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For: McCord RP, Kaplan N, Giorgetti L. Chromosome Conformation Capture and Beyond: Toward an Integrative View of Chromosome Structure and Function. Mol Cell 2020;77:688-708. [PMID: 32001106 DOI: 10.1016/j.molcel.2019.12.021] [Cited by in Crossref: 43] [Cited by in F6Publishing: 31] [Article Influence: 21.5] [Reference Citation Analysis]
Number Citing Articles
1 Zuin J, Roth G, Zhan Y, Cramard J, Redolfi J, Piskadlo E, Mach P, Kryzhanovska M, Tihanyi G, Kohler H, Eder M, Leemans C, van Steensel B, Meister P, Smallwood S, Giorgetti L. Nonlinear control of transcription through enhancer-promoter interactions. Nature 2022. [PMID: 35418676 DOI: 10.1038/s41586-022-04570-y] [Cited by in Crossref: 22] [Cited by in F6Publishing: 6] [Article Influence: 22.0] [Reference Citation Analysis]
2 Chua EHZ, Yasar S, Harmston N. The importance of considering regulatory domains in genome-wide analyses - the nearest gene is often wrong! Biol Open 2022;11:bio059091. [PMID: 35377406 DOI: 10.1242/bio.059091] [Reference Citation Analysis]
3 Neguembor MV, Martin L, Castells-García Á, Gómez-García PA, Vicario C, Carnevali D, AlHaj Abed J, Granados A, Sebastian-Perez R, Sottile F, Solon J, Wu CT, Lakadamyali M, Cosma MP. Transcription-mediated supercoiling regulates genome folding and loop formation. Mol Cell 2021;81:3065-3081.e12. [PMID: 34297911 DOI: 10.1016/j.molcel.2021.06.009] [Cited by in Crossref: 1] [Cited by in F6Publishing: 1] [Article Influence: 1.0] [Reference Citation Analysis]
4 Das P, Shen T, McCord RP. Inferring chromosome radial organization from Hi-C data. BMC Bioinformatics 2020;21:511. [PMID: 33167851 DOI: 10.1186/s12859-020-03841-7] [Cited by in Crossref: 2] [Cited by in F6Publishing: 1] [Article Influence: 1.0] [Reference Citation Analysis]
5 Franke M, De la Calle-Mustienes E, Neto A, Almuedo-Castillo M, Irastorza-Azcarate I, Acemel RD, Tena JJ, Santos-Pereira JM, Gómez-Skarmeta JL. CTCF knockout in zebrafish induces alterations in regulatory landscapes and developmental gene expression. Nat Commun 2021;12:5415. [PMID: 34518536 DOI: 10.1038/s41467-021-25604-5] [Cited by in Crossref: 1] [Article Influence: 1.0] [Reference Citation Analysis]
6 Pigolotti S, Jensen MH, Zhan Y, Tiana G. Bifractal nature of chromosome contact maps. Phys Rev Research 2020;2. [DOI: 10.1103/physrevresearch.2.043078] [Cited by in Crossref: 1] [Cited by in F6Publishing: 1] [Article Influence: 0.5] [Reference Citation Analysis]
7 Jost D. Polymer Modeling of 3D Epigenome Folding: Application to Drosophila. Methods Mol Biol 2022;2301:293-305. [PMID: 34415542 DOI: 10.1007/978-1-0716-1390-0_15] [Reference Citation Analysis]
8 Boninsegna L, Yildirim A, Polles G, Zhan Y, Quinodoz SA, Finn EH, Guttman M, Zhou XJ, Alber F. Integrative genome modeling platform reveals essentiality of rare contact events in 3D genome organizations. Nat Methods 2022. [PMID: 35817938 DOI: 10.1038/s41592-022-01527-x] [Reference Citation Analysis]
9 Yi X, Zheng Z, Xu H, Zhou Y, Huang D, Wang J, Feng X, Zhao K, Fan X, Zhang S, Dong X, Wang Z, Shen Y, Cheng H, Shi L, Li MJ. Interrogating cell type-specific cooperation of transcriptional regulators in 3D chromatin. iScience 2021;24:103468. [PMID: 34888502 DOI: 10.1016/j.isci.2021.103468] [Reference Citation Analysis]
10 Xiao JY, Hafner A, Boettiger AN. How subtle changes in 3D structure can create large changes in transcription. Elife 2021;10:e64320. [PMID: 34240703 DOI: 10.7554/eLife.64320] [Cited by in Crossref: 6] [Cited by in F6Publishing: 2] [Article Influence: 6.0] [Reference Citation Analysis]
11 Arnould C, Rocher V, Finoux AL, Clouaire T, Li K, Zhou F, Caron P, Mangeot PE, Ricci EP, Mourad R, Haber JE, Noordermeer D, Legube G. Loop extrusion as a mechanism for formation of DNA damage repair foci. Nature 2021;590:660-5. [PMID: 33597753 DOI: 10.1038/s41586-021-03193-z] [Cited by in Crossref: 20] [Cited by in F6Publishing: 13] [Article Influence: 20.0] [Reference Citation Analysis]
12 Bennett C, Amin V, Kim D, Cobanoglu MC, Malladi V. TReNCo: Topologically associating domain (TAD) aware regulatory network construction. F1000Res 2022;11:426. [DOI: 10.12688/f1000research.110936.1] [Reference Citation Analysis]
13 Mateo LJ, Sinnott-Armstrong N, Boettiger AN. Tracing DNA paths and RNA profiles in cultured cells and tissues with ORCA. Nat Protoc 2021;16:1647-713. [PMID: 33619390 DOI: 10.1038/s41596-020-00478-x] [Cited by in Crossref: 2] [Cited by in F6Publishing: 2] [Article Influence: 2.0] [Reference Citation Analysis]
14 Istace B, Belser C, Falentin C, Labadie K, Boideau F, Deniot G, Maillet L, Cruaud C, Bertrand L, Chèvre AM, Wincker P, Rousseau-Gueutin M, Aury JM. Sequencing and Chromosome-Scale Assembly of Plant Genomes, Brassica rapa as a Use Case. Biology (Basel) 2021;10:732. [PMID: 34439964 DOI: 10.3390/biology10080732] [Reference Citation Analysis]
15 Robles-Rebollo I, Cuartero S, Canellas-Socias A, Wells S, Karimi MM, Mereu E, Chivu AG, Heyn H, Whilding C, Dormann D, Marguerat S, Rioja I, Prinjha RK, Stumpf MPH, Fisher AG, Merkenschlager M. Cohesin couples transcriptional bursting probabilities of inducible enhancers and promoters. Nat Commun 2022;13:4342. [PMID: 35896525 DOI: 10.1038/s41467-022-31192-9] [Reference Citation Analysis]
16 [DOI: 10.1101/2020.09.08.282707] [Cited by in Crossref: 2] [Cited by in F6Publishing: 1] [Reference Citation Analysis]
17 Cohen CJ, Davidson C, Selmi C, Bowness P, Knight JC, Wordsworth BP, Vecellio M. Disruption of c-MYC Binding and Chromosomal Looping Involving Genetic Variants Associated With Ankylosing Spondylitis Upstream of the RUNX3 Promoter. Front Genet 2021;12:741867. [PMID: 35069677 DOI: 10.3389/fgene.2021.741867] [Reference Citation Analysis]
18 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 DOI: 10.3390/polym14091918] [Cited by in Crossref: 1] [Cited by in F6Publishing: 1] [Article Influence: 1.0] [Reference Citation Analysis]
19 Weiss FD, Calderon L, Wang YF, Georgieva R, Guo Y, Cvetesic N, Kaur M, Dharmalingam G, Krantz ID, Lenhard B, Fisher AG, Merkenschlager M. Neuronal genes deregulated in Cornelia de Lange Syndrome respond to removal and re-expression of cohesin. Nat Commun 2021;12:2919. [PMID: 34006846 DOI: 10.1038/s41467-021-23141-9] [Cited by in Crossref: 2] [Cited by in F6Publishing: 2] [Article Influence: 2.0] [Reference Citation Analysis]
20 Yan J, Huangfu D. Epigenome rewiring in human pluripotent stem cells. Trends Cell Biol 2021:S0962-8924(21)00247-6. [PMID: 34955367 DOI: 10.1016/j.tcb.2021.12.001] [Reference Citation Analysis]
21 Panigrahi A, O'Malley BW. Mechanisms of enhancer action: the known and the unknown. Genome Biol 2021;22:108. [PMID: 33858480 DOI: 10.1186/s13059-021-02322-1] [Cited by in Crossref: 5] [Cited by in F6Publishing: 5] [Article Influence: 5.0] [Reference Citation Analysis]
22 Bouwman BAM, Crosetto N, Bienko M. The era of 3D and spatial genomics. Trends Genet 2022:S0168-9525(22)00118-4. [PMID: 35680466 DOI: 10.1016/j.tig.2022.05.010] [Reference Citation Analysis]
23 Mitter M, Takacs Z, Köcher T, Micura R, Langer CCH, Gerlich DW. Sister chromatid-sensitive Hi-C to map the conformation of replicated genomes. Nat Protoc 2022. [PMID: 35478248 DOI: 10.1038/s41596-022-00687-6] [Reference Citation Analysis]
24 Loda A, Collombet S, Heard E. Gene regulation in time and space during X-chromosome inactivation. Nat Rev Mol Cell Biol 2022. [PMID: 35013589 DOI: 10.1038/s41580-021-00438-7] [Cited by in Crossref: 8] [Cited by in F6Publishing: 4] [Article Influence: 8.0] [Reference Citation Analysis]
25 Mäkelä J, Sherratt D. SMC complexes organize the bacterial chromosome by lengthwise compaction. Curr Genet 2020;66:895-9. [PMID: 32300862 DOI: 10.1007/s00294-020-01076-w] [Cited by in Crossref: 8] [Cited by in F6Publishing: 5] [Article Influence: 4.0] [Reference Citation Analysis]
26 Marti-Marimon M, Vialaneix N, Lahbib-Mansais Y, Zytnicki M, Camut S, Robelin D, Yerle-Bouissou M, Foissac S. Major Reorganization of Chromosome Conformation During Muscle Development in Pig. Front Genet 2021;12:748239. [PMID: 34675966 DOI: 10.3389/fgene.2021.748239] [Reference Citation Analysis]
27 Higashijima Y, Kanki Y. Potential roles of super enhancers in inflammatory gene transcription. FEBS J 2021. [PMID: 34173323 DOI: 10.1111/febs.16089] [Cited by in Crossref: 1] [Cited by in F6Publishing: 1] [Article Influence: 1.0] [Reference Citation Analysis]
28 Bystricky K, Merkenschlager M. Editorial overview: Diving into the Genome. Curr Opin Genet Dev 2020;61:iii-vi. [PMID: 32950132 DOI: 10.1016/j.gde.2020.06.001] [Reference Citation Analysis]
29 Hao N, Sullivan AE, Shearwin KE, Dodd IB. The loopometer: a quantitative in vivo assay for DNA-looping proteins. Nucleic Acids Res 2021;49:e39. [PMID: 33511418 DOI: 10.1093/nar/gkaa1284] [Cited by in Crossref: 1] [Cited by in F6Publishing: 1] [Article Influence: 1.0] [Reference Citation Analysis]
30 Xiao K, Xiong D, Chen G, Yu J, Li Y, Chen K, Zhang L, Xu Y, Xu Q, Huang X, Gao A, Cao K, Yan K, Dai J, Hu X, Ruan Y, Fu Z, Li G, Cao G. RUNX1-mediated alphaherpesvirus-host trans-species chromatin interaction promotes viral transcription. Sci Adv 2021;7:eabf8962. [PMID: 34162542 DOI: 10.1126/sciadv.abf8962] [Cited by in F6Publishing: 1] [Reference Citation Analysis]
31 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:BST20201004. [PMID: 34282837 DOI: 10.1042/BST20201004] [Reference Citation Analysis]
32 Bartolomé A. Stem Cell-Derived β Cells: A Versatile Research Platform to Interrogate the Genetic Basis of β Cell Dysfunction. Int J Mol Sci 2022;23:501. [PMID: 35008927 DOI: 10.3390/ijms23010501] [Cited by in Crossref: 2] [Cited by in F6Publishing: 2] [Article Influence: 2.0] [Reference Citation Analysis]
33 Claringbould A, Zaugg JB. Enhancers in disease: molecular basis and emerging treatment strategies. Trends Mol Med 2021;27:1060-73. [PMID: 34420874 DOI: 10.1016/j.molmed.2021.07.012] [Reference Citation Analysis]
34 Gogou C, Japaridze A, Dekker C. Mechanisms for Chromosome Segregation in Bacteria. Front Microbiol 2021;12:685687. [PMID: 34220773 DOI: 10.3389/fmicb.2021.685687] [Reference Citation Analysis]
35 Espinola SM, Götz M, Bellec M, Messina O, Fiche JB, Houbron C, Dejean M, Reim I, Cardozo Gizzi AM, Lagha M, Nollmann M. Cis-regulatory chromatin loops arise before TADs and gene activation, and are independent of cell fate during early Drosophila development. Nat Genet 2021;53:477-86. [PMID: 33795867 DOI: 10.1038/s41588-021-00816-z] [Cited by in Crossref: 12] [Cited by in F6Publishing: 11] [Article Influence: 12.0] [Reference Citation Analysis]
36 Wolff J, Backofen R, Grüning B. Robust and efficient single-cell Hi-C clustering with approximate k-nearest neighbor graphs. Bioinformatics 2021:btab394. [PMID: 34021764 DOI: 10.1093/bioinformatics/btab394] [Reference Citation Analysis]
37 Xu H, Zhang S, Yi X, Plewczynski D, Li MJ. Exploring 3D chromatin contacts in gene regulation: The evolution of approaches for the identification of functional enhancer-promoter interaction. Comput Struct Biotechnol J 2020;18:558-70. [PMID: 32226593 DOI: 10.1016/j.csbj.2020.02.013] [Cited by in Crossref: 8] [Cited by in F6Publishing: 8] [Article Influence: 4.0] [Reference Citation Analysis]
38 Xu L, Yin L, Qi Y, Tan X, Gao M, Peng J. 3D disorganization and rearrangement of genome provide insights into pathogenesis of NAFLD by integrated Hi-C, Nanopore, and RNA sequencing. Acta Pharm Sin B 2021;11:3150-64. [PMID: 34729306 DOI: 10.1016/j.apsb.2021.03.022] [Cited by in Crossref: 1] [Cited by in F6Publishing: 1] [Article Influence: 1.0] [Reference Citation Analysis]
39 Pitman M, Melters DP, Dalal Y. Job Opening for Nucleosome Mechanic: Flexibility Required. Cells 2020;9:E580. [PMID: 32121488 DOI: 10.3390/cells9030580] [Cited by in Crossref: 4] [Cited by in F6Publishing: 4] [Article Influence: 2.0] [Reference Citation Analysis]
40 Meng L, Wang C, Shi Y, Luo Q. Si-C is a method for inferring super-resolution intact genome structure from single-cell Hi-C data. Nat Commun 2021;12:4369. [PMID: 34272403 DOI: 10.1038/s41467-021-24662-z] [Cited by in F6Publishing: 1] [Reference Citation Analysis]
41 Sedat J, McDonald A, Cang H, Lucas J, Arigovindan M, Kam Z, Murre C, Elbaum M. A proposed unified interphase nucleus chromosome structure: Preliminary preponderance of evidence. Proc Natl Acad Sci U S A 2022;119:e2119101119. [PMID: 35749363 DOI: 10.1073/pnas.2119101119] [Reference Citation Analysis]
42 Xie L, Liu Z. Single-cell imaging of genome organization and dynamics. Mol Syst Biol 2021;17:e9653. [PMID: 34232558 DOI: 10.15252/msb.20209653] [Cited by in F6Publishing: 1] [Reference Citation Analysis]
43 Sanders JT, Golloshi R, Das P, Xu Y, Terry PH, Nash DG, Dekker J, McCord RP. Loops, topologically associating domains, compartments, and territories are elastic and robust to dramatic nuclear volume swelling. Sci Rep 2022;12:4721. [PMID: 35304523 DOI: 10.1038/s41598-022-08602-5] [Cited by in Crossref: 1] [Article Influence: 1.0] [Reference Citation Analysis]
44 Wolff J, Rabbani L, Gilsbach R, Richard G, Manke T, Backofen R, Grüning BA. Galaxy HiCExplorer 3: a web server for reproducible Hi-C, capture Hi-C and single-cell Hi-C data analysis, quality control and visualization. Nucleic Acids Res 2020;48:W177-84. [PMID: 32301980 DOI: 10.1093/nar/gkaa220] [Cited by in Crossref: 26] [Cited by in F6Publishing: 14] [Article Influence: 13.0] [Reference Citation Analysis]
45 Tena JJ, Santos-Pereira JM. Topologically Associating Domains and Regulatory Landscapes in Development, Evolution and Disease. Front Cell Dev Biol 2021;9:702787. [PMID: 34295901 DOI: 10.3389/fcell.2021.702787] [Reference Citation Analysis]
46 Shinkai S, Onami S, Nakato R. Toward understanding the dynamic state of 3D genome. Comput Struct Biotechnol J 2020;18:2259-69. [PMID: 32952939 DOI: 10.1016/j.csbj.2020.08.014] [Cited by in Crossref: 1] [Article Influence: 0.5] [Reference Citation Analysis]
47 Lambert É, Puwakdandawa K, Tao YF, Robert F. From structure to molecular condensates: emerging mechanisms for Mediator function. FEBS J 2021. [PMID: 34698446 DOI: 10.1111/febs.16250] [Reference Citation Analysis]
48 Nazer E, Gómez Acuña L, Kornblihtt AR. Seeking the truth behind the myth: Argonaute tales from "nuclearland". Mol Cell 2021:S1097-2765(21)00955-2. [PMID: 34856122 DOI: 10.1016/j.molcel.2021.11.005] [Cited by in Crossref: 3] [Cited by in F6Publishing: 2] [Article Influence: 3.0] [Reference Citation Analysis]
49 Huang Z, Wang C, Treuter E, Fan R. An optimized 4C-seq protocol based on cistrome and epigenome data in the mouse RAW264.7 macrophage cell line. STAR Protocols 2022;3:101338. [DOI: 10.1016/j.xpro.2022.101338] [Reference Citation Analysis]
50 Cildir G, Yip KH, Pant H, Tergaonkar V, Lopez AF, Tumes DJ. Understanding mast cell heterogeneity at single cell resolution. Trends Immunol 2021;42:523-35. [PMID: 33962887 DOI: 10.1016/j.it.2021.04.004] [Cited by in Crossref: 1] [Cited by in F6Publishing: 3] [Article Influence: 1.0] [Reference Citation Analysis]
51 Oudelaar AM, Higgs DR. The relationship between genome structure and function. Nat Rev Genet 2021;22:154-68. [PMID: 33235358 DOI: 10.1038/s41576-020-00303-x] [Cited by in Crossref: 8] [Cited by in F6Publishing: 4] [Article Influence: 4.0] [Reference Citation Analysis]
52 Deshpande AS, Ulahannan N, Pendleton M, Dai X, Ly L, Behr JM, Schwenk S, Liao W, Augello MA, Tyer C, Rughani P, Kudman S, Tian H, Otis HG, Adney E, Wilkes D, Mosquera JM, Barbieri CE, Melnick A, Stoddart D, Turner DJ, Juul S, Harrington E, Imieliński M. Identifying synergistic high-order 3D chromatin conformations from genome-scale nanopore concatemer sequencing. Nat Biotechnol. [DOI: 10.1038/s41587-022-01289-z] [Cited by in Crossref: 1] [Article Influence: 1.0] [Reference Citation Analysis]
53 Maslova A, Krasikova A. FISH Going Meso-Scale: A Microscopic Search for Chromatin Domains. Front Cell Dev Biol 2021;9:753097. [PMID: 34805161 DOI: 10.3389/fcell.2021.753097] [Cited by in Crossref: 1] [Article Influence: 1.0] [Reference Citation Analysis]