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

Evolution and Impact of Subclonal Mutations in Chronic Lymphocytic Leukemia

(2013) Dan A. Landau et al.   CELL

Criteria for Inference of Chromothripsis in Cancer Genomes

(2013) Jan O. Korbel et al.   CELL

An algorithmic approach for breakage-fusion-bridge detection in tumor genomes

(2013) S. Zakov et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genomic dark matter: the reliability of short read mapping illustrated by the genome mappability score

(2012) Hayan Lee et al.   BIOINFORMATICS

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

(2012) X. Su et al.   BIOINFORMATICS

Reconstructing cancer genomes from paired-end sequencing data

(2012) Layla Oesper et al.   BMC BIOINFORMATICS

Single-Cell Exome Sequencing Reveals Single-Nucleotide Mutation Characteristics of a Kidney Tumor

(2012) Xun Xu et al.   CELL

Single-Cell Exome Sequencing and Monoclonal Evolution of a JAK2-Negative Myeloproliferative Neoplasm

(2012) Yong Hou et al.   CELL

The Life History of 21 Breast Cancers

(2012) Serena Nik-Zainal et al.   CELL

nFuse: Discovery of complex genomic rearrangements in cancer using high-throughput sequencing

(2012) A. McPherson et al.   GENOME RESEARCH

VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing

(2012) D. C. Koboldt et al.   GENOME RESEARCH

Clonal evolution in cancer

(2012) Mel Greaves et al.   NATURE

Clonal evolution in relapsed acute myeloid leukaemia revealed by whole-genome sequencing

(2012) Li Ding et al.   NATURE

Absolute quantification of somatic DNA alterations in human cancer

(2012) Scott L Carter et al.   NATURE BIOTECHNOLOGY

Genome-wide copy number analysis of single cells

(2012) Timour Baslan et al.   Nature Protocols

Intratumor Heterogeneity and Branched Evolution Revealed by Multiregion Sequencing

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

Heterogeneity and Tumor History

(2012) D. Shibata   SCIENCE

Quantitative Image Analysis of Cellular Heterogeneity in Breast Tumors Complements Genomic Profiling

(2012) Y. Yuan et al.   Science Translational Medicine

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

Detecting copy number status and uncovering subclonal markers in heterogeneous tumor biopsies

(2011) Fabio Parisi et al.   BMC GENOMICS

Calling amplified haplotypes in next generation tumor sequence data

(2011) N. Dewal et al.   GENOME RESEARCH

Estimation of rearrangement phylogeny for cancer genomes

(2011) C. D. Greenman et al.   GENOME RESEARCH

Tumour evolution inferred by single-cell sequencing

(2011) Nicholas Navin et al.   NATURE

ReadDepth: A Parallel R Package for Detecting Copy Number Alterations from Short Sequencing Reads

(2011) Christopher A. Miller et al.   PLoS One

Copy number variation detection in whole-genome sequencing data using the Bayesian information criterion

(2011) R. Xi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Robust unmixing of tumor states in array comparative genomic hybridization data

(2010) David Tolliver et al.   BIOINFORMATICS

Analysis of next-generation genomic data in cancer: accomplishments and challenges

(2010) L. Ding et al.   HUMAN MOLECULAR GENETICS

Advances in understanding cancer genomes through second-generation sequencing

(2010) Matthew Meyerson et al.   NATURE REVIEWS GENETICS

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

A geometric approach for classification and comparison of structural variants

(2009) S. Sindi et al.   BIOINFORMATICS

PICNIC: an algorithm to predict absolute allelic copy number variation with microarray cancer data

(2009) C. D. Greenman et al.   BIOSTATISTICS

Inferring tumor progression from genomic heterogeneity

(2009) N. Navin et al.   GENOME RESEARCH

BreakDancer: an algorithm for high-resolution mapping of genomic structural variation

(2009) Ken Chen et al.   NATURE METHODS

SNP Arrays in Heterogeneous Tissue: Highly Accurate Collection of Both Germline and Somatic Genetic Information from Unpaired Single Tumor Samples

(2008) Guillaume Assié et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Genome-wide analysis identifies 16q deletion associated with survival, molecular subtypes, mRNA expression, and germline haplotypes in breast cancer patients

(2008) Silje H. Nordgard et al.   GENES CHROMOSOMES & CANCER

Many different tumor types have polyclonal tumor origin: Evidence and implications

(2008) B PARSONS   MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH

High-resolution mapping of copy-number alterations with massively parallel sequencing

(2008) Derek Y Chiang et al.   NATURE METHODS

Genomic Analysis of the Clonal Origins of Relapsed Acute Lymphoblastic Leukemia

(2008) C. G. Mullighan et al.   SCIENCE

Evaluation of Paired-End Sequencing Strategies for Detection of Genome Rearrangements in Cancer

(2008) Ali Bashir et al.   PLoS Computational Biology