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Nucleosomes  
PLOS Computational Biology  
Role of diffusion and reaction of the constituents in spreading of histone modification marks

Vinoth Manivannan, Mandar M. Inamdar, Ranjith Padinhateeri

Research Article | published 11 Jul 2024 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1012235

Views: 532Citations: 0Saves: 0 • Shares: 0

A genome-wide comprehensive analysis of nucleosome positioning in yeast

Leo Zeitler, Kévin André, Adriana Alberti, Cyril Denby Wilkes, Julie Soutourina, Arach Goldar

Research Article | published 24 Jan 2024 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1011799

Views: 1179Citations: 0Saves: 0 • Shares: 0

Identifying promoter sequence architectures via a chunking-based algorithm using non-negative matrix factorisation

Sarvesh Nikumbh, Boris Lenhard

Methods | published 20 Nov 2023 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1011491

Views: 1093Citations: 2Saves: 11 • Shares: 16

Combining molecular dynamics simulations and scoring method to computationally model ubiquitylated linker histones in chromatosomes

Kevin Sawade, Andreas Marx, Christine Peter, Oleksandra Kukharenko

Research Article | published 01 Aug 2023 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1010531

Views: 1147Citations: 0Saves: 7 • Shares: 1

An associative memory Hamiltonian model for DNA and nucleosomes

Weiqi Lu, José N. Onuchic, Michele Di Pierro

Research Article | published 27 Mar 2023 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1011013

Views: 1556Citations: 4Saves: 7 • Shares: 2

A quantitative modelling approach for DNA repair on a population scale

Leo Zeitler, Cyril Denby Wilkes, Arach Goldar, Julie Soutourina

Research Article | published 12 Sep 2022 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1010488

Views: 1789Citations: 3Saves: 2 • Shares: 1

NucleoMap: A computational tool for identifying nucleosomes in ultra-high resolution contact maps

Yuanhao Huang, Bingjiang Wang, Jie Liu

Research Article | published 14 Jul 2022 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1010265

Views: 2086Citations: 1Saves: 13 • Shares: 5

Epigenetic cell memory: The gene’s inner chromatin modification circuit

Simone Bruno, Ruth J. Williams, Domitilla Del Vecchio

Research Article | published 06 Apr 2022 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1009961

Views: 4784Citations: 36Saves: 0 • Shares: 0

High fidelity epigenetic inheritance: Information theoretic model predicts threshold filling of histone modifications post replication

Nithya Ramakrishnan, Sibi Raj B. Pillai, Ranjith Padinhateeri

Research Article | published 17 Feb 2022 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1009861

Views: 2762Citations: 7Saves: 15 • Shares: 15

Slow nucleosome dynamics set the transcriptional speed limit and induce RNA polymerase II traffic jams and bursts

Robert C. Mines, Tomasz Lipniacki, Xiling Shen

Research Article | published 10 Feb 2022 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1009811

Views: 2264Citations: 9Saves: 10 • Shares: 4

The Impact of the HydroxyMethylCytosine epigenetic signature on DNA structure and function

Federica Battistini, Pablo D. Dans, Montserrat Terrazas, Chiara L. Castellazzi, Guillem Portella, Mireia Labrador, Núria Villegas, Isabelle Brun-Heath, Carlos González, Modesto Orozco

Research Article | published 08 Nov 2021 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1009547

Views: 2202Citations: 8Saves: 26 • Shares: 14

Computational identification and experimental characterization of preferred downstream positions in human core promoters

René Dreos, Anna Sloutskin, Nati Malachi, Diana Ideses, Philipp Bucher, Tamar Juven-Gershon

Research Article | published 12 Aug 2021 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1009256

Views: 2407Citations: 4Saves: 0 • Shares: 0

The kinetic landscape of nucleosome assembly: A coarse-grained molecular dynamics study

Giovanni B. Brandani, Cheng Tan, Shoji Takada

Research Article | published 27 Jul 2021 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1009253

Views: 2924Citations: 25Saves: 35 • Shares: 9

Histone tails cooperate to control the breathing of genomic nucleosomes

Jan Huertas, Hans Robert Schöler, Vlad Cojocaru

Research Article | published 03 Jun 2021 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1009013

Views: 4149Citations: 26Saves: 48 • Shares: 18

Thermodynamic modeling of genome-wide nucleosome depleted regions in yeast

Hungyo Kharerin, Lu Bai

Research Article | published 11 Jan 2021 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1008560

Views: 2541Citations: 16Saves: 18 • Shares: 3

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