Job Dekker to Chromosomes
This is a "connection" page, showing publications Job Dekker has written about Chromosomes.
Connection Strength
12.393
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Dekker J, Mirny LA. The chromosome folding problem and how cells solve it. Cell. 2024 Nov 14; 187(23):6424-6450.
Score: 0.845
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Hildebrand EM, Polovnikov K, Dekker B, Liu Y, Lafontaine DL, Fox AN, Li Y, Venev SV, Mirny LA, Dekker J. Mitotic chromosomes are self-entangled and disentangle through a topoisomerase-II-dependent two-stage exit from mitosis. Mol Cell. 2024 Apr 18; 84(8):1422-1441.e14.
Score: 0.808
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Mirny L, Dekker J. Mechanisms of Chromosome Folding and Nuclear Organization: Their Interplay and Open Questions. Cold Spring Harb Perspect Biol. 2022 07 01; 14(7).
Score: 0.717
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Nand A, Zhan Y, Salazar OR, Aranda M, Voolstra CR, Dekker J. Genetic and spatial organization of the unusual chromosomes of the dinoflagellate Symbiodinium microadriaticum. Nat Genet. 2021 05; 53(5):618-629.
Score: 0.661
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Hildebrand EM, Dekker J. Mechanisms and Functions of Chromosome Compartmentalization. Trends Biochem Sci. 2020 05; 45(5):385-396.
Score: 0.609
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Gibcus JH, Samejima K, Goloborodko A, Samejima I, Naumova N, Nuebler J, Kanemaki MT, Xie L, Paulson JR, Earnshaw WC, Mirny LA, Dekker J. A pathway for mitotic chromosome formation. Science. 2018 02 09; 359(6376).
Score: 0.527
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Oomen ME, Dekker J. Epigenetic characteristics of the mitotic chromosome in 1D and 3D. Crit Rev Biochem Mol Biol. 2017 Apr; 52(2):185-204.
Score: 0.494
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Dekker J. Mapping the 3D genome: Aiming for consilience. Nat Rev Mol Cell Biol. 2016 Nov 21; 17(12):741-742.
Score: 0.486
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Dekker J, Guttman M, Lomvardas S. A Guide to Packing Your DNA. Cell. 2016 Apr 07; 165(2):259-61.
Score: 0.466
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Dekker J, Mirny L. The 3D Genome as Moderator of Chromosomal Communication. Cell. 2016 Mar 10; 164(6):1110-1121.
Score: 0.463
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Belton JM, Dekker J. Randomized ligation control for chromosome conformation capture. Cold Spring Harb Protoc. 2015 Jun 01; 2015(6):587-92.
Score: 0.439
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Belton JM, Dekker J. Chromosome Conformation Capture Carbon Copy (5C) in Budding Yeast. Cold Spring Harb Protoc. 2015 Jun 01; 2015(6):593-8.
Score: 0.439
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Dekker J, Mirny L. Biological techniques: Chromosomes captured one by one. Nature. 2013 Oct 03; 502(7469):45-6.
Score: 0.391
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Sanyal A, Ba? D, Mart?-Renom MA, Dekker J. Chromatin globules: a common motif of higher order chromosome structure? Curr Opin Cell Biol. 2011 Jun; 23(3):325-31.
Score: 0.329
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van Steensel B, Dekker J. Genomics tools for unraveling chromosome architecture. Nat Biotechnol. 2010 Oct; 28(10):1089-95.
Score: 0.318
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Miele A, Dekker J. Mapping cis- and trans- chromatin interaction networks using chromosome conformation capture (3C). Methods Mol Biol. 2009; 464:105-21.
Score: 0.281
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Miele A, Dekker J. Long-range chromosomal interactions and gene regulation. Mol Biosyst. 2008 Nov; 4(11):1046-57.
Score: 0.274
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Dekker J. Gene regulation in the third dimension. Science. 2008 Mar 28; 319(5871):1793-4.
Score: 0.267
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Dostie J, Zhan Y, Dekker J. Chromosome conformation capture carbon copy technology. Curr Protoc Mol Biol. 2007 Oct; Chapter 21:Unit 21.14.
Score: 0.258
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Miele A, Gheldof N, Tabuchi TM, Dostie J, Dekker J. Mapping chromatin interactions by chromosome conformation capture. Curr Protoc Mol Biol. 2006 May; Chapter 21:Unit 21.11.
Score: 0.234
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Dekker J. The three 'C' s of chromosome conformation capture: controls, controls, controls. Nat Methods. 2006 Jan; 3(1):17-21.
Score: 0.229
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Samejima K, Gibcus JH, Abraham S, Cisneros-Soberanis F, Samejima I, Beckett AJ, Pucekov? N, Abad MA, Spanos C, Medina-Pritchard B, Paulson JR, Xie L, Jeyaprakash AA, Prior IA, Mirny LA, Dekker J, Goloborodko A, Earnshaw WC. Rules of engagement for condensins and cohesins guide mitotic chromosome formation. Science. 2025 04 11; 388(6743):eadq1709.
Score: 0.217
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Zhou CY, Dekker B, Liu Z, Cabrera H, Ryan J, Dekker J, Heald R. Mitotic chromosomes scale to nuclear-cytoplasmic ratio and cell size in Xenopus. Elife. 2023 04 25; 12.
Score: 0.190
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Yang L, Akgol Oksuz B, Dekker J, Gibcus JH. Capturing Chromosome Conformation Across Length Scales. J Vis Exp. 2023 01 20; (191).
Score: 0.186
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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 03 18; 12(1):4721.
Score: 0.176
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Leidescher S, Ribisel J, Ullrich S, Feodorova Y, Hildebrand E, Galitsyna A, Bultmann S, Link S, Thanisch K, Mulholland C, Dekker J, Leonhardt H, Mirny L, Solovei I. Spatial organization of transcribed eukaryotic genes. Nat Cell Biol. 2022 03; 24(3):327-339.
Score: 0.175
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Choppakatla P, Dekker B, Cutts EE, Vannini A, Dekker J, Funabiki H. Linker histone H1.8 inhibits chromatin binding of condensins and DNA topoisomerase II to tune chromosome length and individualization. Elife. 2021 08 18; 10.
Score: 0.169
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Lafontaine DL, Yang L, Dekker J, Gibcus JH. Hi-C 3.0: Improved Protocol for Genome-Wide Chromosome Conformation Capture. Curr Protoc. 2021 Jul; 1(7):e198.
Score: 0.167
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Fitz-James MH, Tong P, Pidoux AL, Ozadam H, Yang L, White SA, Dekker J, Allshire RC. Large domains of heterochromatin direct the formation of short mitotic chromosome loops. Elife. 2020 09 11; 9.
Score: 0.158
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Dekker J, Belmont AS, Guttman M, Leshyk VO, Lis JT, Lomvardas S, Mirny LA, O'Shea CC, Park PJ, Ren B, Politz JCR, Shendure J, Zhong S. The 4D nucleome project. Nature. 2017 09 13; 549(7671):219-226.
Score: 0.129
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Belaghzal H, Dekker J, Gibcus JH. Hi-C 2.0: An optimized Hi-C procedure for high-resolution genome-wide mapping of chromosome conformation. Methods. 2017 07 01; 123:56-65.
Score: 0.125
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Servant N, Varoquaux N, Lajoie BR, Viara E, Chen CJ, Vert JP, Heard E, Dekker J, Barillot E. HiC-Pro: an optimized and flexible pipeline for Hi-C data processing. Genome Biol. 2015 Dec 01; 16:259.
Score: 0.114
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Dekker J, Misteli T. Long-Range Chromatin Interactions. Cold Spring Harb Perspect Biol. 2015 Oct 01; 7(10):a019356.
Score: 0.112
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Belton JM, Dekker J. Chromosome Conformation Capture (3C) in Budding Yeast. Cold Spring Harb Protoc. 2015 Jun 01; 2015(6):580-6.
Score: 0.110
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Giorgetti L, Galupa R, Nora EP, Piolot T, Lam F, Dekker J, Tiana G, Heard E. Predictive polymer modeling reveals coupled fluctuations in chromosome conformation and transcription. Cell. 2014 May 08; 157(4):950-63.
Score: 0.102
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Gibcus JH, Dekker J. The hierarchy of the 3D genome. Mol Cell. 2013 Mar 07; 49(5):773-82.
Score: 0.094
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Noble WS, Blau CA, Dekker J, Duan ZJ, Mao Y. The structure and function of chromatin and chromosomes. Pac Symp Biocomput. 2012; 434-40.
Score: 0.087
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Naumova N, Dekker J. Integrating one-dimensional and three-dimensional maps of genomes. J Cell Sci. 2010 Jun 15; 123(Pt 12):1979-88.
Score: 0.078
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van Berkum NL, Lieberman-Aiden E, Williams L, Imakaev M, Gnirke A, Mirny LA, Dekker J, Lander ES. Hi-C: a method to study the three-dimensional architecture of genomes. J Vis Exp. 2010 May 06; (39).
Score: 0.077
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Dekker J. Mapping in vivo chromatin interactions in yeast suggests an extended chromatin fiber with regional variation in compaction. J Biol Chem. 2008 Dec 12; 283(50):34532-40.
Score: 0.069
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Lanzuolo C, Roure V, Dekker J, Bantignies F, Orlando V. Polycomb response elements mediate the formation of chromosome higher-order structures in the bithorax complex. Nat Cell Biol. 2007 Oct; 9(10):1167-74.
Score: 0.064
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Hag?ge H, Klous P, Braem C, Splinter E, Dekker J, Cathala G, de Laat W, Forn? T. Quantitative analysis of chromosome conformation capture assays (3C-qPCR). Nat Protoc. 2007; 2(7):1722-33.
Score: 0.061
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Kleckner N, Zickler D, Jones GH, Dekker J, Padmore R, Henle J, Hutchinson J. A mechanical basis for chromosome function. Proc Natl Acad Sci U S A. 2004 Aug 24; 101(34):12592-7.
Score: 0.052
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Stevens L, Moya ND, Tanny RE, Gibson SB, Tracey A, Na H, Chitrakar R, Dekker J, Walhout AJM, Baugh LR, Andersen EC. Chromosome-Level Reference Genomes for Two Strains of Caenorhabditis briggsae: An Improved Platform for Comparative Genomics. Genome Biol Evol. 2022 04 10; 14(4).
Score: 0.044
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Brossas C, Valton AL, Venev SV, Chilaka S, Counillon A, Laurent M, Goncalves C, Duriez B, Picard F, Dekker J, Prioleau MN. Clustering of strong replicators associated with active promoters is sufficient to establish an early-replicating domain. EMBO J. 2020 11 02; 39(21):e99520.
Score: 0.040
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Finn EH, Pegoraro G, Brand?o HB, Valton AL, Oomen ME, Dekker J, Mirny L, Misteli T. Extensive Heterogeneity and Intrinsic Variation in Spatial Genome Organization. Cell. 2019 03 07; 176(6):1502-1515.e10.
Score: 0.036
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Kind J, Pagie L, de Vries SS, Nahidiazar L, Dey SS, Bienko M, Zhan Y, Lajoie B, de Graaf CA, Amendola M, Fudenberg G, Imakaev M, Mirny LA, Jalink K, Dekker J, van Oudenaarden A, van Steensel B. Genome-wide maps of nuclear lamina interactions in single human cells. Cell. 2015 Sep 24; 163(1):134-47.
Score: 0.028