Topologically associating domains are stable units of replication-timing regulation

Identification of alternative topological domains in chromatin

(2014) Darya Filippova et al.   Algorithms for Molecular Biology

Single-Cell Dynamics of Genome-Nuclear Lamina Interactions

(2013) Jop Kind et al.   CELL

Architectural Protein Subclasses Shape 3D Organization of Genomes during Lineage Commitment

(2013) Jennifer E. Phillips-Cremins et al.   CELL

Quantitative, Genome-Wide Analysis of Eukaryotic Replication Initiation and Termination

(2013) Sean R. McGuffee et al.   MOLECULAR CELL

Human Genome Replication Proceeds through Four Chromatin States

(2013) Hanna Julienne et al.   PLoS Computational Biology

Abnormal developmental control of replication-timing domains in pediatric acute lymphoblastic leukemia

(2012) T. Ryba et al.   GENOME RESEARCH

Constitutive nuclear lamina-genome interactions are highly conserved and associated with A/T-rich sequence

(2012) W. Meuleman et al.   GENOME RESEARCH

Replication-timing boundaries facilitate cell-type and species-specific regulation of a rearranged human chromosome in mouse

(2012) Benjamin D. Pope et al.   HUMAN MOLECULAR GENETICS

Independence of Repressive Histone Marks and Chromatin Compaction during Senescent Heterochromatic Layer Formation

(2012) Tamir Chandra et al.   MOLECULAR CELL

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Topological domains in mammalian genomes identified by analysis of chromatin interactions

(2012) Jesse R. Dixon et al.   NATURE

Spatial partitioning of the regulatory landscape of the X-inactivation centre

(2012) Elphège P. Nora et al.   NATURE

Iterative correction of Hi-C data reveals hallmarks of chromosome organization

(2012) Maxim Imakaev et al.   NATURE METHODS

ChromHMM: automating chromatin-state discovery and characterization

(2012) Jason Ernst et al.   NATURE METHODS

Unraveling cell type–specific and reprogrammable human replication origin signatures associated with G-quadruplex consensus motifs

(2012) Emilie Besnard et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

(2012) Shlomit Farkash-Amar et al.   PLoS One

Chromatin-interaction compartment switch at developmentally regulated chromosomal domains reveals an unusual principle of chromatin folding

(2012) S.-i. Takebayashi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

An encyclopedia of mouse DNA elements (Mouse ENCODE)

(2012) et al.   GENOME BIOLOGY

Genome-scale analysis of metazoan replication origins reveals their organization in specific but flexible sites defined by conserved features

(2011) C. Cayrou et al.   GENOME RESEARCH

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

(2011) Tyrone Ryba et al.   Nature Protocols

DNA Replication Timing Is Maintained Genome-Wide in Primary Human Myoblasts Independent of D4Z4 Contraction in FSH Muscular Dystrophy

(2011) Benjamin D. Pope et al.   PLoS One

Replication Timing: A Fingerprint for Cell Identity and Pluripotency

(2011) Tyrone Ryba et al.   PLoS Computational Biology

c-Myc Regulates Transcriptional Pause Release

(2010) Peter B. Rahl et al.   CELL

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

(2010) Guillaume J. Filion et al.   CELL

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

(2010) T. Ryba et al.   GENOME RESEARCH

G2 phase chromatin lacks determinants of replication timing

(2010) Junjie Lu et al.   JOURNAL OF CELL BIOLOGY

High-Resolution Whole-Genome Sequencing Reveals That Specific Chromatin Domains from Most Human Chromosomes Associate with Nucleoli

(2010) Silvana van Koningsbruggen et al.   MOLECULAR BIOLOGY OF THE CELL

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

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

Characterization of an antagonistic switch between histone H3 lysine 27 methylation and acetylation in the transcriptional regulation of Polycomb group target genes

(2010) Diego Pasini et al.   NUCLEIC ACIDS RESEARCH

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

(2010) Eitan Yaffe et al.   PLoS Genetics

Initial Genomics of the Human Nucleolus

(2010) Attila Németh et al.   PLoS Genetics

Reconciling stochastic origin firing with defined replication timing

(2009) Nicholas Rhind et al.   CHROMOSOME RESEARCH

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

(2009) I. Hiratani et al.   GENOME RESEARCH

ChIP-seq accurately predicts tissue-specific activity of enhancers

(2009) Axel Visel et al.   NATURE

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

(2009) Benjamin Audit et al.   NUCLEIC ACIDS RESEARCH

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

Integration of External Signaling Pathways with the Core Transcriptional Network in Embryonic Stem Cells

(2008) Xi Chen et al.   CELL

EZH1 Mediates Methylation on Histone H3 Lysine 27 and Complements EZH2 in Maintaining Stem Cell Identity and Executing Pluripotency

(2008) Xiaohua Shen et al.   MOLECULAR CELL

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

(2008) Lars Guelen et al.   NATURE

The ground state of embryonic stem cell self-renewal

(2008) Qi-Long Ying et al.   NATURE

Global Reorganization of Replication Domains During Embryonic Stem Cell Differentiation

(2008) Ichiro Hiratani et al.   PLOS BIOLOGY