Hi-C-constrained physical models of human chromosomes recover functionally-related properties of genome organization

Structural Fluctuations of the Chromatin Fiber within Topologically Associating Domains

(2016) Guido Tiana et al.   BIOPHYSICAL JOURNAL

Formation of Chromosomal Domains by Loop Extrusion

(2016) Geoffrey Fudenberg et al.   Cell Reports

Polymer physics of chromosome large-scale 3D organisation

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

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

(2015) François Serra et al.   FEBS LETTERS

Chromatin-Driven Behavior of Topologically Associating Domains

(2015) Filippo Ciabrelli et al.   JOURNAL OF MOLECULAR BIOLOGY

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

Comparative 3D Genome Structure Analysis of the Fission and the Budding Yeast

(2015) Ke Gong et al.   PLoS One

Predictive Polymer Modeling Reveals Coupled Fluctuations in Chromosome Conformation and Transcription

(2014) Luca Giorgetti 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

Models of chromosome structure

(2014) Mario Nicodemi et al.   CURRENT OPINION IN CELL BIOLOGY

Telomere position effect: regulation of gene expression with progressive telomere shortening over long distances

(2014) Jérôme D. Robin et al.   GENES & DEVELOPMENT

Distinct structural transitions of chromatin topological domains correlate with coordinated hormone-induced gene regulation

(2014) François Le Dily et al.   GENES & DEVELOPMENT

Statistical confidence estimation for Hi-C data reveals regulatory chromatin contacts

(2014) F. Ay et al.   GENOME RESEARCH

Statistical Mechanics of the Denatured State of a Protein Using Replica-Averaged Metadynamics

(2014) Carlo Camilloni et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

3D genome reconstruction from chromosomal contacts

(2014) Annick Lesne et al.   NATURE METHODS

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

(2014) Daniel Jost et al.   NUCLEIC ACIDS RESEARCH

Chromosome conformation by crosslinking

(2014) Jörg Langowski   Nucleus

Single-Cell Dynamics of Genome-Nuclear Lamina Interactions

(2013) Jop Kind et al.   CELL

Genome Architecture: Domain Organization of Interphase Chromosomes

(2013) Wendy A. Bickmore et al.   CELL

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

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

Physical tethering and volume exclusion determine higher-order genome organization in budding yeast

(2012) H. Tjong et al.   GENOME RESEARCH

Topological domains in mammalian genomes identified by analysis of chromatin interactions

(2012) Jesse R. Dixon et al.   NATURE

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

(2012) Maxim Imakaev et al.   NATURE METHODS

Recovering ensembles of chromatin conformations from contact probabilities

(2012) Dario Meluzzi et al.   NUCLEIC ACIDS RESEARCH

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

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

(2011) Eitan Yaffe et al.   NATURE GENETICS

Systematic bias in high-throughput sequencing data and its correction by BEADS

(2011) Ming-Sin Cheung et al.   NUCLEIC ACIDS RESEARCH

Conformation Regulation of the X Chromosome Inactivation Center: A Model

(2011) Antonio Scialdone et al.   PLoS Computational Biology

Bridging the Resolution Gap in Structural Modeling of 3D Genome Organization

(2011) Marc A. Marti-Renom et al.   PLoS Computational Biology

Looping Probabilities in Model Interphase Chromosomes

(2010) Angelo Rosa et al.   BIOPHYSICAL JOURNAL

Structure determination of genomic domains by satisfaction of spatial restraints

(2010) Davide Baù et al.   CHROMOSOME RESEARCH

Contrasting GC-content dynamics across 33 mammalian genomes: Relationship with life-history traits and chromosome sizes

(2010) J. Romiguier et al.   GENOME RESEARCH

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR CELL

A three-dimensional model of the yeast genome

(2010) Zhijun Duan et al.   NATURE

PLUMED: A portable plugin for free-energy calculations with molecular dynamics

(2009) Massimiliano Bonomi et al.   COMPUTER PHYSICS COMMUNICATIONS

Topological origins of chromosomal territories

(2009) Julien Dorier et al.   NUCLEIC ACIDS RESEARCH

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

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

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

The Meaning of Gene Positioning

(2008) Takumi Takizawa et al.   CELL

The radial arrangement of the human chromosome 7 in the lymphocyte cell nucleus is associated with chromosomal band gene density

(2008) Concetta Federico et al.   CHROMOSOMA

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

(2008) Lars Guelen et al.   NATURE

Rapid telomere motions in live human cells analyzed by highly time-resolved microscopy

(2008) Xueying Wang et al.   Epigenetics & Chromatin

Structure and Dynamics of Interphase Chromosomes

(2008) Angelo Rosa et al.   PLoS Computational Biology