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

Replication-Associated Mutational Asymmetry in the Human Genome

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

CTCF-mediated functional chromatin interactome in pluripotent cells

(2011) Lusy Handoko et al.   NATURE GENETICS

Evidence for Sequential and Increasing Activation of Replication Origins along Replication Timing Gradients in the Human Genome

(2011) Guillaume Guilbaud et al.   PLoS Computational Biology

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

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

Evolutionarily conserved replication timing profiles predict long-range chromatin interactions and distinguish closely related cell types

(2010) T. Ryba et al.   GENOME RESEARCH

Bubble-chip analysis of human origin distributions demonstrates on a genomic scale significant clustering into zones and significant association with transcription

(2010) L. D. Mesner et al.   GENOME RESEARCH

Evaluating genome-scale approaches to eukaryotic DNA replication

(2010) David M. Gilbert   NATURE REVIEWS GENETICS

Eukaryotic DNA replication origins: many choices for appropriate answers

(2010) Marcel Méchali   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Mathematical modelling of whole chromosome replication

(2010) Alessandro P. S. de Moura et al.   NUCLEIC ACIDS RESEARCH

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

Cell type specificity of chromatin organization mediated by CTCF and cohesin

(2010) Chunhui Hou et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Comparative Analysis of DNA Replication Timing Reveals Conserved Large-Scale Chromosomal Architecture

(2010) Eitan Yaffe et al.   PLoS Genetics

Wavelet-based method to disentangle transcription- and replication-associated strand asymmetries in mammalian genomes

(2009) Antoine Baker et al.   APPLIED AND COMPUTATIONAL HARMONIC ANALYSIS

Does CTCF mediate between nuclear organization and gene expression?

(2009) Rolf Ohlsson et al.   BIOESSAYS

CTCF: Master Weaver of the Genome

(2009) Jennifer E. Phillips et al.   CELL

A winding road to origin discovery

(2009) Joyce L. Hamlin et al.   CHROMOSOME RESEARCH

Predictable dynamic program of timing of DNA replication in human cells

(2009) R. Desprat et al.   GENOME RESEARCH

Genome-wide dynamics of replication timing revealed by in vitro models of mouse embryogenesis

(2009) I. Hiratani et al.   GENOME RESEARCH

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

(2009) Benjamin Audit et al.   NUCLEIC ACIDS RESEARCH

Universal Temporal Profile of Replication Origin Activation in Eukaryotes

(2009) Arach Goldar et al.   PLoS One

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

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

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

F-Seq: a feature density estimator for high-throughput sequence tags

(2008) A. P. Boyle et al.   BIOINFORMATICS

High-Resolution Mapping and Characterization of Open Chromatin across the Genome

(2008) Alan P. Boyle et al.   CELL

Global organization of replication time zones of the mouse genome

(2008) S. Farkash-Amar et al.   GENOME RESEARCH

A revisionist replicon model for higher eukaryotic genomes

(2008) J.L. Hamlin et al.   JOURNAL OF CELLULAR BIOCHEMISTRY

Replication fork movement sets chromatin loop size and origin choice in mammalian cells

(2008) Sylvain Courbet et al.   NATURE

DNA methylation landscapes: provocative insights from epigenomics

(2008) Miho M. Suzuki et al.   NATURE REVIEWS GENETICS

Genome-wide studies highlight indirect links between human replication origins and gene regulation

(2008) J.-C. Cadoret et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Global Reorganization of Replication Domains During Embryonic Stem Cell Differentiation

(2008) Ichiro Hiratani et al.   PLOS BIOLOGY