.   IMMUNITY

Expansion and Activation of CD103 + Dendritic Cell Progenitors at the Tumor Site Enhances Tumor Responses to Therapeutic PD-L1 and BRAF Inhibition

(2016) Hélène Salmon et al.   IMMUNITY

Regulatory T Cells Exhibit Distinct Features in Human Breast Cancer

(2016) George Plitas 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 Fates Zipped Up: How the Bach2 Basic Leucine Zipper Transcriptional Repressor Directs T Cell Differentiation and Function

(2016) Martin J. Richer et al.   JOURNAL OF IMMUNOLOGY

Density of immunogenic antigens does not explain the presence or absence of the T-cell–inflamed tumor microenvironment in melanoma

(2016) Stefani Spranger et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Tumor Heterogeneity and Tumor Immunity: A Chicken-and-Egg Problem

(2016) Stefani Spranger   TRENDS IN IMMUNOLOGY

Molecular and Genetic Properties of Tumors Associated with Local Immune Cytolytic Activity

(2015) Michael S. Rooney et al.   CELL

Comprehensive genomic characterization of head and neck squamous cell carcinomas

(2015)   NATURE

IL-17-producing γδ T cells and neutrophils conspire to promote breast cancer metastasis

(2015) Seth B. Coffelt et al.   NATURE

The prognostic landscape of genes and infiltrating immune cells across human cancers

(2015) Andrew J Gentles et al.   NATURE MEDICINE

Robust enumeration of cell subsets from tissue expression profiles

(2015) Aaron M Newman et al.   NATURE METHODS

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

Dissecting the Tumor Myeloid Compartment Reveals Rare Activating Antigen-Presenting Cells Critical for T Cell Immunity

(2014) Miranda L. Broz et al.   CANCER CELL

Neo-antigens predicted by tumor genome meta-analysis correlate with increased patient survival

(2014) S. D. Brown et al.   GENOME RESEARCH

Multiplexed ion beam imaging of human breast tumors

(2014) Michael Angelo et al.   NATURE MEDICINE

voom: precision weights unlock linear model analysis tools for RNA-seq read counts

(2014) Charity W Law et al.   GENOME BIOLOGY

Cancer immunotherapy strategies based on overcoming barriers within the tumor microenvironment

(2013) Thomas F Gajewski et al.   CURRENT OPINION IN IMMUNOLOGY

Modulation of Treg cells/T effector function by GITR signaling is context-dependent

(2013) Amal Ephrem et al.   EUROPEAN JOURNAL OF IMMUNOLOGY

Spatiotemporal Dynamics of Intratumoral Immune Cells Reveal the Immune Landscape in Human Cancer

(2013) Gabriela Bindea et al.   IMMUNITY

Tumor-associated macrophages: functional diversity, clinical significance, and open questions

(2013) Subhra K. Biswas et al.   Seminars in Immunopathology

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

Hallmarks of Cancer: The Next Generation

(2011) Douglas Hanahan et al.   CELL

A scaling normalization method for differential expression analysis of RNA-seq data

(2010) Mark D Robinson et al.   GENOME BIOLOGY

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Plasticity of CD4+ T Cell Lineage Differentiation

(2009) Liang Zhou et al.   IMMUNITY

Identification of a dendritic cell receptor that couples sensing of necrosis to immunity

(2009) David Sancho et al.   NATURE