Modeling epigenome folding: formation and dynamics of topologically associated chromatin domains

Chromosome positioning from activity-based segregation

(2014) Nirmalendu Ganai et al.   NUCLEIC ACIDS RESEARCH

Bifurcation in epigenetics: Implications in development, proliferation, and diseases

(2014) Daniel Jost   PHYSICAL REVIEW E

Ring Polymers in the Melt State: The Physics of Crumpling

(2014) Angelo Rosa et al.   PHYSICAL REVIEW LETTERS

Genome-wide Chromatin State Transitions Associated with Developmental and Environmental Cues

(2013) Jiang Zhu et al.   CELL

Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes

(2013) Warren A. Whyte et al.   CELL

LBR and Lamin A/C Sequentially Tether Peripheral Heterochromatin and Inversely Regulate Differentiation

(2013) Irina Solovei et al.   CELL

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

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

SAM Domain Polymerization Links Subnuclear Clustering of PRC1 to Gene Silencing

(2013) Kyoichi Isono et al.   DEVELOPMENTAL CELL

Cohesin-mediated interactions organize chromosomal domain architecture

(2013) Sevil Sofueva et al.   EMBO JOURNAL

High-throughput chromatin motion tracking in living yeast reveals the flexibility of the fiber throughout the genome

(2013) Houssam Hajjoul et al.   GENOME RESEARCH

Single-cell Hi-C reveals cell-to-cell variability in chromosome structure

(2013) Takashi Nagano et al.   NATURE

A conformational switch in HP1 releases auto-inhibition to drive heterochromatin assembly

(2013) Daniele Canzio et al.   NATURE

Simulation of stochastic network dynamics via entropic matching

(2013) Tiago Ramalho et al.   PHYSICAL REVIEW E

Organization of the Mitotic Chromosome

(2013) N. Naumova et al.   SCIENCE

Colocalization of Coregulated Genes: A Steered Molecular Dynamics Study of Human Chromosome 19

(2013) Marco Di Stefano et al.   PLoS Computational Biology

Three-Dimensional Folding and Functional Organization Principles of the Drosophila Genome

(2012) Tom Sexton et al.   CELL

A Predictive Computational Model of the Dynamic 3D Interphase Yeast Nucleus

(2012) Hua Wong et al.   CURRENT BIOLOGY

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

(2012) Tamir Chandra et al.   MOLECULAR CELL

A Bridging Model for Persistence of a Polycomb Group Protein Complex through DNA Replication In Vitro

(2012) Stanley M. Lo et al.   MOLECULAR CELL

Gene Density, Transcription, and Insulators Contribute to the Partition of the Drosophila Genome into Physical Domains

(2012) Chunhui Hou et al.   MOLECULAR CELL

Topological domains in mammalian genomes identified by analysis of chromatin interactions

(2012) Jesse R. Dixon et al.   NATURE

Recovering ensembles of chromatin conformations from contact probabilities

(2012) Dario Meluzzi et al.   NUCLEIC ACIDS RESEARCH

Expression-Dependent Folding of Interphase Chromatin

(2012) Hansjoerg Jerabek et al.   PLoS One

Complexity of chromatin folding is captured by the strings and binders switch model

(2012) M. Barbieri et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Integrative epigenomic mapping defines four main chromatin states in Arabidopsis

(2011) François Roudier et al.   EMBO JOURNAL

Chromatin: constructing the big picture

(2011) Bas van Steensel   EMBO JOURNAL

Molecular dynamics simulation study of nonconcatenated ring polymers in a melt. I. Statics

(2011) Jonathan D. Halverson et al.   JOURNAL OF CHEMICAL PHYSICS

Are Biological Systems Poised at Criticality?

(2011) Thierry Mora et al.   JOURNAL OF STATISTICAL PHYSICS

A view of the chromatin landscape

(2011) Lindsy M. Rapkin et al.   MICRON

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

(2011) Jason Ernst et al.   NATURE

Enhancer function: new insights into the regulation of tissue-specific gene expression

(2011) Chin-Tong Ong et al.   NATURE REVIEWS GENETICS

Theoretical analysis of the role of chromatin interactions in long-range action of enhancers and insulators

(2011) S. Mukhopadhyay et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Dynamic Architecture of Hox Gene Clusters

(2011) D. Noordermeer et al.   SCIENCE

Looping Probabilities in Model Interphase Chromosomes

(2010) Angelo Rosa et al.   BIOPHYSICAL JOURNAL

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

(2010) Guillaume J. Filion et al.   CELL

Distinct Epigenomic Landscapes of Pluripotent and Lineage-Committed Human Cells

(2010) R. David Hawkins et al.   Cell Stem Cell

Comprehensive analysis of the chromatin landscape in Drosophila melanogaster

(2010) Peter V. Kharchenko et al.   NATURE

Mediator and cohesin connect gene expression and chromatin architecture

(2010) Michael H. Kagey et al.   NATURE

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

(2010) Kashif Ahmed et al.   PLoS One

Diffusion-Driven Looping Provides a Consistent Framework for Chromatin Organization

(2010) Manfred Bohn et al.   PLoS One

Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project

(2010) M. B. Gerstein et al.   SCIENCE

Nuclear Pore Proteins Nup153 and Megator Define Transcriptionally Active Regions in the Drosophila Genome

(2010) Juan M. Vaquerizas et al.   PLoS Genetics

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

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

Structure and Dynamics of Interphase Chromosomes

(2008) Angelo Rosa et al.   PLoS Computational Biology