Single-cell RNA-seq enables comprehensive tumour and immune cell profiling in primary breast cancer

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

(2016) I. Tirosh et al.   SCIENCE

B cell regulation of the anti-tumor response and role in carcinogenesis

(2016) Marc Schwartz et al.   Journal for ImmunoTherapy of Cancer

Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets

(2015) Evan Z. Macosko et al.   CELL

The first five years of single-cell cancer genomics and beyond

(2015) Nicholas E. Navin   GENOME RESEARCH

Immune Checkpoint Blockade in Cancer Therapy

(2015) Michael A. Postow et al.   JOURNAL OF CLINICAL ONCOLOGY

Single-cell analysis reveals a stem-cell program in human metastatic breast cancer cells

(2015) Devon A. Lawson et al.   NATURE

Fluorescent in situ sequencing (FISSEQ) of RNA for gene expression profiling in intact cells and tissues

(2015) Je Hyuk Lee et al.   Nature Protocols

Delineating cancer evolution with single-cell sequencing

(2015) Nicholas E. Navin   Science Translational Medicine

T-cell exhaustion in the tumor microenvironment

(2015) Y Jiang et al.   Cell Death & Disease

Intra-tumor genetic heterogeneity and alternative driver genetic alterations in breast cancers with heterogeneous HER2 gene amplification

(2015) Charlotte KY Ng et al.   GENOME BIOLOGY

Single-cell mRNA sequencing identifies subclonal heterogeneity in anti-cancer drug responses of lung adenocarcinoma cells

(2015) Kyu-Tae Kim et al.   GENOME BIOLOGY

Inhibitory Receptors Beyond T Cell Exhaustion

(2015) Silvia A. Fuertes Marraco et al.   Frontiers in Immunology

The evaluation of tumor-infiltrating lymphocytes (TILs) in breast cancer: recommendations by an International TILs Working Group 2014

(2014) R. Salgado et al.   ANNALS OF ONCOLOGY

Transfer of clinically relevant gene expression signatures in breast cancer: from Affymetrix microarray to Illumina RNA-Sequencing technology

(2014) Debora Fumagalli et al.   BMC GENOMICS

The Immunoreceptor TIGIT Regulates Antitumor and Antiviral CD8 + T Cell Effector Function

(2014) Robert J. Johnston et al.   CANCER CELL

Tumor-Associated Macrophages: From Mechanisms to Therapy

(2014) Roy Noy et al.   IMMUNITY

Clonal evolution in breast cancer revealed by single nucleus genome sequencing

(2014) Yong Wang et al.   NATURE

Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma

(2014) A. P. Patel et al.   SCIENCE

GSVA: gene set variation analysis for microarray and RNA-Seq data

(2013) Sonja Hänzelmann et al.   BMC BIOINFORMATICS

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

(2013) Gabriela Bindea et al.   IMMUNITY

Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples

(2013) Kristian Cibulskis et al.   NATURE BIOTECHNOLOGY

Innate and adaptive immune cells in the tumor microenvironment

(2013) Thomas F Gajewski et al.   NATURE IMMUNOLOGY

Quantitative assessment of single-cell RNA-sequencing methods

(2013) Angela R Wu et al.   NATURE METHODS

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

(2013) Kosuke Yoshihara et al.   Nature Communications

RNA-SeQC: RNA-seq metrics for quality control and process optimization

(2012) David S. DeLuca et al.   BIOINFORMATICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

A Three-Gene Model to Robustly Identify Breast Cancer Molecular Subtypes

(2012) Benjamin Haibe-Kains et al.   JNCI-Journal of the National Cancer Institute

Sequence analysis of mutations and translocations across breast cancer subtypes

(2012) Shantanu Banerji et al.   NATURE

Comprehensive molecular portraits of human breast tumours

(2012) Daniel C. Koboldt et al.   NATURE

Control-FREEC: a tool for assessing copy number and allelic content using next-generation sequencing data

(2011) Valentina Boeva et al.   BIOINFORMATICS

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

(2011) Bo Li et al.   BMC BIOINFORMATICS

The prognostic significance of B lymphocytes in invasive carcinoma of the breast

(2011) S. M. A. Mahmoud et al.   BREAST CANCER RESEARCH AND TREATMENT

Targeted therapies for breast cancer

(2011) Michaela J. Higgins et al.   JOURNAL OF CLINICAL INVESTIGATION

Identification of human triple-negative breast cancer subtypes and preclinical models for selection of targeted therapies

(2011) Brian D. Lehmann et al.   JOURNAL OF CLINICAL INVESTIGATION

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

(2011) Mark A DePristo et al.   NATURE GENETICS

Mechanisms of Endocrine Resistance in Breast Cancer

(2010) C. Kent Osborne et al.   Annual Review of Medicine

A flexible R package for nonnegative matrix factorization

(2010) Renaud Gaujoux et al.   BMC BIOINFORMATICS

Cancer-Associated Fibroblasts Are Activated in Incipient Neoplasia to Orchestrate Tumor-Promoting Inflammation in an NF-κB-Dependent Manner

(2010) Neta Erez et al.   CANCER CELL

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Triple-Negative Breast Cancer: Distinguishing between Basal and Nonbasal Subtypes

(2009) E. A. Rakha et al.   CLINICAL CANCER RESEARCH

Genetic Alterations and Oncogenic Pathways Associated with Breast Cancer Subtypes

(2009) X. Hu et al.   MOLECULAR CANCER RESEARCH

Biological Processes Associated with Breast Cancer Clinical Outcome Depend on the Molecular Subtypes

(2008) C. Desmedt et al.   CLINICAL CANCER RESEARCH

Development of the 21-Gene Assay and Its Application in Clinical Practice and Clinical Trials

(2008) Joseph A. Sparano et al.   JOURNAL OF CLINICAL ONCOLOGY

Clinical Application of the 70-Gene Profile: The MINDACT Trial

(2008) Fatima Cardoso et al.   JOURNAL OF CLINICAL ONCOLOGY

Stromal gene expression predicts clinical outcome in breast cancer

(2008) Greg Finak et al.   NATURE MEDICINE