4D nucleome modeling

Chromosome dynamics during interphase: a biophysical perspective

(2020) Maxime MC Tortora et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

4D Genome Rewiring during Oncogene-Induced and Replicative Senescence

(2020) Satish Sati et al.   MOLECULAR CELL

Three-dimensional genome restructuring across timescales of activity-induced neuronal gene expression

(2020) Jonathan A. Beagan et al.   NATURE NEUROSCIENCE

Transcriptional activation during cell reprogramming correlates with the formation of 3D open chromatin hubs

(2020) Marco Di Stefano et al.   Nature Communications

Predicting cell lineages using autoencoders and optimal transport

(2020) Karren Dai Yang et al.   PLoS Computational Biology

Chromosome organization by one-sided and two-sided loop extrusion

(2020) Edward J Banigan et al.   eLife

Loop extrusion: theory meets single-molecule experiments

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

3D mapping and accelerated super-resolution imaging of the human genome using in situ sequencing

(2020) Huy Q. Nguyen et al.   NATURE METHODS

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

(2020) Mattia Conte et al.   Nature Communications

Coupling chromatin structure and dynamics by live super-resolution imaging

(2020) R. Barth et al.   Science Advances

Long-range interactions between topologically associating domains shape the four-dimensional genome during differentiation

(2019) Jonas Paulsen et al.   NATURE GENETICS

Rouse model with transient intramolecular contacts on a timescale of seconds recapitulates folding and fluctuation of yeast chromosomes

(2019) Marius Socol et al.   NUCLEIC ACIDS RESEARCH

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

Statistics of chromatin organization during cell differentiation revealed by heterogeneous cross-linked polymers

(2019) O. Shukron et al.   Nature Communications

Control of DNA replication timing in the 3D genome

(2019) Claire Marchal et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Chromatin structure dynamics during the mitosis-to-G1 phase transition

(2019) Haoyue Zhang et al.   NATURE

A chromosome folding intermediate at the condensin-to-cohesin transition during telophase

(2019) Kristin Abramo et al.   NATURE CELL BIOLOGY

DNA loop extrusion by human cohesin

(2019) Iain F. Davidson et al.   SCIENCE

Human cohesin compacts DNA by loop extrusion

(2019) Yoori Kim et al.   SCIENCE

Chromatin Configuration Affects the Dynamics and Distribution of a Transiently Interacting Protein

(2018) Assaf Amitai   BIOPHYSICAL JOURNAL

Polycomb-Dependent Chromatin Looping Contributes to Gene Silencing during Drosophila Development

(2018) Yuki Ogiyama et al.   MOLECULAR CELL

Transcription factors orchestrate dynamic interplay between genome topology and gene regulation during cell reprogramming

(2018) Ralph Stadhouders et al.   NATURE GENETICS

Anomalous diffusion, spatial coherence, and viscoelasticity from the energy landscape of human chromosomes

(2018) Michele Di Pierro et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A pathway for mitotic chromosome formation

(2018) Johan H. Gibcus et al.   SCIENCE

Theoretical principles of transcription factor traffic on folded chromatin

(2018) Ruggero Cortini et al.   Nature Communications

How epigenome drives chromatin folding and dynamics, insights from efficient coarse-grained models of chromosomes

(2018) Surya K. Ghosh et al.   PLoS Computational Biology

Challenges and guidelines toward 4D nucleome data and model standards

(2018) Marc A. Marti-Renom et al.   NATURE GENETICS

Interphase human chromosome exhibits out of equilibrium glassy dynamics

(2018) Guang Shi et al.   Nature Communications

Organizational principles of 3D genome architecture

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

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

(2018) Bogdan Bintu et al.   SCIENCE

Chromatin conformation analysis of primary patient tissue using a low input Hi-C method

(2018) Noelia Díaz et al.   Nature Communications

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

The 4D nucleome project

(2017) Job Dekker et al.   NATURE

Cell-cycle dynamics of chromosomal organization at single-cell resolution

(2017) Takashi Nagano et al.   NATURE

ChromEMT: Visualizing 3D chromatin structure and compaction in interphase and mitotic cells

(2017) Horng D. Ou et al.   SCIENCE

Chromosome Intermingling: Mechanical Hotspots for Genome Regulation

(2017) Caroline Uhler et al.   TRENDS IN CELL BIOLOGY

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

(2016) Alistair N. Boettiger et al.   NATURE

Erratum: Organization and function of the 3D genome

(2016) Boyan Bonev et al.   NATURE REVIEWS GENETICS

Formation of Chromosomal Domains by Loop Extrusion

(2016) Geoffrey Fudenberg et al.   Cell Reports

Compaction and segregation of sister chromatids via active loop extrusion

(2016) Anton Goloborodko et al.   eLife

Chromatin Fibers Are Formed by Heterogeneous Groups of Nucleosomes In Vivo

(2015) Maria Aurelia Ricci et al.   CELL

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

(2015) François Serra et al.   FEBS LETTERS

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

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

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

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

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