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Items: 13

1.

Interphase human chromosome exhibits out of equilibrium glassy dynamics.

Shi G, Liu L, Hyeon C, Thirumalai D.

Nat Commun. 2018 Aug 8;9(1):3161. doi: 10.1038/s41467-018-05606-6.

2.

Chain organization of human interphase chromosome determines the spatiotemporal dynamics of chromatin loci.

Liu L, Shi G, Thirumalai D, Hyeon C.

PLoS Comput Biol. 2018 Dec 3;14(12):e1006617. doi: 10.1371/journal.pcbi.1006617. eCollection 2018 Dec.

3.

MrTADFinder: A network modularity based approach to identify topologically associating domains in multiple resolutions.

Yan KK, Lou S, Gerstein M.

PLoS Comput Biol. 2017 Jul 24;13(7):e1005647. doi: 10.1371/journal.pcbi.1005647. eCollection 2017 Jul.

4.

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

Brackley CA, Johnson J, Kelly S, Cook PR, Marenduzzo D.

Nucleic Acids Res. 2016 May 5;44(8):3503-12. doi: 10.1093/nar/gkw135. Epub 2016 Apr 8.

5.

InTAD: chromosome conformation guided analysis of enhancer target genes.

Okonechnikov K, Erkek S, Korbel JO, Pfister SM, Chavez L.

BMC Bioinformatics. 2019 Jan 31;20(1):60. doi: 10.1186/s12859-019-2655-2.

6.

Are TADs supercoiled?

Racko D, Benedetti F, Dorier J, Stasiak A.

Nucleic Acids Res. 2019 Jan 25;47(2):521-532. doi: 10.1093/nar/gky1091.

7.

Large Scale Chromosome Folding Is Stable against Local Changes in Chromatin Structure.

Florescu AM, Therizols P, Rosa A.

PLoS Comput Biol. 2016 Jun 13;12(6):e1004987. doi: 10.1371/journal.pcbi.1004987. eCollection 2016 Jun.

8.

Molecular Dynamics Simulation of a Feather-Boa Model of a Bacterial Chromosome.

Chaudhuri D, Mulder BM.

Methods Mol Biol. 2018;1837:403-415. doi: 10.1007/978-1-4939-8675-0_20.

PMID:
30109621
9.

Identifying topologically associating domains and subdomains by Gaussian Mixture model And Proportion test.

Yu W, He B, Tan K.

Nat Commun. 2017 Sep 14;8(1):535. doi: 10.1038/s41467-017-00478-8.

10.

Genomic 3D compartments emerge from unfolding mitotic chromosomes.

Kumar R, Lizana L, Stenberg P.

Chromosoma. 2019 Mar;128(1):15-20. doi: 10.1007/s00412-018-0684-7. Epub 2018 Oct 24.

11.

Quantifying the similarity of topological domains across normal and cancer human cell types.

Sauerwald N, Kingsford C.

Bioinformatics. 2018 Jul 1;34(13):i475-i483. doi: 10.1093/bioinformatics/bty265.

12.

BPscore: An Effective Metric for Meaningful Comparisons of Structural Chromosome Segmentations.

Zaborowski R, WilczyƄski B.

J Comput Biol. 2019 Apr;26(4):305-314. doi: 10.1089/cmb.2018.0162. Epub 2019 Feb 27.

PMID:
30810370
13.

Extensile motor activity drives coherent motions in a model of interphase chromatin.

Saintillan D, Shelley MJ, Zidovska A.

Proc Natl Acad Sci U S A. 2018 Nov 6;115(45):11442-11447. doi: 10.1073/pnas.1807073115. Epub 2018 Oct 22.

PMID:
30348795

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