Dorier J - Search Results

1

Boolean regulatory network reconstruction using literature based knowledge with a genetic algorithm optimization method.

Dorier J, Crespo I, Niknejad A, Liechti R, Ebeling M, Xenarios I. Dorier J, et al. BMC Bioinformatics. 2016 Oct 6;17(1):410. doi: 10.1186/s12859-016-1287-z. BMC Bioinformatics. 2016. PMID: 27716031 Free PMC article.

2

SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools.

Chaouiya C, Bérenguier D, Keating SM, Naldi A, van Iersel MP, Rodriguez N, Dräger A, Büchel F, Cokelaer T, Kowal B, Wicks B, Gonçalves E, Dorier J, Page M, Monteiro PT, von Kamp A, Xenarios I, de Jong H, Hucka M, Klamt S, Thieffry D, Le Novère N, Saez-Rodriguez J, Helikar T. Chaouiya C, et al. Among authors: dorier j. BMC Syst Biol. 2013 Dec 10;7:135. doi: 10.1186/1752-0509-7-135. BMC Syst Biol. 2013. PMID: 24321545 Free PMC article.

3

Efficient computation of minimal perturbation sets in gene regulatory networks.

Garg A, Mohanram K, Di Cara A, Degueurce G, Ibberson M, Dorier J, Xenarios I. Garg A, et al. Among authors: dorier j. Front Physiol. 2013 Dec 17;4:361. doi: 10.3389/fphys.2013.00361. eCollection 2013. Front Physiol. 2013. PMID: 24391592 Free PMC article.

4

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.

5

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 PMC article. Review.

6

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

7

Models that include supercoiling of topological domains reproduce several known features of interphase chromosomes.

Benedetti F, Dorier J, Burnier Y, Stasiak A. Benedetti F, et al. Among authors: dorier j. Nucleic Acids Res. 2014 Mar;42(5):2848-55. doi: 10.1093/nar/gkt1353. Epub 2013 Dec 23. Nucleic Acids Res. 2014. PMID: 24366878 Free PMC article.

8

Studies of global and local entanglements of individual protein chains using the concept of knotoids.

Goundaroulis D, Dorier J, Benedetti F, Stasiak A. Goundaroulis D, et al. Among authors: dorier j. Sci Rep. 2017 Jul 24;7(1):6309. doi: 10.1038/s41598-017-06649-3. Sci Rep. 2017. PMID: 28740166 Free PMC article.

9

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.

10

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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