Systematic Determination of Replication Activity Type Highlights Interconnections between Replication, Chromatin Structure and Nuclear Localization

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

Late-replicating heterochromatin is characterized by decreased cytosine methylation in the human genome

(2011) M. Suzuki et al.   GENOME RESEARCH

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

(2011) Jason Ernst et al.   NATURE

Cell-type-specific replication initiation programs set fragility of the FRA3B fragile site

(2011) Anne Letessier et al.   NATURE

Genome-scale analysis of replication timing: from bench to bioinformatics

(2011) Tyrone Ryba et al.   Nature Protocols

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

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

(2010) T. Ryba et al.   GENOME RESEARCH

Dynamic changes in the human methylome during differentiation

(2010) L. Laurent et al.   GENOME RESEARCH

Chromatin signatures of the Drosophila replication program

(2010) M. L. Eaton et al.   GENOME RESEARCH

Replication timing-related and gene body-specific methylation of active human genes

(2010) Dvir Aran et al.   HUMAN MOLECULAR GENETICS

Conserved Antagonism between JMJD2A/KDM4A and HP1γ during Cell Cycle Progression

(2010) Joshua C. Black et al.   MOLECULAR CELL

Molecular Maps of the Reorganization of Genome-Nuclear Lamina Interactions during Differentiation

(2010) Daan Peric-Hupkes et al.   MOLECULAR CELL

Ab initio reconstruction of cell type–specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs

(2010) Mitchell Guttman et al.   NATURE BIOTECHNOLOGY

Charting histone modifications and the functional organization of mammalian genomes

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

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

(2010) Eitan Yaffe et al.   PLoS Genetics

S Phase Progression in Human Cells Is Dictated by the Genetic Continuity of DNA Foci

(2010) Apolinar Maya-Mendoza et al.   PLoS Genetics

Genome-wide analysis of the replication program in mammals

(2009) Shlomit Farkash-Amar et al.   CHROMOSOME RESEARCH

Characterization of human epigenomes

(2009) Zhibin Wang et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

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

Decreased replication origin activity in temporal transition regions

(2009) Zeqiang Guan et al.   JOURNAL OF CELL BIOLOGY

Shifts in Replication Timing Actively Affect Histone Acetylation during Nucleosome Reassembly

(2009) Laura Lande-Diner et al.   MOLECULAR CELL

Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals

(2009) Mitchell Guttman et al.   NATURE

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

Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression

(2009) Ahmad M. Khalil 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

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

(2008) Alan P. Boyle et al.   CELL

DNA replication timing of the human  -globin domain is controlled by histone modification at the origin

(2008) A. Goren et al.   GENES & DEVELOPMENT

Global organization of replication time zones of the mouse genome

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

Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions

(2008) Lars Guelen et al.   NATURE

Combinatorial patterns of histone acetylations and methylations in the human genome

(2008) Zhibin Wang et al.   NATURE GENETICS

Global Reorganization of Replication Domains During Embryonic Stem Cell Differentiation

(2008) Ichiro Hiratani et al.   PLOS BIOLOGY