Quantifying tumor-infiltrating immune cells from transcriptomics data

Elements of cancer immunity and the cancer–immune set point

(2017) Daniel S. Chen et al.   NATURE

A Critical Survey of Deconvolution Methods for Separating Cell Types in Complex Tissues

(2017) Shahin Mohammadi et al.   PROCEEDINGS OF THE IEEE

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

(2017) Max Schelker et al.   Nature Communications

Inference of immune cell composition on the expression profiles of mouse tissue

(2017) Ziyi Chen et al.   Scientific Reports

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

New strategies for cancer immunotherapy: targeting regulatory T cells

(2017) Francesca Finotello et al.   Genome Medicine

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

(2017) Julien Racle et al.   eLife

ImmQuant: a user-friendly tool for inferring immune cell-type composition from gene-expression data

(2016) Amit Frishberg et al.   BIOINFORMATICS

Computational genomics tools for dissecting tumour–immune cell interactions

(2016) Hubert Hackl et al.   NATURE REVIEWS GENETICS

RNA-seq mixology: designing realistic control experiments to compare protocols and analysis methods

(2016) Aliaksei Z. Holik et al.   NUCLEIC ACIDS RESEARCH

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

(2016) I. Tirosh et al.   SCIENCE

Patterns of Immune Infiltration in Breast Cancer and Their Clinical Implications: A Gene-Expression-Based Retrospective Study

(2016) H. Raza Ali et al.   PLOS MEDICINE

The BLUEPRINT Data Analysis Portal

(2016) José María Fernández et al.   Cell Systems

CoD: inferring immune-cell quantities related to disease states

(2015) Amit Frishberg et al.   BIOINFORMATICS

ISOpureR: an R implementation of a computational purification algorithm of mixed tumour profiles

(2015) Catalina V Anghel et al.   BMC BIOINFORMATICS

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

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

Gateways to the FANTOM5 promoter level mammalian expression atlas

(2015) Marina Lizio et al.   GENOME BIOLOGY

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

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

Digital cell quantification identifies global immune cell dynamics during influenza infection

(2014) Z. Altboum et al.   Molecular Systems Biology

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

(2014) Charity W Law et al.   GENOME BIOLOGY

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

DeMix: deconvolution for mixed cancer transcriptomes using raw measured data

(2013) Jaeil Ahn et al.   BIOINFORMATICS

CellMix: a comprehensive toolbox for gene expression deconvolution

(2013) R. Gaujoux et al.   BIOINFORMATICS

DeconRNASeq: a statistical framework for deconvolution of heterogeneous tissue samples based on mRNA-Seq data

(2013) Ting Gong et al.   BIOINFORMATICS

Digital sorting of complex tissues for cell type-specific gene expression profiles

(2013) Yi Zhong et al.   BMC BIOINFORMATICS

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

(2013) Sonja Hänzelmann et al.   BMC BIOINFORMATICS

An expression atlas of human primary cells: inference of gene function from coexpression networks

(2013) Neil A Mabbott et al.   BMC GENOMICS

Computational deconvolution: extracting cell type-specific information from heterogeneous samples

(2013) Shai S Shen-Orr et al.   CURRENT OPINION IN IMMUNOLOGY

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

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

Oncology Meets Immunology: The Cancer-Immunity Cycle

(2013) Daniel S. Chen et al.   IMMUNITY

The Cancer Genome Atlas Pan-Cancer analysis project

(2013) John N Weinstein et al.   NATURE GENETICS

Computational purification of individual tumor gene expression profiles leads to significant improvements in prognostic prediction

(2013) Gerald Quon et al.   Genome Medicine

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

PERT: A Method for Expression Deconvolution of Human Blood Samples from Varied Microenvironmental and Developmental Conditions

(2012) Wenlian Qiao et al.   PLoS Computational Biology

Densely Interconnected Transcriptional Circuits Control Cell States in Human Hematopoiesis

(2011) Noa Novershtern et al.   CELL

Semi-supervised Nonnegative Matrix Factorization for gene expression deconvolution: A case study

(2011) Renaud Gaujoux et al.   INFECTION GENETICS AND EVOLUTION

Gene expression deconvolution in linear space

(2011) Yi Zhong et al.   NATURE METHODS

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

(2011) Ting Gong et al.   PLoS One

Biomarker discovery in heterogeneous tissue samples -taking the in-silico deconfounding approach

(2010) Dirk Repsilber et al.   BMC BIOINFORMATICS

Systematic RNA interference reveals that oncogenic KRAS-driven cancers require TBK1

(2009) David A. Barbie et al.   NATURE

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

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

Next-generation DNA sequencing

(2008) Jay Shendure et al.   NATURE BIOTECHNOLOGY

Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing

(2008) Qun Pan et al.   NATURE GENETICS