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Polymer Simulations of Heteromorphic Chromatin Predict the 3D Folding of Complex Genomic Loci

Molecular cell, 2018-11, Vol.72 (4), p.786-797.e11

2018

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

Proceedings of the National Academy of Sciences - PNAS, 2013-09, Vol.110 (38), p.E3605-E3611

2013

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Transcription modulates chromatin dynamics and locus configuration sampling

Nature structural & molecular biology, 2023-09, Vol.30 (9), p.1275

2023

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Polymer Modeling Predicts Chromosome Reorganization in Senescence

Cell reports (Cambridge), 2019-09, Vol.28 (12), p.3212-3223.e6

2019

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Exploiting native forces to capture chromosome conformation in mammalian cell nuclei

Molecular systems biology, 2016-12, Vol.12 (12), p.891-n/a

2016

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The dynamics of supply and demand in mRNA translation

PLoS computational biology, 2011-10, Vol.7 (10), p.e1002203-e1002203

2011

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Simulating the chromatin-mediated phase separation of model proteins with multiple domains

Biophysical journal, 2022-07, Vol.121 (13), p.2600-2612

2022

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A computational model for microbial colonization of an antifouling surface

Frontiers in microbiology, 2022-09, Vol.13, p.920014-920014

2022

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Nucleosome positions alone can be used to predict domains in yeast chromosomes

Proceedings of the National Academy of Sciences - PNAS, 2019-08, Vol.116 (35), p.17307-17315

2019

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

Nucleic acids research, 2016-05, Vol.44 (8), p.3503

2016

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Evolutionarily conserved enhancer-associated features within the MYEOV locus suggest a regulatory role for this non-coding DNA region in cancer

Frontiers in cell and developmental biology, 2024-07, Vol.12, p.1294510

2024

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Ephemeral Protein Binding to DNA Shapes Stable Nuclear Bodies and Chromatin Domains

Biophysical journal, 2017-03, Vol.112 (6), p.1085-1093

2017

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Predicting genome organisation and function with mechanistic modelling

Trends in genetics, 2022-04, Vol.38 (4), p.364-378

2022

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Effect of DNA conformation on facilitated diffusion

Biochemical Society transactions, 2013-04, Vol.41 (2), p.582

2013

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Model for Quorum-Sensing Mediated Stochastic Biofilm Nucleation

Physical review letters, 2022-11, Vol.129 (19), p.198102-198102, Article 198102

2022

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Transcriptional Bursts in a Nonequilibrium Model for Gene Regulation by Supercoiling

Biophysical journal, 2019-07, Vol.117 (2), p.369-376

2019

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HMGB2 Loss upon Senescence Entry Disrupts Genomic Organization and Induces CTCF Clustering across Cell Types

Molecular cell, 2018-05, Vol.70 (4), p.730-744.e6

2018

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capC-MAP: software for analysis of Capture-C data

Bioinformatics, 2019-11, Vol.35 (22), p.4773-4775

2019

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Predictive Polymer Models for 3D Chromosome Organization

Methods in molecular biology (Clifton, N.J.), 2022, Vol.2301, p.267

2022

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Nonequilibrium dynamics and action at a distance in transcriptionally driven DNA supercoiling

Proceedings of the National Academy of Sciences - PNAS, 2021-03, Vol.118 (10), p.1

2021

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Predicting the three-dimensional folding of cis-regulatory regions in mammalian genomes using bioinformatic data and polymer models

Genome Biology, 2016-03, Vol.17 (1), p.59-59, Article 59

2016

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Computational design of probes to detect bacterial genomes by multivalent binding

Proceedings of the National Academy of Sciences - PNAS, 2020-04, Vol.117 (16), p.8719-8726

2020

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Vertebrate centromeres in mitosis are functionally bipartite structures stabilized by cohesin

Cell, 2024-06, Vol.187 (12), p.3006-3023.e26

2024

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Community control in cellular protein production: consequences for amino acid starvation

Philosophical transactions of the Royal Society of London. Series A: Mathematical, physical, and engineering sciences, 2015-12, Vol.373 (2056), p.20150107

2015

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A max-plus model of ribosome dynamics during mRNA translation

Journal of theoretical biology, 2012-06, Vol.303, p.128-140

2012

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Polymer Simulations of Heteromorphic Chromatin Predict the 3D Folding of Complex Genomic Loci

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

Transcription modulates chromatin dynamics and locus configuration sampling

Polymer Modeling Predicts Chromosome Reorganization in Senescence

Exploiting native forces to capture chromosome conformation in mammalian cell nuclei

The dynamics of supply and demand in mRNA translation

Simulating the chromatin-mediated phase separation of model proteins with multiple domains

A computational model for microbial colonization of an antifouling surface

Nucleosome positions alone can be used to predict domains in yeast chromosomes

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

Evolutionarily conserved enhancer-associated features within the MYEOV locus suggest a regulatory role for this non-coding DNA region in cancer

Ephemeral Protein Binding to DNA Shapes Stable Nuclear Bodies and Chromatin Domains

Predicting genome organisation and function with mechanistic modelling

Effect of DNA conformation on facilitated diffusion

Model for Quorum-Sensing Mediated Stochastic Biofilm Nucleation

Transcriptional Bursts in a Nonequilibrium Model for Gene Regulation by Supercoiling

HMGB2 Loss upon Senescence Entry Disrupts Genomic Organization and Induces CTCF Clustering across Cell Types

capC-MAP: software for analysis of Capture-C data

Predictive Polymer Models for 3D Chromosome Organization

Nonequilibrium dynamics and action at a distance in transcriptionally driven DNA supercoiling

Predicting the three-dimensional folding of cis-regulatory regions in mammalian genomes using bioinformatic data and polymer models

Computational design of probes to detect bacterial genomes by multivalent binding

Vertebrate centromeres in mitosis are functionally bipartite structures stabilized by cohesin

Community control in cellular protein production: consequences for amino acid starvation

A max-plus model of ribosome dynamics during mRNA translation

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