A reference profile-free deconvolution method to infer cancer cell-intrinsic subtypes and tumor-type-specific stromal profiles

Characterization of Tumor-Suppressor Gene Inactivation Events in 33 Cancer Types

(2019) Peilin Jia et al.   Cell Reports

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

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

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

(2019) Francesca Finotello et al.   Genome Medicine

Comprehensive evaluation of transcriptome-based cell-type quantification methods for immuno-oncology

(2019) Gregor Sturm et al.   BIOINFORMATICS

A new method for constructing tumor specific gene co-expression networks based on samples with tumor purity heterogeneity

(2018) Francesca Petralia et al.   BIOINFORMATICS

The Immune Landscape of Cancer

(2018) Vésteinn Thorsson et al.   IMMUNITY

Right data for right patient—a precisionFDA NCI–CPTAC Multi-omics Mislabeling Challenge

(2018) Emily Boja et al.   NATURE MEDICINE

Single-cell transcriptomes from human kidneys reveal the cellular identity of renal tumors

(2018) Matthew D. Young et al.   SCIENCE

EMT- and stroma-related gene expression and resistance to PD-1 blockade in urothelial cancer

(2018) Li Wang et al.   Nature Communications

Pan-cancer deconvolution of tumour composition using DNA methylation

(2018) Ankur Chakravarthy et al.   Nature Communications

Reference component analysis of single-cell transcriptomes elucidates cellular heterogeneity in human colorectal tumors

(2017) Huipeng Li et al.   NATURE GENETICS

Selective analysis of cancer-cell intrinsic transcriptional traits defines novel clinically relevant subtypes of colorectal cancer

(2017) Claudio Isella 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

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

(2017) Julien Racle et al.   eLife

Targeting Wnt signaling in colorectal cancer. A Review in the Theme: Cell Signaling: Proteins, Pathways and Mechanisms

(2015) Laura Novellasdemunt et al.   AMERICAN JOURNAL OF PHYSIOLOGY-CELL PHYSIOLOGY

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

(2015) Catalina V Anghel et al.   BMC BIOINFORMATICS

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

(2015) Evan Z. Macosko 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

Computational and analytical challenges in single-cell transcriptomics

(2015) Oliver Stegle et al.   NATURE REVIEWS GENETICS

Systematic pan-cancer analysis of tumour purity

(2015) Dvir Aran et al.   Nature Communications

Discovery and saturation analysis of cancer genes across 21 tumour types

(2014) Michael S. Lawrence et al.   NATURE

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

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

(2013) Yi Zhong et al.   BMC BIOINFORMATICS

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

(2013) Kosuke Yoshihara et al.   Nature Communications

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

(2013) Gerald Quon et al.   Genome Medicine

A Molecular Taxonomy for Urothelial Carcinoma

(2012) G. Sjodahl et al.   CLINICAL CANCER RESEARCH

Absolute quantification of somatic DNA alterations in human cancer

(2012) Scott L Carter et al.   NATURE BIOTECHNOLOGY

Identification of Genes Upregulated in ALK-Positive and EGFR/KRAS/ALK-Negative Lung Adenocarcinomas

(2011) H. Okayama et al.   CANCER RESEARCH

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

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

GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers

(2011) Craig H Mermel et al.   GENOME BIOLOGY

Cell type–specific gene expression differences in complex tissues

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

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

(2009) David A. Barbie et al.   NATURE

Breast Cancer Subtype Approximated by Estrogen Receptor, Progesterone Receptor, and HER-2 Is Associated With Local and Distant Recurrence After Breast-Conserving Therapy

(2008) Paul L. Nguyen et al.   JOURNAL OF CLINICAL ONCOLOGY

Lung adenocarcinoma: guiding EGFR-targeted therapy and beyond

(2008) Marc Ladanyi et al.   MODERN PATHOLOGY

Comprehensive genomic characterization defines human glioblastoma genes and core pathways

(2008) Roger McLendon et al.   NATURE