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For: Chakraborty A, Wang JG, Ay F. dcHiC detects differential compartments across multiple Hi-C datasets. Nat Commun 2022;13:6827. [PMID: 36369226 PMCID: PMC9652325 DOI: 10.1038/s41467-022-34626-6] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 11/01/2022] [Indexed: 11/13/2022]  Open
Number Cited by Other Article(s)
1
Yao Z, Fang K, Liu G, Bjørås M, Jin VX, Wang J. Integrated analysis of differential intra-chromosomal community interactions: A study of breast cancer. Artif Intell Med 2025;167:103180. [PMID: 40449144 DOI: 10.1016/j.artmed.2025.103180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2024] [Revised: 05/15/2025] [Accepted: 05/23/2025] [Indexed: 06/02/2025]
2
Gregoricchio S, Kojic A, Hoogstraat M, Schuurman K, Stelloo S, Severson TM, O'Mara TA, Droog M, Singh AA, Glubb DM, Wessels LFA, Vermeulen M, van Leeuwen FE, Zwart W. Endometrial tumorigenesis involves epigenetic plasticity demarcating non-coding somatic mutations and 3D-genome alterations. Genome Biol 2025;26:124. [PMID: 40346709 PMCID: PMC12063248 DOI: 10.1186/s13059-025-03596-5] [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: 06/10/2024] [Accepted: 04/28/2025] [Indexed: 05/11/2025]  Open
3
Lee DI, Roy S. Examining the dynamics of three-dimensional genome organization with multitask matrix factorization. Genome Res 2025;35:1179-1193. [PMID: 40113262 PMCID: PMC12047540 DOI: 10.1101/gr.279930.124] [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: 08/15/2024] [Accepted: 02/20/2025] [Indexed: 03/22/2025]
4
Lee J, Mo HL, Ha Y, Nam DY, Lim G, Park JW, Park S, Choi WY, Lee HJ, Rhee JK. Unraveling the three-dimensional genome structure using machine learning. BMB Rep 2025;58:203-208. [PMID: 40058875 PMCID: PMC12123201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 03/07/2024] [Accepted: 09/06/2024] [Indexed: 05/29/2025]  Open
5
Choppavarapu L, Fang K, Liu T, Ohihoin AG, Jin VX. Hi-C profiling in tissues reveals 3D chromatin-regulated breast tumor heterogeneity informing a looping-mediated therapeutic avenue. Cell Rep 2025;44:115450. [PMID: 40112000 PMCID: PMC12103084 DOI: 10.1016/j.celrep.2025.115450] [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: 08/23/2024] [Revised: 01/12/2025] [Accepted: 02/28/2025] [Indexed: 03/22/2025]  Open
6
Hildebrand EM, Cowell IG, Khazeem MM, Sambare S, Uyan O, Dekker J, Austin CA. TOP2B is required for compartment strength changes upon retinoic acid treatment in SH-SY5Y cells. Chromosome Res 2025;33:5. [PMID: 40183884 PMCID: PMC11971153 DOI: 10.1007/s10577-025-09764-4] [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: 09/17/2024] [Revised: 02/16/2025] [Accepted: 03/17/2025] [Indexed: 04/05/2025]
7
Li Y, Xiao P, Boadu F, Goldkamp AK, Nirgude S, Cheng J, Hagen DE, Kalish JM, Rivera RM. Beckwith-Wiedemann syndrome and large offspring syndrome involve alterations in methylome, transcriptome, and chromatin configuration. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2025:2023.12.14.23299981. [PMID: 38168424 PMCID: PMC10760283 DOI: 10.1101/2023.12.14.23299981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
8
Jorge E, Foissac S, Neuvial P, Zytnicki M, Vialaneix N. A comprehensive review and benchmark of differential analysis tools for Hi-C data. Brief Bioinform 2025;26:bbaf074. [PMID: 40037641 PMCID: PMC11879411 DOI: 10.1093/bib/bbaf074] [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: 09/26/2024] [Revised: 01/24/2025] [Accepted: 02/10/2025] [Indexed: 03/06/2025]  Open
9
Grant ZL, Kuang S, Zhang S, Horrillo AJ, Rao KS, Kameswaran V, Joubran C, Lau PK, Dong K, Yang B, Bartosik WM, Zemke NR, Ren B, Kathiriya IS, Pollard KS, Bruneau BG. Dose-dependent sensitivity of human 3D chromatin to a heart disease-linked transcription factor. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.01.09.632202. [PMID: 39829922 PMCID: PMC11741296 DOI: 10.1101/2025.01.09.632202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/22/2025]
10
Wall BPG, Nguyen M, Harrell JC, Dozmorov MG. Machine and Deep Learning Methods for Predicting 3D Genome Organization. Methods Mol Biol 2025;2856:357-400. [PMID: 39283464 DOI: 10.1007/978-1-0716-4136-1_22] [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] [Indexed: 09/25/2024]
11
Chen X, Li K, Wu X, Li Z, Jiang Q, Cui X, Gao Z, Wu Y, Jiang R. Descart: a method for detecting spatial chromatin accessibility patterns with inter-cellular correlations. Genome Biol 2024;25:322. [PMID: 39736655 PMCID: PMC11686967 DOI: 10.1186/s13059-024-03458-6] [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: 03/25/2024] [Accepted: 12/09/2024] [Indexed: 01/01/2025]  Open
12
Tavallaee G, Orouji E. Mapping the 3D genome architecture. Comput Struct Biotechnol J 2024;27:89-101. [PMID: 39816913 PMCID: PMC11732852 DOI: 10.1016/j.csbj.2024.12.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2024] [Revised: 12/17/2024] [Accepted: 12/20/2024] [Indexed: 01/18/2025]  Open
13
Chen ZJ, Das SS, Kar A, Lee SHT, Abuhanna KD, Alvarez M, Sukhatme MG, Gelev KZ, Heffel MG, Zhang Y, Avram O, Rahmani E, Sankararaman S, Heinonen S, Peltoniemi H, Halperin E, Pietiläinen KH, Luo C, Pajukanta P. Single-cell DNA methylome and 3D genome atlas of the human subcutaneous adipose tissue. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.11.02.621694. [PMID: 39554055 PMCID: PMC11566006 DOI: 10.1101/2024.11.02.621694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/19/2024]
14
Heffel MG, Zhou J, Zhang Y, Lee DS, Hou K, Pastor-Alonso O, Abuhanna KD, Galasso J, Kern C, Tai CY, Garcia-Padilla C, Nafisi M, Zhou Y, Schmitt AD, Li T, Haeussler M, Wick B, Zhang MJ, Xie F, Ziffra RS, Mukamel EA, Eskin E, Nowakowski TJ, Dixon JR, Pasaniuc B, Ecker JR, Zhu Q, Bintu B, Paredes MF, Luo C. Temporally distinct 3D multi-omic dynamics in the developing human brain. Nature 2024;635:481-489. [PMID: 39385032 PMCID: PMC11560841 DOI: 10.1038/s41586-024-08030-7] [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: 10/24/2022] [Accepted: 09/06/2024] [Indexed: 10/11/2024]
15
Chang L, Xie Y, Taylor B, Wang Z, Sun J, Armand EJ, Mishra S, Xu J, Tastemel M, Lie A, Gibbs ZA, Indralingam HS, Tan TM, Bejar R, Chen CC, Furnari FB, Hu M, Ren B. Droplet Hi-C enables scalable, single-cell profiling of chromatin architecture in heterogeneous tissues. Nat Biotechnol 2024:10.1038/s41587-024-02447-1. [PMID: 39424717 DOI: 10.1038/s41587-024-02447-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 09/24/2024] [Indexed: 10/21/2024]
16
Zemke NR, Lee S, Mamde S, Yang B, Berchtold N, Maximiliano Garduño B, Indralingam HS, Bartosik WM, Lau PK, Dong K, Yang A, Tani Y, Chen C, Zeng Q, Ajith V, Tong L, Seng C, Li D, Wang T, Xu X, Ren B. Epigenetic and 3D genome reprogramming during the aging of human hippocampus. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.10.14.618338. [PMID: 39463924 PMCID: PMC11507755 DOI: 10.1101/2024.10.14.618338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/29/2024]
17
Banerjee A, Zhang S, Bahar I. Genome structural dynamics: insights from Gaussian network analysis of Hi-C data. Brief Funct Genomics 2024;23:525-537. [PMID: 38654598 PMCID: PMC11428154 DOI: 10.1093/bfgp/elae014] [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: 11/02/2023] [Revised: 03/11/2024] [Accepted: 04/02/2024] [Indexed: 04/26/2024]  Open
18
Xue Y, Liu L, Zhang Y, He Y, Wang J, Ma Z, Li TJ, Zhang J, Huang Y, Gao YQ. Unraveling the key role of chromatin structure in cancer development through epigenetic landscape characterization of oral cancer. Mol Cancer 2024;23:190. [PMID: 39243015 PMCID: PMC11378415 DOI: 10.1186/s12943-024-02100-0] [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: 06/28/2024] [Accepted: 08/23/2024] [Indexed: 09/09/2024]  Open
19
Stephenson-Gussinye A, Rendón-Bautista LA, Ruiz-Medina BE, Blanco-Olais E, Pérez-Molina R, Marcial-Medina C, Chavarri-Guerra Y, Soto-Pérez-de-Celis E, Morales-Alfaro A, Esquivel-López A, Candanedo-González F, Gamboa-Domínguez A, Cortes-González R, Alfaro-Goldaracena A, Vázquez-Manjarrez SE, Grajales-Figueroa G, Astudillo-Romero B, Ruiz-Manriquez J, Poot-Hernández AC, Licona-Limón P, Furlan-Magaril M. Obtention of viable cell suspensions from breast cancer tumor biopsies for 3D chromatin conformation and single-cell transcriptome analysis. Front Mol Biosci 2024;11:1420308. [PMID: 39239354 PMCID: PMC11375512 DOI: 10.3389/fmolb.2024.1420308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Accepted: 07/16/2024] [Indexed: 09/07/2024]  Open
20
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]
21
Fang T, Liu Y, Woicik A, Lu M, Jha A, Wang X, Li G, Hristov B, Liu Z, Xu H, Noble WS, Wang S. Enhancing Hi-C contact matrices for loop detection with Capricorn: a multiview diffusion model. Bioinformatics 2024;40:i471-i480. [PMID: 38940142 PMCID: PMC11211821 DOI: 10.1093/bioinformatics/btae211] [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] [Indexed: 06/29/2024]  Open
22
Ma F, Cao Y, Du H, Braikia FZ, Zong L, Ollikainen N, Bayer M, Qiu X, Park B, Roy R, Nandi S, Sarantopoulou D, Ziman A, Bianchi AH, Beerman I, Zhao K, Grosschedl R, Sen R. Three-dimensional chromatin reorganization regulates B cell development during ageing. Nat Cell Biol 2024;26:991-1002. [PMID: 38866970 PMCID: PMC11178499 DOI: 10.1038/s41556-024-01424-9] [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: 11/01/2022] [Accepted: 04/16/2024] [Indexed: 06/14/2024]
23
Chang L, Xie Y, Taylor B, Wang Z, Sun J, Tan TR, Bejar R, Chen CC, Furnari FB, Hu M, Ren B. Droplet Hi-C for Fast and Scalable Profiling of Chromatin Architecture in Single Cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.18.590148. [PMID: 38712075 PMCID: PMC11071305 DOI: 10.1101/2024.04.18.590148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
24
Camerino M, Chang W, Cvekl A. Analysis of long-range chromatin contacts, compartments and looping between mouse embryonic stem cells, lens epithelium and lens fibers. Epigenetics Chromatin 2024;17:10. [PMID: 38643244 PMCID: PMC11031936 DOI: 10.1186/s13072-024-00533-x] [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: 11/15/2023] [Accepted: 03/08/2024] [Indexed: 04/22/2024]  Open
25
Choppavarapu L, Fang K, Liu T, Jin VX. Hi-C profiling in tissues reveals 3D chromatin-regulated breast tumor heterogeneity and tumor-specific looping-mediated biological pathways. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.13.584872. [PMID: 38559097 PMCID: PMC10979939 DOI: 10.1101/2024.03.13.584872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
26
Rapoport R, Greenberg A, Yakhini Z, Simon I. A Cyclic Permutation Approach to Removing Spatial Dependency between Clustered Gene Ontology Terms. BIOLOGY 2024;13:175. [PMID: 38534445 PMCID: PMC10967837 DOI: 10.3390/biology13030175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Revised: 03/04/2024] [Accepted: 03/05/2024] [Indexed: 03/28/2024]
27
Wall BPG, Nguyen M, Harrell JC, Dozmorov MG. Machine and deep learning methods for predicting 3D genome organization. ARXIV 2024:arXiv:2403.03231v1. [PMID: 38495565 PMCID: PMC10942493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
28
Marie P, Bazire M, Ladet J, Ameur LB, Chahar S, Fontrodona N, Sexton T, Auboeuf D, Bourgeois CF, Mortreux F. Gene-to-gene coordinated regulation of transcription and alternative splicing by 3D chromatin remodeling upon NF-κB activation. Nucleic Acids Res 2024;52:1527-1543. [PMID: 38272542 PMCID: PMC10899780 DOI: 10.1093/nar/gkae015] [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: 06/10/2023] [Revised: 12/13/2023] [Accepted: 01/05/2024] [Indexed: 01/27/2024]  Open
29
Wahl N, Espeso-Gil S, Chietera P, Nagel A, Laighneach A, Morris DW, Rajarajan P, Akbarian S, Dechant G, Apostolova G. SATB2 organizes the 3D genome architecture of cognition in cortical neurons. Mol Cell 2024;84:621-639.e9. [PMID: 38244545 PMCID: PMC10923151 DOI: 10.1016/j.molcel.2023.12.024] [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: 01/27/2023] [Revised: 10/02/2023] [Accepted: 12/15/2023] [Indexed: 01/22/2024]
30
Hua D, Gu M, Zhang X, Du Y, Xie H, Qi L, Du X, Bai Z, Zhu X, Tian D. DiffDomain enables identification of structurally reorganized topologically associating domains. Nat Commun 2024;15:502. [PMID: 38218905 PMCID: PMC10787792 DOI: 10.1038/s41467-024-44782-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 01/02/2024] [Indexed: 01/15/2024]  Open
31
Qu Z, Batz Z, Singh N, Marchal C, Swaroop A. Stage-specific dynamic reorganization of genome topology shapes transcriptional neighborhoods in developing human retinal organoids. Cell Rep 2023;42:113543. [PMID: 38048222 PMCID: PMC10790351 DOI: 10.1016/j.celrep.2023.113543] [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: 05/12/2023] [Revised: 09/21/2023] [Accepted: 11/17/2023] [Indexed: 12/06/2023]  Open
32
Hu Y, Salgado Figueroa D, Zhang Z, Veselits M, Bhattacharyya S, Kashiwagi M, Clark MR, Morgan BA, Ay F, Georgopoulos K. Lineage-specific 3D genome organization is assembled at multiple scales by IKAROS. Cell 2023;186:5269-5289.e22. [PMID: 37995656 PMCID: PMC10895928 DOI: 10.1016/j.cell.2023.10.023] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 07/28/2023] [Accepted: 10/25/2023] [Indexed: 11/25/2023]
33
Tian W, Zhou J, Bartlett A, Zeng Q, Liu H, Castanon RG, Kenworthy M, Altshul J, Valadon C, Aldridge A, Nery JR, Chen H, Xu J, Johnson ND, Lucero J, Osteen JK, Emerson N, Rink J, Lee J, Li Y, Siletti K, Liem M, Claffey N, O’Connor C, Yanny AM, Nyhus J, Dee N, Casper T, Shapovalova N, Hirschstein D, Ding SL, Hodge R, Levi BP, Keene CD, Linnarsson S, Lein E, Ren B, Behrens MM, Ecker JR. Single-cell DNA methylation and 3D genome architecture in the human brain. Science 2023;382:eadf5357. [PMID: 37824674 PMCID: PMC10572106 DOI: 10.1126/science.adf5357] [Citation(s) in RCA: 61] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 09/05/2023] [Indexed: 10/14/2023]
34
Kai Y, Liu N, Orkin SH, Yuan GC. Identifying quantitatively differential chromosomal compartmentalization changes and their biological significance from Hi-C data using DARIC. BMC Genomics 2023;24:614. [PMID: 37833630 PMCID: PMC10571287 DOI: 10.1186/s12864-023-09675-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 09/12/2023] [Indexed: 10/15/2023]  Open
35
Raffo A, Paulsen J. The shape of chromatin: insights from computational recognition of geometric patterns in Hi-C data. Brief Bioinform 2023;24:bbad302. [PMID: 37646128 PMCID: PMC10516369 DOI: 10.1093/bib/bbad302] [Citation(s) in RCA: 7] [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: 05/18/2023] [Revised: 07/05/2023] [Accepted: 08/03/2023] [Indexed: 09/01/2023]  Open
36
Gregoricchio S, Zwart W. snHiC: a complete and simplified snakemake pipeline for grouped Hi-C data analysis. BIOINFORMATICS ADVANCES 2023;3:vbad080. [PMID: 37397353 PMCID: PMC10307938 DOI: 10.1093/bioadv/vbad080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 06/12/2023] [Accepted: 06/20/2023] [Indexed: 07/04/2023]
37
Krasikova A, Kulikova T, Rodriguez Ramos JS, Maslova A. Assignment of the somatic A/B compartments to chromatin domains in giant transcriptionally active lampbrush chromosomes. Epigenetics Chromatin 2023;16:24. [PMID: 37322523 DOI: 10.1186/s13072-023-00499-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 06/04/2023] [Indexed: 06/17/2023]  Open
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Kai Y, Liu N, Orkin SH, Yuan GC. Identifying Quantitatively Differential Chromosomal Compartmentalization Changes and Their Biological Significance from Hi-C data using DARIC. RESEARCH SQUARE 2023:rs.3.rs-2814806. [PMID: 37162846 PMCID: PMC10168473 DOI: 10.21203/rs.3.rs-2814806/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
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Kalluchi A, Harris HL, Reznicek TE, Rowley MJ. Considerations and caveats for analyzing chromatin compartments. Front Mol Biosci 2023;10:1168562. [PMID: 37091873 PMCID: PMC10113542 DOI: 10.3389/fmolb.2023.1168562] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 03/27/2023] [Indexed: 04/08/2023]  Open
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Wang C, Liu X, Liang J, Narita Y, Ding W, Li D, Zhang L, Wang H, Leong MML, Hou I, Gerdt C, Jiang C, Zhong Q, Tang Z, Forney C, Kottyan L, Weirauch MT, Gewurz BE, Zeng MS, Jiang S, Teng M, Zhao B. A DNA tumor virus globally reprograms host 3D genome architecture to achieve immortal growth. Nat Commun 2023;14:1598. [PMID: 36949074 PMCID: PMC10033825 DOI: 10.1038/s41467-023-37347-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 03/13/2023] [Indexed: 03/24/2023]  Open
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Plaza-Jennings AL, Valada A, O'Shea C, Iskhakova M, Hu B, Javidfar B, Ben Hutta G, Lambert TY, Murray J, Kassim B, Chandrasekaran S, Chen BK, Morgello S, Won H, Akbarian S. HIV integration in the human brain is linked to microglial activation and 3D genome remodeling. Mol Cell 2022;82:4647-4663.e8. [PMID: 36525955 PMCID: PMC9831062 DOI: 10.1016/j.molcel.2022.11.016] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Revised: 09/12/2022] [Accepted: 11/17/2022] [Indexed: 12/23/2022]
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