Punctuated copy number evolution and clonal stasis in triple-negative breast cancer

Identification of neutral tumor evolution across cancer types

(2016) Marc J Williams et al.   NATURE GENETICS

A Big Bang model of human colorectal tumor growth

(2015) Andrea Sottoriva et al.   NATURE GENETICS

Subclonal diversification of primary breast cancer revealed by multiregion sequencing

(2015) Lucy R Yates et al.   NATURE MEDICINE

Interactive analysis and assessment of single-cell copy-number variations

(2015) Tyler Garvin et al.   NATURE METHODS

Extremely high genetic diversity in a single tumor points to prevalence of non-Darwinian cell evolution

(2015) Shaoping Ling et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

An Evolutionary Approach for Identifying Driver Mutations in Colorectal Cancer

(2015) Jasmine Foo et al.   PLoS Computational Biology

Clonal evolution in breast cancer revealed by single nucleus genome sequencing

(2014) Yong Wang et al.   NATURE

COSMIC: exploring the world's knowledge of somatic mutations in human cancer

(2014) Simon A. Forbes et al.   NUCLEIC ACIDS RESEARCH

Single cell sequencing reveals low levels of aneuploidy across mammalian tissues

(2014) Kristin A. Knouse et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Inference of Tumor Evolution during Chemotherapy by Computational Modeling and In Situ Analysis of Genetic and Phenotypic Cellular Diversity

(2014) Vanessa Almendro et al.   Cell Reports

Copynumber: Efficient algorithms for single- and multi-track copy number segmentation

(2013) Gro Nilsen et al.   BMC GENOMICS

Punctuated Evolution of Prostate Cancer Genomes

(2013) Sylvan C. Baca et al.   CELL

Chromosomal instability and cancer: a complex relationship with therapeutic potential

(2012) Samuel F. Bakhoum et al.   JOURNAL OF CLINICAL INVESTIGATION

Comprehensive molecular portraits of human breast tumours

(2012) Daniel C. Koboldt et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Genome-wide copy number analysis of single cells

(2012) Timour Baslan et al.   Nature Protocols

Massive Genomic Rearrangement Acquired in a Single Catastrophic Event during Cancer Development

(2011) Philip J. Stephens et al.   CELL

Hallmarks of Cancer: The Next Generation

(2011) Douglas Hanahan et al.   CELL

Tumour evolution inferred by single-cell sequencing

(2011) Nicholas Navin et al.   NATURE

An intuitive graphical visualization technique for the interrogation of transcriptome data

(2011) Natascha Bushati et al.   NUCLEIC ACIDS RESEARCH

phangorn: phylogenetic analysis in R

(2010) Klaus Peter Schliep   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Cellular and genetic diversity in the progression of in situ human breast carcinomas to an invasive phenotype

(2010) So Yeon Park et al.   JOURNAL OF CLINICAL INVESTIGATION

Tracing the tumor lineage

(2010) Nicholas E. Navin et al.   Molecular Oncology

Triple-Negative Breast Cancer

(2010) William D. Foulkes et al.   NEW ENGLAND JOURNAL OF MEDICINE

Integrative molecular profiling of triple negative breast cancers identifies amplicon drivers and potential therapeutic targets

(2010) N Turner et al.   ONCOGENE

Proteins Required for Centrosome Clustering in Cancer Cells

(2010) B. Leber et al.   Science Translational Medicine

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Inferring tumor progression from genomic heterogeneity

(2009) N. Navin et al.   GENOME RESEARCH

Mechanisms to suppress multipolar divisions in cancer cells with extra centrosomes

(2008) M. Kwon et al.   GENES & DEVELOPMENT

Basal-Like Breast Cancer: A Critical Review

(2008) Emad A. Rakha et al.   JOURNAL OF CLINICAL ONCOLOGY