Simulated binding of transcription factors to active and inactive regions folds human chromosomes into loops, rosettes and topological domains

Mapping Nucleosome Resolution Chromosome Folding in Yeast by Micro-C

(2015) Tsung-Han S. Hsieh et al.   CELL

CRISPR Inversion of CTCF Sites Alters Genome Topology and Enhancer/Promoter Function

(2015) Ya Guo et al.   CELL

The Role of Chromosome Domains in Shaping the Functional Genome

(2015) Tom Sexton et al.   CELL

The role of loops on the order of eukaryotes and prokaryotes

(2015) Andreas Hofmann et al.   FEBS LETTERS

Restraint-based three-dimensional modeling of genomes and genomic domains

(2015) François Serra et al.   FEBS LETTERS

On the demultiplexing of chromosome capture conformation data

(2015) Ivan Junier et al.   FEBS LETTERS

A simple model for DNA bridging proteins and bacterial or human genomes: bridging-induced attraction and genome compaction

(2015) J Johnson et al.   JOURNAL OF PHYSICS-CONDENSED MATTER

Mapping long-range promoter contacts in human cells with high-resolution capture Hi-C

(2015) Borbala Mifsud et al.   NATURE GENETICS

Assessing the limits of restraint-based 3D modeling of genomes and genomic domains

(2015) Marie Trussart et al.   NUCLEIC ACIDS RESEARCH

Topology, structures, and energy landscapes of human chromosomes

(2015) Bin Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes

(2015) Adrian L. Sanborn et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Multivalency governs HP1α association dynamics with the silent chromatin state

(2015) Sinan Kilic et al.   Nature Communications

A simple biophysical model emulates budding yeast chromosome condensation

(2015) Tammy MK Cheng et al.   eLife

Predictive Polymer Modeling Reveals Coupled Fluctuations in Chromosome Conformation and Transcription

(2014) Luca Giorgetti et al.   CELL

In This Issue

(2014)   CELL

Nuclear bodies: new insights into assembly/dynamics and disease relevance

(2014) Judith E Sleeman et al.   CURRENT OPINION IN CELL BIOLOGY

Genome-wide map of regulatory interactions in the human genome

(2014) Nastaran Heidari et al.   GENOME RESEARCH

Large-scale reconstruction of 3D structures of human chromosomes from chromosomal contact data

(2014) Tuan Trieu et al.   NUCLEIC ACIDS RESEARCH

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

(2014) Daniel Jost et al.   NUCLEIC ACIDS RESEARCH

Depletion of the Chromatin Looping Proteins CTCF and Cohesin Causes Chromatin Compaction: Insight into Chromatin Folding by Polymer Modelling

(2014) Mariliis Tark-Dame et al.   PLoS Computational Biology

Transcription Factories: Genome Organization and Gene Regulation

(2013) Argyris Papantonis et al.   CHEMICAL REVIEWS

Supercoiling in DNA and chromatin

(2013) Nick Gilbert et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

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

(2013) Takashi Nagano et al.   NATURE

A high-resolution map of the three-dimensional chromatin interactome in human cells

(2013) Fulai Jin et al.   NATURE

Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data

(2013) Job Dekker et al.   NATURE REVIEWS GENETICS

Functional implications of genome topology

(2013) Giacomo Cavalli et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Models that include supercoiling of topological domains reproduce several known features of interphase chromosomes

(2013) Fabrizio Benedetti et al.   NUCLEIC ACIDS RESEARCH

Nonspecific bridging-induced attraction drives clustering of DNA-binding proteins and genome organization

(2013) C. A. Brackley et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cohesin and CTCF differentially affect chromatin architecture and gene expression in human cells

(2013) J. Zuin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

High-Resolution Mapping of the Spatial Organization of a Bacterial Chromosome

(2013) T. B. K. Le et al.   SCIENCE

Organization of the Mitotic Chromosome

(2013) N. Naumova et al.   SCIENCE

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

(2012) Tom Sexton et al.   CELL

Extensive Promoter-Centered Chromatin Interactions Provide a Topological Basis for Transcription Regulation

(2012) Guoliang Li et al.   CELL

TNFα signals through specialized factories where responsive coding and miRNA genes are transcribed

(2012) Argyris Papantonis et al.   EMBO JOURNAL

Genome structure determination via 3C-based data integration by the Integrative Modeling Platform

(2012) Davide Baù et al.   METHODS

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

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

Three-dimensional modeling of chromatin structure from interaction frequency data using Markov chain Monte Carlo sampling

(2011) Mathieu Rousseau et al.   BMC BIOINFORMATICS

Influence of mobile DNA-protein-DNA bridges on DNA configurations: Coarse-grained Monte-Carlo simulations

(2011) Renko de Vries   JOURNAL OF CHEMICAL PHYSICS

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

(2011) Jason Ernst et al.   NATURE

Genome architectures revealed by tethered chromosome conformation capture and population-based modeling

(2011) Reza Kalhor et al.   NATURE BIOTECHNOLOGY

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

(2011) Eitan Yaffe et al.   NATURE GENETICS

A three-dimensional model of the yeast genome

(2010) Zhijun Duan et al.   NATURE

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

Spatial and Topological Organization of DNA Chains Induced by Gene Co-localization

(2010) Ivan Junier et al.   PLoS Computational Biology

Topological and entropic repulsion in biopolymers

(2009) D Marenduzzo et al.   JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT

An oestrogen-receptor-α-bound human chromatin interactome

(2009) Melissa J. Fullwood et al.   NATURE

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

(2009) Stefan Schoenfelder et al.   NATURE GENETICS

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

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

The colocalization transition of homologous chromosomes at meiosis

(2008) Mario Nicodemi et al.   PHYSICAL REVIEW E

Structure and Dynamics of Interphase Chromosomes

(2008) Angelo Rosa et al.   PLoS Computational Biology