Compartmentalization with nuclear landmarks yields random, yet precise, genome organization

Phase Separation and Correlated Motions in Motorized Genome

(2022) Zhongling Jiang et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Integrative genome modeling platform reveals essentiality of rare contact events in 3D genome organizations

(2022) Lorenzo Boninsegna et al.   NATURE METHODS

p53 mediates target gene association with nuclear speckles for amplified RNA expression

(2021) Katherine A. Alexander et al.   MOLECULAR CELL

Systematic inference and comparison of multi-scale chromatin sub-compartments connects spatial organization to cell phenotypes

(2021) Yuanlong Liu et al.   Nature Communications

Multiscale modeling of genome organization with maximum entropy optimization

(2021) Xingcheng Lin et al.   JOURNAL OF CHEMICAL PHYSICS

Interphase Chromatin Undergoes a Local Sol-Gel Transition upon Cell Differentiation

(2021) Iraj Eshghi et al.   PHYSICAL REVIEW LETTERS

HP1α is a chromatin crosslinker that controls nuclear and mitotic chromosome mechanics

(2021) Amy R Strom et al.   eLife

RNA promotes the formation of spatial compartments in the nucleus

(2021) Sofia A. Quinodoz et al.   CELL

Four-dimensional chromosome reconstruction elucidates the spatiotemporal reorganization of the mammalian X chromosome

(2021) Anna Lappala et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mesoscale Phase Separation of Chromatin in the Nucleus

(2020) Gaurav Bajpai et al.   BIOPHYSICAL JOURNAL

Mechanisms and Functions of Chromosome Compartmentalization

(2020) Erica M. Hildebrand et al.   TRENDS IN BIOCHEMICAL SCIENCES

Physical and data structure of 3D genome

(2020) Kai Huang et al.   Science Advances

A Lamin Associated Chromatin Model for Chromosome Organization

(2020) Ajoy Maji et al.   BIOPHYSICAL JOURNAL

Ultrastructural Details of Mammalian Chromosome Architecture

(2020) Nils Krietenstein et al.   MOLECULAR CELL

GPSeq reveals the radial organization of chromatin in the cell nucleus

(2020) Gabriele Girelli et al.   NATURE BIOTECHNOLOGY

Mechanistic modeling of chromatin folding to understand function

(2020) Chris A. Brackey et al.   NATURE METHODS

A New View of Genome Organization Through RNA Directed Interactions

(2020) Gabriel Khelifi et al.   Frontiers in Cell and Developmental Biology

Data-Driven Polymer Model for Mechanistic Exploration of Diploid Genome Organization

(2020) Yifeng Qi et al.   BIOPHYSICAL JOURNAL

Genome-Scale Imaging of the 3D Organization and Transcriptional Activity of Chromatin

(2020) Jun-Han Su et al.   CELL

Large-Scale Topological Changes Restrain Malignant Progression in Colorectal Cancer

(2020) Sarah E. Johnstone et al.   CELL

The nucleolus as a multiphase liquid condensate

(2020) Denis L. J. Lafontaine et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Characterizing chromatin folding coordinate and landscape with deep learning

(2020) Wen Jun Xie et al.   PLoS Computational Biology

TSA-seq reveals a largely conserved genome organization relative to nuclear speckles with small position changes tightly correlated with gene expression changes

(2020) Liguo Zhang et al.   GENOME RESEARCH

Protein condensates as aging Maxwell fluids

(2020) Louise Jawerth et al.   SCIENCE

Improving Coarse-Grained Protein Force Fields with Small-Angle X-Ray Scattering Data

(2019) Andrew P. Latham et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Nuclear speckle fusion via long-range directional motion regulates speckle morphology after transcriptional inhibition

(2019) Jiah Kim et al.   JOURNAL OF CELL SCIENCE

How the Genome Folds: The Biophysics of Four-Dimensional Chromatin Organization

(2019) Jyotsana J. Parmar et al.   Annual Review of Biophysics

Learning the Formation Mechanism of Domain-Level Chromatin States with Epigenomics Data

(2019) Wen Jun Xie et al.   BIOPHYSICAL JOURNAL

Genome organization around nuclear speckles

(2019) Yu Chen et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Heterochromatin drives compartmentalization of inverted and conventional nuclei

(2019) Martin Falk et al.   NATURE

Chromosome dynamics near the sol-gel phase transition dictate the timing of remote genomic interactions

(2019) Nimish Khanna et al.   Nature Communications

Predicting three-dimensional genome organization with chromatin states

(2019) Yifeng Qi et al.   PLoS Computational Biology

Mesoscale liquid model of chromatin recapitulates nuclear order of eukaryotes

(2019) Rabia Laghmach et al.   BIOPHYSICAL JOURNAL

Molecular basis and biological function of variability in spatial genome organization

(2019) Elizabeth H. Finn et al.   SCIENCE

Polymer Modeling Predicts Chromosome Reorganization in Senescence

(2019) Michael Chiang et al.   Cell Reports

Theory of Active Chromatin Remodeling

(2019) Zhongling Jiang et al.   PHYSICAL REVIEW LETTERS

Conformational heterogeneity in human interphase chromosome organization reconciles the FISH and Hi-C paradox

(2019) Guang Shi et al.   Nature Communications

Revealing Hi-C subcompartments by imputing inter-chromosomal chromatin interactions

(2019) Kyle Xiong et al.   Nature Communications

Mechanisms for Active Regulation of Biomolecular Condensates

(2019) Johannes Söding et al.   TRENDS IN CELL BIOLOGY

Formation of Chromatin Subcompartments by Phase Separation

(2018) Fabian Erdel et al.   BIOPHYSICAL JOURNAL

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

(2018) Sofia A. Quinodoz et al.   CELL

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

Mapping 3D genome organization relative to nuclear compartments using TSA-Seq as a cytological ruler

(2018) Yu Chen et al.   JOURNAL OF CELL BIOLOGY

Interphase human chromosome exhibits out of equilibrium glassy dynamics

(2018) Guang Shi et al.   Nature Communications

Liquid Nuclear Condensates Mechanically Sense and Restructure the Genome

(2018) Yongdae Shin et al.   CELL

Organizational principles of 3D genome architecture

(2018) M. Jordan Rowley et al.   NATURE REVIEWS GENETICS

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

HiHiMap: single-cell quantitation of histones and histone posttranslational modifications across the cell cycle by high-throughput imaging

(2017) Linda Zane et al.   MOLECULAR BIOLOGY OF THE CELL

Computational construction of 3D chromatin ensembles and prediction of functional interactions of alpha-globin locus from 5C data

(2017) Gamze Gürsoy et al.   NUCLEIC ACIDS RESEARCH

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

Insulated Neighborhoods: Structural and Functional Units of Mammalian Gene Control

(2016) Denes Hnisz et al.   CELL

The 3D Genome as Moderator of Chromosomal Communication

(2016) Job Dekker et al.   CELL

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

(2016) Alistair N. Boettiger et al.   NATURE

Organization and function of the 3D genome

(2016) Boyan Bonev et al.   NATURE REVIEWS GENETICS

Transferable model for chromosome architecture

(2016) Michele Di Pierro 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

Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments

(2016) Neva C. Durand et al.   Cell Systems

Determinants of mammalian nucleolar architecture

(2015) Katherine I. Farley et al.   CHROMOSOMA

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

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

Loss of lamin A function increases chromatin dynamics in the nuclear interior

(2015) I. Bronshtein et al.   Nature Communications

Progressive Chromatin Condensation and H3K9 Methylation Regulate the Differentiation of Embryonic and Hematopoietic Stem Cells

(2015) Fernando Ugarte et al.   Stem Cell Reports

Chromatin Hydrodynamics

(2014) Robijn Bruinsma et al.   BIOPHYSICAL JOURNAL

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

HSP70 Transgene Directed Motion to Nuclear Speckles Facilitates Heat Shock Activation

(2014) Nimish Khanna et al.   CURRENT 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

The Spatial Organization of the Human Genome

(2013) Wendy A. Bickmore   Annual Review of Genomics and Human Genetics

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

(2013) Job Dekker et al.   NATURE REVIEWS GENETICS

Chromatin organization and transcriptional regulation

(2012) Michael R Hübner et al.   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

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

Diffusion-Driven Looping Provides a Consistent Framework for Chromatin Organization

(2010) Manfred Bohn et al.   PLoS One

Nuclear Speckles

(2010) D. L. Spector et al.   Cold Spring Harbor Perspectives in Biology

Transient Anomalous Diffusion of Telomeres in the Nucleus of Mammalian Cells

(2009) I. Bronstein et al.   PHYSICAL REVIEW LETTERS