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

Integrated genomic characterization of endometrial carcinoma

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Interobserver Agreement Among Pathologists for Semiquantitative Hormone Receptor Scoring in Breast Carcinoma

(2012) David A. Cohen et al.   AMERICAN JOURNAL OF CLINICAL PATHOLOGY

PurityEst: estimating purity of human tumor samples using next-generation sequencing data

(2012) X. Su et al.   BIOINFORMATICS

CTen: a web-based platform for identifying enriched cell types from heterogeneous microarray data

(2012) Jason E Shoemaker et al.   BMC GENOMICS

Mapping the Hallmarks of Lung Adenocarcinoma with Massively Parallel Sequencing

(2012) Marcin Imielinski et al.   CELL

The Life History of 21 Breast Cancers

(2012) Serena Nik-Zainal et al.   CELL

High-Risk Ovarian Cancer Based on 126-Gene Expression Signature Is Uniquely Characterized by Downregulation of Antigen Presentation Pathway

(2012) Kosuke Yoshihara et al.   CLINICAL CANCER RESEARCH

Microarray Analysis of Colorectal Cancer Stromal Tissue Reveals Upregulation of Two Oncogenic miRNA Clusters

(2012) N. Nishida et al.   CLINICAL CANCER RESEARCH

MuSiC: Identifying mutational significance in cancer genomes

(2012) N. D. Dees et al.   GENOME RESEARCH

Ipilimumab in Combination With Paclitaxel and Carboplatin As First-Line Treatment in Stage IIIB/IV Non–Small-Cell Lung Cancer: Results From a Randomized, Double-Blind, Multicenter Phase II Study

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Comprehensive molecular characterization of human colon and rectal cancer

(2012)   NATURE

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

(2012) Jordi Barretina et al.   NATURE

Comprehensive molecular portraits of human breast tumours

(2012) Daniel C. Koboldt et al.   NATURE

Comprehensive genomic characterization of squamous cell lung cancers

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Tumour micro-environment elicits innate resistance to RAF inhibitors through HGF secretion

(2012) Ravid Straussman et al.   NATURE

Absolute quantification of somatic DNA alterations in human cancer

(2012) Scott L Carter et al.   NATURE BIOTECHNOLOGY

Intratumor Heterogeneity and Branched Evolution Revealed by Multiregion Sequencing

(2012) Marco Gerlinger et al.   NEW ENGLAND JOURNAL OF MEDICINE

ArrayExpress update—trends in database growth and links to data analysis tools

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Cell subset prediction for blood genomic studies

(2011) Christopher R Bolen et al.   BMC BIOINFORMATICS

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

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pROC: an open-source package for R and S+ to analyze and compare ROC curves

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Hallmarks of Cancer: The Next Generation

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Histopathologic-Based Prognostic Factors of Colorectal Cancers Are Associated With the State of the Local Immune Reaction

(2011) Bernhard Mlecnik et al.   JOURNAL OF CLINICAL ONCOLOGY

Integrated genomic analyses of ovarian carcinoma

(2011) D. Bell et al.   NATURE

Probabilistic analysis of gene expression measurements from heterogeneous tissues

(2010) Timo Erkkilä et al.   BIOINFORMATICS

Integrated Genomic Analysis Identifies Clinically Relevant Subtypes of Glioblastoma Characterized by Abnormalities in PDGFRA, IDH1, EGFR, and NF1

(2010) Roel G.W. Verhaak et al.   CANCER CELL

Immunity, Inflammation, and Cancer

(2010) Sergei I. Grivennikov et al.   CELL

Meta-analysis of genome-wide association scans for genetic susceptibility to endometriosis in Japanese population

(2010) Sosuke Adachi et al.   JOURNAL OF HUMAN GENETICS

Cell type–specific gene expression differences in complex tissues

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

Allele-specific copy number analysis of tumors

(2010) P. Van Loo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Emerging Role of EpCAM in Cancer and Stem Cell Signaling

(2009) M. Munz et al.   CANCER RESEARCH

The basics of epithelial-mesenchymal transition

(2009) Raghu Kalluri et al.   JOURNAL OF CLINICAL INVESTIGATION

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

(2009) David A. Barbie et al.   NATURE

Distilling Free-Form Natural Laws from Experimental Data

(2009) Michael Schmidt et al.   SCIENCE

Novel Molecular Subtypes of Serous and Endometrioid Ovarian Cancer Linked to Clinical Outcome

(2008) R. W. Tothill et al.   CLINICAL CANCER RESEARCH

Prediction of molecular subtypes in acute myeloid leukemia based on gene expression profiling

(2008) R. G.W. Verhaak et al.   HAEMATOLOGICA

Somatic mutations affect key pathways in lung adenocarcinoma

(2008) Li Ding et al.   NATURE

Comprehensive genomic characterization defines human glioblastoma genes and core pathways

(2008) Roger McLendon et al.   NATURE

Gene expression–based survival prediction in lung adenocarcinoma: a multi-site, blinded validation study

(2008) Kerby Shedden et al.   NATURE MEDICINE

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS