Quantifying the large-scale chromosome structural dynamics during the mitosis-to-G1 phase transition of cell cycle

Chromosome organization through the cell cycle at a glance

(2022) Divyaa Srinivasan et al.   JOURNAL OF CELL SCIENCE

Sister chromatids separate during anaphase in a three-stage program as directed by interaxis bridges

(2022) Lingluo Chu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Quantifying Chromosome Structural Reorganizations during Differentiation, Reprogramming, and Transdifferentiation

(2022) Xiakun Chu et al.   PHYSICAL REVIEW LETTERS

Four-Dimensional Chromosome Structure Prediction

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

CTCF and transcription influence chromatin structure re-configuration after mitosis

(2021) Haoyue Zhang et al.   Nature Communications

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

(2021) Xiakun Chu et al.   PLoS Computational Biology

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

(2020) Marco Di Stefano et al.   Nature Communications

The 3D Topography of Mitotic Chromosomes

(2020) Lingluo Chu et al.   MOLECULAR CELL

Mechanistic modeling of chromatin folding to understand function

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

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

(2020) Yifeng Qi et al.   BIOPHYSICAL JOURNAL

One-dimensional spatial patterning along mitotic chromosomes: A mechanical basis for macroscopic morphogenesis

(2020) Lingluo Chu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

A quantitative map of human Condensins provides new insights into mitotic chromosome architecture

(2018) Nike Walther et al.   JOURNAL OF CELL BIOLOGY

A pathway for mitotic chromosome formation

(2018) Johan H. Gibcus et al.   SCIENCE

Single-nucleus Hi-C reveals unique chromatin reorganization at oocyte-to-zygote transition

(2017) Ilya M. Flyamer 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

Role of Conformational Dynamics in the Evolution of Retro-Aldolase Activity

(2017) Adrian Romero-Rivera et al.   ACS Catalysis

CTCF and Cohesin in Genome Folding and Transcriptional Gene Regulation

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

Synergistic Allosteric Mechanism of Fructose-1,6-bisphosphate and Serine for Pyruvate Kinase M2 via Dynamics Fluctuation Network Analysis

(2016) Jingxu Yang et al.   Journal of Chemical Information and Modeling

Chromatin Domains: The Unit of Chromosome Organization

(2016) Jesse R. Dixon et al.   MOLECULAR CELL

Organization and function of the 3D genome

(2016) Boyan Bonev 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

Spatial organization of chromatin domains and compartments in single chromosomes

(2016) Siyuan Wang et al.   SCIENCE

Formation of Chromosomal Domains by Loop Extrusion

(2016) Geoffrey Fudenberg et al.   Cell Reports

Shaping mitotic chromosomes: From classical concepts to molecular mechanisms

(2015) Marc Kschonsak et al.   BIOESSAYS

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

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

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

Topologically associating domains are stable units of replication-timing regulation

(2014) Benjamin D. Pope et al.   NATURE

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

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

Contrasting roles of condensin I and condensin II in mitotic chromosome formation

(2012) L. C. Green et al.   JOURNAL OF CELL SCIENCE

Gene Density, Transcription, and Insulators Contribute to the Partition of the Drosophila Genome into Physical Domains

(2012) Chunhui Hou et al.   MOLECULAR CELL

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

Allosteric pathways in imidazole glycerol phosphate synthase

(2012) I. Rivalta et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2011) Leonid A. Mirny   CHROMOSOME RESEARCH

Condensin and cohesin complexity: the expanding repertoire of functions

(2010) Andrew J. Wood et al.   NATURE REVIEWS GENETICS

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

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

Temporal Organization of the Cell Cycle

(2008) John J. Tyson et al.   CURRENT BIOLOGY

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

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

Structure and Dynamics of Interphase Chromosomes

(2008) Angelo Rosa et al.   PLoS Computational Biology