Fast and scalable inference of multi-sample cancer lineages

Clonality inference in multiple tumor samples using phylogeny

(2015) Salem Malikic et al.   BIOINFORMATICS

PhyloWGS: Reconstructing subclonal composition and evolution from whole-genome sequencing of tumors

(2015) Amit G Deshwar et al.   GENOME BIOLOGY

A combinatorial approach for analyzing intra-tumor heterogeneity from high-throughput sequencing data

(2014) Iman Hajirasouliha et al.   BIOINFORMATICS

Inferring clonal evolution of tumors from single nucleotide somatic mutations

(2014) Wei Jiao et al.   BMC BIOINFORMATICS

Genetic and Clonal Dissection of Murine Small Cell Lung Carcinoma Progression by Genome Sequencing

(2014) David G. McFadden et al.   CELL

TITAN: inference of copy number architectures in clonal cell populations from tumor whole-genome sequence data

(2014) Gavin Ha et al.   GENOME RESEARCH

Dynamics of genomic clones in breast cancer patient xenografts at single-cell resolution

(2014) Peter Eirew et al.   NATURE

Genomic architecture and evolution of clear cell renal cell carcinomas defined by multiregion sequencing

(2014) Marco Gerlinger et al.   NATURE GENETICS

PyClone: statistical inference of clonal population structure in cancer

(2014) Andrew Roth et al.   NATURE METHODS

Spatial and temporal diversity in genomic instability processes defines lung cancer evolution

(2014) E. C. de Bruin et al.   SCIENCE

Mutascope: sensitive detection of somatic mutations from deep amplicon sequencing

(2013) Shawn E. Yost et al.   BIOINFORMATICS

Hierarchy in somatic mutations arising during genomic evolution and progression of follicular lymphoma

(2013) M. R. Green et al.   BLOOD

Cancer heterogeneity: implications for targeted therapeutics

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

Evolution and Impact of Subclonal Mutations in Chronic Lymphocytic Leukemia

(2013) Dan A. Landau et al.   CELL

Genome evolution during progression to breast cancer

(2013) D. E. Newburger et al.   GENOME RESEARCH

Inference of Tumor Phylogenies with Improved Somatic Mutation Discovery

(2013) Raheleh Salari et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Distinct evolutionary trajectories of primary high-grade serous ovarian cancers revealed through spatial mutational profiling

(2013) Ali Bashashati et al.   JOURNAL OF PATHOLOGY

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

(2013) Layla Oesper et al.   GENOME BIOLOGY

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

(2012) Christopher T. Saunders et al.   BIOINFORMATICS

Monitoring chronic lymphocytic leukemia progression by whole genome sequencing reveals heterogeneous clonal evolution patterns

(2012) A. Schuh et al.   BLOOD

The Life History of 21 Breast Cancers

(2012) Serena Nik-Zainal et al.   CELL

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

Evolution of the cancer genome

(2012) Lucy R. Yates et al.   NATURE REVIEWS GENETICS

Intratumor Heterogeneity and Branched Evolution Revealed by Multiregion Sequencing

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

Reliable detection of subclonal single-nucleotide variants in tumour cell populations

(2012) Moritz Gerstung et al.   Nature Communications

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

(2011) David E. Larson et al.   BIOINFORMATICS

The patterns and dynamics of genomic instability in metastatic pancreatic cancer

(2010) Peter J. Campbell et al.   NATURE

Distant metastasis occurs late during the genetic evolution of pancreatic cancer

(2010) Shinichi Yachida et al.   NATURE

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

Subclonal phylogenetic structures in cancer revealed by ultra-deep sequencing

(2008) P. J. Campbell et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA