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

DeMix: deconvolution for mixed cancer transcriptomes using raw measured data

(2013) Jaeil Ahn et al.   BIOINFORMATICS

PurBayes: estimating tumor cellularity and subclonality in next-generation sequencing data

(2013) Nicholas B. Larson et al.   BIOINFORMATICS

EXPANDS: expanding ploidy and allele frequency on nested subpopulations

(2013) Noemi Andor et al.   BIOINFORMATICS

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

(2013) Ting Gong et al.   BIOINFORMATICS

Advances for studying clonal evolution in cancer

(2013) Li Ding et al.   CANCER LETTERS

Evolution and Impact of Subclonal Mutations in Chronic Lymphocytic Leukemia

(2013) Dan A. Landau et al.   CELL

Tumour heterogeneity in the clinic

(2013) Philippe L. Bedard et al.   NATURE

Mutational heterogeneity in cancer and the search for new cancer-associated genes

(2013) Michael S. Lawrence et al.   NATURE

Tumour heterogeneity and cancer cell plasticity

(2013) Corbin E. Meacham et al.   NATURE

The causes and consequences of genetic heterogeneity in cancer evolution

(2013) Rebecca A. Burrell et al.   NATURE

Mutational landscape and significance across 12 major cancer types

(2013) Cyriac Kandoth et al.   NATURE

Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples

(2013) Kristian Cibulskis et al.   NATURE BIOTECHNOLOGY

Characterization of transcriptional networks in blood stem and progenitor cells using high-throughput single-cell gene expression analysis

(2013) Victoria Moignard et al.   NATURE CELL BIOLOGY

TrAp: a tree approach for fingerprinting subclonal tumor composition

(2013) Francesco Strino et al.   NUCLEIC ACIDS RESEARCH

Deconvoluting complex tissues for expression quantitative trait locus-based analyses

(2013) J.-H. Seo et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Aberration in DNA Methylation in B-Cell Lymphomas Has a Complex Origin and Increases with Disease Severity

(2013) Subhajyoti De et al.   PLoS Genetics

Virmid: accurate detection of somatic mutations with sample impurity inference

(2013) Sangwoo Kim et al.   GENOME BIOLOGY

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

(2013) Layla Oesper et al.   GENOME BIOLOGY

JointSNVMix: a probabilistic model for accurate detection of somatic mutations in normal/tumour paired next-generation sequencing data

(2012) Andrew Roth et al.   BIOINFORMATICS

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

(2012) X. Su et al.   BIOINFORMATICS

Strelka: accurate somatic small-variant calling from sequenced tumor–normal sample pairs

(2012) Christopher T. Saunders et al.   BIOINFORMATICS

DNA Sequencing

(2012) Frederick E. Dewey et al.   CIRCULATION

Single-Cell Analysis Reveals that Noncoding RNAs Contribute to Clonal Heterogeneity by Modulating Transcription Factor Recruitment

(2012) Stacie L. Bumgarner et al.   MOLECULAR CELL

Comprehensive molecular portraits of human breast tumours

(2012) Daniel C. Koboldt et al.   NATURE

Absolute quantification of somatic DNA alterations in human cancer

(2012) Scott L Carter et al.   NATURE BIOTECHNOLOGY

Evolutionary Pathways in BRCA1-Associated Breast Tumors

(2012) Filipe C. Martins et al.   Cancer Discovery

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

(2012) Wenlian Qiao et al.   PLoS Computational Biology

Correcting for cancer genome size and tumour cell content enables better estimation of copy number alterations from next-generation sequence data

(2011) Arief Gusnanto et al.   BIOINFORMATICS

SomaticSniper: identification of somatic point mutations in whole genome sequencing data

(2011) David E. Larson et al.   BIOINFORMATICS

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

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

Tumour evolution inferred by single-cell sequencing

(2011) Nicholas Navin et al.   NATURE

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

(2011) Ting Gong et al.   PLoS One

Somatic mosaicism in healthy human tissues

(2011) Subhajyoti De   TRENDS IN GENETICS

Gene expression deconvolution in clinical samples

(2011) Yingdong Zhao et al.   Genome Medicine

Future medical applications of single-cell sequencing in cancer

(2011) Nicholas Navin et al.   Genome Medicine

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

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

Major copy proportion analysis of tumor samples using SNP arrays

(2008) Cheng Li et al.   BMC BIOINFORMATICS