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Items: 1 to 50 of 152

1.

capC-MAP: software for analysis of Capture-C data.

Buckle A, Gilbert N, Marenduzzo D, Brackley CA.

Bioinformatics. 2019 Jun 7. pii: btz480. doi: 10.1093/bioinformatics/btz480. [Epub ahead of print]

PMID:
31173058
2.

Statistical mechanics of a single active slider on a fluctuating interface.

Cagnetta F, Evans MR, Marenduzzo D.

Phys Rev E. 2019 Apr;99(4-1):042124. doi: 10.1103/PhysRevE.99.042124.

PMID:
31108715
3.

Transcriptional Bursts in a Nonequilibrium Model for Gene Regulation by Supercoiling.

Ancona M, Bentivoglio A, Brackley CA, Gonnella G, Marenduzzo D.

Biophys J. 2019 Apr 26. pii: S0006-3495(19)30342-X. doi: 10.1016/j.bpj.2019.04.023. [Epub ahead of print]

PMID:
31103229
4.

Synergy of topoisomerase and structural-maintenance-of-chromosomes proteins creates a universal pathway to simplify genome topology.

Orlandini E, Marenduzzo D, Michieletto D.

Proc Natl Acad Sci U S A. 2019 Apr 23;116(17):8149-8154. doi: 10.1073/pnas.1815394116. Epub 2019 Apr 8.

5.

Lamellar ordering, droplet formation and phase inversion in exotic active emulsions.

Bonelli F, Carenza LN, Gonnella G, Marenduzzo D, Orlandini E, Tiribocchi A.

Sci Rep. 2019 Feb 26;9(1):2801. doi: 10.1038/s41598-019-39190-6.

6.

Physical principles of retroviral integration in the human genome.

Michieletto D, Lusic M, Marenduzzo D, Orlandini E.

Nat Commun. 2019 Feb 4;10(1):575. doi: 10.1038/s41467-019-08333-8.

7.

Rheology and microrheology of deformable droplet suspensions.

Foglino M, Morozov AN, Marenduzzo D.

Soft Matter. 2018 Nov 28;14(46):9361-9367. doi: 10.1039/c8sm01669k.

PMID:
30431641
8.

Polymer Simulations of Heteromorphic Chromatin Predict the 3D Folding of Complex Genomic Loci.

Buckle A, Brackley CA, Boyle S, Marenduzzo D, Gilbert N.

Mol Cell. 2018 Nov 15;72(4):786-797.e11. doi: 10.1016/j.molcel.2018.09.016. Epub 2018 Oct 18.

9.

A growing bacterial colony in two dimensions as an active nematic.

Dell'Arciprete D, Blow ML, Brown AT, Farrell FDC, Lintuvuori JS, McVey AF, Marenduzzo D, Poon WCK.

Nat Commun. 2018 Oct 10;9(1):4190. doi: 10.1038/s41467-018-06370-3.

10.
11.

Mixtures of Blue Phase Liquid Crystal with Simple Liquids: Elastic Emulsions and Cubic Fluid Cylinders.

Lintuvuori JS, Stratford K, Cates ME, Marenduzzo D.

Phys Rev Lett. 2018 Jul 20;121(3):037802. doi: 10.1103/PhysRevLett.121.037802.

PMID:
30085823
12.

Active Growth and Pattern Formation in Membrane-Protein Systems.

Cagnetta F, Evans MR, Marenduzzo D.

Phys Rev Lett. 2018 Jun 22;120(25):258001. doi: 10.1103/PhysRevLett.120.258001.

PMID:
29979071
13.

HMGB2 Loss upon Senescence Entry Disrupts Genomic Organization and Induces CTCF Clustering across Cell Types.

Zirkel A, Nikolic M, Sofiadis K, Mallm JP, Brackley CA, Gothe H, Drechsel O, Becker C, Altmüller J, Josipovic N, Georgomanolis T, Brant L, Franzen J, Koker M, Gusmao EG, Costa IG, Ullrich RT, Wagner W, Roukos V, Nürnberg P, Marenduzzo D, Rippe K, Papantonis A.

Mol Cell. 2018 May 17;70(4):730-744.e6. doi: 10.1016/j.molcel.2018.03.030. Epub 2018 Apr 26.

14.

Non-equilibrium phase transition in a model for supercoiling-dependent DNA transcription.

Bentivoglio A, Ancona M, Brackley CA, Gonnella G, Marenduzzo D.

Soft Matter. 2018 May 9;14(18):3632-3639. doi: 10.1039/c7sm02452e.

PMID:
29691522
15.

Kinetic theory of pattern formation in mixtures of microtubules and molecular motors.

Maryshev I, Marenduzzo D, Goryachev AB, Morozov A.

Phys Rev E. 2018 Feb;97(2-1):022412. doi: 10.1103/PhysRevE.97.022412.

PMID:
29548141
16.

Nonequilibrium Chromosome Looping via Molecular Slip Links.

Brackley CA, Johnson J, Michieletto D, Morozov AN, Nicodemi M, Cook PR, Marenduzzo D.

Phys Rev Lett. 2017 Sep 29;119(13):138101. doi: 10.1103/PhysRevLett.119.138101. Epub 2017 Sep 26.

PMID:
29341686
17.

Extrusion without a motor: a new take on the loop extrusion model of genome organization.

Brackley CA, Johnson J, Michieletto D, Morozov AN, Nicodemi M, Cook PR, Marenduzzo D.

Nucleus. 2018 Jan 1;9(1):95-103. doi: 10.1080/19491034.2017.1421825.

18.

Flow of Deformable Droplets: Discontinuous Shear Thinning and Velocity Oscillations.

Foglino M, Morozov AN, Henrich O, Marenduzzo D.

Phys Rev Lett. 2017 Nov 17;119(20):208002. doi: 10.1103/PhysRevLett.119.208002. Epub 2017 Nov 15.

19.

Shaping epigenetic memory via genomic bookmarking.

Michieletto D, Chiang M, Colì D, Papantonis A, Orlandini E, Cook PR, Marenduzzo D.

Nucleic Acids Res. 2018 Jan 9;46(1):83-93. doi: 10.1093/nar/gkx1200.

20.

Epigenetic Transitions and Knotted Solitons in Stretched Chromatin.

Michieletto D, Orlandini E, Marenduzzo D.

Sci Rep. 2017 Nov 7;7(1):14642. doi: 10.1038/s41598-017-13916-w.

21.

Dynamical Scaling and Phase Coexistence in Topologically Constrained DNA Melting.

Fosado YAG, Michieletto D, Marenduzzo D.

Phys Rev Lett. 2017 Sep 15;119(11):118002. doi: 10.1103/PhysRevLett.119.118002. Epub 2017 Sep 12.

PMID:
28949232
22.

Switching dynamics in cholesteric liquid crystal emulsions.

Fadda F, Gonnella G, Marenduzzo D, Orlandini E, Tiribocchi A.

J Chem Phys. 2017 Aug 14;147(6):064903. doi: 10.1063/1.4997637.

PMID:
28810771
23.

Motility of active nematic films driven by "active anchoring".

Blow ML, Aqil M, Liebchen B, Marenduzzo D.

Soft Matter. 2017 Sep 20;13(36):6137-6144. doi: 10.1039/c7sm00325k.

PMID:
28791336
24.

Ring Polymers: Threadings, Knot Electrophoresis and Topological Glasses.

Michieletto D, Marenduzzo D, Orlandini E, Turner MS.

Polymers (Basel). 2017 Aug 8;9(8). pii: E349. doi: 10.3390/polym9080349. Review.

25.

Anchoring-driven spontaneous rotations in active gel droplets.

Fialho AR, Blow ML, Marenduzzo D.

Soft Matter. 2017 Sep 13;13(35):5933-5941. doi: 10.1039/c7sm01019b.

PMID:
28770268
26.

Entropic elasticity and dynamics of the bacterial chromosome: A simulation study.

Pereira MCF, Brackley CA, Lintuvuori JS, Marenduzzo D, Orlandini E.

J Chem Phys. 2017 Jul 28;147(4):044908. doi: 10.1063/1.4995992.

PMID:
28764377
27.

Role of Correlations in the Collective Behavior of Microswimmer Suspensions.

Stenhammar J, Nardini C, Nash RW, Marenduzzo D, Morozov A.

Phys Rev Lett. 2017 Jul 14;119(2):028005. doi: 10.1103/PhysRevLett.119.028005. Epub 2017 Jul 13.

PMID:
28753351
28.

Colloidal Spherocylinders at an Interface: Flipper Dynamics and Bilayer Formation.

Li T, Brandani G, Marenduzzo D, Clegg PS.

Phys Rev Lett. 2017 Jul 7;119(1):018001. doi: 10.1103/PhysRevLett.119.018001. Epub 2017 Jul 6.

PMID:
28731771
29.

Phoretic Interactions Generically Induce Dynamic Clusters and Wave Patterns in Active Colloids.

Liebchen B, Marenduzzo D, Cates ME.

Phys Rev Lett. 2017 Jun 30;118(26):268001. doi: 10.1103/PhysRevLett.118.268001. Epub 2017 Jun 28.

PMID:
28707925
30.

Hydrodynamic instabilities in active cholesteric liquid crystals.

Whitfield CA, Adhyapak TC, Tiribocchi A, Alexander GP, Marenduzzo D, Ramaswamy S.

Eur Phys J E Soft Matter. 2017 Apr;40(4):50. doi: 10.1140/epje/i2017-11536-2. Epub 2017 Apr 24.

PMID:
28429181
31.

Contractile and chiral activities codetermine the helicity of swimming droplet trajectories.

Tjhung E, Cates ME, Marenduzzo D.

Proc Natl Acad Sci U S A. 2017 May 2;114(18):4631-4636. doi: 10.1073/pnas.1619960114. Epub 2017 Apr 17.

32.

Ephemeral Protein Binding to DNA Shapes Stable Nuclear Bodies and Chromatin Domains.

Brackley CA, Liebchen B, Michieletto D, Mouvet F, Cook PR, Marenduzzo D.

Biophys J. 2017 Mar 28;112(6):1085-1093. doi: 10.1016/j.bpj.2017.01.025.

33.

Genome organization: experiments and modeling.

Gilbert N, Marenduzzo D.

Chromosome Res. 2017 Mar;25(1):1-4. doi: 10.1007/s10577-017-9551-2. Epub 2017 Feb 2. No abstract available.

34.

Pattern Formation in Polymerizing Actin Flocks: Spirals, Spots, and Waves without Nonlinear Chemistry.

Le Goff T, Liebchen B, Marenduzzo D.

Phys Rev Lett. 2016 Dec 2;117(23):238002. Epub 2016 Nov 30.

PMID:
27982656
35.

Exploiting native forces to capture chromosome conformation in mammalian cell nuclei.

Brant L, Georgomanolis T, Nikolic M, Brackley CA, Kolovos P, van Ijcken W, Grosveld FG, Marenduzzo D, Papantonis A.

Mol Syst Biol. 2016 Dec 9;12(12):891. doi: 10.15252/msb.20167311.

36.

A single nucleotide resolution model for large-scale simulations of double stranded DNA.

Fosado YA, Michieletto D, Allan J, Brackley CA, Henrich O, Marenduzzo D.

Soft Matter. 2016 Nov 28;12(47):9458-9470.

37.

Simulating topological domains in human chromosomes with a fitting-free model.

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

Nucleus. 2016 Sep 2;7(5):453-461.

38.

Microfluidic flow of cholesteric liquid crystals.

Wiese O, Marenduzzo D, Henrich O.

Soft Matter. 2016 Nov 16;12(45):9223-9237.

39.

Hydrodynamic oscillations and variable swimming speed in squirmers close to repulsive walls.

Lintuvuori JS, Brown AT, Stratford K, Marenduzzo D.

Soft Matter. 2016 Sep 28;12(38):7959-7968.

PMID:
27714374
40.

Shear dynamics of an inverted nematic emulsion.

Tiribocchi A, Da Re M, Marenduzzo D, Orlandini E.

Soft Matter. 2016 Oct 4;12(39):8195-8213.

PMID:
27714315
41.

Pattern formation in chemically interacting active rotors with self-propulsion.

Liebchen B, Cates ME, Marenduzzo D.

Soft Matter. 2016 Sep 21;12(35):7259-64. doi: 10.1039/c6sm01162d. Epub 2016 Aug 15.

PMID:
27526180
42.

Stochastic Model of Supercoiling-Dependent Transcription.

Brackley CA, Johnson J, Bentivoglio A, Corless S, Gilbert N, Gonnella G, Marenduzzo D.

Phys Rev Lett. 2016 Jul 1;117(1):018101. doi: 10.1103/PhysRevLett.117.018101. Epub 2016 Jun 27.

PMID:
27419594
43.

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.

44.

Correction: Curvature-driven positioning of Turing patterns in phase-separating curved membranes.

Vandin G, Marenduzzo D, Goryachev AB, Orlandini E.

Soft Matter. 2016 Apr 20;12(16):3828. doi: 10.1039/c6sm90059c.

PMID:
27052157
45.

Light-induced self-assembly of active rectification devices.

Stenhammar J, Wittkowski R, Marenduzzo D, Cates ME.

Sci Adv. 2016 Apr 1;2(4):e1501850. doi: 10.1126/sciadv.1501850. eCollection 2016 Apr.

46.

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.

Genome Biol. 2016 Mar 31;17:59. doi: 10.1186/s13059-016-0909-0.

47.

Curvature-driven positioning of Turing patterns in phase-separating curved membranes.

Vandin G, Marenduzzo D, Goryachev AB, Orlandini E.

Soft Matter. 2016 May 7;12(17):3888-96. doi: 10.1039/c6sm00340k. Epub 2016 Mar 24. Erratum in: Soft Matter. 2016 Apr 20;12(16):3828.

PMID:
27010222
48.

A one-dimensional statistical mechanics model for nucleosome positioning on genomic DNA.

Tesoro S, Ali I, Morozov AN, Sulaiman N, Marenduzzo D.

Phys Biol. 2016 Feb 12;13(1):016004. doi: 10.1088/1478-3975/13/1/016004.

PMID:
26871546
49.

Spontaneous flow in polar active fluids: the effect of a phenomenological self propulsion-like term.

Bonelli F, Gonnella G, Tiribocchi A, Marenduzzo D.

Eur Phys J E Soft Matter. 2016 Jan;39(1):1. doi: 10.1140/epje/i2016-16001-2. Epub 2016 Jan 14.

PMID:
26769011
50.

Clustering and Pattern Formation in Chemorepulsive Active Colloids.

Liebchen B, Marenduzzo D, Pagonabarraga I, Cates ME.

Phys Rev Lett. 2015 Dec 18;115(25):258301. doi: 10.1103/PhysRevLett.115.258301. Epub 2015 Dec 16.

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