| Year |
Citation |
Score |
| 2024 |
Samejima K, Gibcus JH, Abraham S, Cisneros-Soberanis F, Samejima I, Beckett AJ, Pučeková N, Abad MA, Medina-Pritchard B, Paulson JR, Xie L, Jeyaprakash AA, Prior IA, Mirny LA, Dekker J, et al. Rules of engagement for condensins and cohesins guide mitotic chromosome formation. Biorxiv : the Preprint Server For Biology. PMID 38659940 DOI: 10.1101/2024.04.18.590027 |
0.415 |
|
| 2024 |
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. Molecular Cell. PMID 38521067 DOI: 10.1016/j.molcel.2024.02.025 |
0.305 |
|
| 2023 |
Yin Q, Yang CH, Strelkova OS, Wu J, Sun Y, Gopalan S, Yang L, Dekker J, Fazzio TG, Li XZ, Gibcus J, Rando OJ. Revisiting chromatin packaging in mouse sperm. Genome Research. PMID 38129076 DOI: 10.1101/gr.277845.123 |
0.355 |
|
| 2023 |
Kocanova S, Raynal F, Goiffon I, Oksuz BA, Baú D, Kamgoué A, Cantaloube S, Zhan Y, Lajoie B, Marti-Renom MA, Dekker J, Bystricky K. Enhancer-driven 3D chromatin domain folding modulates transcription in human mammary tumor cells. Life Science Alliance. 7. PMID 37989525 DOI: 10.26508/lsa.202302154 |
0.34 |
|
| 2023 |
Min J, Zhao J, Zagelbaum J, Lee J, Takahashi S, Cummings P, Schooley A, Dekker J, Gottesman ME, Rabadan R, Gautier J. Mechanisms of insertions at a DNA double-strand break. Molecular Cell. PMID 37402370 DOI: 10.1016/j.molcel.2023.06.016 |
0.319 |
|
| 2023 |
Syed SA, Shqillo K, Nand A, Zhan Y, Dekker J, Imbalzano AN. Protein arginine methyltransferase 5 (Prmt5) localizes to chromatin loop anchors and modulates expression of genes at TAD boundaries during early adipogenesis. Biorxiv : the Preprint Server For Biology. PMID 37398486 DOI: 10.1101/2023.06.13.544859 |
0.344 |
|
| 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 |
0.353 |
|
| 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 |
0.327 |
|
| 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 |
0.369 |
|
| 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 |
0.378 |
|
| 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 |
0.356 |
|
| 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 |
0.324 |
|
| 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 |
0.35 |
|
| 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 |
0.34 |
|
| 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 |
0.34 |
|
| 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 |
0.438 |
|
| 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 |
0.382 |
|
| 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 |
0.461 |
|
| 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 |
0.445 |
|
| 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 |
0.486 |
|
| 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 |
0.519 |
|
| 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 |
0.417 |
|
| 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 |
0.457 |
|
| 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 |
0.41 |
|
| 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 |
0.373 |
|
| 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 |
0.501 |
|
| 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 |
0.401 |
|
| 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 |
0.45 |
|
| 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 |
0.506 |
|
| 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 |
0.458 |
|
| 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 |
0.422 |
|
| 2018 |
Kim TH, Dekker J. 3C-Based Chromatin Interaction Analyses. Cold Spring Harbor Protocols. 2018: pdb.top097832. PMID 30181229 DOI: 10.1101/Pdb.Top097832 |
0.487 |
|
| 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 |
0.318 |
|
| 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 |
0.382 |
|
| 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 |
0.388 |
|
| 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 |
0.391 |
|
| 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 |
0.334 |
|
| 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 |
0.45 |
|
| 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 |
0.328 |
|
| 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 |
0.369 |
|
| 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 |
0.511 |
|
| 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 |
0.518 |
|
| 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 |
0.417 |
|
| 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 |
0.414 |
|
| 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 |
0.446 |
|
| 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 |
0.398 |
|
| 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 |
0.45 |
|
| 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 |
0.481 |
|
| 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 |
0.482 |
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| 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 |
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| 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 |
0.492 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
0.449 |
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| 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 |
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| 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 |
0.454 |
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| 2015 |
Belton JM, Dekker J. Hi-C in Budding Yeast. Cold Spring Harbor Protocols. 2015: pdb.prot085209. PMID 26134906 DOI: 10.1101/Pdb.Prot085209 |
0.452 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
0.502 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
0.423 |
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| 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 |
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| 2013 |
Dekker J, Mirny L. Biological techniques: Chromosomes captured one by one Nature. 502: 45-46. PMID 24067607 DOI: 10.1038/Nature12691 |
0.52 |
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| 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 |
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| 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 |
0.5 |
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| 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 |
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| 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 |
0.456 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
0.443 |
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| 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 |
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| 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 |
0.47 |
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| 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 |
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| 2012 |
Gibcus JH, Dekker J. The context of gene expression regulation. F1000 Biology Reports. 4: 8. PMID 22500194 DOI: 10.3410/B4-8 |
0.355 |
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| 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 |
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| 2012 |
Felsenfeld G, Dekker J. Genome architecture and expression. Current Opinion in Genetics & Development. 22: 59-61. PMID 22483506 DOI: 10.1016/J.Gde.2012.03.003 |
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| 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 |
0.473 |
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| 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 |
0.391 |
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| 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 |
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| 2012 |
Dekker J. Folding principles of genomes Bmc Proceedings. 6. DOI: 10.1186/1756-8935-6-S1-O40 |
0.528 |
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| 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 |
0.412 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
0.548 |
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| 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 |
0.437 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 2010 |
van Steensel B, Dekker J. Genomics tools for unraveling chromosome architecture. Nature Biotechnology. 28: 1089-95. PMID 20944601 DOI: 10.1038/Nbt.1680 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 2008 |
Miele A, Dekker J. Long-range chromosomal interactions and gene regulation. Molecular Biosystems. 4: 1046-57. PMID 18931780 DOI: 10.1039/B803580F |
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| 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 |
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| 2008 |
Dekker J. Gene regulation in the third dimension. Science (New York, N.Y.). 319: 1793-4. PMID 18369139 DOI: 10.1126/Science.1152850 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
0.474 |
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| 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 |
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| 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 |
0.422 |
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| 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 |
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| 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 |
0.631 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
0.763 |
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| 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 |
0.781 |
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| 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 |
0.39 |
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| 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 |
0.367 |
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| 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 |
0.366 |
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