Loop-extrusion and polymer phase-separation can co-exist at the single-molecule level to shape chromatin folding

Bridging-induced phase separation induced by cohesin SMC protein complexes

(2021) Je-Kyung Ryu et al.   Science Advances

CTCF mediates dosage- and sequence-context-dependent transcriptional insulation by forming local chromatin domains

(2021) Hui Huang et al.   NATURE GENETICS

Comparison of the Hi-C, GAM and SPRITE methods using polymer models of chromatin

(2021) Luca Fiorillo et al.   NATURE METHODS

Benchmarking experiments with polymer modeling

(2021) Marc A. Marti-Renom   NATURE METHODS

From Hi-C Contact Map to Three-Dimensional Organization of Interphase Human Chromosomes

(2021) Guang Shi et al.   Physical Review X

Phase separation drives aberrant chromatin looping and cancer development

(2021) Jeong Hyun Ahn et al.   NATURE

A Dynamic Folded Hairpin Conformation Is Associated with α-Globin Activation in Erythroid Cells

(2020) Andrea M. Chiariello et al.   Cell Reports

Loop extrusion: theory meets single-molecule experiments

(2020) Edward J. Banigan et al.   CURRENT OPINION IN CELL BIOLOGY

Computational approaches from polymer physics to investigate chromatin folding

(2020) Simona Bianco et al.   CURRENT OPINION IN CELL BIOLOGY

Polymer physics indicates chromatin folding variability across single-cells results from state degeneracy in phase separation

(2020) Mattia Conte et al.   Nature Communications

Computational modelling of three-dimensional genome structure

(2020) Dariusz Plewczynski et al.   METHODS

DeepC: predicting 3D genome folding using megabase-scale transfer learning

(2020) Ron Schwessinger et al.   NATURE METHODS

Predicting 3D genome folding from DNA sequence with Akita

(2020) Geoff Fudenberg et al.   NATURE METHODS

Capturing cell type-specific chromatin compartment patterns by applying topic modeling to single-cell Hi-C data

(2020) Hyeon-Jin Kim et al.   PLoS Computational Biology

The epigenetic basis of cellular heterogeneity

(2020) Benjamin Carter et al.   NATURE REVIEWS GENETICS

Cohesin depleted cells rebuild functional nuclear compartments after endomitosis

(2020) Marion Cremer et al.   Nature Communications

4D nucleome modeling

(2020) Marco Di Stefano et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Predicting three-dimensional genome organization with chromatin states

(2019) Yifeng Qi et al.   PLoS Computational Biology

Molecular basis and biological function of variability in spatial genome organization

(2019) Elizabeth H. Finn et al.   SCIENCE

Modeling Single-Molecule Conformations of the HoxD Region in Mouse Embryonic Stem and Cortical Neuronal Cells

(2019) Simona Bianco et al.   Cell Reports

HOOMD-blue: A Python package for high-performance molecular dynamics and hard particle Monte Carlo simulations

(2019) Joshua A. Anderson et al.   COMPUTATIONAL MATERIALS SCIENCE

Methods for mapping 3D chromosome architecture

(2019) Rieke Kempfer et al.   NATURE REVIEWS GENETICS

In silico prediction of high-resolution Hi-C interaction matrices

(2019) Shilu Zhang et al.   Nature Communications

Higher-Order Inter-chromosomal Hubs Shape 3D Genome Organization in the Nucleus

(2018) Sofia A. Quinodoz et al.   CELL

Polymer physics predicts the effects of structural variants on chromatin architecture

(2018) Simona Bianco et al.   NATURE GENETICS

Structural variation in the 3D genome

(2018) Malte Spielmann et al.   NATURE REVIEWS 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

Interphase human chromosome exhibits out of equilibrium glassy dynamics

(2018) Guang Shi et al.   Nature Communications

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

(2018) Adam Buckle et al.   MOLECULAR CELL

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

(2018) Bogdan Bintu et al.   SCIENCE

Walking along chromosomes with super-resolution imaging, contact maps, and integrative modeling

(2018) Guy Nir et al.   PLoS Genetics

Two independent modes of chromatin organization revealed by cohesin removal

(2017) Wibke Schwarzer et al.   NATURE

Complex multi-enhancer contacts captured by genome architecture mapping

(2017) Robert A. Beagrie et al.   NATURE

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

(2017) Tim J. Stevens et al.   NATURE

Active and poised promoter states drive folding of the extended HoxB locus in mouse embryonic stem cells

(2017) Mariano Barbieri et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Transcription-induced supercoiling as the driving force of chromatin loop extrusion during formation of TADs in interphase chromosomes

(2017) Dusan Racko et al.   NUCLEIC ACIDS RESEARCH

Nonequilibrium Chromosome Looping via Molecular Slip Links

(2017) C. A. Brackley et al.   PHYSICAL REVIEW LETTERS

Single-cell absolute contact probability detection reveals chromosomes are organized by multiple low-frequency yet specific interactions

(2017) Diego I. Cattoni et al.   Nature Communications

Active and poised promoter states drive folding of the extended HoxB locus in mouse embryonic stem cells

(2017) Mariano Barbieri et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

Chromosome Compaction by Active Loop Extrusion

(2016) Anton Goloborodko et al.   BIOPHYSICAL JOURNAL

The 3D Genome as Moderator of Chromosomal Communication

(2016) Job Dekker et al.   CELL

Chromatin Domains: The Unit of Chromosome Organization

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

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

(2016) Alistair N. Boettiger et al.   NATURE

Regulation of disease-associated gene expression in the 3D genome

(2016) Peter Hugo Lodewijk Krijger et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

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

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

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

(2016) Marco Di Stefano et al.   Scientific Reports

The Role of Chromosome Domains in Shaping the Functional Genome

(2015) Tom Sexton et al.   CELL

Hierarchical folding and reorganization of chromosomes are linked to transcriptional changes in cellular differentiation

(2015) J. Fraser et al.   Molecular Systems 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

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

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

Genome Architecture: Domain Organization of Interphase Chromosomes

(2013) Wendy A. Bickmore et al.   CELL

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

Resolution enhancement techniques in microscopy

(2013) Christoph Cremer et al.   European Physical Journal H

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

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

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

A guide to super-resolution fluorescence microscopy

(2010) Lothar Schermelleh et al.   JOURNAL OF CELL BIOLOGY

Diffusion-Driven Looping Provides a Consistent Framework for Chromatin Organization

(2010) Manfred Bohn et al.   PLoS One

Thermodynamic Pathways to Genome Spatial Organization in the Cell Nucleus

(2009) Mario Nicodemi et al.   BIOPHYSICAL JOURNAL

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