Quantifying Chromosome Structural Reorganizations during Differentiation, Reprogramming, and Transdifferentiation

Cell cycle dynamics and developmental dynamics of the 3D genome: toward linking the two timescales

(2022) Hisashi Miura et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Anomalous collapses of Nares Strait ice arches leads to enhanced export of Arctic sea ice

(2021) G. W. K. Moore et al.   Nature Communications

Replication timing maintains the global epigenetic state in human cells

(2021) Kyle N. Klein et al.   SCIENCE

Four-Dimensional Chromosome Structure Prediction

(2021) Max Highsmith et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Multiscale modeling of genome organization with maximum entropy optimization

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

Deciphering the molecular mechanism of the cancer formation by chromosome structural dynamics

(2021) Xiakun Chu et al.   PLoS Computational Biology

Mechanistic modeling of chromatin folding to understand function

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

Conformational state switching and pathways of chromosome dynamics in cell cycle

(2020) Xiakun Chu et al.   Applied Physics Reviews

Microscopic Chromosomal Structural and Dynamical Origin of Cell Differentiation and Reprogramming

(2020) Xiakun Chu et al.   Advanced Science

The relationship between genome structure and function

(2020) A. Marieke Oudelaar et al.   NATURE REVIEWS GENETICS

Cell Reprogramming: The Many Roads to Success

(2019) Begüm Aydin et al.   Annual Review of Cell and Developmental Biology

The role of 3D genome organization in development and cell differentiation

(2019) Hui Zheng et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Rapid Irreversible Transcriptional Reprogramming in Human Stem Cells Accompanied by Discordance between Replication Timing and Chromatin Compartment

(2019) Vishnu Dileep et al.   Stem Cell Reports

Single-cell DNA replication profiling identifies spatiotemporal developmental dynamics of chromosome organization

(2019) Hisashi Miura et al.   NATURE GENETICS

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

(2019) Kristin Abramo et al.   NATURE CELL BIOLOGY

Cell Cycle-Dependent Control and Roles of DNA Topoisomerase II

(2019) Joyce H. Lee et al.   Genes

Nonequilibrium physics in biology

(2019) Xiaona Fang et al.   REVIEWS OF MODERN PHYSICS

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

(2018) Ralph Stadhouders et al.   NATURE GENETICS

Polymer physics predicts the effects of structural variants on chromatin architecture

(2018) Simona Bianco 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

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

A pathway for mitotic chromosome formation

(2018) Johan H. Gibcus et al.   SCIENCE

Real-time imaging of DNA loop extrusion by condensin

(2018) Mahipal Ganji et al.   SCIENCE

Structural absorption by barbule microstructures of super black bird of paradise feathers

(2018) Dakota E. McCoy et al.   Nature Communications

Challenges and guidelines toward 4D nucleome data and model standards

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

Master equation for coarse-time macroscopic dynamics

(2018) Andrey Krakovsky   AIP Advances

Neuron-specific signatures in the chromosomal connectome associated with schizophrenia risk

(2018) Prashanth Rajarajan et al.   SCIENCE

Chain organization of human interphase chromosome determines the spatiotemporal dynamics of chromatin loci

(2018) Lei Liu et al.   PLoS Computational Biology

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

(2017) Tao Yang et al.   GENOME RESEARCH

Phase separation drives heterochromatin domain formation

(2017) Amy R. Strom et al.   NATURE

The 4D nucleome project

(2017) Job Dekker et al.   NATURE

Liquid droplet formation by HP1α suggests a role for phase separation in heterochromatin

(2017) Adam G. Larson et al.   NATURE

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

(2017) Takashi Nagano et al.   NATURE

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

Mouse embryonic stem cells can differentiate via multiple paths to the same state

(2017) James Alexander Briggs et al.   eLife

Cell-of-Origin-Specific 3D Genome Structure Acquired during Somatic Cell Reprogramming

(2016) Peter Hugo Lodewijk Krijger et al.   Cell Stem Cell

Dissecting direct reprogramming from fibroblast to neuron using single-cell RNA-seq

(2016) Barbara Treutlein et al.   NATURE

Transition states and cell fate decisions in epigenetic landscapes

(2016) Naomi Moris et al.   NATURE REVIEWS GENETICS

SMC complexes: from DNA to chromosomes

(2016) Frank Uhlmann   NATURE REVIEWS MOLECULAR CELL BIOLOGY

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

Formation of Chromosomal Domains by Loop Extrusion

(2016) Geoffrey Fudenberg et al.   Cell Reports

Dynamic Nucleosome Movement Provides Structural Information of Topological Chromatin Domains in Living Human Cells

(2016) Soya Shinkai et al.   PLoS Computational Biology

Landscape and flux theory of non-equilibrium dynamical systems with application to biology

(2015) Jin Wang   ADVANCES IN PHYSICS

Integrative Analyses of Human Reprogramming Reveal Dynamic Nature of Induced Pluripotency

(2015) Davide Cacchiarelli et al.   CELL

A developmental framework for induced pluripotency

(2015) Kazutoshi Takahashi et al.   DEVELOPMENT

Chromatin architecture reorganization during stem cell differentiation

(2015) Jesse R. Dixon et al.   NATURE

Condensin-driven remodelling of X chromosome topology during dosage compensation

(2015) Emily Crane et al.   NATURE

A comparison of genetically matched cell lines reveals the equivalence of human iPSCs and ESCs

(2015) Jiho Choi et al.   NATURE BIOTECHNOLOGY

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

Effects of Collective Histone State Dynamics on Epigenetic Landscape and Kinetics of Cell Reprogramming

(2015) S. S. Ashwin et al.   Scientific Reports

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

(2014) Suhas S.P. Rao et al.   CELL

PLUMED 2: New feathers for an old bird

(2013) Gareth A. Tribello et al.   COMPUTER PHYSICS COMMUNICATIONS

Single-cell Hi-C reveals cell-to-cell variability in chromosome structure

(2013) Takashi Nagano et al.   NATURE

Eddy current and coupled landscapes for nonadiabatic and nonequilibrium complex system dynamics

(2013) K. Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Organization of the Mitotic Chromosome

(2013) N. Naumova et al.   SCIENCE

Time Scales in Epigenetic Dynamics and Phenotypic Heterogeneity of Embryonic Stem Cells

(2013) Masaki Sasai et al.   PLoS Computational Biology

Dynamical Modeling of Three-Dimensional Genome Organization in Interphase Budding Yeast

(2012) Naoko Tokuda et al.   BIOPHYSICAL JOURNAL

Three-Dimensional Folding and Functional Organization Principles of the Drosophila Genome

(2012) Tom Sexton et al.   CELL

Higher-order chromatin structure: bridging physics and biology

(2012) Geoffrey Fudenberg et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Tensegrity and motor-driven effective interactions in a model cytoskeleton

(2012) Shenshen Wang et al.   JOURNAL OF CHEMICAL PHYSICS

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

Communication: Effective temperature and glassy dynamics of active matter

(2011) Shenshen Wang et al.   JOURNAL OF CHEMICAL PHYSICS

Dedifferentiation, transdifferentiation and reprogramming: three routes to regeneration

(2011) Chris Jopling et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Quantifying the Waddington landscape and biological paths for development and differentiation

(2011) J. Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Concise Review: Induced Pluripotent Stem Cells Versus Embryonic Stem Cells: Close Enough or Yet Too Far Apart?

(2011) Josipa Bilic et al.   STEM CELLS

Chromatin Structure and Gene Expression Programs of Human Embryonic and Induced Pluripotent Stem Cells

(2010) Matthew G. Guenther et al.   Cell Stem Cell

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

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

GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

(2008) Berk Hess et al.   Journal of Chemical Theory and Computation

Transcriptome-wide noise controls lineage choice in mammalian progenitor cells

(2008) Hannah H. Chang et al.   NATURE

Potential landscape and flux framework of nonequilibrium networks: Robustness, dissipation, and coherence of biochemical oscillations

(2008) J. Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structure and Dynamics of Interphase Chromosomes

(2008) Angelo Rosa et al.   PLoS Computational Biology