Evidence of selection for an accessible nucleosomal array in human

Chromatin Fibers Are Formed by Heterogeneous Groups of Nucleosomes In Vivo

(2015) Maria Aurelia Ricci et al.   CELL

Ubiquitous human ‘master’ origins of replication are encoded in the DNA sequence via a local enrichment in nucleosome excluding energy barriers

(2015) Guénola Drillon et al.   JOURNAL OF PHYSICS-CONDENSED MATTER

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

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

Embryonic Stem Cell Specific “Master” Replication Origins at the Heart of the Loss of Pluripotency

(2015) Hanna Julienne et al.   PLoS Computational Biology

Mechanisms Underlying Nucleosome Positioning In Vivo

(2014) Amanda L. Hughes et al.   Annual Review of Biophysics

A chromatin structure-based model accurately predicts DNA replication timing in human cells

(2014) Y. Gindin et al.   Molecular Systems Biology

From the chromatin interaction network to the organization of the human genome into replication N/U-domains

(2014) Rasha E Boulos et al.   NEW JOURNAL OF PHYSICS

Recombination initiation maps of individual human genomes

(2014) F. Pratto et al.   SCIENCE

Regulation of the Nucleosome Repeat Length In Vivo by the DNA Sequence, Protein Concentrations and Long-Range Interactions

(2014) Daria A. Beshnova et al.   PLoS Computational Biology

Nucleosomes Shape DNA Polymorphism and Divergence

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

High-resolution analysis of DNA synthesis start sites and nucleosome architecture at efficient mammalian replication origins

(2013) Rodrigo Lombraña et al.   EMBO JOURNAL

Determinants of nucleosome positioning

(2013) Kevin Struhl et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

Human Genome Replication Proceeds through Four Chromatin States

(2013) Hanna Julienne et al.   PLoS Computational Biology

DNA structure, nucleosome placement and chromatin remodelling: a perspective

(2012) Andrew A. Travers et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

New insights into replication origin characteristics in metazoans

(2012) Christelle Cayrou et al.   CELL CYCLE

CpG islands and GC content dictate nucleosome depletion in a transcription-independent manner at mammalian promoters

(2012) R. Fenouil et al.   GENOME RESEARCH

Genome-wide nucleosome positioning during embryonic stem cell development

(2012) Vladimir B Teif et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Fast Computation and Applications of Genome Mappability

(2012) Thomas Derrien et al.   PLoS One

Genome-wide analysis of histone H3.1 and H3.3 variants in Arabidopsis thaliana

(2012) H. Stroud et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Nucleosomes Suppress Spontaneous Mutations Base-Specifically in Eukaryotes

(2012) Xiaoshu Chen et al.   SCIENCE

Replication Fork Polarity Gradients Revealed by Megabase-Sized U-Shaped Replication Timing Domains in Human Cell Lines

(2012) Antoine Baker et al.   PLoS Computational Biology

Influence of the genomic sequence on the primary structure of chromatin

(2012) G. Chevereau et al.   Frontiers in Life Science

Human nucleosomes: special role of CG dinucleotides and Alu-nucleosomes

(2011) Thomas Bettecken et al.   BMC GENOMICS

DNA shape, genetic codes, and evolution

(2011) Stephen CJ Parker et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

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

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

Evolutionary divergence of intrinsic and trans-regulated nucleosome positioning sequences reveals plastic rules for chromatin organization

(2011) A. Tsankov et al.   GENOME RESEARCH

Evolution of Nucleosome Occupancy: Conservation of Global Properties and Divergence of Gene-Specific Patterns

(2011) K. Tsui et al.   MOLECULAR AND CELLULAR BIOLOGY

Replication-Associated Mutational Asymmetry in the Human Genome

(2011) Chun-Long Chen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Determinants of nucleosome organization in primary human cells

(2011) Anton Valouev et al.   NATURE

Impact of chromatin structure on sequence variability in the human genome

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

Alu elements: know the SINEs

(2011) Prescott Deininger   GENOME BIOLOGY

Conserved nucleosome positioning defines replication origins

(2010) M. L. Eaton et al.   GENES & DEVELOPMENT

Functional Conservation of Nucleosome Formation Selectively Biases Presumably Neutral Molecular Variation in Yeast Genomes

(2010) Gregory A. Babbitt et al.   Genome Biology and Evolution

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

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

A map of human genome variation from population-scale sequencing

(2010) Richard M. Durbin et al.   NATURE

Multi-scale coding of genomic information: From DNA sequence to genome structure and function

(2010) Alain Arneodo et al.   PHYSICS REPORTS-REVIEW SECTION OF PHYSICS LETTERS

High Nucleosome Occupancy Is Encoded at Human Regulatory Sequences

(2010) Desiree Tillo et al.   PLoS One

Learning a Weighted Sequence Model of the Nucleosome Core and Linker Yields More Accurate Predictions in Saccharomyces cerevisiae and Homo sapiens

(2010) Sheila M. Reynolds et al.   PLoS Computational Biology

Widespread Compensatory Evolution Conserves DNA-Encoded Nucleosome Organization in Yeast

(2010) Ephraim Kenigsberg et al.   PLoS Computational Biology

Quantitative Test of the Barrier Nucleosome Model for Statistical Positioning of Nucleosomes Up- and Downstream of Transcription Start Sites

(2010) Wolfram Möbius et al.   PLoS Computational Biology

Diversity of Eukaryotic DNA Replication Origins Revealed by Genome-Wide Analysis of Chromatin Structure

(2010) Nicolas M. Berbenetz et al.   PLoS Genetics

Biased Gene Conversion and the Evolution of Mammalian Genomic Landscapes

(2009) Laurent Duret et al.   Annual Review of Genomics and Human Genetics

Depletion Effects Massively Change Chromatin Properties and Influence Genome Folding

(2009) Philipp M. Diesinger et al.   BIOPHYSICAL JOURNAL

G+C content dominates intrinsic nucleosome occupancy

(2009) Desiree Tillo et al.   BMC BIOINFORMATICS

Poly(dA:dT) tracts: major determinants of nucleosome organization

(2009) Eran Segal et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

A novel strategy of transcription regulation by intragenic nucleosome ordering

(2009) C. Vaillant et al.   GENOME RESEARCH

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

Intrinsic histone-DNA interactions are not the major determinant of nucleosome positions in vivo

(2009) Yong Zhang et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Open chromatin encoded in DNA sequence is the signature of ‘master’ replication origins in human cells

(2009) Benjamin Audit et al.   NUCLEIC ACIDS RESEARCH

Nucleosome positioning by genomic excluding-energy barriers

(2009) Pascale Milani et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Nucleosome Geometry and Internucleosomal Interactions Control the Chromatin Fiber Conformation

(2008) Nick Kepper et al.   BIOPHYSICAL JOURNAL

Dynamic Regulation of Nucleosome Positioning in the Human Genome

(2008) Dustin E. Schones et al.   CELL

A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning

(2008) A. Valouev et al.   GENOME RESEARCH

A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome

(2008) T. N. Mavrich et al.   GENOME RESEARCH

Inferring Natural Selection on Fine-Scale Chromatin Organization in Yeast

(2008) G. A. Babbitt et al.   MOLECULAR BIOLOGY AND EVOLUTION

The McDonald-Kreitman Test and Slightly Deleterious Mutations

(2008) J. Charlesworth et al.   MOLECULAR BIOLOGY AND EVOLUTION

The DNA-encoded nucleosome organization of a eukaryotic genome

(2008) Noam Kaplan et al.   NATURE

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

DNA physical properties determine nucleosome occupancy from yeast to fly

(2008) Vincent Miele et al.   NUCLEIC ACIDS RESEARCH

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

Distinct Modes of Regulation by Chromatin Encoded through Nucleosome Positioning Signals

(2008) Yair Field et al.   PLoS Computational Biology

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

(2008) Tobias Warnecke et al.   PLoS Genetics

The Impact of Recombination on Nucleotide Substitutions in the Human Genome

(2008) Laurent Duret et al.   PLoS Genetics