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Histone modification  
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

Learning Micro-C from Hi-C with diffusion models

Tong Liu, Hao Zhu, Zheng Wang

Research Article | published 17 May 2024 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1012136

Views: 1381Citations: 0Saves: 1 • Shares: 2

Diffusion controls local versus dispersed inheritance of histones during replication and shapes epigenomic architecture

Archit Singh, Shaon Chakrabarti

Research Article | published 18 Dec 2023 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1011725

Views: 1055Citations: 4Saves: 8 • Shares: 16

Analyzing histone ChIP-seq data with a bin-based probability of being signal

Vivian Hecht, Kevin Dong, Sreshtaa Rajesh, Polina Shpilker, Siddarth Wekhande, Noam Shoresh

Research Article | published 20 Oct 2023 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1011568

Views: 1392Citations: 1Saves: 8 • Shares: 1

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

Differential contribution to gene expression prediction of histone modifications at enhancers or promoters

Mar González-Ramírez, Cecilia Ballaré, Francesca Mugianesi, Malte Beringer, Alexandra Santanach, Enrique Blanco, Luciano Di Croce

Research Article | published 02 Sep 2021 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1009368

Views: 4507Citations: 11Saves: 35 • Shares: 44

Sequence deeper without sequencing more: Bayesian resolution of ambiguously mapped reads

Rohan N. Shah, Alexander J. Ruthenburg

Research Article | published 19 Apr 2021 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1008926

Views: 4779Citations: 10Saves: 26 • Shares: 24

Epigenome-based splicing prediction using a recurrent neural network

Donghoon Lee, Jing Zhang, Jason Liu, Mark Gerstein

Research Article | published 25 Jun 2020 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1008006

Views: 4630Citations: 31Saves: 62 • Shares: 15

ORSO (Online Resource for Social Omics): A data-driven social network connecting scientists to genomics datasets

Christopher A. Lavender, Andrew J. Shapiro, Frank S. Day, David C. Fargo

Research Article | published 24 Jan 2020 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1007571

Views: 3460Citations: 2Saves: 31 • Shares: 8

Predicting gene expression in the human malaria parasite Plasmodium falciparum using histone modification, nucleosome positioning, and 3D localization features

David F. Read, Kate Cook, Yang Y. Lu, Karine G. Le Roch, William Stafford Noble

Research Article | published 11 Sep 2019 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1007329

Views: 6993Citations: 27Saves: 59 • Shares: 21

Predicting three-dimensional genome organization with chromatin states

Yifeng Qi, Bin Zhang

Research Article | published 10 Jun 2019 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1007024

Views: 10359Citations: 122Saves: 139 • Shares: 22

Spatial clustering and common regulatory elements correlate with coordinated gene expression

Jingyu Zhang, Hengyu Chen, Ruoyan Li, David A. Taft, Guang Yao, Fan Bai, Jianhua Xing

Research Article | published 01 Mar 2019 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1006786

Views: 4796Citations: 28Saves: 51 • Shares: 6

Exploring chromatin hierarchical organization via Markov State Modelling

Zhen Wah Tan, Enrico Guarnera, Igor N. Berezovsky

Research Article | published 31 Dec 2018 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1006686

Views: 5012Citations: 11Saves: 57 • Shares: 9

A likelihood approach to testing hypotheses on the co-evolution of epigenome and genome

Jia Lu, Xiaoyi Cao, Sheng Zhong

Research Article | published 26 Dec 2018 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1006673

Views: 3897Citations: 4Saves: 17 • Shares: 2

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