Benedetti F - Search Results

1

Chromatin Loop Extrusion and Chromatin Unknotting.

Racko D, Benedetti F, Goundaroulis D, Stasiak A. Racko D, et al. Among authors: benedetti f. Polymers (Basel). 2018 Oct 11;10(10):1126. doi: 10.3390/polym10101126. Polymers (Basel). 2018. PMID: 30961051 Free PMC article.

2

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. 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.

3

Effects of supercoiling on enhancer-promoter contacts.

Benedetti F, Dorier J, Stasiak A. Benedetti F, et al. 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.

4

Effects of physiological self-crowding of DNA on shape and biological properties of DNA molecules with various levels of supercoiling.

Benedetti F, Japaridze A, Dorier J, Racko D, Kwapich R, Burnier Y, Dietler G, Stasiak A. Benedetti F, et al. Nucleic Acids Res. 2015 Feb 27;43(4):2390-9. doi: 10.1093/nar/gkv055. Epub 2015 Feb 4. Nucleic Acids Res. 2015. PMID: 25653164 Free PMC article.

5

Generation of supercoils in nicked and gapped DNA drives DNA unknotting and postreplicative decatenation.

Racko D, Benedetti F, Dorier J, Burnier Y, Stasiak A. Racko D, et al. Among authors: benedetti f. Nucleic Acids Res. 2015 Sep 3;43(15):7229-36. doi: 10.1093/nar/gkv683. Epub 2015 Jul 6. Nucleic Acids Res. 2015. PMID: 26150424 Free PMC article.

6

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: benedetti f. Sci Rep. 2017 Jul 24;7(1):6309. doi: 10.1038/s41598-017-06649-3. Sci Rep. 2017. PMID: 28740166 Free PMC article.

7

Molecular Dynamics Simulation of Supercoiled, Knotted, and Catenated DNA Molecules, Including Modeling of Action of DNA Gyrase.

Racko D, Benedetti F, Dorier J, Burnier Y, Stasiak A. Racko D, et al. Among authors: benedetti f. Methods Mol Biol. 2017;1624:339-372. doi: 10.1007/978-1-4939-7098-8_24. Methods Mol Biol. 2017. PMID: 28842894

8

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. Nucleic Acids Res. 2017 Sep 29;45(17):9850-9859. doi: 10.1093/nar/gkx716. Nucleic Acids Res. 2017. PMID: 28973473 Free PMC article.

9

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: benedetti f. Nucleic Acids Res. 2018 Feb 28;46(4):1648-1660. doi: 10.1093/nar/gkx1123. Nucleic Acids Res. 2018. PMID: 29140466 Free PMC article.

10

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. Among authors: benedetti f. Bioinformatics. 2018 Oct 1;34(19):3402-3404. doi: 10.1093/bioinformatics/bty365. Bioinformatics. 2018. PMID: 29722808

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