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

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

(2015) Paz Polak et al.   NATURE

DNMT3A and IDH mutations in acute myeloid leukemia and other myeloid malignancies: associations with prognosis and potential treatment strategies

(2014) A P Im et al.   LEUKEMIA

Genomic Landscape of Human, Bat, and Ex Vivo DNA Transposon Integrations

(2014) Rebeca Campos-Sánchez et al.   MOLECULAR BIOLOGY AND EVOLUTION

Identification of pre-leukaemic haematopoietic stem cells in acute leukaemia

(2014) Liran I. Shlush et al.   NATURE

Epigenetic inheritance of cell fates during embryonic development

(2014) Sirisha Cheedipudi et al.   Frontiers in Genetics

Rhabdoid Tumors: An Initial Clue to the Role of Chromatin Remodeling in Cancer

(2013) Ryan S. Lee et al.   BRAIN PATHOLOGY

Interactome Maps of Mouse Gene Regulatory Domains Reveal Basic Principles of Transcriptional Regulation

(2013) Kyong-Rim Kieffer-Kwon et al.   CELL

Cumulative Haploinsufficiency and Triplosensitivity Drive Aneuploidy Patterns and Shape the Cancer Genome

(2013) Teresa Davoli et al.   CELL

The influence of genomic context on mutation patterns in the human genome inferred from rare variants

(2013) V. M. Schaibley et al.   GENOME RESEARCH

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

(2013) Michael S. Lawrence et al.   NATURE

The mutational landscape of adenoid cystic carcinoma

(2013) Allen S Ho et al.   NATURE GENETICS

H2A.Z Nucleosome Positioning Has No Impact on Genetic Variation in Drosophila Genome

(2013) Yitao Tang et al.   PLoS One

Segmenting the human genome based on states of neutral genetic divergence

(2013) Prabhani Kuruppumullage Don et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Watching DNA breath one molecule at a time

(2013) J. Fei et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2013) Lin Liu et al.   Nature Communications

A Reversible Histone H3 Acetylation Cooperates with Mismatch Repair and Replicative Polymerases in Maintaining Genome Stability

(2013) Lyudmila Y. Kadyrova et al.   PLoS Genetics

TATES: Efficient Multivariate Genotype-Phenotype Analysis for Genome-Wide Association Studies

(2013) Sophie van der Sluis et al.   PLoS Genetics

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

(2012) Jacob J. Michaelson et al.   CELL

A remarkably simple genome underlies highly malignant pediatric rhabdoid cancers

(2012) Ryan S. Lee et al.   JOURNAL OF CLINICAL INVESTIGATION

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

(2012) Benjamin Schuster-Böckler et al.   NATURE

Dissecting the genomic complexity underlying medulloblastoma

(2012) David T. W. Jones et al.   NATURE

Driver mutations in histone H3.3 and chromatin remodelling genes in paediatric glioblastoma

(2012) Jeremy Schwartzentruber 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

Integrative genome analyses identify key somatic driver mutations of small-cell lung cancer

(2012) Martin Peifer et al.   NATURE GENETICS

Nucleosomes Suppress Spontaneous Mutations Base-Specifically in Eukaryotes

(2012) Xiaoshu Chen et al.   SCIENCE

Systematic Localization of Common Disease-Associated Variation in Regulatory DNA

(2012) M. T. Maurano et al.   SCIENCE

Rescuing Alu: Recovery of New Inserts Shows LINE-1 Preserves Alu Activity through A-Tail Expansion

(2012) Bradley J. Wagstaff et al.   PLoS Genetics

Visualising associations between paired ‘omics’ data sets

(2012) Ignacio González et al.   BioData Mining

Genome analyses substantiate male mutation bias in many species

(2011) Melissa A. Wilson Sayres et al.   BIOESSAYS

Primate CpG Islands Are Maintained by Heterogeneous Evolutionary Regimes Involving Minimal Selection

(2011) Netta Mendelson Cohen et al.   CELL

DO VARIATIONS IN SUBSTITUTION RATES AND MALE MUTATION BIAS CORRELATE WITH LIFE-HISTORY TRAITS? A STUDY OF 32 MAMMALIAN GENOMES

(2011) Melissa A. Wilson Sayres et al.   EVOLUTION

Exploiting CpG Hypermutability to Identify Phenotypically Significant Variation Within Human Protein-Coding Genes

(2011) Hua Ying et al.   Genome Biology and Evolution

Widespread signatures of recent selection linked to nucleosome positioning in the human lineage

(2011) J. G. D. Prendergast et al.   GENOME RESEARCH

The large-scale distribution of somatic mutations in cancer genomes

(2011) Alan Hodgkinson et al.   HUMAN MUTATION

Mapping and analysis of chromatin state dynamics in nine human cell types

(2011) Jason Ernst et al.   NATURE

Silencing chromatin: comparing modes and mechanisms

(2011) Christian Beisel et al.   NATURE REVIEWS GENETICS

Variation in the mutation rate across mammalian genomes

(2011) Alan Hodgkinson et al.   NATURE REVIEWS GENETICS

Impact of chromatin structure on sequence variability in the human genome

(2011) Michael Y Tolstorukov et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

A genome-wide view of mutation rate co-variation using multivariate analyses

(2011) Guruprasad Ananda et al.   GENOME BIOLOGY

Integrative analysis of gene expression and copy number alterations using canonical correlation analysis

(2010) Charlotte Soneson et al.   BMC BIOINFORMATICS

Systematic Protein Location Mapping Reveals Five Principal Chromatin Types in Drosophila Cells

(2010) Guillaume J. Filion et al.   CELL

The (r)evolution of SINE versus LINE distributions in primate genomes: Sex chromosomes are important

(2010) E. M. Kvikstad et al.   GENOME RESEARCH

Dynamic changes in the human methylome during differentiation

(2010) L. Laurent et al.   GENOME RESEARCH

Charting histone modifications and the functional organization of mammalian genomes

(2010) Vicky W. Zhou et al.   NATURE REVIEWS GENETICS

Extensive sequence-influenced DNA methylation polymorphism in the human genome

(2010) Asaf Hellman et al.   Epigenetics & Chromatin

Evidence that Localized Variation in Primate Sequence Divergence Arises from an Influence of Nucleosome Placement on DNA Repair

(2009) H. Ying et al.   MOLECULAR BIOLOGY AND EVOLUTION

Human mutation rate associated with DNA replication timing

(2009) John A Stamatoyannopoulos et al.   NATURE GENETICS

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

(2009) E. Lieberman-Aiden et al.   SCIENCE

Transcription induces strand-specific mutations at the 5' end of human genes

(2008) P. Polak et al.   GENOME RESEARCH

Transcription-Induced Mutational Strand Bias and Its Effect on Substitution Rates in Human Genes

(2008) C. F. Mugal et al.   MOLECULAR BIOLOGY AND EVOLUTION

Chromatin-Associated Periodicity in Genetic Variation Downstream of Transcriptional Start Sites

(2008) S. Sasaki et al.   SCIENCE

Evolutionary footprints of nucleosome positions in yeast

(2008) Stefan Washietl et al.   TRENDS IN GENETICS

The Impact of the Nucleosome Code on Protein-Coding Sequence Evolution in Yeast

(2008) Tobias Warnecke et al.   PLoS Genetics

Human-macaque comparisons illuminate variation in neutral substitution rates

(2008) Svitlana Tyekucheva et al.   GENOME BIOLOGY