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Items: 1 to 50 of 71

1.

Models of polymer physics for the architecture of the cell nucleus.

Esposito A, Annunziatella C, Bianco S, Chiariello AM, Fiorillo L, Nicodemi M.

Wiley Interdiscip Rev Syst Biol Med. 2018 Dec 19:e1444. doi: 10.1002/wsbm.1444. [Epub ahead of print] Review.

PMID:
30566285
2.

Single-allele chromatin interactions identify regulatory hubs in dynamic compartmentalized domains.

Oudelaar AM, Davies JOJ, Hanssen LLP, Telenius JM, Schwessinger R, Liu Y, Brown JM, Downes DJ, Chiariello AM, Bianco S, Nicodemi M, Buckle VJ, Dekker J, Higgs DR, Hughes JR.

Nat Genet. 2018 Dec;50(12):1744-1751. doi: 10.1038/s41588-018-0253-2. Epub 2018 Oct 29.

PMID:
30374068
3.

Dynamic 3D chromatin architecture contributes to enhancer specificity and limb morphogenesis.

Kragesteen BK, Spielmann M, Paliou C, Heinrich V, Schöpflin R, Esposito A, Annunziatella C, Bianco S, Chiariello AM, Jerković I, Harabula I, Guckelberger P, Pechstein M, Wittler L, Chan WL, Franke M, Lupiáñez DG, Kraft K, Timmermann B, Vingron M, Visel A, Nicodemi M, Mundlos S, Andrey G.

Nat Genet. 2018 Oct;50(10):1463-1473. doi: 10.1038/s41588-018-0221-x. Epub 2018 Sep 27.

PMID:
30262816
4.

Challenges and guidelines toward 4D nucleome data and model standards.

Marti-Renom MA, Almouzni G, Bickmore WA, Bystricky K, Cavalli G, Fraser P, Gasser SM, Giorgetti L, Heard E, Nicodemi M, Nollmann M, Orozco M, Pombo A, Torres-Padilla ME.

Nat Genet. 2018 Oct;50(10):1352-1358. doi: 10.1038/s41588-018-0236-3. Epub 2018 Sep 27. Review.

PMID:
30262815
5.

Polymer physics predicts the effects of structural variants on chromatin architecture.

Bianco S, Lupiáñez DG, Chiariello AM, Annunziatella C, Kraft K, Schöpflin R, Wittler L, Andrey G, Vingron M, Pombo A, Mundlos S, Nicodemi M.

Nat Genet. 2018 May;50(5):662-667. doi: 10.1038/s41588-018-0098-8. Epub 2018 Apr 16.

PMID:
29662163
6.

Molecular Dynamics simulations of the Strings and Binders Switch model of chromatin.

Annunziatella C, Chiariello AM, Esposito A, Bianco S, Fiorillo L, Nicodemi M.

Methods. 2018 Jun 1;142:81-88. doi: 10.1016/j.ymeth.2018.02.024. Epub 2018 Mar 6. Review.

PMID:
29522804
7.

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
8.

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.

9.

Structure of the human chromosome interaction network.

Sarnataro S, Chiariello AM, Esposito A, Prisco A, Nicodemi M.

PLoS One. 2017 Nov 15;12(11):e0188201. doi: 10.1371/journal.pone.0188201. eCollection 2017.

10.

A Polymer Physics Investigation of the Architecture of the Murine Orthologue of the 7q11.23 Human Locus.

Chiariello AM, Esposito A, Annunziatella C, Bianco S, Fiorillo L, Prisco A, Nicodemi M.

Front Neurosci. 2017 Oct 10;11:559. doi: 10.3389/fnins.2017.00559. eCollection 2017. Review.

11.

RNA polymerase II primes Polycomb-repressed developmental genes throughout terminal neuronal differentiation.

Ferrai C, Torlai Triglia E, Risner-Janiczek JR, Rito T, Rackham OJ, de Santiago I, Kukalev A, Nicodemi M, Akalin A, Li M, Ungless MA, Pombo A.

Mol Syst Biol. 2017 Oct 16;13(10):946. doi: 10.15252/msb.20177754.

12.

Active and poised promoter states drive folding of the extended HoxB locus in mouse embryonic stem cells.

Barbieri M, Xie SQ, Torlai Triglia E, Chiariello AM, Bianco S, de Santiago I, Branco MR, Rueda D, Nicodemi M, Pombo A.

Nat Struct Mol Biol. 2017 Jun;24(6):515-524. doi: 10.1038/nsmb.3402. Epub 2017 Apr 24.

PMID:
28436944
13.

Complex multi-enhancer contacts captured by genome architecture mapping.

Beagrie RA, Scialdone A, Schueler M, Kraemer DC, Chotalia M, Xie SQ, Barbieri M, de Santiago I, Lavitas LM, Branco MR, Fraser J, Dostie J, Game L, Dillon N, Edwards PA, Nicodemi M, Pombo A.

Nature. 2017 Mar 23;543(7646):519-524. doi: 10.1038/nature21411. Epub 2017 Mar 8.

14.

Predicting chromatin architecture from models of polymer physics.

Bianco S, Chiariello AM, Annunziatella C, Esposito A, Nicodemi M.

Chromosome Res. 2017 Mar;25(1):25-34. doi: 10.1007/s10577-016-9545-5. Epub 2017 Jan 9. Review.

PMID:
28070687
15.

Polymer models of the hierarchical folding of the Hox-B chromosomal locus.

Annunziatella C, Chiariello AM, Bianco S, Nicodemi M.

Phys Rev E. 2016 Oct;94(4-1):042402. Epub 2016 Oct 4.

PMID:
27841585
16.

Polymer Physics of the Large-Scale Structure of Chromatin.

Bianco S, Chiariello AM, Annunziatella C, Esposito A, Nicodemi M.

Methods Mol Biol. 2016;1480:201-6. doi: 10.1007/978-1-4939-6380-5_17.

PMID:
27659986
17.

Polymer physics of chromosome large-scale 3D organisation.

Chiariello AM, Annunziatella C, Bianco S, Esposito A, Nicodemi M.

Sci Rep. 2016 Jul 13;6:29775. doi: 10.1038/srep29775.

18.

Erratum to: Single cell analysis of CD4+ T cell differentiation reveals three major cell states and progressive acceleration of proliferation.

Proserpio V, Piccolo A, Haim-Vilmovsky L, Kar G, Lönnberg T, Svensson V, Pramanik J, Natarajan KN, Zhai W, Zhang X, Donati G, Kayikci M, Kotar J, McKenzie AN, Montandon R, James KR, Fernandez-Ruiz D, Heath WR, Haque A, Billker O, Woodhouse S, Cicuta P, Nicodemi M, Teichmann SA.

Genome Biol. 2016 Jun 22;17(1):133. No abstract available.

19.

Single-cell analysis of CD4+ T-cell differentiation reveals three major cell states and progressive acceleration of proliferation.

Proserpio V, Piccolo A, Haim-Vilmovsky L, Kar G, Lönnberg T, Svensson V, Pramanik J, Natarajan KN, Zhai W, Zhang X, Donati G, Kayikci M, Kotar J, McKenzie AN, Montandon R, Billker O, Woodhouse S, Cicuta P, Nicodemi M, Teichmann SA.

Genome Biol. 2016 May 12;17:103. doi: 10.1186/s13059-016-0957-5. Erratum in: Genome Biol. 2016;17(1):133.

20.

Hierarchical folding and reorganization of chromosomes are linked to transcriptional changes in cellular differentiation.

Fraser J, Ferrai C, Chiariello AM, Schueler M, Rito T, Laudanno G, Barbieri M, Moore BL, Kraemer DC, Aitken S, Xie SQ, Morris KJ, Itoh M, Kawaji H, Jaeger I, Hayashizaki Y, Carninci P, Forrest AR; FANTOM Consortium, Semple CA, Dostie J, Pombo A, Nicodemi M.

Mol Syst Biol. 2015 Dec 23;11(12):852. doi: 10.15252/msb.20156492.

21.

Physical mechanisms behind the large scale features of chromatin organization.

Pombo A, Nicodemi M.

Transcription. 2014;5(2):e28447. doi: 10.4161/trns.28447. Review.

22.

Dynamic membrane patterning, signal localization and polarity in living cells.

Zamparo M, Chianale F, Tebaldi C, Cosentino-Lagomarsino M, Nicodemi M, Gamba A.

Soft Matter. 2015 Feb 7;11(5):838-49. doi: 10.1039/c4sm02157f. Epub 2015 Jan 7. Review.

PMID:
25563791
23.

Models of chromosome structure.

Nicodemi M, Pombo A.

Curr Opin Cell Biol. 2014 Jun;28:90-5. doi: 10.1016/j.ceb.2014.04.004. Epub 2014 May 4. Review.

PMID:
24804566
24.

Single-cell states in the estrogen response of breast cancer cell lines.

Casale FP, Giurato G, Nassa G, Armond JW, Oates CJ, Corá D, Gamba A, Mukherjee S, Weisz A, Nicodemi M.

PLoS One. 2014 Feb 25;9(2):e88485. doi: 10.1371/journal.pone.0088485. eCollection 2014.

25.

A stochastic model dissects cell states in biological transition processes.

Armond JW, Saha K, Rana AA, Oates CJ, Jaenisch R, Nicodemi M, Mukherjee S.

Sci Rep. 2014 Jan 17;4:3692. doi: 10.1038/srep03692.

26.

A polymer model explains the complexity of large-scale chromatin folding.

Barbieri M, Fraser J, Lavitas LM, Chotalia M, Dostie J, Pombo A, Nicodemi M.

Nucleus. 2013 Jul-Aug;4(4):267-73. doi: 10.4161/nucl.25432. Epub 2013 Jun 19.

27.

Polymer models of chromatin organization.

Barbieri M, Scialdone A, Piccolo A, Chiariello AM, di Lanno C, Prisco A, Pombo A, Nicodemi M.

Front Genet. 2013 Jun 20;4:113. doi: 10.3389/fgene.2013.00113. eCollection 2013. No abstract available.

28.

A model of the large-scale organization of chromatin.

Barbieri M, Chotalia M, Fraser J, Lavitas LM, Dostie J, Pombo A, Nicodemi M.

Biochem Soc Trans. 2013 Apr;41(2):508-12. doi: 10.1042/BST20120238. Review.

PMID:
23514144
29.

Colocalization of multiple DNA loci: a physical mechanism.

Bianco V, Scialdone A, Nicodemi M.

Biophys J. 2012 Nov 21;103(10):2223-32. doi: 10.1016/j.bpj.2012.08.056. Epub 2012 Nov 20.

30.

Complexity of chromatin folding is captured by the strings and binders switch model.

Barbieri M, Chotalia M, Fraser J, Lavitas LM, Dostie J, Pombo A, Nicodemi M.

Proc Natl Acad Sci U S A. 2012 Oct 2;109(40):16173-8. doi: 10.1073/pnas.1204799109. Epub 2012 Sep 17.

31.

Critical behavior and axis defining symmetry breaking in Hydra embryonic development.

Gamba A, Nicodemi M, Soriano J, Ott A.

Phys Rev Lett. 2012 Apr 13;108(15):158103. Epub 2012 Apr 10.

PMID:
22587289
32.

Jamming phase diagram for frictional particles.

Ciamarra MP, Pastore R, Nicodemi M, Coniglio A.

Phys Rev E Stat Nonlin Soft Matter Phys. 2011 Oct;84(4 Pt 1):041308. Epub 2011 Oct 28.

PMID:
22181136
33.

Conformation regulation of the X chromosome inactivation center: a model.

Scialdone A, Cataudella I, Barbieri M, Prisco A, Nicodemi M.

PLoS Comput Biol. 2011 Oct;7(10):e1002229. doi: 10.1371/journal.pcbi.1002229. Epub 2011 Oct 27.

34.

Stochastic transitions and jamming in granular pipe flow.

Brand S, Ball RC, Nicodemi M.

Phys Rev E Stat Nonlin Soft Matter Phys. 2011 Mar;83(3 Pt 1):031309. Epub 2011 Mar 30.

PMID:
21517496
35.

Diffusion-based DNA target colocalization by thermodynamic mechanisms.

Scialdone A, Nicodemi M.

Development. 2010 Nov;137(22):3877-85. doi: 10.1242/dev.053322.

36.

A novel approach to simulate gene-environment interactions in complex diseases.

Amato R, Pinelli M, D'Andrea D, Miele G, Nicodemi M, Raiconi G, Cocozza S.

BMC Bioinformatics. 2010 Jan 5;11:8. doi: 10.1186/1471-2105-11-8.

37.

Aggregation of fibrils and plaques in amyloid molecular systems.

Nicodemi M, de Candia A, Coniglio A.

Phys Rev E Stat Nonlin Soft Matter Phys. 2009 Oct;80(4 Pt 1):041914. Epub 2009 Oct 12.

PMID:
19905349
38.

Symmetry breaking mechanism for epithelial cell polarization.

Veglio A, Gamba A, Nicodemi M, Bussolino F, Serini G.

Phys Rev E Stat Nonlin Soft Matter Phys. 2009 Sep;80(3 Pt 1):031919. Epub 2009 Sep 29.

PMID:
19905158
39.

DNA loci cross-talk through thermodynamics.

Scialdone A, Nicodemi M.

J Biomed Biotechnol. 2009;2009:516723. doi: 10.1155/2009/516723. Epub 2009 Sep 16.

40.

Thermodynamic pathways to genome spatial organization in the cell nucleus.

Nicodemi M, Prisco A.

Biophys J. 2009 Mar 18;96(6):2168-77. doi: 10.1016/j.bpj.2008.12.3919.

41.

Mechanics and dynamics of X-chromosome pairing at X inactivation.

Scialdone A, Nicodemi M.

PLoS Comput Biol. 2008 Dec;4(12):e1000244. doi: 10.1371/journal.pcbi.1000244. Epub 2008 Dec 26.

42.

The colocalization transition of homologous chromosomes at meiosis.

Nicodemi M, Panning B, Prisco A.

Phys Rev E Stat Nonlin Soft Matter Phys. 2008 Jun;77(6 Pt 1):061913. Epub 2008 Jun 17.

PMID:
18643306
43.

A thermodynamic switch for chromosome colocalization.

Nicodemi M, Panning B, Prisco A.

Genetics. 2008 May;179(1):717-21. doi: 10.1534/genetics.107.083154.

44.

Flow, ordering, and jamming of sheared granular suspensions.

Grebenkov DS, Ciamarra MP, Nicodemi M, Coniglio A.

Phys Rev Lett. 2008 Feb 22;100(7):078001. Epub 2008 Feb 19.

PMID:
18352596
45.

Shear- and vibration-induced order-disorder transitions in granular media.

Pica Ciamarra M, Coniglio A, De Martino D, Nicodemi M.

Eur Phys J E Soft Matter. 2007 Dec;24(4):411-5. doi: 10.1140/epje/i2007-10256-6. Epub 2008 Jan 17.

PMID:
18202820
46.

Self-assembly and DNA binding of the blocking factor in x chromosome inactivation.

Nicodemi M, Prisco A.

PLoS Comput Biol. 2007 Nov;3(11):e210. Epub 2007 Sep 18.

47.

Granular dynamics, jamming, rheology and instabilities.

Richard P, Nicodemi M.

Eur Phys J E Soft Matter. 2007 Mar;22(3):193. No abstract available.

PMID:
17426937
48.

Symmetry-breaking model for X-chromosome inactivation.

Nicodemi M, Prisco A.

Phys Rev Lett. 2007 Mar 9;98(10):108104. Epub 2007 Mar 7.

PMID:
17358571
49.

Granular packs under vertical tapping: structure evolution, grain motion, and dynamical heterogeneities.

Pica Ciamarra M, Nicodemi M, Coniglio A.

Phys Rev E Stat Nonlin Soft Matter Phys. 2007 Feb;75(2 Pt 1):021303. Epub 2007 Feb 23.

PMID:
17358333
50.

Phenomenology and theory of horizontally oscillated granular mixtures.

Pica Ciamarra M, Coniglio A, Nicodemi M.

Eur Phys J E Soft Matter. 2007 Mar;22(3):227-34. Epub 2007 Feb 21.

PMID:
17318290

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