The biology and polymer physics underlying large-scale chromosome organization

Complex multi-enhancer contacts captured by genome architecture mapping

(2017) Robert A. Beagrie et al.   NATURE

The 4D nucleome project

(2017) Job Dekker 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

SMC complexes differentially compact mitotic chromosomes according to genomic context

(2017) Stephanie Andrea Schalbetter et al.   NATURE CELL BIOLOGY

Super-resolution microscopy with DNA-PAINT

(2017) Joerg Schnitzbauer et al.   Nature Protocols

Small Activity Differences Drive Phase Separation in Active-Passive Polymer Mixtures

(2017) Jan Smrek et al.   PHYSICAL REVIEW LETTERS

Binding, sliding, and function of cohesin during transcriptional activation

(2017) Melinda S. Borrie et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

3D organization of synthetic and scrambled chromosomes

(2017) Guillaume Mercy et al.   SCIENCE

Bacillus subtilis SMC complexes juxtapose chromosome arms as they travel from origin to terminus

(2017) Xindan Wang et al.   SCIENCE

Transcription dynamics stabilizes nucleus-like layer structure in chromatin brush

(2017) Tetsuya Yamamoto et al.   Soft Matter

Dynamics of active Rouse chains

(2017) Dino Osmanović et al.   Soft Matter

The Nucleoskeleton

(2017) Stephen A. Adam   Cold Spring Harbor Perspectives in Biology

The dynamic three-dimensional organization of the diploid yeast genome

(2017) Seungsoo Kim et al.   eLife

Topologically associated domains: a successful scaffold for the evolution of gene regulation in animals

(2017) Rafael D. Acemel et al.   Wiley Interdisciplinary Reviews-Developmental Biology

CTCF and Cohesin in Genome Folding and Transcriptional Gene Regulation

(2016) Matthias Merkenschlager et al.   Annual Review of Genomics and Human Genetics

Extruding Loops to Make Loopy Globules?

(2016) Alexander Y. Grosberg   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

How to rule the nucleus: divide et impera

(2016) Irina Solovei et al.   CURRENT OPINION IN CELL BIOLOGY

The three-dimensional genome: principles and roles of long-distance interactions

(2016) M Jordan Rowley et al.   CURRENT OPINION IN CELL BIOLOGY

Insulators and domains of gene expression

(2016) Tamer Ali et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Examining Topological Domain Influence on Enhancer Function

(2016) Robert A. Beagrie et al.   DEVELOPMENTAL CELL

Ancient Eukaryotic Origin and Evolutionary Plasticity of Nuclear Lamina

(2016) Ludek Koreny et al.   Genome Biology and Evolution

CRISPR-Cas9 nuclear dynamics and target recognition in living cells

(2016) Hanhui Ma et al.   JOURNAL OF CELL BIOLOGY

Self-Similar Conformations and Dynamics in Entangled Melts and Solutions of Nonconcatenated Ring Polymers

(2016) Ting Ge et al.   MACROMOLECULES

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

(2016) Alistair N. Boettiger et al.   NATURE

Centromeric DNA replication reconstitution reveals DNA loops and ATR checkpoint suppression

(2016) Antoine Aze et al.   NATURE CELL BIOLOGY

Enhancer–promoter interactions are encoded by complex genomic signatures on looping chromatin

(2016) Sean Whalen et al.   NATURE GENETICS

SMC complexes: from DNA to chromosomes

(2016) Frank Uhlmann   NATURE REVIEWS MOLECULAR CELL BIOLOGY

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

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

Different enhancer classes in Drosophila bind distinct architectural proteins and mediate unique chromatin interactions and 3D architecture

(2016) Caelin Cubeñas-Potts 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

Single-molecule decoding of combinatorially modified nucleosomes

(2016) E. Shema et al.   SCIENCE

Spatial organization of chromatin domains and compartments in single chromosomes

(2016) Siyuan Wang et al.   SCIENCE

Spatial organization of theSchizosaccharomyces pombegenome within the nucleus

(2016) Atsushi Matsuda et al.   YEAST

Minimal Surfaces on Unconcatenated Polymer Rings in Melt

(2016) Jan Smrek et al.   ACS Macro Letters

Formation of Chromosomal Domains by Loop Extrusion

(2016) Geoffrey Fudenberg et al.   Cell Reports

Evidence for cohesin sliding along budding yeast chromosomes

(2016) Maria Ocampo-Hafalla et al.   Open Biology

Of Rings and Rods: Regulating Cohesin Entrapment of DNA to Generate Intra- and Intermolecular Tethers

(2016) Robert V. Skibbens   PLoS Genetics

Compaction and segregation of sister chromatids via active loop extrusion

(2016) Anton Goloborodko et al.   eLife

Multiplexing Genetic and Nucleosome Positioning Codes: A Computational Approach

(2016) Behrouz Eslami-Mossallam et al.   PLoS One

A CTCF Code for 3D Genome Architecture

(2015) Michael H. Nichols et al.   CELL

Mapping Nucleosome Resolution Chromosome Folding in Yeast by Micro-C

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

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

(2015) Darío G. Lupiáñez et al.   CELL

Structural and functional diversity of Topologically Associating Domains

(2015) Job Dekker et al.   FEBS LETTERS

Condensin promotes the juxtaposition of DNA flanking its loading site inBacillus subtilis

(2015) Xindan Wang et al.   GENES & DEVELOPMENT

DNA loops generate intracentromere tension in mitosis

(2015) Josh Lawrimore et al.   JOURNAL OF CELL BIOLOGY

The Hitchhiker’s guide to Hi-C analysis: Practical guidelines

(2015) Bryan R. Lajoie et al.   METHODS

An Organizational Hub of Developmentally Regulated Chromatin Loops in the Drosophila Antennapedia Complex

(2015) Mo Li et al.   MOLECULAR AND CELLULAR BIOLOGY

Condensin- and Replication-Mediated Bacterial Chromosome Folding and Origin Condensation Revealed by Hi-C and Super-resolution Imaging

(2015) Martial Marbouty et al.   MOLECULAR CELL

The Ku heterodimer: Function in DNA repair and beyond

(2015) Victoria L. Fell et al.   MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH

The yeast genome undergoes significant topological reorganization in quiescence

(2015) Mark T. Rutledge et al.   NUCLEIC ACIDS RESEARCH

Nuclear dynamical deformation induced hetero- and euchromatin positioning

(2015) Akinori Awazu   PHYSICAL REVIEW E

Nonequilibrium statistical mechanics of mixtures of particles in contact with different thermostats

(2015) A. Y. Grosberg et al.   PHYSICAL REVIEW E

CASFISH: CRISPR/Cas9-mediated in situ labeling of genomic loci in fixed cells

(2015) Wulan Deng 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

Theory in Biology: Figure 1 or Figure 7?

(2015) Rob Phillips   TRENDS IN CELL BIOLOGY

Genetic Tailors: CTCF and Cohesin Shape the Genome During Evolution

(2015) Matteo Vietri Rudan et al.   TRENDS IN GENETICS

Single-molecule super-resolution imaging of chromosomes and in situ haplotype visualization using Oligopaint FISH probes

(2015) Brian J. Beliveau et al.   Nature Communications

The International Nucleome Consortium

(2015) Satoshi Tashiro et al.   Nucleus

The International Nucleome Consortium

(2015) Satoshi Tashiro et al.   Nucleus

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

(2015) Ke Gong et al.   PLoS One

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

(2014) Suhas S.P. Rao et al.   CELL

Deciphering the Evolutionary History of Open and Closed Mitosis

(2014) Shelley Sazer et al.   CURRENT BIOLOGY

Chromosome Organization: Original Condensins

(2014) Diego I. Cattoni et al.   CURRENT BIOLOGY

Nucleolus and nuclear periphery: Velcro for heterochromatin

(2014) Jan Padeken et al.   CURRENT OPINION IN CELL BIOLOGY

Transcription in the context of the 3D nucleus

(2014) Kerstin S. Wendt et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Crumpled globule formation during collapse of a long flexible and semiflexible polymer in poor solvent

(2014) A. Chertovich et al.   JOURNAL OF CHEMICAL PHYSICS

Cohesin-dependent globules and heterochromatin shape 3D genome architecture in S. pombe

(2014) Takeshi Mizuguchi et al.   NATURE

The biogenesis of chromosome translocations

(2014) Vassilis Roukos et al.   NATURE CELL BIOLOGY

Histone core modifications regulating nucleosome structure and dynamics

(2014) Peter Tessarz et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

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

LBR and Lamin A/C Sequentially Tether Peripheral Heterochromatin and Inversely Regulate Differentiation

(2013) Irina Solovei et al.   CELL

Genome organization and long-range regulation of gene expression by enhancers

(2013) Andrea Smallwood et al.   CURRENT OPINION IN CELL BIOLOGY

DNA Looping in Prokaryotes: Experimental and Theoretical Approaches

(2013) A. Cournac et al.   JOURNAL OF BACTERIOLOGY

On the stability of fractal globules

(2013) Raoul D. Schram et al.   JOURNAL OF CHEMICAL PHYSICS

A novel family of space-filling curves in their relation to chromosome conformation in eukaryotes

(2013) Jan Smrek et al.   PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS

Organization of the Mitotic Chromosome

(2013) N. Naumova et al.   SCIENCE

Annealed lattice animal model and Flory theory for the melt of non-concatenated rings: towards the physics of crumpling

(2013) Alexander Y. Grosberg   Soft Matter

When untethered, something silent inside comes

(2013) Joan C. Ritland Politz et al.   Nucleus

Nuclear Aggregation of Olfactory Receptor Genes Governs Their Monogenic Expression

(2012) E. Josephine Clowney et al.   CELL

CTCF: insights into insulator function during development

(2012) M. Herold et al.   DEVELOPMENT

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

(2012) H. Tjong et al.   GENOME RESEARCH

Effect of Topology on the Conformations of Ring Polymers

(2012) M. Lang et al.   MACROMOLECULES

Self-organization of domain structures by DNA-loop-extruding enzymes

(2012) E. Alipour et al.   NUCLEIC ACIDS RESEARCH

Telomeres, tethers and trypanosomes

(2012) Mark C. Field et al.   Nucleus

Molecular dynamics simulation study of nonconcatenated ring polymers in a melt. II. Dynamics

(2011) Jonathan D. Halverson et al.   JOURNAL OF CHEMICAL PHYSICS

Molecular dynamics simulation study of nonconcatenated ring polymers in a melt. I. Statics

(2011) Jonathan D. Halverson et al.   JOURNAL OF CHEMICAL PHYSICS

Breaking the Diffraction Barrier: Super-Resolution Imaging of Cells

(2010) Bo Huang et al.   CELL

Nuclear Membrane: Nuclear Envelope PORosity in Fission Yeast Meiosis

(2010) Shelley Sazer   CURRENT BIOLOGY

A three-dimensional model of the yeast genome

(2010) Zhijun Duan et al.   NATURE

Living without 30nm chromatin fibers

(2010) Eden Fussner et al.   TRENDS IN BIOCHEMICAL SCIENCES

Chromosome Territories

(2010) T. Cremer et al.   Cold Spring Harbor Perspectives in Biology

Cohesin: Its Roles and Mechanisms

(2009) Kim Nasmyth et al.   Annual Review of Genetics

Loss of the insulator protein CTCF during nematode evolution

(2009) Peter Heger et al.   BMC MOLECULAR BIOLOGY

Nuclear Architecture of Rod Photoreceptor Cells Adapts to Vision in Mammalian Evolution

(2009) Irina Solovei et al.   CELL

Entropic organization of interphase chromosomes

(2009) Peter R. Cook et al.   JOURNAL OF CELL BIOLOGY

Nucleosome positioning and gene regulation: advances through genomics

(2009) Cizhong Jiang et al.   NATURE REVIEWS GENETICS

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

Examination of Interchromosomal Interactions in Vegetatively Growing Diploid Schizosaccharomyces pombe Cells by Cre/loxP Site-Specific Recombination

(2008) Monika Molnar et al.   GENETICS

PcG Proteins, DNA Methylation, and Gene Repression by Chromatin Looping

(2008) Vijay K Tiwari et al.   PLOS BIOLOGY

Structure and Dynamics of Interphase Chromosomes

(2008) Angelo Rosa et al.   PLoS Computational Biology