MutationalPatterns: comprehensive genome-wide analysis of mutational processes

HRDetect is a predictor of BRCA1 and BRCA2 deficiency based on mutational signatures

(2017) Helen Davies et al.   NATURE MEDICINE

Use of CRISPR-modified human stem cell organoids to study the origin of mutational signatures in cancer

(2017) Jarno Drost et al.   SCIENCE

signeR: an empirical Bayesian approach to mutational signature discovery

(2016) Rafael A. Rosales et al.   BIOINFORMATICS

MutSpec: a Galaxy toolbox for streamlined analyses of somatic mutation spectra in human and mouse cancer genomes

(2016) Maude Ardin et al.   BMC BIOINFORMATICS

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

(2016) Nicholas J. Haradhvala et al.   CELL

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

(2016) Radhakrishnan Sabarinathan et al.   NATURE

Differential DNA repair underlies mutation hotspots at active promoters in cancer genomes

(2016) Dilmi Perera et al.   NATURE

Tissue-specific mutation accumulation in human adult stem cells during life

(2016) Francis Blokzijl et al.   NATURE

Somatic ERCC2 mutations are associated with a distinct genomic signature in urothelial tumors

(2016) Jaegil Kim et al.   NATURE GENETICS

Mutational signatures associated with tobacco smoking in human cancer

(2016) L. B. Alexandrov et al.   SCIENCE

The DNA cytosine deaminase APOBEC3B promotes tamoxifen resistance in ER-positive breast cancer

(2016) E. K. Law et al.   Science Advances

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

(2015) Fran Supek et al.   NATURE

The UCSC Genome Browser database: 2016 update

(2015) Matthew L. Speir et al.   NUCLEIC ACIDS RESEARCH

A Simple Model-Based Approach to Inferring and Visualizing Cancer Mutation Signatures

(2015) Yuichi Shiraishi et al.   PLoS Genetics

C. eleganswhole-genome sequencing reveals mutational signatures related to carcinogens and DNA repair deficiency

(2014) Bettina Meier et al.   GENOME RESEARCH

Exonuclease mutations in DNA polymerase epsilon reveal replication strand specific mutation patterns and human origins of replication

(2014) Eve Shinbrot et al.   GENOME RESEARCH

Transcription Restores DNA Repair to Heterochromatin, Determining Regional Mutation Rates in Cancer Genomes

(2014) Christina L. Zheng et al.   Cell Reports

Elevated APOBEC3B Correlates with Poor Outcomes for Estrogen-Receptor-Positive Breast Cancers

(2014) Anieta M. Sieuwerts et al.   Hormones & Cancer

DNA repair mechanisms in dividing and non-dividing cells

(2013) Teruaki Iyama et al.   DNA REPAIR

Signatures of mutational processes in human cancer

(2013) Ludmil B. Alexandrov et al.   NATURE

Software for Computing and Annotating Genomic Ranges

(2013) Michael Lawrence et al.   PLoS Computational Biology

EMu: probabilistic inference of mutational processes and their localization in the cancer genome

(2013) Andrej Fischer et al.   GENOME BIOLOGY

Mutational Processes Molding the Genomes of 21 Breast Cancers

(2012) Serena Nik-Zainal et al.   CELL

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

ggplot2: Elegant Graphics for Data Analysis by WICKHAM, H.

(2011) Leland Wilkinson   BIOMETRICS

Hallmarks of Cancer: The Next Generation

(2011) Douglas Hanahan et al.   CELL

A flexible R package for nonnegative matrix factorization

(2010) Renaud Gaujoux et al.   BMC BIOINFORMATICS

DNA Damage, Aging, and Cancer

(2009) Jan H.J. Hoeijmakers   NEW ENGLAND JOURNAL OF MEDICINE

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