Pervasive lesion segregation shapes cancer genome evolution

Pan-cancer analysis of whole genomes

(2020)   NATURE

The repertoire of mutational signatures in human cancer

(2020) Ludmil B. Alexandrov et al.   NATURE

Resolving genetic heterogeneity in cancer

(2019) Samra Turajlic et al.   NATURE REVIEWS GENETICS

Characterizing Mutational Signatures in Human Cancer Cell Lines Reveals Episodic APOBEC Mutagenesis

(2019) Mia Petljak et al.   CELL

A Compendium of Mutational Signatures of Environmental Agents

(2019) Jill E. Kucab et al.   CELL

OncodriveCLUSTL: a sequence-based clustering method to identify cancer drivers

(2019) Claudia Arnedo-Pac et al.   BIOINFORMATICS

Transcription-Coupled Repair: From Cells to Single Molecules and Back Again

(2019) T.R. Strick et al.   JOURNAL OF MOLECULAR BIOLOGY

Mutational landscape of a chemically-induced mouse model of liver cancer

(2018) Frances Connor et al.   JOURNAL OF HEPATOLOGY

Strelka2: fast and accurate calling of germline and somatic variants

(2018) Sangtae Kim et al.   NATURE METHODS

MutationalPatterns: comprehensive genome-wide analysis of mutational processes

(2018) Francis Blokzijl et al.   Genome Medicine

Sixteen diverse laboratory mouse reference genomes define strain-specific haplotypes and novel functional loci

(2018) Jingtao Lilue et al.   NATURE GENETICS

Quantification of somatic mutation flow across individual cell division events by lineage sequencing

(2018) Yehuda Brody et al.   GENOME RESEARCH

Ensembl 2019

(2018) Fiona Cunningham et al.   NUCLEIC ACIDS RESEARCH

Genetic Load and Potential Mutational Meltdown in Cancer Cell Populations

(2018) Yuezheng Zhang et al.   MOLECULAR BIOLOGY AND EVOLUTION

Single-cell sequencing data reveal widespread recurrence and loss of mutational hits in the life histories of tumors

(2017) Jack Kuipers et al.   GENOME RESEARCH

Whole-genome landscapes of major melanoma subtypes

(2017) Nicholas K. Hayward et al.   NATURE

The evolution of tumour phylogenetics: principles and practice

(2017) Russell Schwartz et al.   NATURE REVIEWS GENETICS

Mutational Strand Asymmetries in Cancer Genomes Reveal Mechanisms of DNA Damage and Repair

(2016) Nicholas J. Haradhvala et al.   CELL

Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

CNVkit: Genome-Wide Copy Number Detection and Visualization from Targeted DNA Sequencing

(2016) Eric Talevich et al.   PLoS Computational Biology

Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments

(2016) Neva C. Durand et al.   Cell Systems

Clusters of Multiple Mutations: Incidence and Molecular Mechanisms

(2015) Kin Chan et al.   Annual Review of Genetics

Genome-wide analysis of human global and transcription-coupled excision repair of UV damage at single-nucleotide resolution

(2015) Jinchuan Hu et al.   GENES & DEVELOPMENT

Comparative Hi-C Reveals that CTCF Underlies Evolution of Chromosomal Domain Architecture

(2015) Matteo Vietri Rudan et al.   Cell Reports

changepoint: AnRPackage for Changepoint Analysis

(2015) Rebecca Killick et al.   Journal of Statistical Software

Is homologous recombination really an error-free process?

(2014) Josée Guirouilh-Barbat et al.   Frontiers in Genetics

Signatures of mutational processes in human cancer

(2013) Ludmil B. Alexandrov et al.   NATURE

Mutational Processes Molding the Genomes of 21 Breast Cancers

(2012) Serena Nik-Zainal et al.   CELL

Clustered Mutations in Yeast and in Human Cancers Can Arise from Damaged Long Single-Strand DNA Regions

(2012) Steven A. Roberts et al.   MOLECULAR CELL

PROMoter uPstream Transcripts share characteristics with mRNAs and are produced upstream of all three major types of mammalian promoters

(2011) Pascal Preker et al.   NUCLEIC ACIDS RESEARCH

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

International network of cancer genome projects

(2010) Thomas J. Hudson (Chairperson) et al.   NATURE

Proliferative and Nonproliferative Lesions of the Rat and Mouse Hepatobiliary System

(2010) Bob Thoolen et al.   TOXICOLOGIC PATHOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Use of high throughput sequencing to observe genome dynamics at a single cell level

(2009) D. Parkhomchuk et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Biological Basis of Differential Susceptibility to Hepatocarcinogenesis among Mouse Strains

(2009) Robert R. Maronpot   Journal of Toxicologic Pathology

Lineage-Specific Biology Revealed by a Finished Genome Assembly of the Mouse

(2009) Deanna M. Church et al.   PLOS BIOLOGY

Divergent Transcription from Active Promoters

(2008) Amy C. Seila et al.   SCIENCE

Differential selection for B-raf and Ha-ras mutated liver tumors in mice with high and low susceptibility to hepatocarcinogenesis

(2007) Albrecht Buchmann et al.   MUTATION RESEARCH-FUNDAMENTAL AND MOLECULAR MECHANISMS OF MUTAGENESIS