Microscopic Chromosomal Structural and Dynamical Origin of Cell Differentiation and Reprogramming

Re-epithelialization and immune cell behaviour in an ex vivo human skin model

(2020) Ana Rakita et al.   Scientific Reports

Conformational state switching and pathways of chromosome dynamics in cell cycle

(2020) Xiakun Chu et al.   Applied Physics Reviews

Principles of genome folding into topologically associating domains

(2019) Quentin Szabo et al.   Science Advances

Predicting three-dimensional genome organization with chromatin states

(2019) Yifeng Qi et al.   PLoS Computational Biology

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

(2019) Hisashi Miura et al.   NATURE GENETICS

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

(2019) Haoyue Zhang et al.   NATURE

A transient absence of SMC-mediated loops after mitosis

(2019) Ning Qing Liu et al.   NATURE CELL BIOLOGY

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

(2019) Kristin Abramo et al.   NATURE CELL BIOLOGY

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

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

(2018) Lei Liu et al.   PLoS Computational Biology

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

Liquid-like behavior of chromatin

(2016) Kazuhiro Maeshima et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

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

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

A Compendium of Chromatin Contact Maps Reveals Spatially Active Regions in the Human Genome

(2016) Anthony D. Schmitt 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

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

Functional organization of the human 4D Nucleome

(2015) Haiming Chen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

Functional and topological characteristics of mammalian regulatory domains

(2014) O. Symmons et al.   GENOME RESEARCH

Topologically associating domains are stable units of replication-timing regulation

(2014) Benjamin D. Pope et al.   NATURE

Epigenetics of Reprogramming to Induced Pluripotency

(2013) Bernadett Papp et al.   CELL

Genome Architecture: Domain Organization of Interphase Chromosomes

(2013) Wendy A. Bickmore et al.   CELL

Epigenomic Analysis of Multilineage Differentiation of Human Embryonic Stem Cells

(2013) Wei Xie et al.   CELL

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

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

Quantifying Waddington landscapes and paths of non-adiabatic cell fate decisions for differentiation, reprogramming and transdifferentiation

(2013) C. Li et al.   Journal of the Royal Society Interface

Deterministic direct reprogramming of somatic cells to pluripotency

(2013) Yoach Rais et al.   NATURE

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

(2013) Takashi Nagano et al.   NATURE

Chromatin dynamics during cellular reprogramming

(2013) Effie Apostolou et al.   NATURE

Functional implications of genome topology

(2013) Giacomo Cavalli et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Organization of the Mitotic Chromosome

(2013) N. Naumova et al.   SCIENCE

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

(2012) Tom Sexton et al.   CELL

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

FGF2 Sustains NANOG and Switches the Outcome of BMP4-Induced Human Embryonic Stem Cell Differentiation

(2011) Pengzhi Yu et al.   Cell Stem Cell

The fractal globule as a model of chromatin architecture in the cell

(2011) Leonid A. Mirny   CHROMOSOME RESEARCH

Communication: Effective temperature and glassy dynamics of active matter

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

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

Global epigenetic changes during somatic cell reprogramming to iPS cells

(2011) Anna Mattout et al.   Journal of Molecular Cell Biology

Pluripotency and Cellular Reprogramming: Facts, Hypotheses, Unresolved Issues

(2010) Jacob H. Hanna et al.   CELL

Distinct Epigenomic Landscapes of Pluripotent and Lineage-Committed Human Cells

(2010) R. David Hawkins et al.   Cell Stem Cell

Induced pluripotency: history, mechanisms, and applications

(2010) M. Stadtfeld et al.   GENES & DEVELOPMENT

Adiabatic and Non-Adiabatic Non-Equilibrium Stochastic Dynamics of Single Regulating Genes

(2010) Haidong Feng et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Epigenetic reprogramming and induced pluripotency

(2009) K. Hochedlinger et al.   DEVELOPMENT

Direct cell reprogramming is a stochastic process amenable to acceleration

(2009) Jacob Hanna et al.   NATURE

Transient Anomalous Diffusion of Telomeres in the Nucleus of Mammalian Cells

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

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

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

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