Mutational Biases Drive Elevated Rates of Substitution at Regulatory Sites across Cancer Types

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

Activation of proto-oncogenes by disruption of chromosome neighborhoods

(2016) D. Hnisz et al.   SCIENCE

CRISPR Inversion of CTCF Sites Alters Genome Topology and Enhancer/Promoter Function

(2015) Ya Guo et al.   CELL

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

(2015) Fran Supek et al.   NATURE

Lagging-strand replication shapes the mutational landscape of the genome

(2015) Martin A. M. Reijns 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

Recurrent somatic mutations in regulatory regions of human cancer genomes

(2015) Collin Melton et al.   NATURE GENETICS

CTCF/cohesin-binding sites are frequently mutated in cancer

(2015) Riku Katainen et al.   NATURE GENETICS

The effects of chromatin organization on variation in mutation rates in the genome

(2015) Kateryna D. Makova et al.   NATURE REVIEWS GENETICS

A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping

(2014) Suhas S.P. Rao et al.   CELL

Multiplatform Analysis of 12 Cancer Types Reveals Molecular Classification within and across Tissues of Origin

(2014) Katherine A. Hoadley et al.   CELL

Discovery and saturation analysis of cancer genes across 21 tumour types

(2014) Michael S. Lawrence et al.   NATURE

Genome-wide analysis of noncoding regulatory mutations in cancer

(2014) Nils Weinhold et al.   NATURE GENETICS

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

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

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

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

Signatures of mutational processes in human cancer

(2013) Ludmil B. Alexandrov et al.   NATURE

JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles

(2013) Anthony Mathelier et al.   NUCLEIC ACIDS RESEARCH

Highly Recurrent TERT Promoter Mutations in Human Melanoma

(2013) F. W. Huang et al.   SCIENCE

Comprehensive identification of mutational cancer driver genes across 12 tumor types

(2013) David Tamborero et al.   Scientific Reports

Whole-Genome Sequencing in Autism Identifies Hot Spots for De Novo Germline Mutation

(2012) Jacob J. Michaelson et al.   CELL

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

(2012) Benjamin Schuster-Böckler et al.   NATURE

An expansive human regulatory lexicon encoded in transcription factor footprints

(2012) Shane Neph et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

The accessible chromatin landscape of the human genome

(2012) Robert E. Thurman et al.   NATURE

ChromHMM: automating chromatin-state discovery and characterization

(2012) Jason Ernst et al.   NATURE METHODS

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

High order chromatin architecture shapes the landscape of chromosomal alterations in cancer

(2011) Geoff Fudenberg et al.   NATURE BIOTECHNOLOGY

Analysis of genomic variation in non-coding elements using population-scale sequencing data from the 1000 Genomes Project

(2011) Xinmeng Jasmine Mu et al.   NUCLEIC ACIDS RESEARCH

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

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

High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells

(2010) A. P. Boyle et al.   GENOME RESEARCH

Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data

(2010) R. Pique-Regi et al.   GENOME RESEARCH

International network of cancer genome projects

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

GREAT improves functional interpretation of cis-regulatory regions

(2010) Cory Y McLean et al.   NATURE BIOTECHNOLOGY

The UCSC Genome Browser database: update 2011

(2010) P. A. Fujita et al.   NUCLEIC ACIDS RESEARCH

The cancer genome

(2009) Michael R. Stratton et al.   NATURE