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For: Lin D, Sanders J, Noble WS. HiCRep.py: fast comparison of Hi-C contact matrices in Python. Bioinformatics 2021;37:2996-2997. [PMID: 33576390 PMCID: PMC8479650 DOI: 10.1093/bioinformatics/btab097] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 12/17/2020] [Accepted: 02/08/2021] [Indexed: 02/02/2023]  Open
Number Cited by Other Article(s)
1
Shi C, Zhao D, Butler J, Frantzeskos A, Rossi S, Ding J, Ferrazzano C, Wynn C, Hum RM, Richards E, Gupta M, Patel K, Yap CF, Plant D, Grencis R, Martin P, Adamson A, Eyre S, Bowes J, Barton A, Ho P, Rattray M, Orozco G. Multi-omics analysis in primary T cells elucidates mechanisms behind disease-associated genetic loci. Genome Biol 2025;26:26. [PMID: 39930543 PMCID: PMC11808986 DOI: 10.1186/s13059-025-03492-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 01/29/2025] [Indexed: 02/14/2025]  Open
2
Ma N, Li X, Ci D, Zeng HY, Zhang C, Xie X, Zhong C, Deng XW, Li D, He H. Chromatin Topological Domains Associate With the Rapid Formation of Tandem Duplicates in Plants. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2025;12:e2408861. [PMID: 39731323 DOI: 10.1002/advs.202408861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2024] [Revised: 11/25/2024] [Indexed: 12/29/2024]
3
Wang X, Zhang Y, Ray S, Jha A, Fang T, Hang S, Doulatov S, Noble WS, Wang S. A generalizable Hi-C foundation model for chromatin architecture, single-cell and multi-omics analysis across species. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.12.16.628821. [PMID: 39763871 PMCID: PMC11702576 DOI: 10.1101/2024.12.16.628821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/19/2025]
4
Chiliński M, Plewczynski D. HiCDiffusion - diffusion-enhanced, transformer-based prediction of chromatin interactions from DNA sequences. BMC Genomics 2024;25:964. [PMID: 39407104 PMCID: PMC11481779 DOI: 10.1186/s12864-024-10885-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2024] [Accepted: 10/09/2024] [Indexed: 10/19/2024]  Open
5
Rossini R, Oshaghi M, Nekrasov M, Bellanger A, Domaschenz R, Dijkwel Y, Abdelhalim M, Collas P, Tremethick D, Paulsen J. Loss of multi-level 3D genome organization during breast cancer progression. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.26.568711. [PMID: 38076897 PMCID: PMC10705249 DOI: 10.1101/2023.11.26.568711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
6
Das M, Semple JI, Haemmerli A, Volodkina V, Scotton J, Gitchev T, Annan A, Campos J, Statzer C, Dakhovnik A, Ewald CY, Mozziconacci J, Meister P. Condensin I folds the Caenorhabditis elegans genome. Nat Genet 2024;56:1737-1749. [PMID: 39039278 DOI: 10.1038/s41588-024-01832-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 06/13/2024] [Indexed: 07/24/2024]
7
Bittner N, Shi C, Zhao D, Ding J, Southam L, Swift D, Kreitmaier P, Tutino M, Stergiou O, Cheung JTS, Katsoula G, Hankinson J, Wilkinson JM, Orozco G, Zeggini E. Primary osteoarthritis chondrocyte map of chromatin conformation reveals novel candidate effector genes. Ann Rheum Dis 2024;83:1048-1059. [PMID: 38479789 PMCID: PMC11287644 DOI: 10.1136/ard-2023-224945] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 02/29/2024] [Indexed: 07/17/2024]
8
Cheng G, Pratto F, Brick K, Li X, Alleva B, Huang M, Lam G, Camerini-Otero RD. High resolution maps of chromatin reorganization through mouse meiosis reveal novel features of the 3D meiotic structure. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.25.586627. [PMID: 38903112 PMCID: PMC11188084 DOI: 10.1101/2024.03.25.586627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/22/2024]
9
Xing M, Xiong Y, Zhang Y. Ku80 is indispensable for repairing DNA double-strand breaks at highly methylated sites in human HCT116 cells. DNA Repair (Amst) 2024;134:103627. [PMID: 38219597 DOI: 10.1016/j.dnarep.2024.103627] [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: 09/16/2023] [Revised: 01/01/2024] [Accepted: 01/03/2024] [Indexed: 01/16/2024]
10
Abbas A, Chandratre K, Gao Y, Yuan J, Zhang MQ, Mani RS. ChIPr: accurate prediction of cohesin-mediated 3D genome organization from 2D chromatin features. Genome Biol 2024;25:15. [PMID: 38217027 PMCID: PMC10785520 DOI: 10.1186/s13059-023-03158-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 12/22/2023] [Indexed: 01/14/2024]  Open
11
Krug B, Hu B, Chen H, Ptack A, Chen X, Gretarsson KH, Deshmukh S, Kabir N, Andrade AF, Jabbour E, Harutyunyan AS, Lee JJY, Hulswit M, Faury D, Russo C, Xu X, Johnston MJ, Baguette A, Dahl NA, Weil AG, Ellezam B, Dali R, Blanchette M, Wilson K, Garcia BA, Soni RK, Gallo M, Taylor MD, Kleinman CL, Majewski J, Jabado N, Lu C. H3K27me3 spreading organizes canonical PRC1 chromatin architecture to regulate developmental programs. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.28.567931. [PMID: 38116029 PMCID: PMC10729739 DOI: 10.1101/2023.11.28.567931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
12
Li H, He X, Kurowski L, Zhang R, Zhao D, Zeng J. Improving comparative analyses of Hi-C data via contrastive self-supervised learning. Brief Bioinform 2023;24:bbad193. [PMID: 37287135 DOI: 10.1093/bib/bbad193] [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: 02/06/2023] [Revised: 04/12/2023] [Accepted: 04/27/2023] [Indexed: 06/09/2023]  Open
13
Li K, Zhang P, Wang Z, Shen W, Sun W, Xu J, Wen Z, Li L. iEnhance: a multi-scale spatial projection encoding network for enhancing chromatin interaction data resolution. Brief Bioinform 2023;24:bbad245. [PMID: 37381618 DOI: 10.1093/bib/bbad245] [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: 03/21/2023] [Revised: 06/06/2023] [Accepted: 06/12/2023] [Indexed: 06/30/2023]  Open
14
Zhang Y, Blanchette M. Reference panel-guided super-resolution inference of Hi-C data. Bioinformatics 2023;39:i386-i393. [PMID: 37387127 DOI: 10.1093/bioinformatics/btad266] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/01/2023]  Open
15
Hill L, Wutz G, Jaritz M, Tagoh H, Calderón L, Peters JM, Goloborodko A, Busslinger M. Igh and Igk loci use different folding principles for V gene recombination due to distinct chromosomal architectures of pro-B and pre-B cells. Nat Commun 2023;14:2316. [PMID: 37085514 PMCID: PMC10121685 DOI: 10.1038/s41467-023-37994-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 04/04/2023] [Indexed: 04/23/2023]  Open
16
Lambuta RA, Nanni L, Liu Y, Diaz-Miyar J, Iyer A, Tavernari D, Katanayeva N, Ciriello G, Oricchio E. Whole-genome doubling drives oncogenic loss of chromatin segregation. Nature 2023;615:925-933. [PMID: 36922594 PMCID: PMC10060163 DOI: 10.1038/s41586-023-05794-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Accepted: 02/03/2023] [Indexed: 03/17/2023]
17
Chai H, Tjong H, Li P, Liao W, Wang P, Wong CH, Ngan CY, Leonard WJ, Wei CL, Ruan Y. ChIATAC is an efficient strategy for multi-omics mapping of 3D epigenomes from low-cell inputs. Nat Commun 2023;14:213. [PMID: 36639381 PMCID: PMC9839710 DOI: 10.1038/s41467-023-35879-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 01/05/2023] [Indexed: 01/15/2023]  Open
18
Thulson E, Davis ES, D’Costa S, Coryell PR, Kramer NE, Mohlke KL, Loeser RF, Diekman BO, Phanstiel DH. 3D chromatin structure in chondrocytes identifies putative osteoarthritis risk genes. Genetics 2022;222:iyac141. [PMID: 36099032 PMCID: PMC9713432 DOI: 10.1093/genetics/iyac141] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 08/29/2022] [Indexed: 12/13/2022]  Open
19
Nagano M, Hu B, Yokobayashi S, Yamamura A, Umemura F, Coradin M, Ohta H, Yabuta Y, Ishikura Y, Okamoto I, Ikeda H, Kawahira N, Nosaka Y, Shimizu S, Kojima Y, Mizuta K, Kasahara T, Imoto Y, Meehan K, Stocsits R, Wutz G, Hiraoka Y, Murakawa Y, Yamamoto T, Tachibana K, Peters J, Mirny LA, Garcia BA, Majewski J, Saitou M. Nucleome programming is required for the foundation of totipotency in mammalian germline development. EMBO J 2022;41:e110600. [PMID: 35703121 PMCID: PMC9251848 DOI: 10.15252/embj.2022110600] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 04/27/2022] [Accepted: 04/29/2022] [Indexed: 11/09/2022]  Open
20
Li J, Xiang Y, Zhang L, Qi X, Zheng Z, Zhou P, Tang Z, Jin Y, Zhao Q, Fu Y, Zhao Y, Li X, Fu L, Zhao S. Enhancer-promoter interaction maps provide insights into skeletal muscle-related traits in pig genome. BMC Biol 2022;20:136. [PMID: 35681201 PMCID: PMC9185926 DOI: 10.1186/s12915-022-01322-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 05/06/2022] [Indexed: 12/03/2022]  Open
21
Gong W, Wee J, Wu MC, Sun X, Li C, Xia K. Persistent spectral simplicial complex-based machine learning for chromosomal structural analysis in cellular differentiation. Brief Bioinform 2022;23:6583209. [PMID: 35536545 DOI: 10.1093/bib/bbac168] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 04/12/2022] [Accepted: 03/13/2022] [Indexed: 11/13/2022]  Open
22
Liu Y, Ding B, Zheng L, Xu P, Liu Z, Chen Z, Wu P, Zhao Y, Pan Q, Guo Y, Wang W, Wei W. Regulatory elements can be essential for maintaining broad chromatin organization and cell viability. Nucleic Acids Res 2022;50:4340-4354. [PMID: 35390162 PMCID: PMC9071426 DOI: 10.1093/nar/gkac197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 03/03/2022] [Accepted: 03/15/2022] [Indexed: 11/14/2022]  Open
23
Swygert SG, Lin D, Portillo-Ledesma S, Lin PY, Hunt DR, Kao CF, Schlick T, Noble WS, Tsukiyama T. Local chromatin fiber folding represses transcription and loop extrusion in quiescent cells. eLife 2021;10:e72062. [PMID: 34734806 PMCID: PMC8598167 DOI: 10.7554/elife.72062] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 11/03/2021] [Indexed: 12/16/2022]  Open
24
Jo H, Kim T, Chun Y, Jung I, Lee D. A compendium of chromatin contact maps reflecting regulation by chromatin remodelers in budding yeast. Nat Commun 2021;12:6380. [PMID: 34737268 PMCID: PMC8569116 DOI: 10.1038/s41467-021-26629-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 10/14/2021] [Indexed: 11/09/2022]  Open
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