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

Fast and Elegant Numerical Linear Algebra Using theRcppEigenPackage

(2015) Douglas Bates et al.   Journal of Statistical Software

UNDO: a Bioconductor R package for unsupervised deconvolution of mixed gene expressions in tumor samples

(2014) Niya Wang et al.   BIOINFORMATICS

An assessment of computational methods for estimating purity and clonality using genomic data derived from heterogeneous tumor tissue samples

(2014) V. K. Yadav et al.   BRIEFINGS IN BIOINFORMATICS

Predictive Performance of Microarray Gene Signatures: Impact of Tumor Heterogeneity and Multiple Mechanisms of Drug Resistance

(2014) C. K. Y. Ng et al.   CANCER RESEARCH

Global optimization of somatic variant identification in cancer genomes with a global community challenge

(2014) Paul C Boutros et al.   NATURE GENETICS

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

Structural analysis on mutation residues and interfacial water molecules for human TIM disease understanding

(2013) Zhenhua Li et al.   BMC BIOINFORMATICS

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

(2013) Yi Zhong et al.   BMC BIOINFORMATICS

Cancer heterogeneity: implications for targeted therapeutics

(2013) R Fisher et al.   BRITISH JOURNAL OF CANCER

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

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

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

(2013) Gerald Quon et al.   Genome Medicine

THetA: inferring intra-tumor heterogeneity from high-throughput DNA sequencing data

(2013) Layla Oesper et al.   GENOME BIOLOGY

Absolute quantification of somatic DNA alterations in human cancer

(2012) Scott L Carter et al.   NATURE BIOTECHNOLOGY

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

(2012) Wenlian Qiao et al.   PLoS Computational Biology

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

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

Population-specific expression analysis (PSEA) reveals molecular changes in diseased brain

(2011) Alexandre Kuhn et al.   NATURE METHODS

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

Robust unmixing of tumor states in array comparative genomic hybridization data

(2010) David Tolliver et al.   BIOINFORMATICS

Statistical expression deconvolution from mixed tissue samples

(2010) J. Clarke et al.   BIOINFORMATICS

Probabilistic analysis of gene expression measurements from heterogeneous tissues

(2010) Timo Erkkilä et al.   BIOINFORMATICS

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

(2010) Dirk Repsilber et al.   BMC BIOINFORMATICS

In silico Estimates of Tissue Components in Surgical Samples Based on Expression Profiling Data

(2010) Y. Wang et al.   CANCER RESEARCH

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

ISOLATE: a computational strategy for identifying the primary origin of cancers using high-throughput sequencing

(2009) G. Quon et al.   BIOINFORMATICS

Supervised Risk Predictor of Breast Cancer Based on Intrinsic Subtypes

(2009) Joel S. Parker et al.   JOURNAL OF CLINICAL ONCOLOGY

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

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

Tumor Immunobiological Differences in Prostate Cancer between African-American and European-American Men

(2008) T. A. Wallace et al.   CANCER RESEARCH

Genome-wide transcriptional analysis of the human cell cycle identifies genes differentially regulated in normal and cancer cells

(2008) Z. Bar-Joseph et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA