Predicting three-dimensional genome organization with chromatin states

Polymer physics predicts the effects of structural variants on chromatin architecture

(2018) Simona Bianco et al.   NATURE GENETICS

Chromatin organization by an interplay of loop extrusion and compartmental segregation

(2018) Johannes Nuebler et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Polymer Simulations of Heteromorphic Chromatin Predict the 3D Folding of Complex Genomic Loci

(2018) Adam Buckle et al.   MOLECULAR CELL

Bottom–up modeling of chromatin segregation due to epigenetic modifications

(2018) Quinn MacPherson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Super-resolution chromatin tracing reveals domains and cooperative interactions in single cells

(2018) Bogdan Bintu et al.   SCIENCE

HiCRep: assessing the reproducibility of Hi-C data using a stratum-adjusted correlation coefficient

(2017) Tao Yang et al.   GENOME RESEARCH

Two independent modes of chromatin organization revealed by cohesin removal

(2017) Wibke Schwarzer et al.   NATURE

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

(2017) Ilya M. Flyamer et al.   NATURE

FISH-ing for captured contacts: towards reconciling FISH and 3C

(2017) Geoffrey Fudenberg et al.   NATURE METHODS

De novo prediction of human chromosome structures: Epigenetic marking patterns encode genome architecture

(2017) Michele Di Pierro et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Automatic analysis and 3D-modelling of Hi-C data using TADbit reveals structural features of the fly chromatin colors

(2017) François Serra et al.   PLoS Computational Biology

Structural Fluctuations of the Chromatin Fiber within Topologically Associating Domains

(2016) Guido Tiana et al.   BIOPHYSICAL JOURNAL

Chromosome Compaction by Active Loop Extrusion

(2016) Anton Goloborodko et al.   BIOPHYSICAL JOURNAL

Insulated Neighborhoods: Structural and Functional Units of Mammalian Gene Control

(2016) Denes Hnisz et al.   CELL

Chromatin Domains: The Unit of Chromosome Organization

(2016) Jesse R. Dixon et al.   MOLECULAR CELL

Capturing pairwise and multi-way chromosomal conformations using chromosomal walks

(2016) Pedro Olivares-Chauvet et al.   NATURE

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

(2016) Alistair N. Boettiger et al.   NATURE

ATAC-see reveals the accessible genome by transposase-mediated imaging and sequencing

(2016) Xingqi Chen et al.   NATURE METHODS

De novo deciphering three-dimensional chromatin interaction and topological domains by wavelet transformation of epigenetic profiles

(2016) Yong Chen et al.   NUCLEIC ACIDS RESEARCH

Shape Transitions and Chiral Symmetry Breaking in the Energy Landscape of the Mitotic Chromosome

(2016) Bin Zhang et al.   PHYSICAL REVIEW LETTERS

Transferable model for chromosome architecture

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

Population-based 3D genome structure analysis reveals driving forces in spatial genome organization

(2016) Harianto Tjong 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

Mining 3D genome structure populations identifies major factors governing the stability of regulatory communities

(2016) Chao Dai et al.   Nature Communications

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

A High-Resolution Imaging Approach to Investigate Chromatin Architecture in Complex Tissues

(2015) Michael W. Linhoff et al.   CELL

Identification of Gene Positioning Factors Using High-Throughput Imaging Mapping

(2015) Sigal Shachar et al.   CELL

CTCF-Mediated Human 3D Genome Architecture Reveals Chromatin Topology for Transcription

(2015) Zhonghui Tang et al.   CELL

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

(2015) Ya Guo et al.   CELL

The 4D nucleome: Evidence for a dynamic nuclear landscape based on co-aligned active and inactive nuclear compartments

(2015) Thomas Cremer et al.   FEBS LETTERS

CTCF Binding Polarity Determines Chromatin Looping

(2015) Elzo de Wit et al.   MOLECULAR CELL

Condensin-driven remodelling of X chromosome topology during dosage compensation

(2015) Emily Crane et al.   NATURE

Three-dimensional genome architecture: players and mechanisms

(2015) Ana Pombo et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

A predictive modeling approach for cell line-specific long-range regulatory interactions

(2015) Sushmita Roy 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

A statistical approach for inferring the 3D structure of the genome

(2014) N. Varoquaux et al.   BIOINFORMATICS

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

The 3D Genome in Transcriptional Regulation and Pluripotency

(2014) David U. Gorkin et al.   Cell Stem Cell

Spatial genome organization: contrasting views from chromosome conformation capture and fluorescence in situ hybridization

(2014) Iain Williamson et al.   GENES & DEVELOPMENT

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

(2014) F. Ay et al.   GENOME RESEARCH

CTCF: an architectural protein bridging genome topology and function

(2014) Chin-Tong Ong et al.   NATURE REVIEWS GENETICS

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

(2014) Gamze Gürsoy et al.   NUCLEIC ACIDS RESEARCH

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

(2014) Daniel Jost et al.   NUCLEIC ACIDS RESEARCH

Global view of enhancer-promoter interactome in human cells

(2014) B. He et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cryo-EM Study of the Chromatin Fiber Reveals a Double Helix Twisted by Tetranucleosomal Units

(2014) F. Song et al.   SCIENCE

Dynamic Imaging of Genomic Loci in Living Human Cells by an Optimized CRISPR/Cas System

(2013) Baohui Chen et al.   CELL

Genome Architecture: Domain Organization of Interphase Chromosomes

(2013) Wendy A. Bickmore et al.   CELL

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

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

Large-scale chromatin organization: the good, the surprising, and the still perplexing

(2013) Andrew S Belmont   CURRENT OPINION IN CELL BIOLOGY

Molecular recognition of DNA by ligands: Roughness and complexity of the free energy profile

(2013) Wenwei Zheng et al.   JOURNAL OF CHEMICAL PHYSICS

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

(2013) Job Dekker et al.   NATURE REVIEWS GENETICS

Systematic discovery and characterization of regulatory motifs in ENCODE TF binding experiments

(2013) P. Kheradpour 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

Combinatorial complexity in chromatin structure and function: revisiting the histone code

(2012) Oliver J Rando   CURRENT OPINION IN GENETICS & DEVELOPMENT

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

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

(2012) Maxim Imakaev et al.   NATURE METHODS

ChromHMM: automating chromatin-state discovery and characterization

(2012) Jason Ernst et al.   NATURE METHODS

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

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

(2011) Leonid A. Mirny   CHROMOSOME RESEARCH

Determination of reaction coordinates via locally scaled diffusion map

(2011) Mary A. Rohrdanz et al.   JOURNAL OF CHEMICAL PHYSICS

Delineation of Folding Pathways of a β-Sheet Miniprotein

(2011) Wenwei Zheng et al.   JOURNAL OF PHYSICAL CHEMISTRY B

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

(2011) Eitan Yaffe et al.   NATURE GENETICS

Discovery and characterization of chromatin states for systematic annotation of the human genome

(2010) Jason Ernst et al.   NATURE BIOTECHNOLOGY

The NIH Roadmap Epigenomics Mapping Consortium

(2010) Bradley E Bernstein et al.   NATURE BIOTECHNOLOGY

Charting histone modifications and the functional organization of mammalian genomes

(2010) Vicky W. Zhou et al.   NATURE REVIEWS GENETICS

Diffusion-Driven Looping Provides a Consistent Framework for Chromatin Organization

(2010) Manfred Bohn et al.   PLoS One

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

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

Diffusion Maps, Reduction Coordinates, and Low Dimensional Representation of Stochastic Systems

(2008) R. R. Coifman et al.   MULTISCALE MODELING & SIMULATION

Structure and Dynamics of Interphase Chromosomes

(2008) Angelo Rosa et al.   PLoS Computational Biology