Marenduzzo D - Search Results

1

Predictive Polymer Models for 3D Chromosome Organization.

Chiang M, Forte G, Gilbert N, Marenduzzo D, Brackley CA. Chiang M, et al. Among authors: marenduzzo d. Methods Mol Biol. 2022;2301:267-291. doi: 10.1007/978-1-0716-1390-0_14. Methods Mol Biol. 2022. PMID: 34415541 Review.

2

Facilitated diffusion on mobile DNA: configurational traps and sequence heterogeneity.

Brackley CA, Cates ME, Marenduzzo D. Brackley CA, et al. Among authors: marenduzzo d. Phys Rev Lett. 2012 Oct 19;109(16):168103. doi: 10.1103/PhysRevLett.109.168103. Epub 2012 Oct 17. Phys Rev Lett. 2012. PMID: 23215135

3

Effect of DNA conformation on facilitated diffusion.

Brackley CA, Cates ME, Marenduzzo D. Brackley CA, et al. Among authors: marenduzzo d. Biochem Soc Trans. 2013 Apr;41(2):582-8. doi: 10.1042/BST20120234. Biochem Soc Trans. 2013. PMID: 23514158 Review.

4

Nonspecific bridging-induced attraction drives clustering of DNA-binding proteins and genome organization.

Brackley CA, Taylor S, Papantonis A, Cook PR, Marenduzzo D. Brackley CA, et al. Among authors: marenduzzo d. Proc Natl Acad Sci U S A. 2013 Sep 17;110(38):E3605-11. doi: 10.1073/pnas.1302950110. Epub 2013 Sep 3. Proc Natl Acad Sci U S A. 2013. PMID: 24003126 Free PMC article.

5

Models for twistable elastic polymers in Brownian dynamics, and their implementation for LAMMPS.

Brackley CA, Morozov AN, Marenduzzo D. Brackley CA, et al. Among authors: marenduzzo d. J Chem Phys. 2014 Apr 7;140(13):135103. doi: 10.1063/1.4870088. J Chem Phys. 2014. PMID: 24712817

6

Intracellular facilitated diffusion: searchers, crowders, and blockers.

Brackley CA, Cates ME, Marenduzzo D. Brackley CA, et al. Among authors: marenduzzo d. Phys Rev Lett. 2013 Sep 6;111(10):108101. doi: 10.1103/PhysRevLett.111.108101. Epub 2013 Sep 3. Phys Rev Lett. 2013. PMID: 25166711

7

Topological constraints strongly affect chromatin reconstitution in silico.

Brackley CA, Allan J, Keszenman-Pereyra D, Marenduzzo D. Brackley CA, et al. Among authors: marenduzzo d. Nucleic Acids Res. 2015 Jan;43(1):63-73. doi: 10.1093/nar/gku1085. Epub 2014 Nov 28. Nucleic Acids Res. 2015. PMID: 25432958 Free PMC article.

8

A simple model for DNA bridging proteins and bacterial or human genomes: bridging-induced attraction and genome compaction.

Johnson J, Brackley CA, Cook PR, Marenduzzo D. Johnson J, et al. Among authors: marenduzzo d. J Phys Condens Matter. 2015 Feb 18;27(6):064119. doi: 10.1088/0953-8984/27/6/064119. Epub 2015 Jan 7. J Phys Condens Matter. 2015. PMID: 25563801 Free article.

9

Predicting the three-dimensional folding of cis-regulatory regions in mammalian genomes using bioinformatic data and polymer models.

Brackley CA, Brown JM, Waithe D, Babbs C, Davies J, Hughes JR, Buckle VJ, Marenduzzo D. Brackley CA, et al. Among authors: marenduzzo d. Genome Biol. 2016 Mar 31;17:59. doi: 10.1186/s13059-016-0909-0. Genome Biol. 2016. PMID: 27036497 Free PMC article.

10

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. Brackley CA, et al. Among authors: marenduzzo d. Nucleic Acids Res. 2016 May 5;44(8):3503-12. doi: 10.1093/nar/gkw135. Epub 2016 Apr 8. Nucleic Acids Res. 2016. PMID: 27060145 Free PMC article.

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