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Job Dekker PhD

TitleProfessor
Endowed TitleJoseph J. Byrne Chair in Biomedical Research
InstitutionUMass Chan Medical School
DepartmentSystems Biology
AddressUMass Chan Medical School
368 Plantation Street AS5-1049
Worcester MA 01605
Phone508-856-4371
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    Other Positions
    InstitutionT.H. Chan School of Medicine
    DepartmentBiochemistry and Molecular Biotechnology

    InstitutionT.H. Chan School of Medicine
    DepartmentSystems Biology

    InstitutionMorningside Graduate School of Biomedical Sciences
    DepartmentBiochemistry and Molecular Pharmacology

    InstitutionMorningside Graduate School of Biomedical Sciences
    DepartmentBioinformatics and Computational Biology

    InstitutionMorningside Graduate School of Biomedical Sciences
    DepartmentInterdisciplinary Graduate Program

    InstitutionMorningside Graduate School of Biomedical Sciences
    DepartmentMD/PhD Program

    InstitutionUMass Chan Programs, Centers and Institutes
    DepartmentBioinformatics and Integrative Biology


    Collapse Biography 
    Collapse education and training
    Utrecht University, Utrecht, , NetherlandsMSBiology
    Utrecht University, Utrecht, , NetherlandsPHDPhysiological Chemistry
    Collapse awards and honors
    2020Elected EMBO Associate Member
    2018International Award of the Biochemical Society
    2018Novitski Prize of the Genetics Society of America
    2015Investigator, Howard Hughes Medical Institute
    2014Elected Fellow of the American Association for the Advancement of Science (AAAS)
    2011American Society for Biochemistry and Molecular Biology Young Investigator Award
    2007W.M. Keck Foundation Distinguished Young Scholar in Medical Research Award

    Collapse Overview 
    Collapse Rotation Projects
    ?

    Rotation Projects

    Multiple rotation projects are available in several areas related to long-range gene regulation and higher order chromosome organization.  Projects include thorough analyses of the biochemical mechanisms of long-range gene regulation of specific disease-related genes, as well as large-scale analyses of chromosome organization using high-throughput genomics technologies (5C and Hi-C).  The lab employs a wide range of experimental approaches, including cell culture, protein biochemistry, microscopy, genomics as well computational approaches such as bioinformatics and modeling.  Specific rotation projects are determined dependent on the interest of the student.



    Collapse Bibliographic 
    Collapse selected publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
    Newest   |   Oldest   |   Most Cited   |   Most Discussed   |   Timeline   |   Field Summary   |   Plain Text
    PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Stevens L, Moya ND, Tanny RE, Gibson SB, Tracey A, Na H, Chitrakar R, Dekker J, Walhout AJM, Baugh LR, Andersen EC. Chromosome-Level Reference Genomes for Two Strains of Caenorhabditis briggsae: An Improved Platform for Comparative Genomics. Genome Biol Evol. 2022 Apr 10; 14(4). PMID: 35348662.
      Citations:    Fields:    Translation:AnimalsCells
    2. Sanders JT, Golloshi R, Das P, Xu Y, Terry PH, Nash DG, Dekker J, McCord RP. Loops, topologically associating domains, compartments, and territories are elastic and robust to dramatic nuclear volume swelling. Sci Rep. 2022 03 18; 12(1):4721. PMID: 35304523.
      Citations:    Fields:    
    3. Leidescher S, Ribisel J, Ullrich S, Feodorova Y, Hildebrand E, Galitsyna A, Bultmann S, Link S, Thanisch K, Mulholland C, Dekker J, Leonhardt H, Mirny L, Solovei I. Spatial organization of transcribed eukaryotic genes. Nat Cell Biol. 2022 Mar; 24(3):327-339. PMID: 35177821.
      Citations: 2     Fields:    Translation:AnimalsCells
    4. Cha HJ, Uyan Ö, Kai Y, Liu T, Zhu Q, Tothova Z, Botten GA, Xu J, Yuan GC, Dekker J, Orkin SH. Inner nuclear protein Matrin-3 coordinates cell differentiation by stabilizing chromatin architecture. Nat Commun. 2021 10 29; 12(1):6241. PMID: 34716321.
      Citations: 2     Fields:    Translation:AnimalsCells
    5. Mirny L, Dekker J. Mechanisms of Chromosome Folding and Nuclear Organization: Their Interplay and Open Questions. Cold Spring Harb Perspect Biol. 2021 Sep 13. PMID: 34518339.
      Citations: 3     Fields:    
    6. Voolstra CR, Aranda M, Zhan Y, Dekker J. Symbiodinium microadriaticum (coral microalgal endosymbiont). Trends Genet. 2021 11; 37(11):1044-1045. PMID: 34518054.
      Citations:    Fields:    Translation:Animals
    7. 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. Systematic evaluation of chromosome conformation capture assays. Nat Methods. 2021 09; 18(9):1046-1055. PMID: 34480151.
      Citations: 4     Fields:    Translation:HumansCells
    8. Choppakatla P, Dekker B, Cutts EE, Vannini A, Dekker J, Funabiki H. Linker histone H1.8 inhibits chromatin binding of condensins and DNA topoisomerase II to tune chromosome length and individualization. Elife. 2021 08 18; 10. PMID: 34406118.
      Citations: 4     Fields:    Translation:AnimalsCells
    9. Tigano A, Jacobs A, Wilder AP, Nand A, Zhan Y, Dekker J, Therkildsen NO. Erratum to: Chromosome-Level Assembly of the Atlantic Silverside Genome Reveals Extreme Levels of Sequence Diversity and Structural Genetic Variation. Genome Biol Evol. 2021 Jul 06; 13(7). PMID: 34332503.
      Citations: 1     Fields:    
    10. Lafontaine DL, Yang L, Dekker J, Gibcus JH. Hi-C 3.0: Improved Protocol for Genome-Wide Chromosome Conformation Capture. Curr Protoc. 2021 Jul; 1(7):e198. PMID: 34286910.
      Citations: 3     Fields:    Translation:AnimalsCells
    11. Tigano A, Jacobs A, Wilder AP, Nand A, Zhan Y, Dekker J, Therkildsen NO. Chromosome-Level Assembly of the Atlantic Silverside Genome Reveals Extreme Levels of Sequence Diversity and Structural Genetic Variation. Genome Biol Evol. 2021 06 08; 13(6). PMID: 33964136.
      Citations:    Fields:    Translation:Animals
    12. Nand A, Zhan Y, Salazar OR, Aranda M, Voolstra CR, Dekker J. Genetic and spatial organization of the unusual chromosomes of the dinoflagellate Symbiodinium microadriaticum. Nat Genet. 2021 05; 53(5):618-629. PMID: 33927399.
      Citations: 2     Fields:    Translation:AnimalsCells
    13. 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. Nat Genet. 2021 03; 53(3):367-378. PMID: 33574602.
      Citations: 15     Fields:    Translation:HumansCells
    14. Tothova Z, Valton AL, Gorelov RA, Vallurupalli M, Krill-Burger JM, Holmes A, Landers CC, Haydu JE, Malolepsza E, Hartigan C, Donahue M, Popova KD, Koochaki S, Venev SV, Rivera J, Chen E, Lage K, Schenone M, D'Andrea AD, Carr SA, Morgan EA, Dekker J, Ebert BL. Cohesin mutations alter DNA damage repair and chromatin structure and create therapeutic vulnerabilities in MDS/AML. JCI Insight. 2021 02 08; 6(3). PMID: 33351783.
      Citations: 10     Fields:    Translation:HumansAnimalsCells
    15. Oomen ME, Hedger AK, Watts JK, Dekker J. Detecting chromatin interactions between and along sister chromatids with SisterC. Nat Methods. 2020 10; 17(10):1002-1009. PMID: 32968250.
      Citations: 5     Fields:    Translation:AnimalsCells
    16. Brossas C, Valton AL, Venev SV, Chilaka S, Counillon A, Laurent M, Goncalves C, Duriez B, Picard F, Dekker J, Prioleau MN. Clustering of strong replicators associated with active promoters is sufficient to establish an early-replicating domain. EMBO J. 2020 11 02; 39(21):e99520. PMID: 32935369.
      Citations: 2     Fields:    Translation:HumansCells
    17. 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. Nat Struct Mol Biol. 2020 12; 27(12):1105-1114. PMID: 32929283.
      Citations: 8     Fields:    Translation:HumansCells
    18. Fitz-James MH, Tong P, Pidoux AL, Ozadam H, Yang L, White SA, Dekker J, Allshire RC. Large domains of heterochromatin direct the formation of short mitotic chromosome loops. Elife. 2020 09 11; 9. PMID: 32915140.
      Citations: 7     Fields:    Translation:HumansAnimalsCells
    19. 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. Mol Cell. 2020 05 07; 78(3):554-565.e7. PMID: 32213324.
      Citations: 82     Fields:    Translation:HumansAnimalsCells
    20. Hildebrand EM, Dekker J. Mechanisms and Functions of Chromosome Compartmentalization. Trends Biochem Sci. 2020 05; 45(5):385-396. PMID: 32311333.
      Citations: 35     Fields:    Translation:Cells
    21. Dossin F, Pinheiro I, ?ylicz 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. 2020 02; 578(7795):455-460. PMID: 32025035.
      Citations: 45     Fields:    Translation:AnimalsCells
    22. 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. Mol Cell. 2020 01 16; 77(2):324-337.e8. PMID: 31704182.
      Citations: 23     Fields:    Translation:AnimalsCells
    23. Abramo K, Valton AL, Venev SV, Ozadam H, Fox AN, Dekker J. A chromosome folding intermediate at the condensin-to-cohesin transition during telophase. Nat Cell Biol. 2019 11; 21(11):1393-1402. PMID: 31685986.
      Citations: 47     Fields:    Translation:HumansCells
    24. 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. Nat Commun. 2019 10 03; 10(1):4485. PMID: 31582763.
      Citations: 13     Fields:    Translation:AnimalsCells
    25. 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, Mirny LA, Wu CT. The genome-wide multi-layered architecture of chromosome pairing in early Drosophila embryos. Nat Commun. 2019 10 03; 10(1):4486. PMID: 31582744.
      Citations: 11     Fields:    Translation:AnimalsCells
    26. 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, Baslan T, Ott CJ, Pe'er D, Dekker J, Koche R, Levine RL. Cohesin Members Stag1 and Stag2 Display Distinct Roles in Chromatin Accessibility and Topological Control of HSC Self-Renewal and Differentiation. Cell Stem Cell. 2019 11 07; 25(5):682-696.e8. PMID: 31495782.
      Citations: 39     Fields:    Translation:HumansAnimalsCells
    27. Falk M, Feodorova Y, Naumova N, Imakaev M, Lajoie BR, Leonhardt H, Joffe B, Dekker J, Fudenberg G, Solovei I, Mirny LA. Publisher Correction: Heterochromatin drives compartmentalization of inverted and conventional nuclei. Nature. 2019 Aug; 572(7771):E22. PMID: 31375785.
      Citations:    Fields:    
    28. 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, Dalton S, Corces VG, Gilbert DM. Rapid Irreversible Transcriptional Reprogramming in Human Stem Cells Accompanied by Discordance between Replication Timing and Chromatin Compartment. Stem Cell Reports. 2019 07 09; 13(1):193-206. PMID: 31231024.
      Citations: 6     Fields:    Translation:HumansCells
    29. 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. 2019 06; 570(7761):395-399. PMID: 31168090.
      Citations: 141     Fields:    Translation:AnimalsCells
    30. Yard?mc? 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, Taylor J, Yue F, Dekker J, Noble WS. Measuring the reproducibility and quality of Hi-C data. Genome Biol. 2019 03 19; 20(1):57. PMID: 30890172.
      Citations: 38     Fields:    Translation:HumansCells
    31. 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. 2019 03 07; 176(6):1502-1515.e10. PMID: 30799036.
      Citations: 131     Fields:    Translation:HumansCells
    32. Oomen ME, Hansen AS, Liu Y, Darzacq X, Dekker J. CTCF sites display cell cycle-dependent dynamics in factor binding and nucleosome positioning. Genome Res. 2019 02; 29(2):236-249. PMID: 30655336.
      Citations: 39     Fields:    Translation:HumansCells
    33. 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. Nat Commun. 2019 01 03; 10(1):30. PMID: 30604745.
      Citations: 35     Fields:    Translation:AnimalsCells
    34. Metkar M, Ozadam H, Lajoie BR, Imakaev M, Mirny LA, Dekker J, Moore MJ. Higher-Order Organization Principles of Pre-translational mRNPs. Mol Cell. 2018 11 15; 72(4):715-726.e3. PMID: 30415953.
      Citations: 21     Fields:    Translation:HumansCells
    35. 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. Nat Genet. 2018 12; 50(12):1744-1751. PMID: 30374068.
      Citations: 45     Fields:    Translation:AnimalsCells
    36. Dixon JR, Xu J, Dileep V, Zhan Y, Song F, Le VT, Yard?mc? GG, Chakraborty A, Bann DV, Wang Y, Clark R, Zhang L, Yang H, Liu T, Iyyanki S, An L, Pool C, Sasaki T, Rivera-Mulia JC, Ozadam H, Lajoie BR, Kaul R, Buckley M, Lee K, Diegel M, Pezic D, Ernst C, Hadjur S, Odom DT, Stamatoyannopoulos JA, Broach JR, Hardison RC, Ay F, Noble WS, Dekker J, Gilbert DM, Yue F. Integrative detection and analysis of structural variation in cancer genomes. Nat Genet. 2018 10; 50(10):1388-1398. PMID: 30202056.
      Citations: 82     Fields:    Translation:HumansCells
    37. Kim TH, Dekker J. 5C Analysis of 3C, ChIP-Loop, and Control Libraries. Cold Spring Harb Protoc. 2018 09 04; 2018(9). PMID: 30181223.
      Citations:    Fields:    
    38. Kim TH, Dekker J. 4C Analysis of 3C, ChIP-Loop, and Control Libraries. Cold Spring Harb Protoc. 2018 09 04; 2018(9). PMID: 30181222.
      Citations:    Fields:    
    39. Kim TH, Dekker J. 3C-Based Chromatin Interaction Analyses. Cold Spring Harb Protoc. 2018 09 04; 2018(9). PMID: 30181229.
      Citations: 5     Fields:    Translation:Cells
    40. Kim TH, Dekker J. Polymerase Chain Reaction (PCR) Detection of 3C Ligation Products Present in 3C, ChIP-Loop, and Control Libraries: Library Titration and Interaction Frequency Analysis. Cold Spring Harb Protoc. 2018 09 04; 2018(9). PMID: 30181221.
      Citations:    Fields:    Translation:Humans
    41. 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. CBF?-SMMHC Inhibition Triggers Apoptosis by Disrupting MYC Chromatin Dynamics in Acute Myeloid Leukemia. Cell. 2018 08 23; 174(5):1325. PMID: 30142347.
      Citations: 9     Fields:    
    42. Kim TH, Dekker J. Generation of 3C Libraries from Cross-Linked Cells. Cold Spring Harb Protoc. 2018 08 01; 2018(8). PMID: 30068590.
      Citations:    Fields:    Translation:Cells
    43. Kim TH, Dekker J. Generation of ChIP-Loop Libraries. Cold Spring Harb Protoc. 2018 08 01; 2018(8). PMID: 30068591.
      Citations:    Fields:    Translation:Cells
    44. Kim TH, Dekker J. Generation of Control Ligation Product Libraries for 3C Analyses. Cold Spring Harb Protoc. 2018 08 01; 2018(8). PMID: 30068592.
      Citations: 1     Fields:    Translation:HumansAnimalsCells
    45. 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. Mol Cell. 2018 07 05; 71(1):191. PMID: 29979966.
      Citations: 10     Fields:    
    46. 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. CBF?-SMMHC Inhibition Triggers Apoptosis by Disrupting MYC Chromatin Dynamics in Acute Myeloid Leukemia. Cell. 2018 06 28; 174(1):172-186.e21. PMID: 29958106.
      Citations: 27     Fields:    Translation:HumansAnimalsCells
    47. 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. Nat Methods. 2018 06; 15(6):433-436. PMID: 29735996.
      Citations: 45     Fields:    Translation:HumansCells
    48. Kim TH, Dekker J. Chromatin Immunoprecipitation (ChIP) Analysis of Protein-DNA Interactions. Cold Spring Harb Protoc. 2018 05 01; 2018(5). PMID: 29717056.
      Citations: 1     Fields:    Translation:Cells
    49. Kim TH, Dekker J. ChIP-chip. Cold Spring Harb Protoc. 2018 05 01; 2018(5). PMID: 29717045.
      Citations: 1     Fields:    Translation:HumansAnimals
    50. Kim TH, Dekker J. ChIP-seq. Cold Spring Harb Protoc. 2018 05 01; 2018(5). PMID: 29717046.
      Citations: 1     Fields:    
    51. Kim TH, Dekker J. ChIP-Quantitative Polymerase Chain Reaction (ChIP-qPCR). Cold Spring Harb Protoc. 2018 05 01; 2018(5). PMID: 29717044.
      Citations: 10     Fields:    
    52. Kim TH, Dekker J. Preparation of Cross-Linked Chromatin for ChIP. Cold Spring Harb Protoc. 2018 04 02; 2018(4). PMID: 29610358.
      Citations:    Fields:    Translation:HumansCells
    53. Kim TH, Dekker J. ChIP. Cold Spring Harb Protoc. 2018 04 02; 2018(4). PMID: 29610359.
      Citations: 1     Fields:    Translation:Humans
    54. Kim TH, Dekker J. Formaldehyde Cross-Linking. Cold Spring Harb Protoc. 2018 04 02; 2018(4). PMID: 29610357.
      Citations: 1     Fields:    Translation:HumansCells
    55. Gibcus JH, Samejima K, Goloborodko A, Samejima I, Naumova N, Nuebler J, Kanemaki MT, Xie L, Paulson JR, Earnshaw WC, Mirny LA, Dekker J. A pathway for mitotic chromosome formation. Science. 2018 02 09; 359(6376). PMID: 29348367.
      Citations: 207     Fields:    Translation:AnimalsCells
    56. 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. Corrigendum: The 4D nucleome project. Nature. 2017 12 14; 552(7684):278. PMID: 29168505.
      Citations: 1     Fields:    
    57. 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 Dev. 2017 11 15; 31(22):2264-2281. PMID: 29273679.
      Citations: 46     Fields:    Translation:AnimalsCells
    58. Dekker J, Belmont AS, Guttman M, Leshyk VO, Lis JT, Lomvardas S, Mirny LA, O'Shea CC, Park PJ, Ren B, Politz JCR, Shendure J, Zhong S. The 4D nucleome project. Nature. 2017 09 13; 549(7671):219-226. PMID: 28905911.
      Citations: 185     Fields:    Translation:HumansAnimalsCells
    59. 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. Nat Cell Biol. 2017 Sep; 19(9):1071-1080. PMID: 28825700.
      Citations: 52     Fields:    Translation:AnimalsCells
    60. Narendra V, Bulaji? M, Dekker J, Mazzoni EO, Reinberg D. Corrigendum: CTCF-mediated topological boundaries during development foster appropriate gene regulation. Genes Dev. 2017 08 15; 31(16):1714. PMID: 28947498.
      Citations: 1     Fields:    
    61. 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. 2017 May 18; 169(5):930-944.e22. PMID: 28525758.
      Citations: 480     Fields:    Translation:AnimalsCells
    62. Mizuguchi T, Taneja N, Matsuda E, Belton JM, FitzGerald P, Dekker J, Grewal SIS. Shelterin components mediate genome reorganization in response to replication stress. Proc Natl Acad Sci U S A. 2017 05 23; 114(21):5479-5484. PMID: 28490498.
      Citations: 8     Fields:    Translation:AnimalsCells
    63. Belaghzal H, Dekker J, Gibcus JH. Hi-C 2.0: An optimized Hi-C procedure for high-resolution genome-wide mapping of chromosome conformation. Methods. 2017 07 01; 123:56-65. PMID: 28435001.
      Citations: 86     Fields:    Translation:HumansCells
    64. Oomen ME, Dekker J. Epigenetic characteristics of the mitotic chromosome in 1D and 3D. Crit Rev Biochem Mol Biol. 2017 Apr; 52(2):185-204. PMID: 28228067.
      Citations: 12     Fields:    Translation:HumansAnimalsCells
    65. 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. Mol Cell. 2017 Feb 02; 65(3):432-446.e5. PMID: 28157505.
      Citations: 109     Fields:    Translation:HumansAnimalsCells
    66. McGeachie MJ, Yates KP, Zhou X, Guo F, Sternberg AL, Van Natta ML, Wise RA, Szefler SJ, Sharma S, Kho AT, Cho MH, Croteau-Chonka DC, Castaldi PJ, Jain G, Sanyal A, Zhan Y, Lajoie BR, Dekker J, Stamatoyannopoulos J, Covar RA, Zeiger RS, Adkinson NF, Williams PV, Kelly HW, Grasemann H, Vonk JM, Koppelman GH, Postma DS, Raby BA, Houston I, Lu Q, Fuhlbrigge AL, Tantisira KG, Silverman EK, Tonascia J, Strunk RC, Weiss ST. Genetics and Genomics of Longitudinal Lung Function Patterns in Individuals with Asthma. Am J Respir Crit Care Med. 2016 12 15; 194(12):1465-1474. PMID: 27367781.
      Citations: 9     Fields:    Translation:Humans
    67. Narendra V, Bulaji? M, Dekker J, Mazzoni EO, Reinberg D. CTCF-mediated topological boundaries during development foster appropriate gene regulation. Genes Dev. 2016 12 15; 30(24):2657-2662. PMID: 28087711.
      Citations: 59     Fields:    Translation:AnimalsCells
    68. Dekker J. Mapping the 3D genome: Aiming for consilience. Nat Rev Mol Cell Biol. 2016 Nov 21; 17(12):741-742. PMID: 27869158.
      Citations: 30     Fields:    Translation:HumansCells
    69. 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. Proc Natl Acad Sci U S A. 2016 10 25; 113(43):E6572-E6581. PMID: 27791029.
      Citations: 7     Fields:    Translation:AnimalsCells
    70. 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. Biochim Biophys Acta. 2016 11; 1859(11):1389-1397. PMID: 27514584.
      Citations: 28     Fields:    Translation:HumansCells
    71. 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 Res. 2016 09; 26(9):1188-201. PMID: 27435934.
      Citations: 45     Fields:    Translation:HumansCells
    72. 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. 2016 07 28; 535(7613):575-9. PMID: 27437574.
      Citations: 167     Fields:    Translation:AnimalsCells
    73. 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. 2016 05 05; 18(5):611-24. PMID: 27152443.
      Citations: 50     Fields:    Translation:AnimalsCells
    74. Valton AL, Dekker J. TAD disruption as oncogenic driver. Curr Opin Genet Dev. 2016 02; 36:34-40. PMID: 27111891.
      Citations: 76     Fields:    Translation:HumansCells
    75. Dekker J, Guttman M, Lomvardas S. A Guide to Packing Your DNA. Cell. 2016 Apr 07; 165(2):259-61. PMID: 27058655.
      Citations: 1     Fields:    Translation:AnimalsCells
    76. Dekker J, Mirny L. The 3D Genome as Moderator of Chromosomal Communication. Cell. 2016 Mar 10; 164(6):1110-1121. PMID: 26967279.
      Citations: 338     Fields:    Translation:HumansAnimalsCells
    77. 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, Young RA. Activation of proto-oncogenes by disruption of chromosome neighborhoods. Science. 2016 Mar 25; 351(6280):1454-1458. PMID: 26940867.
      Citations: 375     Fields:    Translation:HumansCells
    78. 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 Rep. 2016 Feb 02; 14(4):896-906. PMID: 26804913.
      Citations: 31     Fields:    Translation:AnimalsCells
    79. 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. Am J Hum Genet. 2016 Jan 07; 98(1):185-201. PMID: 26748519.
      Citations: 70     Fields:    Translation:HumansCells
    80. Servant N, Varoquaux N, Lajoie BR, Viara E, Chen CJ, Vert JP, Heard E, Dekker J, Barillot E. HiC-Pro: an optimized and flexible pipeline for Hi-C data processing. Genome Biol. 2015 Dec 01; 16:259. PMID: 26619908.
      Citations: 525     Fields:    Translation:HumansCells
    81. 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 Rep. 2015 Dec 01; 13(9):1855-67. PMID: 26655901.
      Citations: 13     Fields:    Translation:AnimalsCells
    82. 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. Mol Cell. 2015 Oct 01; 60(1):146-62. PMID: 26431028.
      Citations: 43     Fields:    Translation:AnimalsCells
    83. Dekker J, Misteli T. Long-Range Chromatin Interactions. Cold Spring Harb Perspect Biol. 2015 Oct 01; 7(10):a019356. PMID: 26430217.
      Citations: 101     Fields:    Translation:HumansAnimalsCells
    84. 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 Biol. 2015 Sep 28; 16:214. PMID: 26415882.
      Citations: 84     Fields:    Translation:HumansCells
    85. Kind J, Pagie L, de Vries SS, Nahidiazar L, Dey SS, Bienko M, Zhan Y, Lajoie B, de Graaf CA, Amendola M, Fudenberg G, Imakaev M, Mirny LA, Jalink K, Dekker J, van Oudenaarden A, van Steensel B. Genome-wide maps of nuclear lamina interactions in single human cells. Cell. 2015 Sep 24; 163(1):134-47. PMID: 26365489.
      Citations: 165     Fields:    Translation:HumansCells
    86. Dekker J, Heard E. Structural and functional diversity of Topologically Associating Domains. FEBS Lett. 2015 Oct 07; 589(20 Pt A):2877-84. PMID: 26348399.
      Citations: 104     Fields:    Translation:HumansAnimalsCells
    87. 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 Dev. 2015 Aug 01; 29(15):1661-75. PMID: 26253537.
      Citations: 84     Fields:    Translation:Cells
    88. Rutledge MT, Russo M, Belton JM, Dekker J, Broach JR. The yeast genome undergoes significant topological reorganization in quiescence. Nucleic Acids Res. 2015 Sep 30; 43(17):8299-313. PMID: 26202961.
      Citations: 35     Fields:    Translation:AnimalsCells
    89. Belton JM, Dekker J. Measuring Chromatin Structure in Budding Yeast. Cold Spring Harb Protoc. 2015 Jul 01; 2015(7):614-8. PMID: 26134912.
      Citations: 2     Fields:    Translation:AnimalsCells
    90. Belton JM, Dekker J. Hi-C in Budding Yeast. Cold Spring Harb Protoc. 2015 Jul 01; 2015(7):649-61. PMID: 26134906.
      Citations: 6     Fields:    Translation:AnimalsCells
    91. Hsieh TH, Weiner A, Lajoie B, Dekker J, Friedman N, Rando OJ. Mapping Nucleosome Resolution Chromosome Folding in Yeast by Micro-C. Cell. 2015 Jul 02; 162(1):108-19. PMID: 26119342.
      Citations: 214     Fields:    Translation:AnimalsCells
    92. 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. 2015 Jul 09; 523(7559):240-4. PMID: 26030525.
      Citations: 310     Fields:    Translation:AnimalsCells
    93. Belton JM, Dekker J. Chromosome Conformation Capture Carbon Copy (5C) in Budding Yeast. Cold Spring Harb Protoc. 2015 Jun 01; 2015(6):593-8. PMID: 26034306.
      Citations:    Fields:    Translation:AnimalsCells
    94. Belton JM, Dekker J. Randomized ligation control for chromosome conformation capture. Cold Spring Harb Protoc. 2015 Jun 01; 2015(6):587-92. PMID: 26034305.
      Citations: 1     Fields:    Translation:AnimalsCells
    95. Belton JM, Dekker J. Chromosome Conformation Capture (3C) in Budding Yeast. Cold Spring Harb Protoc. 2015 Jun 01; 2015(6):580-6. PMID: 26034304.
      Citations: 4     Fields:    Translation:AnimalsCells
    96. 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 Res. 2015 Apr; 25(4):504-13. PMID: 25677180.
      Citations: 76     Fields:    Translation:AnimalsCells
    97. Dekker J. Two ways to fold the genome during the cell cycle: insights obtained with chromosome conformation capture. Epigenetics Chromatin. 2014; 7(1):25. PMID: 25435919.
      Citations: 39     Fields:    
    98. Lajoie BR, Dekker J, Kaplan N. The Hitchhiker's guide to Hi-C analysis: practical guidelines. Methods. 2015 Jan 15; 72:65-75. PMID: 25448293.
      Citations: 134     Fields:    Translation:HumansCells
    99. Mizuguchi T, Fudenberg G, Mehta S, Belton JM, Taneja N, Folco HD, FitzGerald P, Dekker J, Mirny L, Barrowman J, Grewal SIS. Cohesin-dependent globules and heterochromatin shape 3D genome architecture in S. pombe. Nature. 2014 Dec 18; 516(7531):432-435. PMID: 25307058.
      Citations: 119     Fields:    Translation:AnimalsCells
    100. Giorgetti L, Galupa R, Nora EP, Piolot T, Lam F, Dekker J, Tiana G, Heard E. Predictive polymer modeling reveals coupled fluctuations in chromosome conformation and transcription. Cell. 2014 May 08; 157(4):950-63. PMID: 24813616.
      Citations: 174     Fields:    Translation:AnimalsCells
    101. 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, Giddings MC, Gilbert DM, Gingeras TR, Green ED, Guigo R, Hubbard T, Kent J, Lieb JD, Myers RM, Pazin MJ, Ren B, Stamatoyannopoulos JA, Weng Z, White KP, Hardison RC. Defining functional DNA elements in the human genome. Proc Natl Acad Sci U S A. 2014 Apr 29; 111(17):6131-8. PMID: 24753594.
      Citations: 288     Fields:    Translation:HumansCells
    102. Kaplan N, Dekker J. High-throughput genome scaffolding from in vivo DNA interaction frequency. Nat Biotechnol. 2013 Dec; 31(12):1143-7. PMID: 24270850.
      Citations: 80     Fields:    
    103. Kumar S, Wuerffel R, Achour I, Lajoie B, Sen R, Dekker J, Feeney AJ, Kenter AL. Flexible ordering of antibody class switch and V(D)J joining during B-cell ontogeny. Genes Dev. 2013 Nov 15; 27(22):2439-44. PMID: 24240234.
      Citations: 25     Fields:    Translation:AnimalsCells
    104. Naumova N, Imakaev M, Fudenberg G, Zhan Y, Lajoie BR, Mirny LA, Dekker J. Organization of the mitotic chromosome. Science. 2013 Nov 22; 342(6161):948-53. PMID: 24200812.
      Citations: 386     Fields:    Translation:HumansCells
    105. Dekker J, Mirny L. Biological techniques: Chromosomes captured one by one. Nature. 2013 Oct 03; 502(7469):45-6. PMID: 24067607.
      Citations: 6     Fields:    Translation:AnimalsCells
    106. 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 Res. 2013 Dec; 23(12):2066-77. PMID: 24002784.
      Citations: 165     Fields:    Translation:AnimalsCells
    107. Nora EP, Dekker J, Heard E. Segmental folding of chromosomes: a basis for structural and regulatory chromosomal neighborhoods? Bioessays. 2013 Sep; 35(9):818-28. PMID: 23832846.
      Citations: 82     Fields:    Translation:HumansAnimalsCells
    108. 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, Taylor J, Corces VG. Architectural protein subclasses shape 3D organization of genomes during lineage commitment. Cell. 2013 Jun 06; 153(6):1281-95. PMID: 23706625.
      Citations: 566     Fields:    Translation:AnimalsCells
    109. Dekker J, Marti-Renom MA, Mirny LA. Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data. Nat Rev Genet. 2013 Jun; 14(6):390-403. PMID: 23657480.
      Citations: 475     Fields:    Translation:HumansAnimalsCells
    110. Dekker J, Wysocka J, Mattaj I, Lieberman Aiden E, Pikaard C. Nuclear biology: what's been most surprising? Cell. 2013 Mar 14; 152(6):1207-8. PMID: 23616995.
      Citations: 1     Fields:    Translation:HumansAnimalsCells
    111. Gibcus JH, Dekker J. The hierarchy of the 3D genome. Mol Cell. 2013 Mar 07; 49(5):773-82. PMID: 23473598.
      Citations: 329     Fields:    Translation:HumansAnimalsCells
    112. 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 Res. 2013 Feb; 23(2):260-9. PMID: 23152449.
      Citations: 149     Fields:    Translation:HumansCells
    113. Ferraiuolo MA, Sanyal A, Naumova N, Dekker J, Dostie J. From cells to chromatin: capturing snapshots of genome organization with 5C technology. Methods. 2012 Nov; 58(3):255-67. PMID: 23137922.
      Citations: 27     Fields:    Translation:HumansAnimalsCells
    114. de Laat W, Dekker J. 3C-based technologies to study the shape of the genome. Methods. 2012 Nov; 58(3):189-91. PMID: 23199640.
      Citations: 45     Fields:    Translation:HumansCells
    115. An integrated encyclopedia of DNA elements in the human genome. Nature. 2012 Sep 06; 489(7414):57-74. PMID: 22955616.
      Citations: 6978     Fields:    Translation:HumansAnimalsCells
    116. 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, Canfield TK, Diegel M, Dunn D, Ebersol AK, Frum T, Giste E, Johnson AK, Johnson EM, Kutyavin T, Lajoie B, Lee BK, Lee K, London D, Lotakis D, Neph S, Neri F, Nguyen ED, Qu H, Reynolds AP, Roach V, Safi A, Sanchez ME, Sanyal A, Shafer A, Simon JM, Song L, Vong S, Weaver M, Yan Y, Zhang Z, Zhang Z, Lenhard B, Tewari M, Dorschner MO, Hansen RS, Navas PA, Stamatoyannopoulos G, Iyer VR, Lieb JD, Sunyaev SR, Akey JM, Sabo PJ, Kaul R, Furey TS, Dekker J, Crawford GE, Stamatoyannopoulos JA. The accessible chromatin landscape of the human genome. Nature. 2012 Sep 06; 489(7414):75-82. PMID: 22955617.
      Citations: 1317     Fields:    Translation:HumansCells
    117. Sanyal A, Lajoie BR, Jain G, Dekker J. The long-range interaction landscape of gene promoters. Nature. 2012 Sep 06; 489(7414):109-13. PMID: 22955621.
      Citations: 745     Fields:    Translation:HumansCells
    118. 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. Nat Methods. 2012 Oct; 9(10):999-1003. PMID: 22941365.
      Citations: 511     Fields:    Translation:HumansCells
    119. Servant N, Lajoie BR, Nora EP, Giorgetti L, Chen CJ, Heard E, Dekker J, Barillot E. HiTC: exploration of high-throughput 'C' experiments. Bioinformatics. 2012 Nov 01; 28(21):2843-4. PMID: 22923296.
      Citations: 80     Fields:    Translation:HumansAnimalsCells
    120. Naumova N, Smith EM, Zhan Y, Dekker J. Analysis of long-range chromatin interactions using Chromosome Conformation Capture. Methods. 2012 Nov; 58(3):192-203. PMID: 22903059.
      Citations: 75     Fields:    Translation:HumansAnimalsCells
    121. 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, Byron R, Roach V, Sabo PJ, Sandstrom R, Stehling AS, Thurman RE, Weissman SM, Cayting P, Hariharan M, Lian J, Cheng Y, Landt SG, Ma Z, Wold BJ, Dekker J, Crawford GE, Keller CA, Wu W, Morrissey C, Kumar SA, Mishra T, Jain D, Byrska-Bishop M, Blankenberg D, Lajoie BR, Jain G, Sanyal A, Chen KB, Denas O, Taylor J, Blobel GA, Weiss MJ, Pimkin M, Deng W, Marinov GK, Williams BA, Fisher-Aylor KI, Desalvo G, Kiralusha A, Trout D, Amrhein H, Mortazavi A, Edsall L, McCleary D, Kuan S, Shen Y, Yue F, Ye Z, Davis CA, Zaleski C, Jha S, Xue C, Dobin A, Lin W, Fastuca M, Wang H, Guigo R, Djebali S, Lagarde J, Ryba T, Sasaki T, Malladi VS, Cline MS, Kirkup VM, Learned K, Rosenbloom KR, Kent WJ, Feingold EA, Good PJ, Pazin M, Lowdon RF, Adams LB. An encyclopedia of mouse DNA elements (Mouse ENCODE). Genome Biol. 2012 Aug 13; 13(8):418. PMID: 22889292.
      Citations: 272     Fields:    Translation:HumansAnimals
    122. Belton JM, McCord RP, Gibcus JH, Naumova N, Zhan Y, Dekker J. Hi-C: a comprehensive technique to capture the conformation of genomes. Methods. 2012 Nov; 58(3):268-76. PMID: 22652625.
      Citations: 302     Fields:    Translation:HumansAnimalsCells
    123. Dekker J. CTCF and cohesin help neurons raise their self-awareness. Proc Natl Acad Sci U S A. 2012 Jun 05; 109(23):8799-800. PMID: 22615386.
      Citations: 3     Fields:    Translation:HumansAnimals
    124. 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, Kim JK, Jacobsen SE. MORC family ATPases required for heterochromatin condensation and gene silencing. Science. 2012 Jun 15; 336(6087):1448-51. PMID: 22555433.
      Citations: 138     Fields:    Translation:AnimalsCells
    125. 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. 2012 Apr 11; 485(7398):381-5. PMID: 22495304.
      Citations: 1167     Fields:    Translation:AnimalsCells
    126. Felsenfeld G, Dekker J. Genome architecture and expression. Curr Opin Genet Dev. 2012 Apr; 22(2):59-61. PMID: 22483506.
      Citations: 5     Fields:    Translation:HumansCells
    127. Gibcus JH, Dekker J. The context of gene expression regulation. F1000 Biol Rep. 2012; 4:8. PMID: 22500194.
      Citations:    
    128. 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. 2012 Mar 02; 148(5):908-21. PMID: 22341456.
      Citations: 264     Fields:    Translation:AnimalsCells
    129. 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, Lin C, Bell I, Dumais E, Drenkow J, Tress ML, Gelpí JL, Orozco M, Valencia A, van Berkum NL, Lajoie BR, Vidal M, Stamatoyannopoulos J, Batut P, Dobin A, Harrow J, Hubbard T, Dekker J, Frankish A, Salehi-Ashtiani K, Reymond A, Antonarakis SE, Guigó R, Gingeras TR. Evidence for transcript networks composed of chimeric RNAs in human cells. PLoS One. 2012; 7(1):e28213. PMID: 22238572.
      Citations: 39     Fields:    Translation:HumansCells
    130. Noble WS, Blau CA, Dekker J, Duan ZJ, Mao Y. The structure and function of chromatin and chromosomes. Pac Symp Biocomput. 2012; 434-40. PMID: 22174298.
      Citations: 1     Fields:    Translation:HumansAnimalsCells
    131. 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. Nat Methods. 2011 Oct 30; 8(12):1050-2. PMID: 22037702.
      Citations: 28     Fields:    Translation:HumansCells
    132. 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. Nat Methods. 2011 Oct 30; 8(12):1059-64. PMID: 22037705.
      Citations: 60     Fields:    Translation:HumansAnimals
    133. 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. Mol Cell. 2011 Oct 21; 44(2):252-64. PMID: 22017872.
      Citations: 123     Fields:    Translation:Cells
    134. McCord RP, Dekker J. Translocation mapping exposes the risky lifestyle of B cells. Cell. 2011 Sep 30; 147(1):20-2. PMID: 21962501.
      Citations:    Fields:    
    135. A user's guide to the encyclopedia of DNA elements (ENCODE). PLoS Biol. 2011 Apr; 9(4):e1001046. PMID: 21526222.
      Citations: 723     Fields:    Translation:HumansCells
    136. Sanyal A, Baù D, Martí-Renom MA, Dekker J. Chromatin globules: a common motif of higher order chromosome structure? Curr Opin Cell Biol. 2011 Jun; 23(3):325-31. PMID: 21489772.
      Citations: 32     Fields:    Translation:HumansAnimalsCells
    137. 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. 2011 Apr 07; 472(7341):120-4. PMID: 21423168.
      Citations: 999     Fields:    Translation:HumansAnimalsCells
    138. 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. 2010 Dec 10; 143(6):924-37. PMID: 21145459.
      Citations: 135     Fields:    Translation:AnimalsCells
    139. Baù D, Sanyal A, Lajoie BR, Capriotti E, Byron M, Lawrence JB, Dekker J, Marti-Renom MA. The three-dimensional folding of the ?-globin gene domain reveals formation of chromatin globules. Nat Struct Mol Biol. 2011 Jan; 18(1):107-14. PMID: 21131981.
      Citations: 155     Fields:    Translation:HumansCells
    140. van Steensel B, Dekker J. Genomics tools for unraveling chromosome architecture. Nat Biotechnol. 2010 Oct; 28(10):1089-95. PMID: 20944601.
      Citations: 121     Fields:    Translation:HumansAnimalsCells
    141. 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 Sep 23; 467(7314):430-5. PMID: 20720539.
      Citations: 991     Fields:    Translation:AnimalsCells
    142. Bradner JE, Mak R, Tanguturi SK, Mazitschek R, Haggarty SJ, Ross K, Chang CY, Bosco J, West N, Morse E, Lin K, Shen JP, Kwiatkowski NP, Gheldof N, Dekker J, DeAngelo DJ, Carr SA, Schreiber SL, Golub TR, Ebert BL. Chemical genetic strategy identifies histone deacetylase 1 (HDAC1) and HDAC2 as therapeutic targets in sickle cell disease. Proc Natl Acad Sci U S A. 2010 Jul 13; 107(28):12617-22. PMID: 20616024.
      Citations: 89     Fields:    Translation:Humans
    143. Naumova N, Dekker J. Integrating one-dimensional and three-dimensional maps of genomes. J Cell Sci. 2010 Jun 15; 123(Pt 12):1979-88. PMID: 20519580.
      Citations: 32     Fields:    Translation:HumansAnimalsCells
    144. van Berkum NL, Lieberman-Aiden E, Williams L, Imakaev M, Gnirke A, Mirny LA, Dekker J, Lander ES. Hi-C: a method to study the three-dimensional architecture of genomes. J Vis Exp. 2010 May 06; (39). PMID: 20461051.
      Citations: 155     Fields:    Translation:Cells
    145. 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 Res. 2010 Jul; 38(13):4325-36. PMID: 20360044.
      Citations: 52     Fields:    Translation:HumansCells
    146. 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, Stamatoyannopoulos J, Mirny LA, Lander ES, Dekker J. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science. 2009 Oct 09; 326(5950):289-93. PMID: 19815776.
      Citations: 2949     Fields:    Translation:HumansCells
    147. Lajoie BR, van Berkum NL, Sanyal A, Dekker J. My5C: web tools for chromosome conformation capture studies. Nat Methods. 2009 Oct; 6(10):690-1. PMID: 19789528.
      Citations: 46     Fields:    Translation:Cells
    148. 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, Wyss C, Speleman F, De Paepe A, Dekker J, Antonarakis SE, De Baere E. 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 Genet. 2009 Jun; 5(6):e1000522. PMID: 19543368.
      Citations: 36     Fields:    Translation:HumansCells
    149. Chang HY, Cuvier O, Dekker J. Gene dates, parties and galas. Symposium on Chromatin Dynamics and Higher Order Organization. EMBO Rep. 2009 Jul; 10(7):689-93. PMID: 19525922.
      Citations: 2     Fields:    Translation:AnimalsCells
    150. Miele A, Bystricky K, Dekker J. Yeast silent mating type loci form heterochromatic clusters through silencer protein-dependent long-range interactions. PLoS Genet. 2009 May; 5(5):e1000478. PMID: 19424429.
      Citations: 56     Fields:    Translation:AnimalsCells
    151. 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 Dev. 2009 Apr 15; 23(8):912-27. PMID: 19390086.
      Citations: 165     Fields:    Translation:AnimalsCells
    152. Miele A, Dekker J. Mapping cis- and trans- chromatin interaction networks using chromosome conformation capture (3C). Methods Mol Biol. 2009; 464:105-21. PMID: 18951182.
      Citations: 50     Fields:    Translation:HumansAnimalsCells
    153. van Berkum NL, Dekker J. Determining spatial chromatin organization of large genomic regions using 5C technology. Methods Mol Biol. 2009; 567:189-213. PMID: 19588094.
      Citations: 28     Fields:    Translation:HumansAnimalsCells
    154. Dekker J. Mapping in vivo chromatin interactions in yeast suggests an extended chromatin fiber with regional variation in compaction. J Biol Chem. 2008 Dec 12; 283(50):34532-40. PMID: 18930918.
      Citations: 72     Fields:    Translation:AnimalsCells
    155. Miele A, Dekker J. Long-range chromosomal interactions and gene regulation. Mol Biosyst. 2008 Nov; 4(11):1046-57. PMID: 18931780.
      Citations: 79     Fields:    Translation:HumansAnimalsCells
    156. Dekker J. Gene regulation in the third dimension. Science. 2008 Mar 28; 319(5871):1793-4. PMID: 18369139.
      Citations: 131     Fields:    Translation:HumansAnimalsCells
    157. 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. Br J Haematol. 2008 May; 141(3):398-406. PMID: 18318763.
      Citations: 20     Fields:    Translation:HumansAnimalsCells
    158. Dostie J, Zhan Y, Dekker J. Chromosome conformation capture carbon copy technology. Curr Protoc Mol Biol. 2007 Oct; Chapter 21:Unit 21.14. PMID: 18265398.
      Citations: 26     Fields:    Translation:Cells
    159. Lanzuolo C, Roure V, Dekker J, Bantignies F, Orlando V. Polycomb response elements mediate the formation of chromosome higher-order structures in the bithorax complex. Nat Cell Biol. 2007 Oct; 9(10):1167-74. PMID: 17828248.
      Citations: 146     Fields:    Translation:AnimalsCells
    160. 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, Asthana S, Malhotra A, Adzhubei I, Greenbaum JA, Andrews RM, Flicek P, Boyle PJ, Cao H, Carter NP, Clelland GK, Davis S, Day N, Dhami P, Dillon SC, Dorschner MO, Fiegler H, Giresi PG, Goldy J, Hawrylycz M, Haydock A, Humbert R, James KD, Johnson BE, Johnson EM, Frum TT, Rosenzweig ER, Karnani N, Lee K, Lefebvre GC, Navas PA, Neri F, Parker SC, Sabo PJ, Sandstrom R, Shafer A, Vetrie D, Weaver M, Wilcox S, Yu M, Collins FS, Dekker J, Lieb JD, Tullius TD, Crawford GE, Sunyaev S, Noble WS, Dunham I, Denoeud F, Reymond A, Kapranov P, Rozowsky J, Zheng D, Castelo R, Frankish A, Harrow J, Ghosh S, Sandelin A, Hofacker IL, Baertsch R, Keefe D, Dike S, Cheng J, Hirsch HA, Sekinger EA, Lagarde J, Abril JF, Shahab A, Flamm C, Fried C, Hackermüller J, Hertel J, Lindemeyer M, Missal K, Tanzer A, Washietl S, Korbel J, Emanuelsson O, Pedersen JS, Holroyd N, Taylor R, Swarbreck D, Matthews N, Dickson MC, Thomas DJ, Weirauch MT, Gilbert J, Drenkow J, Bell I, Zhao X, Srinivasan KG, Sung WK, Ooi HS, Chiu KP, Foissac S, Alioto T, Brent M, Pachter L, Tress ML, Valencia A, Choo SW, Choo CY, Ucla C, Manzano C, Wyss C, Cheung E, Clark TG, Brown JB, Ganesh M, Patel S, Tammana H, Chrast J, Henrichsen CN, Kai C, Kawai J, Nagalakshmi U, Wu J, Lian Z, Lian J, Newburger P, Zhang X, Bickel P, Mattick JS, Carninci P, Hayashizaki Y, Weissman S, Hubbard T, Myers RM, Rogers J, Stadler PF, Lowe TM, Wei CL, Ruan Y, Struhl K, Gerstein M, Antonarakis SE, Fu Y, Green ED, Karaöz U, Siepel A, Taylor J, Liefer LA, Wetterstrand KA, Good PJ, Feingold EA, Guyer MS, Cooper GM, Asimenos G, Dewey CN, Hou M, Nikolaev S, Montoya-Burgos JI, Löytynoja A, Whelan S, Pardi F, Massingham T, Huang H, Zhang NR, Holmes I, Mullikin JC, Ureta-Vidal A, Paten B, Seringhaus M, Church D, Rosenbloom K, Kent WJ, Stone EA, Batzoglou S, Goldman N, Hardison RC, Haussler D, Miller W, Sidow A, Trinklein ND, Zhang ZD, Barrera L, Stuart R, King DC, Ameur A, Enroth S, Bieda MC, Kim J, Bhinge AA, Jiang N, Liu J, Yao F, Vega VB, Lee CW, Ng P, Shahab A, Yang A, Moqtaderi Z, Zhu Z, Xu X, Squazzo S, Oberley MJ, Inman D, Singer MA, Richmond TA, Munn KJ, Rada-Iglesias A, Wallerman O, Komorowski J, Fowler JC, Couttet P, Bruce AW, Dovey OM, Ellis PD, Langford CF, Nix DA, Euskirchen G, Hartman S, Urban AE, Kraus P, Van Calcar S, Heintzman N, Kim TH, Wang K, Qu C, Hon G, Luna R, Glass CK, Rosenfeld MG, Aldred SF, Cooper SJ, Halees A, Lin JM, Shulha HP, Zhang X, Xu M, Haidar JN, Yu Y, Ruan Y, Iyer VR, Green RD, Wadelius C, Farnham PJ, Ren B, Harte RA, Hinrichs AS, Trumbower H, Clawson H, Hillman-Jackson J, Zweig AS, Smith K, Thakkapallayil A, Barber G, Kuhn RM, Karolchik D, Armengol L, Bird CP, de Bakker PI, Kern AD, Lopez-Bigas N, Martin JD, Stranger BE, Woodroffe A, Davydov E, Dimas A, Eyras E, Hallgrímsdóttir IB, Huppert J, Zody MC, Abecasis GR, Estivill X, Bouffard GG, Guan X, Hansen NF, Idol JR, Maduro VV, Maskeri B, McDowell JC, Park M, Thomas PJ, Young AC, Blakesley RW, Muzny DM, Sodergren E, Wheeler DA, Worley KC, Jiang H, Weinstock GM, Gibbs RA, Graves T, Fulton R, Mardis ER, Wilson RK, Clamp M, Cuff J, Gnerre S, Jaffe DB, Chang JL, Lindblad-Toh K, Lander ES, Koriabine M, Nefedov M, Osoegawa K, Yoshinaga Y, Zhu B, de Jong PJ. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature. 2007 Jun 14; 447(7146):799-816. PMID: 17571346.
      Citations: 2543     Fields:    Translation:HumansCells
    161. Dostie J, Dekker J. Mapping networks of physical interactions between genomic elements using 5C technology. Nat Protoc. 2007; 2(4):988-1002. PMID: 17446898.
      Citations: 98     Fields:    Translation:Cells
    162. Dekker J. GC- and AT-rich chromatin domains differ in conformation and histone modification status and are differentially modulated by Rpd3p. Genome Biol. 2007; 8(6):R116. PMID: 17577398.
      Citations: 29     Fields:    Translation:AnimalsCells
    163. 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). Nat Protoc. 2007; 2(7):1722-33. PMID: 17641637.
      Citations: 375     Fields:    Translation:AnimalsCells
    164. 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 Res. 2006 Oct; 16(10):1299-309. PMID: 16954542.
      Citations: 520     Fields:    Translation:HumansCells
    165. 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. Proc Natl Acad Sci U S A. 2006 Aug 15; 103(33):12463-8. PMID: 16891414.
      Citations: 35     Fields:    Translation:HumansCells
    166. Miele A, Gheldof N, Tabuchi TM, Dostie J, Dekker J. Mapping chromatin interactions by chromosome conformation capture. Curr Protoc Mol Biol. 2006 May; Chapter 21:Unit 21.11. PMID: 18265379.
      Citations: 49     Fields:    Translation:AnimalsCells
    167. Dekker J. The three 'C' s of chromosome conformation capture: controls, controls, controls. Nat Methods. 2006 Jan; 3(1):17-21. PMID: 16369547.
      Citations: 190     Fields:    Translation:Cells
    168. 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. Mol Cell. 2005 Feb 04; 17(3):453-62. PMID: 15694345.
      Citations: 257     Fields:    Translation:HumansAnimalsCells
    169. Kleckner N, Zickler D, Jones GH, Dekker J, Padmore R, Henle J, Hutchinson J. A mechanical basis for chromosome function. Proc Natl Acad Sci U S A. 2004 Aug 24; 101(34):12592-7. PMID: 15299144.
      Citations: 157     Fields:    Translation:HumansAnimalsCells
    170. Dekker J. A closer look at long-range chromosomal interactions. Trends Biochem Sci. 2003 Jun; 28(6):277-80. PMID: 12826398.
      Citations: 25     Fields:    Translation:HumansAnimalsCells
    171. Dekker J, Rippe K, Dekker M, Kleckner N. Capturing chromosome conformation. Science. 2002 Feb 15; 295(5558):1306-11. PMID: 11847345.
      Citations: 1511     Fields:    Translation:AnimalsCells
    172. 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 Dev. 2000 Feb 15; 14(4):493-503. PMID: 10691741.
      Citations: 105     Fields:    Translation:AnimalsCells
    173. 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. J Mol Biol. 1998 Apr 10; 277(4):825-38. PMID: 9545375.
      Citations: 5     Fields:    Translation:AnimalsCells
    174. 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. EMBO J. 1997 Mar 17; 16(6):1455-63. PMID: 9135160.
      Citations: 20     Fields:    Translation:AnimalsCells
    175. 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. Mol Cell Biol. 1996 Aug; 16(8):4073-80. PMID: 8754805.
      Citations: 6     Fields:    Translation:AnimalsCells
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