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For: Fiorillo L, Bianco S, Esposito A, Conte M, Sciarretta R, Musella F, Chiariello AM. A modern challenge of polymer physics: Novel ways to study, interpret, and reconstruct chromatin structure. WIREs Comput Mol Sci 2019. [DOI: 10.1002/wcms.1454] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Number Cited by Other Article(s)
1
Meng L, Sheong FK, Luo Q. Linking DNA-packing density distribution and TAD boundary locations. Proc Natl Acad Sci U S A 2025;122:e2418456122. [PMID: 39999165 PMCID: PMC11892626 DOI: 10.1073/pnas.2418456122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2024] [Accepted: 01/21/2025] [Indexed: 02/27/2025]  Open
2
Fontana A, Tafuri F, Abraham A, Bianco S, Esposito A, Conte M, Vercellone F, Pierno FD, Guha S, Carluccio CD, Chiariello AM. Polymer models of chromatin organization in virally infected cells. Biochem Soc Trans 2025;53:BST20240598. [PMID: 39927819 DOI: 10.1042/bst20240598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2025] [Revised: 01/16/2025] [Accepted: 01/21/2025] [Indexed: 02/11/2025]
3
Conte M, Abraham A, Esposito A, Yang L, Gibcus JH, Parsi KM, Vercellone F, Fontana A, Di Pierno F, Dekker J, Nicodemi M. Polymer Physics Models Reveal Structural Folding Features of Single-Molecule Gene Chromatin Conformations. Int J Mol Sci 2024;25:10215. [PMID: 39337699 PMCID: PMC11432541 DOI: 10.3390/ijms251810215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2024] [Revised: 09/17/2024] [Accepted: 09/22/2024] [Indexed: 09/30/2024]  Open
4
Conte M, Abraham A, Esposito A, Yang L, Gibcus JH, Parsi KM, Vercellone F, Fontana A, Pierno FD, Dekker J, Nicodemi M. Polymer physics models reveal structural folding features of single-molecule gene chromatin conformations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.16.603769. [PMID: 39071404 PMCID: PMC11275793 DOI: 10.1101/2024.07.16.603769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
5
Wei J, Xue Y, Liu Y, Tian H, Shao Y, Gao YQ. Steric repulsion introduced by loop constraints modulates the microphase separation of chromatins. J Chem Phys 2024;160:054904. [PMID: 38341710 DOI: 10.1063/5.0189692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 01/15/2024] [Indexed: 02/13/2024]  Open
6
Unveiling the Machinery behind Chromosome Folding by Polymer Physics Modeling. Int J Mol Sci 2023;24:ijms24043660. [PMID: 36835064 PMCID: PMC9967178 DOI: 10.3390/ijms24043660] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 02/06/2023] [Accepted: 02/09/2023] [Indexed: 02/16/2023]  Open
7
Gong H, Li M, Ji M, Zhang X, Yuan Z, Zhang S, Yang Y, Li C, Chen Y. MINE is a method for detecting spatial density of regulatory chromatin interactions based on a multi-modal network. CELL REPORTS METHODS 2023;3:100386. [PMID: 36814847 PMCID: PMC9939382 DOI: 10.1016/j.crmeth.2022.100386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 09/15/2022] [Accepted: 12/16/2022] [Indexed: 06/18/2023]
8
Madsen-Østerbye J, Bellanger A, Galigniana NM, Collas P. Biology and Model Predictions of the Dynamics and Heterogeneity of Chromatin-Nuclear Lamina Interactions. Front Cell Dev Biol 2022;10:913458. [PMID: 35693945 PMCID: PMC9178083 DOI: 10.3389/fcell.2022.913458] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 05/12/2022] [Indexed: 11/13/2022]  Open
9
Esposito A, Abraham A, Conte M, Vercellone F, Prisco A, Bianco S, Chiariello AM. The Physics of DNA Folding: Polymer Models and Phase-Separation. Polymers (Basel) 2022;14:1918. [PMID: 35567087 PMCID: PMC9104579 DOI: 10.3390/polym14091918] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 04/23/2022] [Accepted: 04/27/2022] [Indexed: 02/04/2023]  Open
10
Laghmach R, Di Pierro M, Potoyan D. A Liquid State Perspective on Dynamics of Chromatin Compartments. Front Mol Biosci 2022;8:781981. [PMID: 35096966 PMCID: PMC8793688 DOI: 10.3389/fmolb.2021.781981] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 12/22/2021] [Indexed: 12/11/2022]  Open
11
Esposito A, Bianco S, Fiorillo L, Conte M, Abraham A, Musella F, Nicodemi M, Prisco A, Chiariello AM. Polymer models are a versatile tool to study chromatin 3D organization. Biochem Soc Trans 2021;49:1675-1684. [PMID: 34282837 DOI: 10.1042/bst20201004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 06/21/2021] [Accepted: 06/25/2021] [Indexed: 11/17/2022]
12
Wei J, Tian H, Zhou R, Shao Y, Song F, Gao YQ. Topological Constraints with Optimal Length Promote the Formation of Chromosomal Territories at Weakened Degree of Phase Separation. J Phys Chem B 2021;125:9092-9101. [PMID: 34351763 DOI: 10.1021/acs.jpcb.1c03523] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
13
Chiariello AM, Corberi F, Salerno M. The Interplay between Phase Separation and Gene-Enhancer Communication: A Theoretical Study. Biophys J 2020;119:873-883. [PMID: 32738219 PMCID: PMC7451901 DOI: 10.1016/j.bpj.2020.07.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 07/01/2020] [Accepted: 07/06/2020] [Indexed: 12/14/2022]  Open
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