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Are TADs supercoiled?

Racko D, Benedetti F, Dorier J, Stasiak A. Racko D, et al. Among authors: dorier j. Nucleic Acids Res. 2019 Jan 25;47(2):521-532. doi: 10.1093/nar/gky1091. Nucleic Acids Res. 2019. PMID: 30395328 Free PMC article. Review.

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Closing the DNA replication cycle: from simple circular molecules to supercoiled and knotted DNA catenanes.

Schvartzman JB, Hernández P, Krimer DB, Dorier J, Stasiak A. Schvartzman JB, et al. Among authors: dorier j. Nucleic Acids Res. 2019 Aug 22;47(14):7182-7198. doi: 10.1093/nar/gkz586. Nucleic Acids Res. 2019. PMID: 31276584 Free PMC article. Review.

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KnotProt 2.0: a database of proteins with knots and other entangled structures.

Dabrowski-Tumanski P, Rubach P, Goundaroulis D, Dorier J, Sulkowski P, Millett KC, Rawdon EJ, Stasiak A, Sulkowska JI. Dabrowski-Tumanski P, et al. Among authors: dorier j. Nucleic Acids Res. 2019 Jan 8;47(D1):D367-D375. doi: 10.1093/nar/gky1140. Nucleic Acids Res. 2019. PMID: 30508159 Free PMC article.

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SBML Level 3: an extensible format for the exchange and reuse of biological models.

Keating SM, Waltemath D, König M, Zhang F, Dräger A, Chaouiya C, Bergmann FT, Finney A, Gillespie CS, Helikar T, Hoops S, Malik-Sheriff RS, Moodie SL, Moraru II, Myers CJ, Naldi A, Olivier BG, Sahle S, Schaff JC, Smith LP, Swat MJ, Thieffry D, Watanabe L, Wilkinson DJ, Blinov ML, Begley K, Faeder JR, Gómez HF, Hamm TM, Inagaki Y, Liebermeister W, Lister AL, Lucio D, Mjolsness E, Proctor CJ, Raman K, Rodriguez N, Shaffer CA, Shapiro BE, Stelling J, Swainston N, Tanimura N, Wagner J, Meier-Schellersheim M, Sauro HM, Palsson B, Bolouri H, Kitano H, Funahashi A, Hermjakob H, Doyle JC, Hucka M; SBML Level 3 Community members. Keating SM, et al. Mol Syst Biol. 2020 Aug;16(8):e9110. doi: 10.15252/msb.20199110. Mol Syst Biol. 2020. PMID: 32845085 Free article. Review.

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Effects of supercoiling on enhancer-promoter contacts.

Benedetti F, Dorier J, Stasiak A. Benedetti F, et al. Among authors: dorier j. Nucleic Acids Res. 2014;42(16):10425-32. doi: 10.1093/nar/gku759. Epub 2014 Aug 14. Nucleic Acids Res. 2014. PMID: 25123662 Free PMC article.

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Expert curation for building network-based dynamical models: a case study on atherosclerotic plaque formation.

Bekkar A, Estreicher A, Niknejad A, Casals-Casas C, Bridge A, Xenarios I, Dorier J, Crespo I. Bekkar A, et al. Among authors: dorier j. Database (Oxford). 2018 Jan 1;2018:bay031. doi: 10.1093/database/bay031. Database (Oxford). 2018. PMID: 29688381 Free PMC article.

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Knoto-ID: a tool to study the entanglement of open protein chains using the concept of knotoids.

Dorier J, Goundaroulis D, Benedetti F, Stasiak A. Dorier J, et al. Bioinformatics. 2018 Oct 1;34(19):3402-3404. doi: 10.1093/bioinformatics/bty365. Bioinformatics. 2018. PMID: 29722808

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Transcription-induced supercoiling as the driving force of chromatin loop extrusion during formation of TADs in interphase chromosomes.

Racko D, Benedetti F, Dorier J, Stasiak A. Racko D, et al. Among authors: dorier j. Nucleic Acids Res. 2018 Feb 28;46(4):1648-1660. doi: 10.1093/nar/gkx1123. Nucleic Acids Res. 2018. PMID: 29140466 Free PMC article.

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Transcription-induced supercoiling explains formation of self-interacting chromatin domains in S. pombe.

Benedetti F, Racko D, Dorier J, Burnier Y, Stasiak A. Benedetti F, et al. Among authors: dorier j. Nucleic Acids Res. 2017 Sep 29;45(17):9850-9859. doi: 10.1093/nar/gkx716. Nucleic Acids Res. 2017. PMID: 28973473 Free PMC article.

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Topological origins of chromosomal territories.

Dorier J, Stasiak A. Dorier J, et al. Nucleic Acids Res. 2009 Oct;37(19):6316-22. doi: 10.1093/nar/gkp702. Epub 2009 Sep 2. Nucleic Acids Res. 2009. PMID: 19726582 Free PMC article.

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