Polymer model with Epigenetic Recoloring Reveals a Pathway for the de novo Establishment and 3D Organization of Chromatin Domains

Chromosome Compaction by Active Loop Extrusion

(2016) Anton Goloborodko et al.   BIOPHYSICAL JOURNAL

A Systems Approach to Reverse Engineer Lifespan Extension by Dietary Restriction

(2016) Lei Hou et al.   Cell Metabolism

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

(2016) Alistair N. Boettiger et al.   NATURE

Simulated binding of transcription factors to active and inactive regions folds human chromosomes into loops, rosettes and topological domains

(2016) Chris A. Brackley et al.   NUCLEIC ACIDS RESEARCH

Achieving diverse and monoallelic olfactory receptor selection through dual-objective optimization design

(2016) Xiao-Jun Tian et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The physics of epigenetics

(2016) Ruggero Cortini et al.   REVIEWS OF MODERN PHYSICS

Compaction and segregation of sister chromatids via active loop extrusion

(2016) Anton Goloborodko et al.   eLife

Metachronal waves in the flagellar beating ofVolvoxand their hydrodynamic origin

(2015) Douglas R. Brumley et al.   Journal of the Royal Society Interface

Ising-model description of long-range correlations in DNA sequences

(2015) A. Colliva et al.   PHYSICAL REVIEW E

Phylogenetic analyses of melanoma reveal complex patterns of metastatic dissemination

(2015) J. Zachary Sanborn et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Regulation of gene transcription by Polycomb proteins

(2015) S. Aranda et al.   Science Advances

Predictive Polymer Modeling Reveals Coupled Fluctuations in Chromosome Conformation and Transcription

(2014) Luca Giorgetti et al.   CELL

Folding mechanism of a polymer chain with short-range attractions

(2014) Christian Leitold et al.   JOURNAL OF CHEMICAL PHYSICS

Clocks for all seasons: unwinding the roles and mechanisms of circadian and interval timers in the hypothalamus and pituitary

(2014) Shona Wood et al.   JOURNAL OF ENDOCRINOLOGY

Specificity, propagation, and memory of pericentric heterochromatin

(2014) K. Muller-Ott et al.   Molecular Systems Biology

Modeling epigenome folding: formation and dynamics of topologically associated chromatin domains

(2014) Daniel Jost et al.   NUCLEIC ACIDS RESEARCH

Bifurcation in epigenetics: Implications in development, proliferation, and diseases

(2014) Daniel Jost   PHYSICAL REVIEW E

Statistical Mechanics Model for the Dynamics of Collective Epigenetic Histone Modification

(2014) Hang Zhang et al.   PHYSICAL REVIEW LETTERS

Mechanistic stochastic model of histone modification pattern formation

(2014) Lisette C M Anink-Groenen et al.   Epigenetics & Chromatin

Retrieving the intracellular topology from multi-scale protein mobility mapping in living cells

(2014) Michael Baum et al.   Nature Communications

Establishing epigenetic domains via chromatin-bound histone modifiers

(2013) Fabian Erdel et al.   Annals of the New York Academy of Sciences

Regulation of nucleosome dynamics by histone modifications

(2013) Gabriel E Zentner et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Intracellular Facilitated Diffusion: Searchers, Crowders, and Blockers

(2013) C. A. Brackley et al.   PHYSICAL REVIEW LETTERS

Nonspecific bridging-induced attraction drives clustering of DNA-binding proteins and genome organization

(2013) C. A. Brackley et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A polymer model explains the complexity of large-scale chromatin folding

(2013) Mariano Barbieri et al.   Nucleus

Dynamics and Memory of Heterochromatin in Living Cells

(2012) Nathaniel A. Hathaway et al.   CELL

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

(2012) Tom Sexton et al.   CELL

Spreading of X chromosome inactivation via a hierarchy of defined Polycomb stations

(2012) S. F. Pinter et al.   GENOME RESEARCH

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

Folding kinetics of a polymer

(2012) Štěpán Růžička et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Multistability with a Metastable Mixed State

(2012) Kim Sneppen et al.   PHYSICAL REVIEW LETTERS

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

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

(2011) Leonid A. Mirny   CHROMOSOME RESEARCH

HJURP is a CENP-A chromatin assembly factor sufficient to form a functional de novo kinetochore

(2011) Meghan C. Barnhart et al.   JOURNAL OF CELL BIOLOGY

Barriers and Silencers: A Theoretical Toolkit for Control and Containment of Nucleosome-Based Epigenetic States

(2011) Ian B. Dodd et al.   JOURNAL OF MOLECULAR BIOLOGY

A Polycomb-based switch underlying quantitative epigenetic memory

(2011) Andrew Angel et al.   NATURE

Jarid2 and PRC2, partners in regulating gene expression

(2010) G. Li et al.   GENES & DEVELOPMENT

The genetics of ageing

(2010) Cynthia J. Kenyon   NATURE

Thermodynamics and dynamics of systems with long-range interactions

(2010) Freddy Bouchet et al.   PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS

Fast signals and slow marks: the dynamics of histone modifications

(2010) Teresa K. Barth et al.   TRENDS IN BIOCHEMICAL SCIENCES

High-resolution analysis of epigenetic changes associated with X inactivation

(2009) H. Marks et al.   GENOME RESEARCH

Epigenetic inheritance during the cell cycle

(2009) Aline V. Probst et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

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

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

Ultrasensitive gene regulation by positive feedback loops in nucleosome modification

(2008) Kim Sneppen et al.   Molecular Systems Biology

Structure and Dynamics of Interphase Chromosomes

(2008) Angelo Rosa et al.   PLoS Computational Biology