Recurrent somatic mutations reveal new insights into consequences of mutagenic processes in cancer

Local Determinants of the Mutational Landscape of the Human Genome

(2019) Abel Gonzalez-Perez et al.   CELL

Finding driver mutations in cancer: Elucidating the role of background mutational processes

(2019) Anna-Leigh Brown et al.   PLoS Computational Biology

Perspective on Oncogenic Processes at the End of the Beginning of Cancer Genomics

(2018) Li Ding et al.   CELL

ETS transcription factors induce a unique UV damage signature that drives recurrent mutagenesis in melanoma

(2018) Peng Mao et al.   Nature Communications

Clustering trees: a visualisation for evaluating clusterings at multiple resolutions

(2018) Luke Zappia et al.   GigaScience

Somatic and Germline Mutation Periodicity Follow the Orientation of the DNA Minor Groove around Nucleosomes

(2018) Oriol Pich et al.   CELL

Mutations differ in normal and cancer cells of the oesophagus

(2018) Francesca D. Ciccarelli   NATURE

Somatic mutant clones colonize the human esophagus with age

(2018) Iñigo Martincorena et al.   SCIENCE

Update on immune checkpoint inhibitors in gynecological cancers

(2017) Valerie Heong et al.   Journal of Gynecologic Oncology

Exploring background mutational processes to decipher cancer genetic heterogeneity

(2017) Alexander Goncearenco et al.   NUCLEIC ACIDS RESEARCH

Recurrent promoter mutations in melanoma are defined by an extended context-specific mutational signature

(2017) Nils Johan Fredriksson et al.   PLoS Genetics

Predicting the recurrence of noncoding regulatory mutations in cancer

(2016) Woojin Yang et al.   BMC BIOINFORMATICS

vcfr: a package to manipulate and visualize variant call format data in R

(2016) Brian J. Knaus et al.   Molecular Ecology Resources

Nucleotide excision repair is impaired by binding of transcription factors to DNA

(2016) Radhakrishnan Sabarinathan et al.   NATURE

Mutational signatures in esophageal adenocarcinoma define etiologically distinct subgroups with therapeutic relevance

(2016) Maria Secrier et al.   NATURE GENETICS

Oncotator: Cancer Variant Annotation Tool

(2015) Alex H. Ramos et al.   HUMAN MUTATION

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

(2015) Fran Supek et al.   NATURE

Non-coding recurrent mutations in chronic lymphocytic leukaemia

(2015) Xose S. Puente et al.   NATURE

Cell-of-origin chromatin organization shapes the mutational landscape of cancer

(2015) Paz Polak et al.   NATURE

An APOBEC3A hypermutation signature is distinguishable from the signature of background mutagenesis by APOBEC3B in human cancers

(2015) Kin Chan et al.   NATURE GENETICS

The Microsatellite Instable Subset of Colorectal Cancer Is a Particularly Good Candidate for Checkpoint Blockade Immunotherapy

(2015) Yanping Xiao et al.   Cancer Discovery

Hypermutation takes the driver’s seat

(2015) Matthias Schlesner et al.   Genome Medicine

Comprehensive characterization of complex structural variations in cancer by directly comparing genome sequence reads

(2014) Valentí Moncunill et al.   NATURE BIOTECHNOLOGY

Systematic analysis of noncoding somatic mutations and gene expression alterations across 14 tumor types

(2014) Nils J Fredriksson et al.   NATURE GENETICS

Only three driver gene mutations are required for the development of lung and colorectal cancers

(2014) Cristian Tomasetti et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Prognostic and predictive significance of MSI in stages II/III colon cancer

(2014) Zacharenia Saridaki   WORLD JOURNAL OF GASTROENTEROLOGY

Cancer Evolution Is Associated with Pervasive Positive Selection on Globally Expressed Genes

(2014) Sheli L. Ostrow et al.   PLoS Genetics

MSIsensor: microsatellite instability detection using paired tumor-normal sequence data

(2013) Beifang Niu et al.   BIOINFORMATICS

Signatures of mutational processes in human cancer

(2013) Ludmil B. Alexandrov et al.   NATURE

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

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

A direct characterization of human mutation based on microsatellites

(2012) James X Sun et al.   NATURE GENETICS

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

(2012) Yong H Woo et al.   Nature Communications

Mutation Rates across Budding Yeast Chromosome VI Are Correlated with Replication Timing

(2011) Gregory I. Lang et al.   Genome Biology and Evolution

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

Hypermutability of Damaged Single-Strand DNA Formed at Double-Strand Breaks and Uncapped Telomeres in Yeast Saccharomyces cerevisiae

(2008) Yong Yang et al.   PLoS Genetics