Increasing Nucleosome Occupancy Is Correlated with an Increasing Mutation Rate so Long as DNA Repair Machinery Is Intact

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

(2015) Paz Polak et al.   NATURE

Nucleosomal occupancy changes locally over key regulatory regions during cell differentiation and reprogramming

(2014) Jason A. West et al.   Nature Communications

Nucleosomes Shape DNA Polymorphism and Divergence

(2014) Sasha A. Langley et al.   PLoS Genetics

Comprehensive molecular characterization of clear cell renal cell carcinoma

(2013)   NATURE

Integrated genomic characterization of endometrial carcinoma

(2013) Gad Getz et al.   NATURE

Genomic and Epigenomic Landscapes of Adult De Novo Acute Myeloid Leukemia

(2013)   NEW ENGLAND JOURNAL OF MEDICINE

Fitness landscape for nucleosome positioning

(2013) D. Weghorn 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

Mutation Rates, Spectra, and Genome-Wide Distribution of Spontaneous Mutations in Mismatch Repair Deficient Yeast

(2013) Gregory I. Lang et al.   G3-Genes Genomes Genetics

Conserved Substitution Patterns around Nucleosome Footprints in Eukaryotes and Archaea Derive from Frequent Nucleosome Repositioning through Evolution

(2013) Tobias Warnecke et al.   PLoS Computational Biology

Widespread Existence of Cytosine Methylation in Yeast DNA Measured by Gas Chromatography/Mass Spectrometry

(2012) Yang Tang et al.   ANALYTICAL CHEMISTRY

Base-Resolution Analysis of 5-Hydroxymethylcytosine in the Mammalian Genome

(2012) Miao Yu et al.   CELL

Genome-wide Nucleosome Specificity and Directionality of Chromatin Remodelers

(2012) Kuangyu Yen et al.   CELL

DANPOS: Dynamic analysis of nucleosome position and occupancy by sequencing

(2012) K. Chen et al.   GENOME RESEARCH

VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing

(2012) D. C. Koboldt et al.   GENOME RESEARCH

Micrococcal Nuclease Does Not Substantially Bias Nucleosome Mapping

(2012) James Allan et al.   JOURNAL OF MOLECULAR BIOLOGY

Comprehensive molecular characterization of human colon and rectal cancer

(2012)   NATURE

Comprehensive genomic characterization of squamous cell lung cancers

(2012)   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

An integrated map of genetic variation from 1,092 human genomes

(2012)   NATURE

Rate of de novo mutations and the importance of father’s age to disease risk

(2012) Augustine Kong et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Regulation of the nucleosome unwrapping rate controls DNA accessibility

(2012) Justin A. North et al.   NUCLEIC ACIDS RESEARCH

The UCSC Genome Browser database: extensions and updates 2013

(2012) Laurence R. Meyer et al.   NUCLEIC ACIDS RESEARCH

Nucleosomes Suppress Spontaneous Mutations Base-Specifically in Eukaryotes

(2012) Xiaoshu Chen et al.   SCIENCE

Controls of Nucleosome Positioning in the Human Genome

(2012) Daniel J. Gaffney et al.   PLoS Genetics

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

A high-resolution map of human evolutionary constraint using 29 mammals

(2011) Kerstin Lindblad-Toh et al.   NATURE

Determinants of nucleosome organization in primary human cells

(2011) Anton Valouev et al.   NATURE

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

(2011) Jason Ernst et al.   NATURE

Integrated genomic analyses of ovarian carcinoma

(2011) D. Bell et al.   NATURE

DNA replication timing and long-range DNA interactions predict mutational landscapes of cancer genomes

(2011) Subhajyoti De et al.   NATURE BIOTECHNOLOGY

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

Impact of chromatin structure on sequence variability in the human genome

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

NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy

(2011) K. D. Pruitt et al.   NUCLEIC ACIDS RESEARCH

Ensembl 2012

(2011) P. Flicek et al.   NUCLEIC ACIDS RESEARCH

Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries

(2011) Daniel Aird et al.   GENOME BIOLOGY

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Nucleosomes are preferentially positioned at exons in somatic and sperm cells

(2010) Satu Nahkuri et al.   CELL CYCLE

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Complete Khoisan and Bantu genomes from southern Africa

(2010) Stephan C. Schuster et al.   NATURE

Relationship between nucleosome positioning and DNA methylation

(2010) Ramakrishna K. Chodavarapu et al.   NATURE

Rate, molecular spectrum, and consequences of human mutation

(2010) M. Lynch   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Widespread Compensatory Evolution Conserves DNA-Encoded Nucleosome Organization in Yeast

(2010) Ephraim Kenigsberg et al.   PLoS Computational Biology

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Nucleosomes are well positioned in exons and carry characteristic histone modifications

(2009) R. Andersson et al.   GENOME RESEARCH

Human DNA methylomes at base resolution show widespread epigenomic differences

(2009) Ryan Lister et al.   NATURE

COSMIC (the Catalogue of Somatic Mutations in Cancer): a resource to investigate acquired mutations in human cancer

(2009) Simon A. Forbes et al.   NUCLEIC ACIDS RESEARCH

Oxidatively Generated Damage to the Guanine Moiety of DNA: Mechanistic Aspects and Formation in Cells

(2008) Jean Cadet et al.   ACCOUNTS OF CHEMICAL RESEARCH

Dynamic Regulation of Nucleosome Positioning in the Human Genome

(2008) Dustin E. Schones et al.   CELL

Nucleosome organization in the Drosophila genome

(2008) Travis N. Mavrich et al.   NATURE

The DNA-encoded nucleosome organization of a eukaryotic genome

(2008) Noam Kaplan et al.   NATURE

Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning

(2008) Shawn J. Cokus et al.   NATURE