Differential DNA mismatch repair underlies mutation rate variation across the human genome

Complex correlations: replication timing and mutational landscapes during cancer and genome evolution

(2014) Jiao Sima et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

DNA replication and transcription programs respond to the same chromatin cues

(2014) Y. Lubelsky et al.   GENOME RESEARCH

Comprehensive molecular characterization of gastric adenocarcinoma

(2014) Adam J. Bass et al.   NATURE

Mechanisms underlying mutational signatures in human cancers

(2014) Thomas Helleday et al.   NATURE REVIEWS GENETICS

A comparative analysis of algorithms for somatic SNV detection in cancer

(2013) Nicola D. Roberts et al.   BIOINFORMATICS

Hypermutation of the Inactive X Chromosome Is a Frequent Event in Cancer

(2013) Natalie Jäger et al.   CELL

The Landscape of Microsatellite Instability in Colorectal and Endometrial Cancer Genomes

(2013) Tae-Min Kim et al.   CELL

Integrated genomic characterization of endometrial carcinoma

(2013) Gad Getz et al.   NATURE

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

(2013) Michael S. Lawrence et al.   NATURE

Signatures of mutational processes in human cancer

(2013) Ludmil B. Alexandrov et al.   NATURE

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

(2013) Kristian Cibulskis et al.   NATURE BIOTECHNOLOGY

Genomic and Epigenomic Landscapes of Adult De Novo Acute Myeloid Leukemia

(2013)   NEW ENGLAND JOURNAL OF MEDICINE

Discovery and characterization of artifactual mutations in deep coverage targeted capture sequencing data due to oxidative DNA damage during sample preparation

(2013) Maura Costello et al.   NUCLEIC ACIDS RESEARCH

DNA replication timing and higher-order nuclear organization determine single-nucleotide substitution patterns in cancer genomes

(2013) Lin Liu et al.   Nature Communications

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

(2012) Christopher T. Saunders et al.   BIOINFORMATICS

Chromatin organization is a major influence on regional mutation rates in human cancer cells

(2012) Benjamin Schuster-Böckler et al.   NATURE

Comprehensive molecular characterization of human colon and rectal cancer

(2012)   NATURE

Fast Computation and Applications of Genome Mappability

(2012) Thomas Derrien et al.   PLoS One

Measurement of mRNA abundance using RNA-seq data: RPKM measure is inconsistent among samples

(2012) Günter P. Wagner et al.   THEORY IN BIOSCIENCES

DNA replication timing and selection shape the landscape of nucleotide variation in cancer genomes

(2012) Yong H Woo et al.   Nature Communications

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

The large-scale distribution of somatic mutations in cancer genomes

(2011) Alan Hodgkinson et al.   HUMAN MUTATION

Mismatch Repair, But Not Heteroduplex Rejection, Is Temporally Coupled to DNA Replication

(2011) H. Hombauer et al.   SCIENCE

Impact of replication timing on non-CpG and CpG substitution rates in mammalian genomes

(2010) C. L. Chen et al.   GENOME RESEARCH

Oxidative stress triggers the preferential assembly of base excision repair complexes on open chromatin regions

(2010) Rachel Amouroux et al.   NUCLEIC ACIDS RESEARCH

Genome-wide dynamics of replication timing revealed by in vitro models of mouse embryogenesis

(2009) I. Hiratani et al.   GENOME RESEARCH

A comprehensive catalogue of somatic mutations from a human cancer genome

(2009) Erin D. Pleasance et al.   NATURE

Human mutation rate associated with DNA replication timing

(2009) John A Stamatoyannopoulos et al.   NATURE GENETICS

Histone H3 Lys79 methylation is required for efficient nucleotide excision repair in a silenced locus of Saccharomyces cerevisiae

(2009) Shubho Chaudhuri et al.   NUCLEIC ACIDS RESEARCH

Sequencing newly replicated DNA reveals widespread plasticity in human replication timing

(2009) R. S. Hansen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

DNA mismatch repair efficiency and fidelity are elevated during DNA synthesis in human cells

(2008) Michael A. Edelbrock et al.   MUTATION RESEARCH-FUNDAMENTAL AND MOLECULAR MECHANISMS OF MUTAGENESIS

Global Reorganization of Replication Domains During Embryonic Stem Cell Differentiation

(2008) Ichiro Hiratani et al.   PLOS BIOLOGY