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

Chromatin states in pluripotent, differentiated, and reprogrammed cells

(2011) Cynthia L Fisher et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Variegated gene expression caused by cell-specific long-range DNA interactions

(2011) Daan Noordermeer et al.   NATURE CELL BIOLOGY

Probabilistic modeling of Hi-C contact maps eliminates systematic biases to characterize global chromosomal architecture

(2011) Eitan Yaffe et al.   NATURE GENETICS

Mammalian Genes Are Transcribed with Widely Different Bursting Kinetics

(2011) D. M. Suter et al.   SCIENCE

The Dynamic Architecture of Hox Gene Clusters

(2011) D. Noordermeer et al.   SCIENCE

Chromatin structure: does the 30-nm fibre exist in vivo?

(2010) Kazuhiro Maeshima et al.   CURRENT OPINION IN CELL 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 plasticity of large-scale chromatin structure revealed by self-assembly of engineered chromosome regions

(2010) Paul Sinclair et al.   JOURNAL OF CELL BIOLOGY

Ring1B Compacts Chromatin Structure and Represses Gene Expression Independent of Histone Ubiquitination

(2010) Ragnhild Eskeland et al.   MOLECULAR CELL

Analysis of Active and Inactive X Chromosome Architecture Reveals the Independent Organization of 30 nm and Large-Scale Chromatin Structures

(2010) Catherine Naughton et al.   MOLECULAR CELL

Accessibility of the Drosophila genome discriminates PcG repression, H4K16 acetylation and replication timing

(2010) Oliver Bell et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Global Chromatin Architecture Reflects Pluripotency and Lineage Commitment in the Early Mouse Embryo

(2010) Kashif Ahmed et al.   PLoS One

Living without 30nm chromatin fibers

(2010) Eden Fussner et al.   TRENDS IN BIOCHEMICAL SCIENCES

Role of the Murine Reprogramming Factors in the Induction of Pluripotency

(2009) Rupa Sridharan et al.   CELL

Temporal regulation of DNA replication in mammalian cells

(2009) Juan Méndez   CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY

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

(2009) I. Hiratani et al.   GENOME RESEARCH

Preferential associations between co-regulated genes reveal a transcriptional interactome in erythroid cells

(2009) Stefan Schoenfelder et al.   NATURE GENETICS

Spatially confined folding of chromatin in the interphase nucleus

(2009) J. Mateos-Langerak et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

G9a selectively represses a class of late-replicating genes at the nuclear periphery

(2009) T. Yokochi 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

ReplicationDomain: a visualization tool and comparative database for genome-wide replication timing data

(2008) Nodin Weddington et al.   BMC BIOINFORMATICS

Identification and characterization of subpopulations in undifferentiated ES cell culture

(2008) Y. Toyooka et al.   DEVELOPMENT

Dissecting direct reprogramming through integrative genomic analysis

(2008) Tarjei S. Mikkelsen et al.   NATURE

Pluripotency and nuclear reprogramming

(2008) S. Yamanaka   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Global Reorganization of Replication Domains During Embryonic Stem Cell Differentiation

(2008) Ichiro Hiratani et al.   PLOS BIOLOGY