Molecular and pharmacological modulators of the tumor immune contexture revealed by deconvolution of RNA-seq data

Quantifying tumor-infiltrating immune cells from transcriptomics data

(2018) Francesca Finotello et al.   CANCER IMMUNOLOGY IMMUNOTHERAPY

CXCL9, CXCL10, CXCL11/CXCR3 axis for immune activation – A target for novel cancer therapy

(2018) Ryuma Tokunaga et al.   CANCER TREATMENT REVIEWS

The Immune Landscape of Cancer

(2018) Vésteinn Thorsson et al.   IMMUNITY

Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images

(2018) Joel Saltz et al.   Cell Reports

Quantitative Analyses of the Tumor Microenvironment Composition and Orientation in the Era of Precision Medicine

(2018) Florent Petitprez et al.   Frontiers in Oncology

Multi-Omics Profiling of the Tumor Microenvironment: Paving the Way to Precision Immuno-Oncology

(2018) Francesca Finotello et al.   Frontiers in Oncology

Comprehensive Intrametastatic Immune Quantification and Major Impact of Immunoscore on Survival

(2017) Bernhard Mlecnik et al.   JNCI-Journal of the National Cancer Institute

The benefits of immunotherapy combinations

(2017) Charles Schmidt   NATURE

Elements of cancer immunity and the cancer–immune set point

(2017) Daniel S. Chen et al.   NATURE

The immune contexture in cancer prognosis and treatment

(2017) Wolf H. Fridman et al.   Nature Reviews Clinical Oncology

Dynamic versus static biomarkers in cancer immune checkpoint blockade: unravelling complexity

(2017) W. Joost Lesterhuis et al.   NATURE REVIEWS DRUG DISCOVERY

A molecular portrait of microsatellite instability across multiple cancers

(2017) Isidro Cortes-Ciriano et al.   Nature Communications

Estimation of immune cell content in tumour tissue using single-cell RNA-seq data

(2017) Max Schelker et al.   Nature Communications

Recurrent Tumor Cell–Intrinsic and –Extrinsic Alterations during MAPKi-Induced Melanoma Regression and Early Adaptation

(2017) Chunying Song et al.   Cancer Discovery

Quantitative Multiplex Immunohistochemistry Reveals Myeloid-Inflamed Tumor-Immune Complexity Associated with Poor Prognosis

(2017) Takahiro Tsujikawa et al.   Cell Reports

Pan-cancer Immunogenomic Analyses Reveal Genotype-Immunophenotype Relationships and Predictors of Response to Checkpoint Blockade

(2017) Pornpimol Charoentong et al.   Cell Reports

Simultaneous enumeration of cancer and immune cell types from bulk tumor gene expression data

(2017) Julien Racle et al.   eLife

Comprehensive Intrametastatic Immune Quantification and Major Impact of Immunoscore on Survival

(2017) Bernhard Mlecnik et al.   JNCI-Journal of the National Cancer Institute

Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

Computational genomics tools for dissecting tumour–immune cell interactions

(2016) Hubert Hackl et al.   NATURE REVIEWS GENETICS

Analysis of Immune Signatures in Longitudinal Tumor Samples Yields Insight into Biomarkers of Response and Mechanisms of Resistance to Immune Checkpoint Blockade

(2016) P.-L. Chen et al.   Cancer Discovery

Immunological Effects of Conventional Chemotherapy and Targeted Anticancer Agents

(2015) Lorenzo Galluzzi et al.   CANCER CELL

Genomic Classification of Cutaneous Melanoma

(2015) Rehan Akbani et al.   CELL

The consensus molecular subtypes of colorectal cancer

(2015) Justin Guinney et al.   NATURE MEDICINE

Robust enumeration of cell subsets from tissue expression profiles

(2015) Aaron M Newman et al.   NATURE METHODS

PD-1 Blockade in Tumors with Mismatch-Repair Deficiency

(2015) Dung T. Le et al.   NEW ENGLAND JOURNAL OF MEDICINE

Systematic pan-cancer analysis of tumour purity

(2015) Dvir Aran et al.   Nature Communications

Characterization of the immunophenotypes and antigenomes of colorectal cancers reveals distinct tumor escape mechanisms and novel targets for immunotherapy

(2015) Mihaela Angelova et al.   GENOME BIOLOGY

De novo transcriptome profiling of highly purified human lymphocytes primary cells

(2015) Raoul J.P. Bonnal et al.   Scientific Data

A Cell-Based Systems Biology Assessment of Human Blood to Monitor Immune Responses after Influenza Vaccination

(2015) Kristen L. Hoek et al.   PLoS One

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Measuring differential gene expression with RNA-seq: challenges and strategies for data analysis

(2014) F. Finotello et al.   Briefings in Functional Genomics

MMAD: microarray microdissection with analysis of differences is a computational tool for deconvoluting cell type-specific contributions from tissue samples

(2013) David A. Liebner et al.   BIOINFORMATICS

From single-cell to cell-pool transcriptomes: Stochasticity in gene expression and RNA splicing

(2013) G. K. Marinov et al.   GENOME RESEARCH

Towards the introduction of the ‘Immunoscore’ in the classification of malignant tumours

(2013) Jérôme Galon et al.   JOURNAL OF PATHOLOGY

The Cancer Genome Atlas Pan-Cancer analysis project

(2013) John N Weinstein et al.   NATURE GENETICS

Human housekeeping genes, revisited

(2013) Eli Eisenberg et al.   TRENDS IN GENETICS

The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity

(2012) Jordi Barretina et al.   NATURE

Expression Profiling of Human Immune Cell Subsets Identifies miRNA-mRNA Regulatory Relationships Correlated with Cell Type Specific Expression

(2012) Florence Allantaz et al.   PLoS One

Improved structure, function and compatibility for CellProfiler: modular high-throughput image analysis software

(2011) Lee Kamentsky et al.   BIOINFORMATICS

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

(2011) Bo Li et al.   BMC BIOINFORMATICS

Measuring cell identity in noisy biological systems

(2011) Kenneth D. Birnbaum et al.   NUCLEIC ACIDS RESEARCH

Optimal Deconvolution of Transcriptional Profiling Data Using Quadratic Programming with Application to Complex Clinical Blood Samples

(2011) Ting Gong et al.   PLoS One

Metadata matters: access to image data in the real world

(2010) Melissa Linkert et al.   JOURNAL OF CELL BIOLOGY

Cell type–specific gene expression differences in complex tissues

(2010) Shai S Shen-Orr et al.   NATURE METHODS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Biomolecular Network Reconstruction Identifies T-Cell Homing Factors Associated With Survival in Colorectal Cancer

(2009) Bernhard Mlecnik et al.   GASTROENTEROLOGY

Deconvolution of Blood Microarray Data Identifies Cellular Activation Patterns in Systemic Lupus Erythematosus

(2009) Alexander R. Abbas et al.   PLoS One