Atlas of clinically distinct cell states and ecosystems across human solid tumors

The landscape of tumor cell states and ecosystems in diffuse large B cell lymphoma

(2021) Chloé B. Steen et al.   CANCER CELL

Cancer statistics, 2020

(2020) Rebecca L. Siegel et al.   CA-A CANCER JOURNAL FOR CLINICIANS

The single-cell pathology landscape of breast cancer

(2020) Hartland W. Jackson et al.   NATURE

Regenerative lineages and immune-mediated pruning in lung cancer metastasis

(2020) Ashley M. Laughney et al.   NATURE MEDICINE

The Human Tumor Atlas Network: Charting Tumor Transitions across Space and Time at Single-Cell Resolution

(2020) Orit Rozenblatt-Rosen et al.   CELL

Lineage-dependent gene expression programs influence the immune landscape of colorectal cancer

(2020) Hae-Ock Lee et al.   NATURE GENETICS

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

(2020) David Y. Oh et al.   CELL

Coordinated Cellular Neighborhoods Orchestrate Antitumoral Immunity at the Colorectal Cancer Invasive Front

(2020) Christian M. Schürch et al.   CELL

Deciphering the genomic, epigenomic, and transcriptomic landscapes of pre-invasive lung cancer lesions

(2019) Vitor H. Teixeira et al.   NATURE MEDICINE

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

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

RNA-Seq Signatures Normalized by mRNA Abundance Allow Absolute Deconvolution of Human Immune Cell Types

(2019) Gianni Monaco et al.   Cell Reports

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

(2019) Rapolas Zilionis et al.   IMMUNITY

Determining cell type abundance and expression from bulk tissues with digital cytometry

(2019) Aaron M. Newman et al.   NATURE BIOTECHNOLOGY

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

Immune evasion before tumour invasion in early lung squamous carcinogenesis

(2019) Céline Mascaux et al.   NATURE

SingleCellNet: A Computational Tool to Classify Single Cell RNA-Seq Data Across Platforms and Across Species

(2019) Yuqi Tan et al.   Cell Systems

Gene-expression profiling of single cells from archival tissue with laser-capture microdissection and Smart-3SEQ

(2019) Joseph W Foley et al.   GENOME RESEARCH

Five-Year Survival with Combined Nivolumab and Ipilimumab in Advanced Melanoma

(2019) James Larkin et al.   NEW ENGLAND JOURNAL OF MEDICINE

CLEC5A expressed on myeloid cells as a M2 biomarker relates to immunosuppression and decreased survival in patients with glioma

(2019) Luqing Tong et al.   CANCER GENE THERAPY

5-Fluorouracil treatment induces characteristic T>G mutations in human cancer

(2019) Sharon Christensen et al.   Nature Communications

MIBI-TOF: A multiplexed imaging platform relates cellular phenotypes and tissue structure

(2019) Leeat Keren et al.   Science Advances

Integrative molecular and clinical modeling of clinical outcomes to PD1 blockade in patients with metastatic melanoma

(2019) David Liu et al.   NATURE MEDICINE

ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R

(2018) Emmanuel Paradis et al.   BIOINFORMATICS

Single-Cell Transcriptome Analyses Reveal Endothelial Cell Heterogeneity in Tumors and Changes following Antiangiogenic Treatment

(2018) Qi Zhao et al.   CANCER RESEARCH

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

(2018) Elham Azizi et al.   CELL

EMT Subtype Influences Epithelial Plasticity and Mode of Cell Migration

(2018) Nicole M. Aiello et al.   DEVELOPMENTAL CELL

The Immune Landscape of Cancer

(2018) Vésteinn Thorsson et al.   IMMUNITY

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

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

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

(2018) Xinyi Guo et al.   NATURE MEDICINE

Understanding the tumor immune microenvironment (TIME) for effective therapy

(2018) Mikhail Binnewies et al.   NATURE MEDICINE

Phenotype molding of stromal cells in the lung tumor microenvironment

(2018) Diether Lambrechts et al.   NATURE MEDICINE

scmap: projection of single-cell RNA-seq data across data sets

(2018) Vladimir Yu Kiselev et al.   NATURE METHODS

Cancer immunotherapy using checkpoint blockade

(2018) Antoni Ribas et al.   SCIENCE

Periostin: A Matricellular Protein With Multiple Functions in Cancer Development and Progression

(2018) Laura González-González et al.   Frontiers in Oncology

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

(2018) Leeat Keren et al.   CELL

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

(2018) Sanjeev Mariathasan et al.   NATURE

A Cancer Cell Program Promotes T Cell Exclusion and Resistance to Checkpoint Blockade

(2018) Livnat Jerby-Arnon et al.   CELL

Pan-tumor genomic biomarkers for PD-1 checkpoint blockade–based immunotherapy

(2018) Razvan Cristescu et al.   SCIENCE

S1PR1 on tumor-associated macrophages promotes lymphangiogenesis and metastasis via NLRP3/IL-1β

(2017) Benjamin Weichand et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Comprehensive analysis of normal adjacent to tumor transcriptomes

(2017) Dvir Aran et al.   Nature Communications

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

(2016) I. Tirosh et al.   SCIENCE

Somatic Mutations and Neoepitope Homology in Melanomas Treated with CTLA-4 Blockade

(2016) Tavi Nathanson et al.   Cancer Immunology Research

A cloud-based workflow to quantify transcript-expression levels in public cancer compendia

(2016) PJ Tatlow et al.   Scientific Reports

Alternative preprocessing of RNA-Sequencing data in The Cancer Genome Atlas leads to improved analysis results

(2015) Mumtahena Rahman et al.   BIOINFORMATICS

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

(2015) Michael S. Rooney et al.   CELL

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

Genomic correlates of response to CTLA-4 blockade in metastatic melanoma

(2015) E. M. Van Allen et al.   SCIENCE

A draft network of ligand–receptor-mediated multicellular signalling in human

(2015) Jordan A. Ramilowski et al.   Nature Communications

Foam Cell Formation In Vivo Converts Macrophages to a Pro-Fibrotic Phenotype

(2015) Anita C. Thomas et al.   PLoS One

MISIPI study: Melanoma ImmunoScore evaluation in patients treated with IPIlimumab

(2014) Carlo Bifulco et al.   Journal of Translational Medicine

Diverse roles of ANGPTL2 in physiology and pathophysiology

(2014) Tsuyoshi Kadomatsu et al.   TRENDS IN ENDOCRINOLOGY AND METABOLISM

Carbonic anhydrase IX from cancer-associated fibroblasts drives epithelial-mesenchymal transition in prostate carcinoma cells

(2013) Tania Fiaschi et al.   CELL CYCLE

Human housekeeping genes, revisited

(2013) Eli Eisenberg et al.   TRENDS IN GENETICS

Inferring tumour purity and stromal and immune cell admixture from expression data

(2013) Kosuke Yoshihara et al.   Nature Communications

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Absolute quantification of somatic DNA alterations in human cancer

(2012) Scott L Carter et al.   NATURE BIOTECHNOLOGY

GC-Content Normalization for RNA-Seq Data

(2011) Davide Risso et al.   BMC BIOINFORMATICS

Optimally weighted Z-test is a powerful method for combining probabilities in meta-analysis

(2011) D. V. ZAYKIN   JOURNAL OF EVOLUTIONARY BIOLOGY

A flexible R package for nonnegative matrix factorization

(2010) Renaud Gaujoux et al.   BMC BIOINFORMATICS

Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt

(2009) Steffen Durinck et al.   Nature Protocols

Fast unfolding of communities in large networks

(2008) Vincent D Blondel et al.   JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT