Job Dekker - Publications

Harvard University, Cambridge, MA, United States 

172 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 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 . Elife. 12. PMID 37096661 DOI: 10.7554/eLife.84360  0.354
2023 Zagelbaum J, Schooley A, Zhao J, Schrank BR, Callen E, Zha S, Gottesman ME, Nussenzweig A, Rabadan R, Dekker J, Gautier J. Author Correction: Multiscale reorganization of the genome following DNA damage facilitates chromosome translocations via nuclear actin polymerization. Nature Structural & Molecular Biology. PMID 37059902 DOI: 10.1038/s41594-023-00994-w  0.368
2023 Marlétaz F, de la Calle-Mustienes E, Acemel RD, Paliou C, Naranjo S, Martínez-García PM, Cases I, Sleight VA, Hirschberger C, Marcet-Houben M, Navon D, Andrescavage A, Skvortsova K, Duckett PE, González-Rajal Á, ... ... Dekker J, et al. The little skate genome and the evolutionary emergence of wing-like fins. Nature. PMID 37046085 DOI: 10.1038/s41586-023-05868-1  0.326
2023 Yang L, Akgol Oksuz B, Dekker J, Gibcus JH. Capturing Chromosome Conformation Across Length Scales. Journal of Visualized Experiments : Jove. PMID 36744801 DOI: 10.3791/64001  0.368
2022 Zagelbaum J, Schooley A, Zhao J, Schrank BR, Callen E, Zha S, Gottesman ME, Nussenzweig A, Rabadan R, Dekker J, Gautier J. Multiscale reorganization of the genome following DNA damage facilitates chromosome translocations via nuclear actin polymerization. Nature Structural & Molecular Biology. PMID 36564591 DOI: 10.1038/s41594-022-00893-6  0.379
2022 Spracklin G, Abdennur N, Imakaev M, Chowdhury N, Pradhan S, Mirny LA, Dekker J. Diverse silent chromatin states modulate genome compartmentalization and loop extrusion barriers. Nature Structural & Molecular Biology. 30: 38-51. PMID 36550219 DOI: 10.1038/s41594-022-00892-7  0.355
2022 Dekker B, Dekker J. Regulation of the mitotic chromosome folding machines. The Biochemical Journal. 479: 2153-2173. PMID 36268993 DOI: 10.1042/BCJ20210140  0.342
2022 Liu Y, Dekker J. CTCF-CTCF loops and intra-TAD interactions show differential dependence on cohesin ring integrity. Nature Cell Biology. PMID 36202971 DOI: 10.1038/s41556-022-00992-y  0.325
2022 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. Scientific Reports. 12: 4721. PMID 35304523 DOI: 10.1038/s41598-022-08602-5  0.349
2021 Mirny L, Dekker J. Mechanisms of Chromosome Folding and Nuclear Organization: Their Interplay and Open Questions. Cold Spring Harbor Perspectives in Biology. PMID 34518339 DOI: 10.1101/cshperspect.a040147  0.377
2021 Akgol Oksuz B, Yang L, Abraham S, Venev SV, Krietenstein N, Parsi KM, Ozadam H, Oomen ME, Nand A, Mao H, Genga RMJ, Maehr R, Rando OJ, Mirny LA, Gibcus JH, ... Dekker J, et al. Systematic evaluation of chromosome conformation capture assays. Nature Methods. PMID 34480151 DOI: 10.1038/s41592-021-01248-7  0.339
2021 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. 10. PMID 34406118 DOI: 10.7554/eLife.68918  0.341
2021 Lafontaine DL, Yang L, Dekker J, Gibcus JH. Hi-C 3.0: Improved Protocol for Genome-Wide Chromosome Conformation Capture. Current Protocols. 1: e198. PMID 34286910 DOI: 10.1002/cpz1.198  0.342
2021 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. Nature Genetics. PMID 33927399 DOI: 10.1038/s41588-021-00841-y  0.439
2021 Belaghzal H, Borrman T, Stephens AD, Lafontaine DL, Venev SV, Weng Z, Marko JF, Dekker J. Liquid chromatin Hi-C characterizes compartment-dependent chromatin interaction dynamics. Nature Genetics. PMID 33574602 DOI: 10.1038/s41588-021-00784-4  0.381
2020 Oomen ME, Hedger AK, Watts JK, Dekker J. Detecting chromatin interactions between and along sister chromatids with SisterC. Nature Methods. 17: 1002-1009. PMID 32968250 DOI: 10.1038/s41592-020-0930-9  0.463
2020 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. The Embo Journal. e99520. PMID 32935369 DOI: 10.15252/Embj.201899520  0.446
2020 Tavares-Cadete F, Norouzi D, Dekker B, Liu Y, Dekker J. Multi-contact 3C reveals that the human genome during interphase is largely not entangled. Nature Structural & Molecular Biology. PMID 32929283 DOI: 10.1038/S41594-020-0506-5  0.487
2020 Fitz-James MH, Tong P, Pidoux AL, Ozadam H, Yang L, White SA, Dekker J, Allshire R. Large domains of heterochromatin direct the formation of short mitotic chromosome loops. Elife. 9. PMID 32915140 DOI: 10.7554/Elife.57212  0.52
2020 Moore JE, Purcaro MJ, Pratt HE, Epstein CB, Shoresh N, Adrian J, Kawli T, Davis CA, Dobin A, Kaul R, Halow J, Van Nostrand EL, Freese P, Gorkin DU, ... ... Dekker J, et al. Expanded encyclopaedias of DNA elements in the human and mouse genomes. Nature. 583: 699-710. PMID 32728249 DOI: 10.1038/S41586-020-2493-4  0.416
2020 Hildebrand EM, Dekker J. Mechanisms and Functions of Chromosome Compartmentalization. Trends in Biochemical Sciences. 45: 385-396. PMID 32311333 DOI: 10.1016/J.Tibs.2020.01.002  0.456
2020 Krietenstein N, Abraham S, Venev SV, Abdennur N, Gibcus J, Hsieh TS, Parsi KM, Yang L, Maehr R, Mirny LA, Dekker J, Rando OJ. Ultrastructural Details of Mammalian Chromosome Architecture. Molecular Cell. PMID 32213324 DOI: 10.1016/J.Molcel.2020.03.003  0.495
2020 Dossin F, Pinheiro I, Żylicz JJ, Roensch J, Collombet S, Le Saux A, Chelmicki T, Attia M, Kapoor V, Zhan Y, Dingli F, Loew D, Mercher T, Dekker J, Heard E. SPEN integrates transcriptional and epigenetic control of X-inactivation. Nature. PMID 32025035 DOI: 10.1038/S41586-020-1974-9  0.409
2019 Gisselbrecht SS, Palagi A, Kurland JV, Rogers JM, Ozadam H, Zhan Y, Dekker J, Bulyk ML. Transcriptional Silencers in Drosophila Serve a Dual Role as Transcriptional Enhancers in Alternate Cellular Contexts. Molecular Cell. PMID 31704182 DOI: 10.1016/J.Molcel.2019.10.004  0.372
2019 Abramo K, Valton AL, Venev SV, Ozadam H, Fox AN, Dekker J. A chromosome folding intermediate at the condensin-to-cohesin transition during telophase. Nature Cell Biology. 21: 1393-1402. PMID 31685986 DOI: 10.1038/S41556-019-0406-2  0.502
2019 AlHaj Abed J, Erceg J, Goloborodko A, Nguyen SC, McCole RB, Saylor W, Fudenberg G, Lajoie BR, Dekker J, Mirny LA, Wu CT. Highly structured homolog pairing reflects functional organization of the Drosophila genome. Nature Communications. 10: 4485. PMID 31582763 DOI: 10.1038/S41467-019-12208-3  0.464
2019 Erceg J, AlHaj Abed J, Goloborodko A, Lajoie BR, Fudenberg G, Abdennur N, Imakaev M, McCole RB, Nguyen SC, Saylor W, Joyce EF, Senaratne TN, Hannan MA, Nir G, Dekker J, et al. The genome-wide multi-layered architecture of chromosome pairing in early Drosophila embryos. Nature Communications. 10: 4486. PMID 31582744 DOI: 10.1038/S41467-019-12211-8  0.515
2019 Viny AD, Bowman RL, Liu Y, Lavallée VP, Eisman SE, Xiao W, Durham BH, Navitski A, Park J, Braunstein S, Alija B, Karzai A, Csete IS, Witkin M, Azizi E, ... ... Dekker J, et al. Cohesin Members Stag1 and Stag2 Display Distinct Roles in Chromatin Accessibility and Topological Control of HSC Self-Renewal and Differentiation. Cell Stem Cell. PMID 31495782 DOI: 10.1016/J.Stem.2019.08.003  0.4
2019 Dileep V, Wilson KA, Marchal C, Lyu X, Zhao PA, Li B, Poulet A, Bartlett DA, Rivera-Mulia JC, Qin ZS, Robins AJ, Schulz TC, Kulik MJ, McCord RP, Dekker J, et al. Rapid Irreversible Transcriptional Reprogramming in Human Stem Cells Accompanied by Discordance between Replication Timing and Chromatin Compartment. Stem Cell Reports. PMID 31231024 DOI: 10.1016/J.Stemcr.2019.05.021  0.392
2019 Falk M, Feodorova Y, Naumova N, Imakaev M, Lajoie BR, Leonhardt H, Joffe B, Dekker J, Fudenberg G, Solovei I, Mirny LA. Heterochromatin drives compartmentalization of inverted and conventional nuclei. Nature. PMID 31168090 DOI: 10.1038/S41586-019-1275-3  0.5
2019 Yardımcı GG, Ozadam H, Sauria MEG, Ursu O, Yan KK, Yang T, Chakraborty A, Kaul A, Lajoie BR, Song F, Zhan Y, Ay F, Gerstein M, Kundaje A, Li Q, ... ... Dekker J, et al. Measuring the reproducibility and quality of Hi-C data. Genome Biology. 20: 57. PMID 30890172 DOI: 10.1186/S13059-019-1658-7  0.367
2019 Finn EH, Pegoraro G, Brandão HB, Valton AL, Oomen ME, Dekker J, Mirny L, Misteli T. Extensive Heterogeneity and Intrinsic Variation in Spatial Genome Organization. Cell. PMID 30799036 DOI: 10.1016/J.Cell.2019.01.020  0.449
2019 Oomen ME, Hansen AS, Liu Y, Darzacq X, Dekker J. CTCF sites display cell cycle-dependent dynamics in factor binding and nucleosome positioning. Genome Research. PMID 30655336 DOI: 10.1101/Gr.241547.118  0.342
2019 Gdula MR, Nesterova TB, Pintacuda G, Godwin J, Zhan Y, Ozadam H, McClellan M, Moralli D, Krueger F, Green CM, Reik W, Kriaucionis S, Heard E, Dekker J, Brockdorff N. The non-canonical SMC protein SmcHD1 antagonises TAD formation and compartmentalisation on the inactive X chromosome. Nature Communications. 10: 30. PMID 30604745 DOI: 10.1038/S41467-018-07907-2  0.507
2019 Viny AD, Bowman RL, Liu Y, Lavallee V, Eisman S, Xiao W, Durham BH, Navitski A, Park J, Braunstein S, Alija B, Karzai A, Csete IS, Witkin M, Azizi E, ... ... Dekker J, et al. Stag2 Regulates Hematopoietic Differentiation and Self-Renewal through Alterations in Gene Expression and Topological Control Blood. 134: 279-279. DOI: 10.1182/Blood-2019-123464  0.457
2018 Oudelaar AM, Davies JOJ, Hanssen LLP, Telenius JM, Schwessinger R, Liu Y, Brown JM, Downes DJ, Chiariello AM, Bianco S, Nicodemi M, Buckle VJ, Dekker J, Higgs DR, Hughes JR. Single-allele chromatin interactions identify regulatory hubs in dynamic compartmentalized domains. Nature Genetics. PMID 30374068 DOI: 10.1038/S41588-018-0253-2  0.456
2018 Dixon JR, Xu J, Dileep V, Zhan Y, Song F, Le VT, Yardımcı GG, Chakraborty A, Bann DV, Wang Y, Clark R, Zhang L, Yang H, Liu T, Iyyanki S, ... ... Dekker J, et al. Integrative detection and analysis of structural variation in cancer genomes. Nature Genetics. PMID 30202056 DOI: 10.1038/S41588-018-0195-8  0.421
2018 Kim TH, Dekker J. 3C-Based Chromatin Interaction Analyses. Cold Spring Harbor Protocols. 2018: pdb.top097832. PMID 30181229 DOI: 10.1101/Pdb.Top097832  0.486
2018 Kim TH, Dekker J. 4C Analysis of 3C, ChIP-Loop, and Control Libraries. Cold Spring Harbor Protocols. 2018: pdb.prot097881. PMID 30181222 DOI: 10.1101/Pdb.Prot097881  0.317
2018 Kim TH, Dekker J. Generation of Control Ligation Product Libraries for 3C Analyses. Cold Spring Harbor Protocols. 2018: pdb.prot097865. PMID 30068592 DOI: 10.1101/Pdb.Prot097865  0.381
2018 Kim TH, Dekker J. Generation of ChIP-Loop Libraries. Cold Spring Harbor Protocols. 2018: pdb.prot097857. PMID 30068591 DOI: 10.1101/Pdb.Prot097857  0.333
2018 Kim TH, Dekker J. Generation of 3C Libraries from Cross-Linked Cells. Cold Spring Harbor Protocols. 2018: pdb.prot097840. PMID 30068590 DOI: 10.1101/Pdb.Prot097840  0.341
2018 Pulikkan JA, Hegde M, Ahmad HM, Belaghzal H, Illendula A, Yu J, O'Hagan K, Ou J, Muller-Tidow C, Wolfe SA, Zhu LJ, Dekker J, Bushweller JH, Castilla LH. CBFβ-SMMHC Inhibition Triggers Apoptosis by Disrupting MYC Chromatin Dynamics in Acute Myeloid Leukemia. Cell. 174: 172-186.e21. PMID 29958106 DOI: 10.1016/J.Cell.2018.05.048  0.396
2018 Gao XD, Tu LC, Mir A, Rodriguez T, Ding Y, Leszyk J, Dekker J, Shaffer SA, Zhu LJ, Wolfe SA, Sontheimer EJ. C-BERST: defining subnuclear proteomic landscapes at genomic elements with dCas9-APEX2. Nature Methods. PMID 29735996 DOI: 10.1038/S41592-018-0006-2  0.387
2018 Kim TH, Dekker J. Chromatin Immunoprecipitation (ChIP) Analysis of Protein-DNA Interactions. Cold Spring Harbor Protocols. 2018: pdb.top082586. PMID 29717056 DOI: 10.1101/Pdb.Top082586  0.39
2018 Kim TH, Dekker J. ChIP-Quantitative Polymerase Chain Reaction (ChIP-qPCR). Cold Spring Harbor Protocols. 2018: pdb.prot082628. PMID 29717044 DOI: 10.1101/Pdb.Prot082628  0.333
2018 Kim TH, Dekker J. Preparation of Cross-Linked Chromatin for ChIP. Cold Spring Harbor Protocols. 2018: pdb.prot082602. PMID 29610358 DOI: 10.1101/Pdb.Prot082602  0.366
2018 Kim TH, Dekker J. Formaldehyde Cross-Linking. Cold Spring Harbor Protocols. 2018: pdb.prot082594. PMID 29610357 DOI: 10.1101/Pdb.Prot082594  0.375
2018 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 (New York, N.Y.). PMID 29348367 DOI: 10.1126/Science.Aao6135  0.451
2018 Hedger AK, Oomen ME, Liu V, Moazami MP, Rhind N, Dekker J, Watts JK. Progress toward an amplifiable metabolic label for DNA: conversion of 4-thiothymidine (4sT) to 5-methyl-2′-deoxycytidine and synthesis of a 4sT phosphorodiamidate prodrug Canadian Journal of Chemistry. 96: 636-645. DOI: 10.1139/Cjc-2017-0732  0.302
2018 Gao XD, Tu L, Mir A, Rodriguez T, Ding Y, Leszyk J, Dekker J, Shaffer SA, Zhu LJ, Wolfe SA, Sontheimer EJ. Mapping subnuclear proteomes onto genome architecture via C-BERST Protocol Exchange. DOI: 10.1038/Protex.2018.036  0.327
2017 Rodríguez-Carballo E, Lopez-Delisle L, Zhan Y, Fabre PJ, Beccari L, El-Idrissi I, Huynh THN, Ozadam H, Dekker J, Duboule D. The HoxD cluster is a dynamic and resilient TAD boundary controlling the segregation of antagonistic regulatory landscapes. Genes & Development. 31: 2264-2281. PMID 29273679 DOI: 10.1101/Gad.307769.117  0.384
2017 Narendra V, Bulajić M, Dekker J, Mazzoni EO, Reinberg D. Corrigendum: CTCF-mediated topological boundaries during development foster appropriate gene regulation. Genes & Development. 31: 1714. PMID 28947498 DOI: 10.1101/Gad.306829.117  0.307
2017 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. 549: 219-226. PMID 28905911 DOI: 10.1038/Nature23884  0.368
2017 Schalbetter SA, Goloborodko A, Fudenberg G, Belton JM, Miles C, Yu M, Dekker J, Mirny L, Baxter J. SMC complexes differentially compact mitotic chromosomes according to genomic context. Nature Cell Biology. PMID 28825700 DOI: 10.1038/Ncb3594  0.512
2017 Nora EP, Goloborodko A, Valton AL, Gibcus JH, Uebersohn A, Abdennur N, Dekker J, Mirny LA, Bruneau BG. Targeted Degradation of CTCF Decouples Local Insulation of Chromosome Domains from Genomic Compartmentalization. Cell. 169: 930-944.e22. PMID 28525758 DOI: 10.1016/J.Cell.2017.05.004  0.531
2017 Mizuguchi T, Taneja N, Matsuda E, Belton JM, FitzGerald P, Dekker J, Grewal SIS. Shelterin components mediate genome reorganization in response to replication stress. Proceedings of the National Academy of Sciences of the United States of America. PMID 28490498 DOI: 10.1073/Pnas.1705527114  0.519
2017 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 (San Diego, Calif.). 123: 56-65. PMID 28435001 DOI: 10.1016/J.Ymeth.2017.04.004  0.488
2017 Oomen ME, Dekker J. Epigenetic characteristics of the mitotic chromosome in 1D and 3D. Critical Reviews in Biochemistry and Molecular Biology. 52: 185-204. PMID 28228067 DOI: 10.1080/10409238.2017.1287160  0.475
2017 Kundu S, Ji F, Sunwoo H, Jain G, Lee JT, Sadreyev RI, Dekker J, Kingston RE. Polycomb Repressive Complex 1 Generates Discrete Compacted Domains that Change during Differentiation. Molecular Cell. 65: 432-446.e5. PMID 28157505 DOI: 10.1016/J.Molcel.2017.01.009  0.394
2016 Narendra V, Bulajić M, Dekker J, Mazzoni EO, Reinberg D. CTCF-mediated topological boundaries during development foster appropriate gene regulation. Genes & Development. 30: 2657-2662. PMID 28087711 DOI: 10.1101/Gad.288324.116  0.412
2016 Dekker J. Mapping the 3D genome: Aiming for consilience. Nature Reviews. Molecular Cell Biology. 17: 741-742. PMID 27869158 DOI: 10.1038/Nrm.2016.151  0.416
2016 Liu CF, Brandt GS, Hoang QQ, Naumova N, Lazarevic V, Hwang ES, Dekker J, Glimcher LH, Ringe D, Petsko GA. Crystal structure of the DNA binding domain of the transcription factor T-bet suggests simultaneous recognition of distant genome sites. Proceedings of the National Academy of Sciences of the United States of America. 113: E6572-E6581. PMID 27791029 DOI: 10.1073/Pnas.1613914113  0.357
2016 Barutcu AR, Hong D, Lajoie BR, McCord RP, van Wijnen AJ, Lian JB, Stein JL, Dekker J, Imbalzano AN, Stein GS. RUNX1 contributes to higher-order chromatin organization and gene regulation in breast cancer cells. Biochimica Et Biophysica Acta. PMID 27514584 DOI: 10.1016/J.Bbagrm.2016.08.003  0.412
2016 Giorgetti L, Lajoie BR, Carter AC, Attia M, Zhan Y, Xu J, Chen CJ, Kaplan N, Chang HY, Heard E, Dekker J. Structural organization of the inactive X chromosome in the mouse. Nature. PMID 27437574 DOI: 10.1038/Nature18589  0.534
2016 Barutcu AR, Lajoie BR, Fritz AJ, McCord RP, Nickerson JA, van Wijnen AJ, Lian JB, Stein JL, Dekker J, Stein GS, Imbalzano AN. SMARCA4 regulates gene expression and higher-order chromatin structure in proliferating mammary epithelial cells. Genome Research. PMID 27435934 DOI: 10.1101/Gr.201624.115  0.445
2016 Beagan JA, Gilgenast TG, Kim J, Plona Z, Norton HK, Hu G, Hsu SC, Shields EJ, Lyu X, Apostolou E, Hochedlinger K, Corces VG, Dekker J, Phillips-Cremins JE. Local Genome Topology Can Exhibit an Incompletely Rewired 3D-Folding State during Somatic Cell Reprogramming. Cell Stem Cell. 18: 611-624. PMID 27152443 DOI: 10.1016/J.Stem.2016.04.004  0.397
2016 Valton AL, Dekker J. TAD disruption as oncogenic driver. Current Opinion in Genetics & Development. 36: 34-40. PMID 27111891 DOI: 10.1016/J.Gde.2016.03.008  0.42
2016 Dekker J, Mirny L. The 3D Genome as Moderator of Chromosomal Communication. Cell. 164: 1110-1121. PMID 26967279 DOI: 10.1016/J.Cell.2016.02.007  0.451
2016 Hnisz D, Weintraub AS, Day DS, Valton AL, Bak RO, Li CH, Goldmann J, Lajoie BR, Fan ZP, Sigova AA, Reddy J, Borges-Rivera D, Lee TI, Jaenisch R, Porteus MH, ... Dekker J, et al. Activation of proto-oncogenes by disruption of chromosome neighborhoods. Science (New York, N.Y.). PMID 26940867 DOI: 10.1126/Science.Aad9024  0.421
2016 Montefiori L, Wuerffel R, Roqueiro D, Lajoie B, Guo C, Gerasimova T, De S, Wood W, Becker KG, Dekker J, Liang J, Sen R, Kenter AL. Extremely Long-Range Chromatin Loops Link Topological Domains to Facilitate a Diverse Antibody Repertoire. Cell Reports. PMID 26804913 DOI: 10.1016/J.Celrep.2015.12.083  0.443
2016 Smith EM, Lajoie BR, Jain G, Dekker J. Invariant TAD Boundaries Constrain Cell-Type-Specific Looping Interactions between Promoters and Distal Elements around the CFTR Locus. American Journal of Human Genetics. 98: 185-201. PMID 26748519 DOI: 10.1016/J.Ajhg.2015.12.002  0.482
2016 Dekker J. Abstract IA12: Long-range gene regulation in the context of chromatin domains Cancer Research. 76. DOI: 10.1158/1538-7445.Chromepi15-Ia12  0.517
2015 Belton JM, Lajoie BR, Audibert S, Cantaloube S, Lassadi I, Goiffon I, Baù D, Marti-Renom MA, Bystricky K, Dekker J. The Conformation of Yeast Chromosome III Is Mating Type Dependent and Controlled by the Recombination Enhancer. Cell Reports. 13: 1855-67. PMID 26655901 DOI: 10.1016/J.Celrep.2015.10.063  0.483
2015 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 Biology. 16: 259. PMID 26619908 DOI: 10.1186/S13059-015-0831-X  0.318
2015 Ramírez F, Lingg T, Toscano S, Lam KC, Georgiev P, Chung HR, Lajoie BR, de Wit E, Zhan Y, de Laat W, Dekker J, Manke T, Akhtar A. High-Affinity Sites Form an Interaction Network to Facilitate Spreading of the MSL Complex across the X Chromosome in Drosophila. Molecular Cell. 60: 146-62. PMID 26431028 DOI: 10.1016/J.Molcel.2015.08.024  0.493
2015 Dekker J, Misteli T. Long-Range Chromatin Interactions. Cold Spring Harbor Perspectives in Biology. 7. PMID 26430217 DOI: 10.1101/Cshperspect.A019356  0.509
2015 Barutcu AR, Lajoie BR, McCord RP, Tye CE, Hong D, Messier TL, Browne G, van Wijnen AJ, Lian JB, Stein JL, Dekker J, Imbalzano AN, Stein GS. Chromatin interaction analysis reveals changes in small chromosome and telomere clustering between epithelial and breast cancer cells. Genome Biology. 16: 214. PMID 26415882 DOI: 10.1186/S13059-015-0768-0  0.401
2015 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, et al. Genome-wide Maps of Nuclear Lamina Interactions in Single Human Cells. Cell. 163: 134-47. PMID 26365489 DOI: 10.1016/J.Cell.2015.08.040  0.476
2015 Dekker J, Heard E. Structural and functional diversity of Topologically Associating Domains. Febs Letters. 589: 2877-84. PMID 26348399 DOI: 10.1016/J.Febslet.2015.08.044  0.424
2015 Wang X, Le TB, Lajoie BR, Dekker J, Laub MT, Rudner DZ. Condensin promotes the juxtaposition of DNA flanking its loading site in Bacillus subtilis. Genes & Development. 29: 1661-75. PMID 26253537 DOI: 10.1101/Gad.265876.115  0.45
2015 Rutledge MT, Russo M, Belton JM, Dekker J, Broach JR. The yeast genome undergoes significant topological reorganization in quiescence. Nucleic Acids Research. 43: 8299-313. PMID 26202961 DOI: 10.1093/Nar/Gkv723  0.509
2015 Belton JM, Dekker J. Measuring Chromatin Structure in Budding Yeast. Cold Spring Harbor Protocols. 2015: pdb.top077552. PMID 26134912 DOI: 10.1101/Pdb.Top077552  0.453
2015 Belton JM, Dekker J. Hi-C in Budding Yeast. Cold Spring Harbor Protocols. 2015: pdb.prot085209. PMID 26134906 DOI: 10.1101/Pdb.Prot085209  0.451
2015 Hsieh TH, Weiner A, Lajoie B, Dekker J, Friedman N, Rando OJ. Mapping Nucleosome Resolution Chromosome Folding in Yeast by Micro-C. Cell. 162: 108-19. PMID 26119342 DOI: 10.1016/J.Cell.2015.05.048  0.496
2015 Belton JM, Dekker J. Chromosome Conformation Capture Carbon Copy (5C) in Budding Yeast. Cold Spring Harbor Protocols. 2015: pdb.prot085191. PMID 26034306 DOI: 10.1101/Pdb.Prot085191  0.415
2015 Belton JM, Dekker J. Randomized ligation control for chromosome conformation capture. Cold Spring Harbor Protocols. 2015: pdb.prot085183. PMID 26034305 DOI: 10.1101/Pdb.Prot085183  0.4
2015 Belton JM, Dekker J. Chromosome Conformation Capture (3C) in Budding Yeast. Cold Spring Harbor Protocols. 2015: pdb.prot085175. PMID 26034304 DOI: 10.1101/Pdb.Prot085175  0.494
2015 Crane E, Bian Q, McCord RP, Lajoie BR, Wheeler BS, Ralston EJ, Uzawa S, Dekker J, Meyer BJ. Condensin-driven remodelling of X chromosome topology during dosage compensation. Nature. PMID 26030525 DOI: 10.1038/Nature14450  0.503
2015 Ing-Simmons E, Seitan VC, Faure AJ, Flicek P, Carroll T, Dekker J, Fisher AG, Lenhard B, Merkenschlager M. Spatial enhancer clustering and regulation of enhancer-proximal genes by cohesin. Genome Research. 25: 504-13. PMID 25677180 DOI: 10.1101/Gr.184986.114  0.34
2015 Lajoie BR, Dekker J, Kaplan N. The Hitchhiker's guide to Hi-C analysis: practical guidelines. Methods (San Diego, Calif.). 72: 65-75. PMID 25448293 DOI: 10.1016/J.Ymeth.2014.10.031  0.426
2014 Dekker J. Two ways to fold the genome during the cell cycle: insights obtained with chromosome conformation capture. Epigenetics & Chromatin. 7: 25. PMID 25435919 DOI: 10.1186/1756-8935-7-25  0.516
2014 Mizuguchi T, Fudenberg G, Mehta S, Belton JM, Taneja N, Folco HD, FitzGerald P, Dekker J, Mirny L, Barrowman J, Grewal SI. Cohesin-dependent globules and heterochromatin shape 3D genome architecture in S. pombe. Nature. 516: 432-5. PMID 25307058 DOI: 10.1038/Nature13833  0.543
2014 Kellis M, Wold B, Snyder MP, Bernstein BE, Kundaje A, Marinov GK, Ward LD, Birney E, Crawford GE, Dekker J, Dunham I, Elnitski LL, Farnham PJ, Feingold EA, Gerstein M, et al. Reply to Brunet and Doolittle: Both selected effect and causal role elements can influence human biology and disease. Proceedings of the National Academy of Sciences of the United States of America. 111: E3366. PMID 25275169 DOI: 10.1073/Pnas.1410434111  0.313
2014 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. 157: 950-63. PMID 24813616 DOI: 10.1016/J.Cell.2014.03.025  0.479
2014 Kellis M, Wold B, Snyder MP, Bernstein BE, Kundaje A, Marinov GK, Ward LD, Birney E, Crawford GE, Dekker J, Dunham I, Elnitski LL, Farnham PJ, Feingold EA, Gerstein M, et al. Defining functional DNA elements in the human genome. Proceedings of the National Academy of Sciences of the United States of America. 111: 6131-8. PMID 24753594 DOI: 10.1073/Pnas.1318948111  0.425
2013 Kaplan N, Dekker J. High-throughput genome scaffolding from in vivo DNA interaction frequency. Nature Biotechnology. 31: 1143-7. PMID 24270850 DOI: 10.1038/Nbt.2768  0.422
2013 Naumova N, Imakaev M, Fudenberg G, Zhan Y, Lajoie BR, Mirny LA, Dekker J. Organization of the mitotic chromosome. Science (New York, N.Y.). 342: 948-53. PMID 24200812 DOI: 10.1126/Science.1236083  0.486
2013 Dekker J, Mirny L. Biological techniques: Chromosomes captured one by one Nature. 502: 45-46. PMID 24067607 DOI: 10.1038/Nature12691  0.52
2013 Seitan VC, Faure AJ, Zhan Y, McCord RP, Lajoie BR, Ing-Simmons E, Lenhard B, Giorgetti L, Heard E, Fisher AG, Flicek P, Dekker J, Merkenschlager M. Cohesin-based chromatin interactions enable regulated gene expression within preexisting architectural compartments. Genome Research. 23: 2066-77. PMID 24002784 DOI: 10.1101/Gr.161620.113  0.548
2013 Nora EP, Dekker J, Heard E. Segmental folding of chromosomes: a basis for structural and regulatory chromosomal neighborhoods? Bioessays : News and Reviews in Molecular, Cellular and Developmental Biology. 35: 818-28. PMID 23832846 DOI: 10.1002/Bies.201300040  0.501
2013 Phillips-Cremins JE, Sauria ME, Sanyal A, Gerasimova TI, Lajoie BR, Bell JS, Ong CT, Hookway TA, Guo C, Sun Y, Bland MJ, Wagstaff W, Dalton S, McDevitt TC, Sen R, ... Dekker J, et al. Architectural protein subclasses shape 3D organization of genomes during lineage commitment. Cell. 153: 1281-95. PMID 23706625 DOI: 10.1016/J.Cell.2013.04.053  0.429
2013 Dekker J, Marti-Renom MA, Mirny LA. Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data. Nature Reviews. Genetics. 14: 390-403. PMID 23657480 DOI: 10.1038/Nrg3454  0.455
2013 Gibcus JH, Dekker J. The hierarchy of the 3D genome. Molecular Cell. 49: 773-82. PMID 23473598 DOI: 10.1016/J.Molcel.2013.02.011  0.531
2013 McCord RP, Nazario-Toole A, Zhang H, Chines PS, Zhan Y, Erdos MR, Collins FS, Dekker J, Cao K. Correlated alterations in genome organization, histone methylation, and DNA-lamin A/C interactions in Hutchinson-Gilford progeria syndrome. Genome Research. 23: 260-9. PMID 23152449 DOI: 10.1101/Gr.138032.112  0.307
2013 Belton J, Bau D, Lassardi I, Bystricky K, Marti-Renom M, Dekker J. Mating type specific chromosome conformation in Saccharomyces cerevisiae Epigenetics & Chromatin. 6. DOI: 10.1186/1756-8935-6-S1-P92  0.492
2013 Goloborodko A, Belton JM, Fudenberg G, Imakaev M, Dekker J, Mirny L. S cerevisiae genome as a confined equilibrium polymer brush Epigenetics & Chromatin. 6. DOI: 10.1186/1756-8935-6-S1-P129  0.359
2013 Fudenberg G, Belton J, Goloborodko A, Imakaev M, Dekker J, Mirny L. Polymer models of yeast S. cerevisiae genome organization Epigenetics & Chromatin. 6. DOI: 10.1186/1756-8935-6-S1-P128  0.504
2012 de Laat W, Dekker J. 3C-based technologies to study the shape of the genome Methods. 58: 189-191. PMID 23199640 DOI: 10.1016/J.Ymeth.2012.11.005  0.5
2012 Ferraiuolo MA, Sanyal A, Naumova N, Dekker J, Dostie J. From cells to chromatin: capturing snapshots of genome organization with 5C technology. Methods (San Diego, Calif.). 58: 255-67. PMID 23137922 DOI: 10.1016/J.Ymeth.2012.10.011  0.462
2012 Sanyal A, Lajoie BR, Jain G, Dekker J. The long-range interaction landscape of gene promoters. Nature. 489: 109-13. PMID 22955621 DOI: 10.1038/Nature11279  0.458
2012 Thurman RE, Rynes E, Humbert R, Vierstra J, Maurano MT, Haugen E, Sheffield NC, Stergachis AB, Wang H, Vernot B, Garg K, John S, Sandstrom R, Bates D, Boatman L, ... ... Dekker J, et al. The accessible chromatin landscape of the human genome. Nature. 489: 75-82. PMID 22955617 DOI: 10.1038/Nature11232  0.408
2012 Imakaev M, Fudenberg G, McCord RP, Naumova N, Goloborodko A, Lajoie BR, Dekker J, Mirny LA. Iterative correction of Hi-C data reveals hallmarks of chromosome organization. Nature Methods. 9: 999-1003. PMID 22941365 DOI: 10.1038/Nmeth.2148  0.493
2012 Naumova N, Smith EM, Zhan Y, Dekker J. Analysis of long-range chromatin interactions using Chromosome Conformation Capture. Methods (San Diego, Calif.). 58: 192-203. PMID 22903059 DOI: 10.1016/J.Ymeth.2012.07.022  0.442
2012 Stamatoyannopoulos JA, Snyder M, Hardison R, Ren B, Gingeras T, Gilbert DM, Groudine M, Bender M, Kaul R, Canfield T, Giste E, Johnson A, Zhang M, Balasundaram G, ... ... Dekker J, et al. An encyclopedia of mouse DNA elements (Mouse ENCODE). Genome Biology. 13: 418. PMID 22889292 DOI: 10.1186/Gb-2012-13-8-418  0.39
2012 Belton JM, McCord RP, Gibcus JH, Naumova N, Zhan Y, Dekker J. Hi-C: a comprehensive technique to capture the conformation of genomes. Methods (San Diego, Calif.). 58: 268-76. PMID 22652625 DOI: 10.1016/J.Ymeth.2012.05.001  0.469
2012 Moissiard G, Cokus SJ, Cary J, Feng S, Billi AC, Stroud H, Husmann D, Zhan Y, Lajoie BR, McCord RP, Hale CJ, Feng W, Michaels SD, Frand AR, Pellegrini M, ... Dekker J, et al. MORC family ATPases required for heterochromatin condensation and gene silencing. Science (New York, N.Y.). 336: 1448-51. PMID 22555433 DOI: 10.1126/Science.1221472  0.43
2012 Gibcus JH, Dekker J. The context of gene expression regulation. F1000 Biology Reports. 4: 8. PMID 22500194 DOI: 10.3410/B4-8  0.354
2012 Nora EP, Lajoie BR, Schulz EG, Giorgetti L, Okamoto I, Servant N, Piolot T, Van Berkum NL, Meisig J, Sedat J, Gribnau J, Barillot E, Blüthgen N, Dekker J, Heard E. Spatial partitioning of the regulatory landscape of the X-inactivation centre Nature. 485: 381-385. PMID 22495304 DOI: 10.1038/Nature11049  0.501
2012 Zhang Y, McCord RP, Ho YJ, Lajoie BR, Hildebrand DG, Simon AC, Becker MS, Alt FW, Dekker J. Spatial organization of the mouse genome and its role in recurrent chromosomal translocations. Cell. 148: 908-21. PMID 22341456 DOI: 10.1016/J.Cell.2012.02.002  0.472
2012 Djebali S, Lagarde J, Kapranov P, Lacroix V, Borel C, Mudge JM, Howald C, Foissac S, Ucla C, Chrast J, Ribeca P, Martin D, Murray RR, Yang X, Ghamsari L, ... ... Dekker J, et al. Evidence for transcript networks composed of chimeric RNAs in human cells. Plos One. 7: e28213. PMID 22238572 DOI: 10.1371/Journal.Pone.0028213  0.39
2012 Noble WS, Blau CA, Dekker J, Duan ZJ, Mao Y. The structure and function of chromatin and chromosomes. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 434-40. PMID 22174298  0.337
2012 Dekker J. Folding principles of genomes Bmc Proceedings. 6. DOI: 10.1186/1756-8935-6-S1-O40  0.528
2011 Reece-Hoyes JS, Diallo A, Lajoie B, Kent A, Shrestha S, Kadreppa S, Pesyna C, Dekker J, Myers CL, Walhout AJ. Enhanced yeast one-hybrid assays for high-throughput gene-centered regulatory network mapping. Nature Methods. 8: 1059-64. PMID 22037705 DOI: 10.1038/Nmeth.1748  0.411
2011 Reece-Hoyes JS, Barutcu AR, McCord RP, Jeong JS, Jiang L, MacWilliams A, Yang X, Salehi-Ashtiani K, Hill DE, Blackshaw S, Zhu H, Dekker J, Walhout AJ. Yeast one-hybrid assays for gene-centered human gene regulatory network mapping. Nature Methods. 8: 1050-2. PMID 22037702 DOI: 10.1038/Nmeth.1764  0.392
2011 Umbarger MA, Toro E, Wright MA, Porreca GJ, Baù D, Hong SH, Fero MJ, Zhu LJ, Marti-Renom MA, McAdams HH, Shapiro L, Dekker J, Church GM. The three-dimensional architecture of a bacterial genome and its alteration by genetic perturbation. Molecular Cell. 44: 252-64. PMID 22017872 DOI: 10.1016/j.molcel.2011.09.010  0.412
2011 McCord RP, Dekker J. Translocation mapping exposes the risky lifestyle of B cells. Cell. 147: 20-2. PMID 21962501 DOI: 10.1016/J.Cell.2011.09.005  0.407
2011 Sanyal A, Baù D, Martí-Renom MA, Dekker J. Chromatin globules: a common motif of higher order chromosome structure? Current Opinion in Cell Biology. 23: 325-31. PMID 21489772 DOI: 10.1016/J.Ceb.2011.03.009  0.549
2011 Wang KC, Yang YW, Liu B, Sanyal A, Corces-Zimmerman R, Chen Y, Lajoie BR, Protacio A, Flynn RA, Gupta RA, Wysocka J, Lei M, Dekker J, Helms JA, Chang HY. A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression. Nature. 472: 120-4. PMID 21423168 DOI: 10.1038/Nature09819  0.436
2011 Baù D, Sanyal A, Lajoie BR, Capriotti E, Byron M, Lawrence JB, Dekker J, Marti-Renom MA. The three-dimensional folding of the α-globin gene domain reveals formation of chromatin globules. Nature Structural & Molecular Biology. 18: 107-14. PMID 21131981 DOI: 10.1038/Nsmb.1936  0.414
2011 Bender MA, Bau D, Ragoczy T, Byron R, Zhan Y, Lajoie B, Marti-Renom MA, Dekker J, Groudine MT. Integrating Structural and Functional Studies Leads to a New Model of β-Globin Activation That Suggests Distinct Initiation and Maintenance States Blood. 118: 349-349. DOI: 10.1182/Blood.V118.21.349.349  0.386
2011 Kagey MH, Newman JJ, Bilodeau S, Zhan Y, Orlando DA, Van Berkum NL, Ebmeier CC, Goossens J, Rahl PB, Levine SS, Taatjes DJ, Dekker J, Young RA. Mediator and cohesin connect gene expression and chromatin architecture (Nature (2010) 467 (430-435)) Nature. 472: 247. DOI: 10.1038/Nature09930  0.342
2010 Kim KP, Weiner BM, Zhang L, Jordan A, Dekker J, Kleckner N. Sister cohesion and structural axis components mediate homolog bias of meiotic recombination. Cell. 143: 924-37. PMID 21145459 DOI: 10.1016/J.Cell.2010.11.015  0.716
2010 van Steensel B, Dekker J. Genomics tools for unraveling chromosome architecture. Nature Biotechnology. 28: 1089-95. PMID 20944601 DOI: 10.1038/Nbt.1680  0.507
2010 Kagey MH, Newman JJ, Bilodeau S, Zhan Y, Orlando DA, van Berkum NL, Ebmeier CC, Goossens J, Rahl PB, Levine SS, Taatjes DJ, Dekker J, Young RA. Mediator and cohesin connect gene expression and chromatin architecture. Nature. 467: 430-5. PMID 20720539 DOI: 10.1038/nature09380  0.306
2010 Naumova N, Dekker J. Integrating one-dimensional and three-dimensional maps of genomes. Journal of Cell Science. 123: 1979-88. PMID 20519580 DOI: 10.1242/Jcs.051631  0.486
2010 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. Journal of Visualized Experiments : Jove. PMID 20461051 DOI: 10.3791/1869  0.551
2010 Gheldof N, Smith EM, Tabuchi TM, Koch CM, Dunham I, Stamatoyannopoulos JA, Dekker J. Cell-type-specific long-range looping interactions identify distant regulatory elements of the CFTR gene Nucleic Acids Research. 38: 4325-4336. PMID 20360044 DOI: 10.1093/Nar/Gkq175  0.397
2010 van Berkum NL, Dekker J. Determining spatial chromatin organization of large genomic regions using 5C technology. Methods in Molecular Biology (Clifton, N.J.). 567: 189-213. PMID 19588094 DOI: 10.1007/978-1-60327-414-2_13  0.438
2010 Miele A, Dekker J. Mapping cis- and trans- chromatin interaction networks using chromosome conformation capture (3C). Methods in Molecular Biology (Clifton, N.J.). 464: 105-21. PMID 18951182 DOI: 10.1007/978-1-60327-461-6_7  0.546
2009 Lieberman-Aiden E, van Berkum NL, Williams L, Imakaev M, Ragoczy T, Telling A, Amit I, Lajoie BR, Sabo PJ, Dorschner MO, Sandstrom R, Bernstein B, Bender MA, Groudine M, Gnirke A, ... ... Dekker J, et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science (New York, N.Y.). 326: 289-93. PMID 19815776 DOI: 10.1126/Science.1181369  0.446
2009 Lajoie BR, van Berkum NL, Sanyal A, Dekker J. My5C: web tools for chromosome conformation capture studies. Nature Methods. 6: 690-1. PMID 19789528 DOI: 10.1038/Nmeth1009-690  0.449
2009 D'haene B, Attanasio C, Beysen D, Dostie J, Lemire E, Bouchard P, Field M, Jones K, Lorenz B, Menten B, Buysse K, Pattyn F, Friedli M, Ucla C, Rossier C, ... ... Dekker J, et al. Disease-causing 7.4 kb cis-regulatory deletion disrupting conserved non-coding sequences and their interaction with the FOXL2 promotor: implications for mutation screening. Plos Genetics. 5: e1000522. PMID 19543368 DOI: 10.1371/Journal.Pgen.1000522  0.39
2009 Chang HY, Cuvier O, Dekker J. Gene dates, parties and galas. Symposium on Chromatin Dynamics and Higher Order Organization. Embo Reports. 10: 689-93. PMID 19525922 DOI: 10.1038/Embor.2009.136  0.385
2009 Miele A, Bystricky K, Dekker J. Yeast silent mating type loci form heterochromatic clusters through silencer protein-dependent long-range interactions. Plos Genetics. 5: e1000478. PMID 19424429 DOI: 10.1371/Journal.Pgen.1000478  0.417
2009 Oza P, Jaspersen SL, Miele A, Dekker J, Peterson CL. Mechanisms that regulate localization of a DNA double-strand break to the nuclear periphery. Genes & Development. 23: 912-27. PMID 19390086 DOI: 10.1101/Gad.1782209  0.5
2008 Miele A, Dekker J. Long-range chromosomal interactions and gene regulation. Molecular Biosystems. 4: 1046-57. PMID 18931780 DOI: 10.1039/B803580F  0.492
2008 Dekker J. Mapping in vivo chromatin interactions in yeast suggests an extended chromatin fiber with regional variation in compaction. The Journal of Biological Chemistry. 283: 34532-40. PMID 18930918 DOI: 10.1074/Jbc.M806479200  0.415
2008 Dekker J. Gene regulation in the third dimension. Science (New York, N.Y.). 319: 1793-4. PMID 18369139 DOI: 10.1126/Science.1152850  0.479
2008 Keys JR, Tallack MR, Zhan Y, Papathanasiou P, Goodnow CC, Gaensler KM, Crossley M, Dekker J, Perkins AC. A mechanism for Ikaros regulation of human globin gene switching British Journal of Haematology. 141: 398-406. PMID 18318763 DOI: 10.1111/J.1365-2141.2008.07065.X  0.385
2008 Dekker J. GC- and AT-rich chromatin domains differ in conformation and histone modification status and are differentially modulated by Rpd3p. Genome Biology. 8: R116. PMID 17577398 DOI: 10.1186/Gb-2007-8-6-R116  0.444
2007 Dostie J, Zhan Y, Dekker J. Chromosome conformation capture carbon copy technology. Current Protocols in Molecular Biology / Edited by Frederick M. Ausubel ... [Et Al.]. Unit 21.14. PMID 18265398 DOI: 10.1002/0471142727.Mb2114S80  0.525
2007 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 Nature Cell Biology. 9: 1167-1174. PMID 17828248 DOI: 10.1038/Ncb1637  0.446
2007 Hagège H, Klous P, Braem C, Splinter E, Dekker J, Cathala G, de Laat W, Forné T. Quantitative analysis of chromosome conformation capture assays (3C-qPCR). Nature Protocols. 2: 1722-1733. PMID 17641637 DOI: 10.1038/Nprot.2007.243  0.419
2007 Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, Thurman RE, Kuehn MS, Taylor CM, Neph S, Koch CM, ... ... Dekker J, et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature. 447: 799-816. PMID 17571346 DOI: 10.1038/Nature05874  0.402
2007 Dostie J, Dekker J. Mapping networks of physical interactions between genomic elements using 5C technology. Nature Protocols. 2: 988-1002. PMID 17446898 DOI: 10.1038/Nprot.2007.116  0.459
2007 Perkins AC, Tallack M, Zhan Y, Papathanasiou P, Goodnow C, Gaensler K, Crossley PM, Dekker J, Keys JR. Ikaros Drives Human Haemoglobin Switching by Facilitating Active Chromatin Hub Formation. Blood. 110: 1772-1772. DOI: 10.1182/Blood.V110.11.1772.1772  0.372
2007 Dekker J. Regulation of gene expression through chromatin interaction networks Blood Cells, Molecules, and Diseases. 38: 135. DOI: 10.1016/J.Bcmd.2006.10.039  0.336
2006 Miele A, Gheldof N, Tabuchi TM, Dostie J, Dekker J. Mapping chromatin interactions by chromosome conformation capture. Current Protocols in Molecular Biology / Edited by Frederick M. Ausubel ... [Et Al.]. Unit 21.11. PMID 18265379 DOI: 10.1002/0471142727.Mb2111S74  0.51
2006 Dostie J, Richmond TA, Arnaout RA, Selzer RR, Lee WL, Honan TA, Rubio ED, Krumm A, Lamb J, Nusbaum C, Green RD, Dekker J. Chromosome Conformation Capture Carbon Copy (5C): a massively parallel solution for mapping interactions between genomic elements. Genome Research. 16: 1299-309. PMID 16954542 DOI: 10.1101/Gr.5571506  0.473
2006 Gheldof N, Tabuchi TM, Dekker J. The active FMR1 promoter is associated with a large domain of altered chromatin conformation with embedded local histone modifications. Proceedings of the National Academy of Sciences of the United States of America. 103: 12463-8. PMID 16891414 DOI: 10.1073/Pnas.0605343103  0.434
2006 Dekker J. The three 'C' s of chromosome conformation capture: controls, controls, controls. Nature Methods. 3: 17-21. PMID 16369547 DOI: 10.1038/Nmeth823  0.421
2005 Vakoc CR, Letting DL, Gheldof N, Sawado T, Bender MA, Groudine M, Weiss MJ, Dekker J, Blobel GA. Proximity among distant regulatory elements at the beta-globin locus requires GATA-1 and FOG-1. Molecular Cell. 17: 453-62. PMID 15694345 DOI: 10.1016/J.Molcel.2004.12.028  0.363
2004 Kleckner N, Zickler D, Jones GH, Dekker J, Padmore R, Henle J, Hutchinson J. A mechanical basis for chromosome function. Proceedings of the National Academy of Sciences of the United States of America. 101: 12592-7. PMID 15299144 DOI: 10.1073/Pnas.0402724101  0.635
2004 Vakoc C, Dekker J, Blobel GA. GATA-1 Directly Induces Physical Proximity between the LCR and β Globin Promoter in Erythroid Cells. Blood. 104: 1612-1612. DOI: 10.1182/Blood.V104.11.1612.1612  0.423
2003 Dekker J. A closer look at long-range chromosomal interactions. Trends in Biochemical Sciences. 28: 277-80. PMID 12826398 DOI: 10.1016/S0968-0004(03)00089-6  0.475
2002 Dekker J, Rippe K, Dekker M, Kleckner N. Capturing chromosome conformation. Science (New York, N.Y.). 295: 1306-11. PMID 11847345 DOI: 10.1126/Science.1067799  0.68
2000 Cha RS, Weiner BM, Keeney S, Dekker J, Kleckner N. Progression of meiotic DNA replication is modulated by interchromosomal interaction proteins, negatively by Spo11p and positively by Rec8p. Genes & Development. 14: 493-503. PMID 10691741  0.761
2000 Cha RS, Weiner BM, Keeney S, Dekker J, Kleckner N. Progression of meiotic DNA replication is modulated by interchromosomal interaction proteins, negatively by Spo11p and positively by Rec8p Genes & Development. 14: 493-503. DOI: 10.1101/Gad.14.4.493  0.779
1998 Dekker J, Kanellopoulos PN, van Oosterhout JA, Stier G, Tucker PA, van der Vliet PC. ATP-independent DNA unwinding by the adenovirus single-stranded DNA binding protein requires a flexible DNA binding loop. Journal of Molecular Biology. 277: 825-38. PMID 9545375 DOI: 10.1006/Jmbi.1998.1652  0.392
1997 Dekker J, Kanellopoulos PN, Loonstra AK, van Oosterhout JA, Leonard K, Tucker PA, van der Vliet PC. Multimerization of the adenovirus DNA-binding protein is the driving force for ATP-independent DNA unwinding during strand displacement synthesis. The Embo Journal. 16: 1455-63. PMID 9135160 DOI: 10.1093/Emboj/16.6.1455  0.368
1996 Dekker J, van Oosterhout JA, van der Vliet PC. Two regions within the DNA binding domain of nuclear factor I interact with DNA and stimulate adenovirus DNA replication independently. Molecular and Cellular Biology. 16: 4073-80. PMID 8754805 DOI: 10.1128/Mcb.16.8.4073  0.367
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