How epigenome drives chromatin folding and dynamics, insights from efficient coarse-grained models of chromosomes

Simulation of ring polymer melts with GPU acceleration

(2018) R.D. Schram et al.   JOURNAL OF COMPUTATIONAL PHYSICS

Epigenomics in 3D: importance of long-range spreading and specific interactions in epigenomic maintenance

(2018) Daniel Jost et al.   NUCLEIC ACIDS RESEARCH

TADs are 3D structural units of higher-order chromosome organization in Drosophila

(2018) Quentin Szabo et al.   Science Advances

Reciprocal insulation analysis of Hi-C data shows that TADs represent a functionally but not structurally privileged scale in the hierarchical folding of chromosomes

(2017) Yinxiu Zhan et al.   GENOME RESEARCH

Single-nucleus Hi-C reveals unique chromatin reorganization at oocyte-to-zygote transition

(2017) Ilya M. Flyamer et al.   NATURE

3D structures of individual mammalian genomes studied by single-cell Hi-C

(2017) Tim J. Stevens et al.   NATURE

Cell-cycle dynamics of chromosomal organization at single-cell resolution

(2017) Takashi Nagano et al.   NATURE

Structural Fluctuations of the Chromatin Fiber within Topologically Associating Domains

(2016) Guido Tiana et al.   BIOPHYSICAL JOURNAL

Formation of new chromatin domains determines pathogenicity of genomic duplications

(2016) Martin Franke et al.   NATURE

Super-resolution imaging reveals distinct chromatin folding for different epigenetic states

(2016) Alistair N. Boettiger et al.   NATURE

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

(2016) Chris A. Brackley et al.   NUCLEIC ACIDS RESEARCH

Transferable model for chromosome architecture

(2016) Michele Di Pierro et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Spatial organization of chromatin domains and compartments in single chromosomes

(2016) Siyuan Wang et al.   SCIENCE

Constructing 3D interaction maps from 1D epigenomes

(2016) Yun Zhu et al.   Nature Communications

Chromatin topology is coupled to Polycomb group protein subnuclear organization

(2016) Ajazul H. Wani et al.   Nature Communications

Formation of Chromosomal Domains by Loop Extrusion

(2016) Geoffrey Fudenberg et al.   Cell Reports

Large Scale Chromosome Folding Is Stable against Local Changes in Chromatin Structure

(2016) Ana-Maria Florescu et al.   PLoS Computational Biology

Computational Identification of Genomic Features That Influence 3D Chromatin Domain Formation

(2016) Raphaël Mourad et al.   PLoS Computational Biology

Compaction and segregation of sister chromatids via active loop extrusion

(2016) Anton Goloborodko et al.   eLife

Polymer physics of chromosome large-scale 3D organisation

(2016) Andrea M. Chiariello et al.   Scientific Reports

Disruptions of Topological Chromatin Domains Cause Pathogenic Rewiring of Gene-Enhancer Interactions

(2015) Darío G. Lupiáñez et al.   CELL

The Role of Chromosome Domains in Shaping the Functional Genome

(2015) Tom Sexton et al.   CELL

Chromosome dynamics and folding in eukaryotes: Insights from live cell microscopy

(2015) Kerstin Bystricky   FEBS LETTERS

Active chromatin and transcription play a key role in chromosome partitioning into topologically associating domains

(2015) Sergey V. Ulianov et al.   GENOME RESEARCH

Anomalous Diffusion in Fractal Globules

(2015) M. V. Tamm et al.   PHYSICAL REVIEW LETTERS

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

Effects of topological constraints on globular polymers

(2015) Maxim V. Imakaev et al.   Soft Matter

Global Reorganization of the Nuclear Landscape in Senescent Cells

(2015) Tamir Chandra et al.   Cell Reports

Predictive Polymer Modeling Reveals Coupled Fluctuations in Chromosome Conformation and Transcription

(2014) Luca Giorgetti et al.   CELL

3D Trajectories Adopted by Coding and Regulatory DNA Elements: First-Passage Times for Genomic Interactions

(2014) Joseph S. Lucas et al.   CELL

A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping

(2014) Suhas S.P. Rao et al.   CELL

Differential spatial and structural organization of the X chromosome underlies dosage compensation inC. elegans

(2014) Rahul Sharma et al.   GENES & DEVELOPMENT

Comparative analysis of metazoan chromatin organization

(2014) Joshua W. K. Ho et al.   NATURE

CRISPR-Cas systems for editing, regulating and targeting genomes

(2014) Jeffry D Sander et al.   NATURE BIOTECHNOLOGY

Spatial confinement is a major determinant of the folding landscape of human chromosomes

(2014) Gamze Gürsoy et al.   NUCLEIC ACIDS RESEARCH

Chromosome positioning from activity-based segregation

(2014) Nirmalendu Ganai et al.   NUCLEIC ACIDS RESEARCH

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

(2014) Daniel Jost et al.   NUCLEIC ACIDS RESEARCH

Ring Polymers in the Melt State: The Physics of Crumpling

(2014) Angelo Rosa et al.   PHYSICAL REVIEW LETTERS

From a melt of rings to chromosome territories: the role of topological constraints in genome folding

(2014) Jonathan D Halverson et al.   REPORTS ON PROGRESS IN PHYSICS

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

SAM Domain Polymerization Links Subnuclear Clustering of PRC1 to Gene Silencing

(2013) Kyoichi Isono et al.   DEVELOPMENTAL CELL

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

(2013) Houssam Hajjoul et al.   GENOME RESEARCH

The genome folding mechanism in yeast

(2013) Hajime Kimura et al.   JOURNAL OF BIOCHEMISTRY

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

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

(2013) Fabrizio Benedetti et al.   NUCLEIC ACIDS RESEARCH

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

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

Recovering ensembles of chromatin conformations from contact probabilities

(2012) Dario Meluzzi et al.   NUCLEIC ACIDS RESEARCH

Lattice animal model of chromosome organization

(2012) Balaji V. S. Iyer et al.   PHYSICAL REVIEW E

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

Progressive Polycomb Assembly on H3K27me3 Compartments Generates Polycomb Bodies with Developmentally Regulated Motion

(2012) Thierry Cheutin et al.   PLoS Genetics

Polycomb-Dependent Regulatory Contacts between Distant Hox Loci in Drosophila

(2011) Frédéric Bantignies et al.   CELL

The fractal globule as a model of chromatin architecture in the cell

(2011) Leonid A. Mirny   CHROMOSOME RESEARCH

Capturing the essence of folding and functions of biomolecules using coarse-grained models

(2011) Changbong Hyeon et al.   Nature Communications

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

A three-dimensional model of the yeast genome

(2010) Zhijun Duan et al.   NATURE

Stable Morphology, but Dynamic Internal Reorganisation, of Interphase Human Chromosomes in Living Cells

(2010) Iris Müller et al.   PLoS One

BioNumbers—the database of key numbers in molecular and cell biology

(2009) Ron Milo et al.   NUCLEIC ACIDS RESEARCH

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

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

Viscoelasticity and primitive path analysis of entangled polymer liquids: From F-actin to polyethylene

(2008) Nariya Uchida et al.   JOURNAL OF CHEMICAL PHYSICS

Amphiphilic Multiblock Copolymers: From Intramolecular Pearl Necklace to Layered Structures

(2008) Virginie Hugouvieux et al.   MACROMOLECULES

Structure and Dynamics of Interphase Chromosomes

(2008) Angelo Rosa et al.   PLoS Computational Biology