Physical modeling of the spreading of epigenetic modifications through transient DNA looping

A fluorogenic array for temporally unlimited single-molecule tracking

(2019) Rajarshi P. Ghosh et al.   Nature Chemical Biology

Epigenomics in 3D: importance of long-range spreading and specific interactions in epigenomic maintenance

(2018) Daniel Jost et al.   NUCLEIC ACIDS RESEARCH

An archaeal primase functions as a nanoscale caliper to define primer length

(2018) Jiangyu Yan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Nucleosome Turnover Regulates Histone Methylation Patterns over the Genome

(2018) Emma J. Chory et al.   MOLECULAR CELL

Bottom–up modeling of chromatin segregation due to epigenetic modifications

(2018) Quinn MacPherson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Crowding and hopping in a protein’s diffusive transport on DNA

(2017) Elena F Koslover et al.   Journal of Physics A-Mathematical and Theoretical

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

(2017) Adam G. Larson 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

Physical Modeling of Dynamic Coupling between Chromosomal Loci

(2016) Thomas J. Lampo et al.   BIOPHYSICAL JOURNAL

Generalized nucleation and looping model for epigenetic memory of histone modifications

(2016) Fabian Erdel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2016) D. Michieletto et al.   Physical Review X

Polymer physics of chromosome large-scale 3D organisation

(2016) Andrea M. Chiariello et al.   Scientific Reports

Interplay of Protein Binding Interactions, DNA Mechanics, and Entropy in DNA Looping Kinetics

(2015) Peter J. Mulligan et al.   BIOPHYSICAL JOURNAL

Physical Modeling of Chromosome Segregation in Escherichia coli Reveals Impact of Force and DNA Relaxation

(2015) Thomas J. Lampo et al.   BIOPHYSICAL JOURNAL

Thermodynamic model of heterochromatin formation through epigenetic regulation

(2015) Peter J Mulligan et al.   JOURNAL OF PHYSICS-CONDENSED MATTER

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

(2014) Suhas S.P. Rao et al.   CELL

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

Multiscale dynamics of semiflexible polymers from a universal coarse-graining procedure

(2014) Elena F. Koslover et al.   PHYSICAL REVIEW E

Modulation of DNA loop lifetimes by the free energy of loop formation

(2014) Yi-Ju Chen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Systematic Coarse-Graining of Microscale Polymer Models as Effective Elastic Chains

(2013) Elena F. Koslover et al.   MACROMOLECULES

High-Resolution Mapping of the Spatial Organization of a Bacterial Chromosome

(2013) T. B. K. Le et al.   SCIENCE

Discretizing elastic chains for coarse-grained polymer models

(2013) Elena F. Koslover et al.   Soft Matter

The statistical-mechanics of chromosome conformation capture

(2013) Justin M O'Sullivan et al.   Nucleus

Analytical Tools To Distinguish the Effects of Localization Error, Confinement, and Medium Elasticity on the Velocity Autocorrelation Function

(2012) Stephanie C. Weber et al.   BIOPHYSICAL JOURNAL

Dynamics and Memory of Heterochromatin in Living Cells

(2012) Nathaniel A. Hathaway et al.   CELL

Chromatin architectures at fission yeast transcriptional promoters and replication origins

(2012) Robert M. Givens et al.   NUCLEIC ACIDS RESEARCH

Dynamics of inherently bounded histone modification domains

(2012) C. Hodges et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Nonthermal ATP-dependent fluctuations contribute to the in vivo motion of chromosomal loci

(2012) S. C. Weber et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Theoretical and Computational Modeling of Target-Site Search Kinetics In Vitro and In Vivo

(2011) Elena F. Koslover et al.   BIOPHYSICAL JOURNAL

Chromodomain-Mediated Oligomerization of HP1 Suggests a Nucleosome-Bridging Mechanism for Heterochromatin Assembly

(2011) Daniele Canzio et al.   MOLECULAR CELL

Looping Probabilities in Model Interphase Chromosomes

(2010) Angelo Rosa et al.   BIOPHYSICAL JOURNAL

Dynamic Strategies for Target-Site Search by DNA-Binding Proteins

(2010) Mario A. Díaz de la Rosa et al.   BIOPHYSICAL JOURNAL

A Subset of the Histone H3 Lysine 9 Methyltransferases Suv39h1, G9a, GLP, and SETDB1 Participate in a Multimeric Complex

(2010) Lauriane Fritsch et al.   MOLECULAR CELL

Subdiffusive motion of a polymer composed of subdiffusive monomers

(2010) Stephanie C. Weber et al.   PHYSICAL REVIEW E

Bacterial Chromosomal Loci Move Subdiffusively through a Viscoelastic Cytoplasm

(2010) Stephanie C. Weber et al.   PHYSICAL REVIEW LETTERS

Genome-Wide Kinetics of Nucleosome Turnover Determined by Metabolic Labeling of Histones

(2010) R. B. Deal et al.   SCIENCE

In VivoResidue-specific Histone Methylation Dynamics

(2009) Barry M. Zee et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

End-to-end distribution for a wormlike chain in arbitrary dimensions

(2008) Shafigh Mehraeen et al.   PHYSICAL REVIEW E

Structure and Dynamics of Interphase Chromosomes

(2008) Angelo Rosa et al.   PLoS Computational Biology