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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 Biotechnology

    InstitutionMorningside Graduate School of Biomedical Sciences
    DepartmentBiophysical Chemical and Computational Biology

    InstitutionMorningside Graduate School of Biomedical Sciences
    DepartmentInterdisciplinary Graduate Program

    InstitutionMorningside Graduate School of Biomedical Sciences
    DepartmentMD/PhD Program

    InstitutionMorningside Graduate School of Biomedical Sciences
    DepartmentSystems Computational and Quantitative Biology

    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
    2022Member National Academy of Sciences
    2021Member National Academy of Medicine
    2020EMBO Associate Member
    2018International Award of the Biochemical Society
    2018Novitski Prize of the Genetics Society of America
    2015Investigator, Howard Hughes Medical Institute
    2014Fellow 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. Samejima K, Gibcus JH, Abraham S, Cisneros-Soberanis F, Samejima I, Beckett AJ, Pucekov? N, Abad MA, Spanos C, Medina-Pritchard B, Paulson JR, Xie L, Jeyaprakash AA, Prior IA, Mirny LA, Dekker J, Goloborodko A, Earnshaw WC. Rules of engagement for condensins and cohesins guide mitotic chromosome formation. Science. 2025 04 11; 388(6743):eadq1709. PMID: 40208986.
      Citations:    
    2. Hildebrand EM, Cowell IG, Khazeem MM, Sambare S, Uyan O, Dekker J, Austin CA. TOP2B is required for compartment strength changes upon retinoic acid treatment in SH-SY5Y cells. Chromosome Res. 2025 Apr 04; 33(1):5. PMID: 40183884.
      Citations:    
    3. Dekker J, Mirny LA. The chromosome folding problem and how cells solve it. Cell. 2024 Nov 14; 187(23):6424-6450. PMID: 39547207.
      Citations:    
    4. Dekker J, Oksuz BA, Zhang Y, Wang Y, Minsk MK, Kuang S, Yang L, Gibcus JH, Krietenstein N, Rando OJ, Xu J, Janssens DH, Henikoff S, Kukalev A, Willemin A, Winick-Ng W, Kempfer R, Pombo A, Yu M, Kumar P, Zhang L, Belmont AS, Sasaki T, van Schaik T, Brueckner L, Peric-Hupkes D, van Steensel B, Wang P, Chai H, Kim M, Ruan Y, Zhang R, Quinodoz SA, Bhat P, Guttman M, Zhao W, Chien S, Liu Y, Venev SV, Plewczynski D, Azcarate II, Szab? D, Thieme CJ, Szczepinska T, Chilinski M, Sengupta K, Conte M, Esposito A, Abraham A, Zhang R, Wang Y, Wen X, Wu Q, Yang Y, Liu J, Boninsegna L, Yildirim A, Zhan Y, Chiariello AM, Bianco S, Lee L, Hu M, Li Y, Barnett RJ, Cook AL, Emerson DJ, Marchal C, Zhao P, Park P, Alver BH, Schroeder A, Navelkar R, Bakker C, Ronchetti W, Ehmsen S, Veit A, Gehlenborg N, Wang T, Li D, Wang X, Nicodemi M, Ren B, Zhong S, Phillips-Cremins JE, Gilbert DM, Pollard KS, Alber F, Ma J, Noble WS, Yue F. An integrated view of the structure and function of the human 4D nucleome. bioRxiv. 2024 Oct 27. PMID: 39484446.
      Citations:    
    5. Conte M, Abraham A, Esposito A, Yang L, Gibcus JH, Parsi KM, Vercellone F, Fontana A, Di Pierno F, Dekker J, Nicodemi M. Polymer Physics Models Reveal Structural Folding Features of Single-Molecule Gene Chromatin Conformations. Int J Mol Sci. 2024 Sep 23; 25(18). PMID: 39337699.
      Citations:    
    6. Schooley A, Venev SV, Aksenova V, Navarrete E, Dasso M, Dekker J. Interphase chromosome conformation is specified by distinct folding programs inherited via mitotic chromosomes or through the cytoplasm. bioRxiv. 2024 Sep 16. PMID: 39345587.
      Citations:    
    7. Conte M, Abraham A, Esposito A, Yang L, Gibcus JH, Parsi KM, Vercellone F, Fontana A, Pierno FD, Dekker J, Nicodemi M. Polymer physics models reveal structural folding features of single-molecule gene chromatin conformations. bioRxiv. 2024 Jul 16. PMID: 39071404.
      Citations:    
    8. Samejima K, Gibcus JH, Abraham S, Cisneros-Soberanis F, Samejima I, Beckett AJ, Pucekov? N, Abad MA, Medina-Pritchard B, Paulson JR, Xie L, Jeyaprakash AA, Prior IA, Mirny LA, Dekker J, Goloborodko A, Earnshaw WC. Rules of engagement for condensins and cohesins guide mitotic chromosome formation. bioRxiv. 2024 Apr 30. PMID: 38659940.
      Citations:    
    9. Hildebrand EM, Polovnikov K, Dekker B, Liu Y, Lafontaine DL, Fox AN, Li Y, Venev SV, Mirny LA, Dekker J. Mitotic chromosomes are self-entangled and disentangle through a topoisomerase-II-dependent two-stage exit from mitosis. Mol Cell. 2024 Apr 18; 84(8):1422-1441.e14. PMID: 38521067.
      Citations:    
    10. Watson EV, Lee JJ, Gulhan DC, Melloni GEM, Venev SV, Magesh RY, Frederick A, Chiba K, Wooten EC, Naxerova K, Dekker J, Park PJ, Elledge SJ. Chromosome evolution screens recapitulate tissue-specific tumor aneuploidy patterns. Nat Genet. 2024 May; 56(5):900-912. PMID: 38388848.
      Citations:    
    11. Calvo-Roitberg E, Carroll CL, Venev SV, Kim G, Mick ST, Dekker J, Fiszbein A, Pai AA. mRNA initiation and termination are spatially coordinated. bioRxiv. 2024 Jan 07. PMID: 38260419.
      Citations:    
    12. 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 Res. 2023 Dec 27; 33(12):2079-2093. PMID: 38129076.
      Citations: 3     Fields:    
    13. Pourmorady AD, Bashkirova EV, Chiariello AM, Belagzhal H, Kodra A, Duffi? R, Kahiapo J, Monahan K, Pulupa J, Schieren I, Osterhoudt A, Dekker J, Nicodemi M, Lomvardas S. RNA-mediated symmetry breaking enables singular olfactory receptor choice. Nature. 2024 Jan; 625(7993):181-188. PMID: 38123679.
      Citations:    Fields:    Translation:Cells
    14. Kocanova S, Raynal F, Goiffon I, Oksuz BA, Ba? D, Kamgou? 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 Sci Alliance. 2024 02; 7(2). PMID: 37989525.
      Citations: 1     Fields:    Translation:HumansCells
    15. Gentien D, Saberi-Ansari E, Servant N, Jolly A, de la Grange P, N?mati F, Liot G, Saule S, Teissandier A, Bourc'his D, Girard E, Wong J, Masliah-Planchon J, Narmanli E, Liu Y, Torun E, Goulancourt R, Rodrigues M, Gaud? LV, Reyes C, Bazire M, Chenegros T, Henry E, Rapinat A, Bohec M, Baulande S, M'kacher R, Jeandidier E, Nicolas A, Ciriello G, Margueron R, Decaudin D, Cassoux N, Piperno-Neumann S, Stern MH, Gibcus JH, Dekker J, Heard E, Roman-Roman S, Waterfall JJ. Multi-omics comparison of malignant and normal uveal melanocytes reveals molecular features of uveal melanoma. Cell Rep. 2023 09 26; 42(9):113132. PMID: 37708024.
      Citations:    Fields:    Translation:HumansCells
    16. Cavalli G, Dekker J. Editorial overview: Multiscale regulation of genome folding in space, time, and across the tree of life. Curr Opin Genet Dev. 2023 10; 82:102095. PMID: 37595408.
      Citations:    Fields:    
    17. Dekker J, Alber F, Aufmkolk S, Beliveau BJ, Bruneau BG, Belmont AS, Bintu L, Boettiger A, Calandrelli R, Disteche CM, Gilbert DM, Gregor T, Hansen AS, Huang B, Huangfu D, Kalhor R, Leslie CS, Li W, Li Y, Ma J, Noble WS, Park PJ, Phillips-Cremins JE, Pollard KS, Rafelski SM, Ren B, Ruan Y, Shav-Tal Y, Shen Y, Shendure J, Shu X, Strambio-De-Castillia C, Vertii A, Zhang H, Zhong S. Spatial and temporal organization of the genome: Current state and future aims of the 4D nucleome project. Mol Cell. 2023 08 03; 83(15):2624-2640. PMID: 37419111.
      Citations: 3     Fields:    Translation:Cells
    18. 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. Mol Cell. 2023 07 20; 83(14):2434-2448.e7. PMID: 37402370.
      Citations: 3     Fields:    Translation:HumansCells
    19. 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. Nat Struct Mol Biol. 2023 Jul; 30(7):1048. PMID: 37059902.
      Citations:    Fields:    
    20. 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. 2023 Jun 14. PMID: 37398486.
      Citations:    
    21. Zhou CY, Dekker B, Liu Z, Cabrera H, Ryan J, Dekker J, Heald R. Mitotic chromosomes scale to nuclear-cytoplasmic ratio and cell size in Xenopus. Elife. 2023 04 25; 12. PMID: 37096661.
      Citations: 1     Fields:    Translation:AnimalsCells
    22. Marl?taz F, de la Calle-Mustienes E, Acemel RD, Paliou C, Naranjo S, Mart?nez-Garc?a PM, Cases I, Sleight VA, Hirschberger C, Marcet-Houben M, Navon D, Andrescavage A, Skvortsova K, Duckett PE, Gonz?lez-Rajal ?, Bogdanovic O, Gibcus JH, Yang L, Gallardo-Fuentes L, Sospedra I, Lopez-Rios J, Darbellay F, Visel A, Dekker J, Shubin N, Gabald?n T, Nakamura T, Tena JJ, Lupi??ez DG, Rokhsar DS, G?mez-Skarmeta JL. The little skate genome and the evolutionary emergence of wing-like fins. Nature. 2023 04; 616(7957):495-503. PMID: 37046085.
      Citations: 6     Fields:    Translation:Animals
    23. Yang L, Akgol Oksuz B, Dekker J, Gibcus JH. Capturing Chromosome Conformation Across Length Scales. J Vis Exp. 2023 01 20; (191). PMID: 36744801.
      Citations:    Fields:    Translation:Cells
    24. Spracklin G, Yang L, Pradhan S, Dekker J. Measuring Inaccessible Chromatin Genome-Wide Using Protect-seq. Methods Mol Biol. 2023; 2611:53-61. PMID: 36807063.
      Citations:    Fields:    Translation:Cells
    25. 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. Nat Struct Mol Biol. 2023 01; 30(1):99-106. PMID: 36564591.
      Citations: 8     Fields:    Translation:HumansCells
    26. 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. Nat Struct Mol Biol. 2023 Jan; 30(1):38-51. PMID: 36550219.
      Citations: 16     Fields:    Translation:Cells
    27. Valton AL, Venev SV, Mair B, Khokhar ES, Tong AHY, Usaj M, Chan K, Pai AA, Moffat J, Dekker J. A cohesin traffic pattern genetically linked to gene regulation. Nat Struct Mol Biol. 2022 12; 29(12):1239-1251. PMID: 36482254.
      Citations: 11     Fields:    Translation:Cells
    28. Dekker B, Dekker J. Regulation of the mitotic chromosome folding machines. Biochem J. 2022 10 28; 479(20):2153-2173. PMID: 36268993.
      Citations: 2     Fields:    Translation:Cells
    29. Liu Y, Dekker J. CTCF-CTCF loops and intra-TAD interactions show differential dependence on cohesin ring integrity. Nat Cell Biol. 2022 10; 24(10):1516-1527. PMID: 36202971.
      Citations: 2     Fields:    Translation:Cells
    30. Mirny L, Dekker J. Mechanisms of Chromosome Folding and Nuclear Organization: Their Interplay and Open Questions. Cold Spring Harb Perspect Biol. 2022 07 01; 14(7). PMID: 34518339.
      Citations: 23     Fields:    Translation:Cells
    31. Emerson DJ, Zhao PA, Cook AL, Barnett RJ, Klein KN, Saulebekova D, Ge C, Zhou L, Simandi Z, Minsk MK, Titus KR, Wang W, Gong W, Zhang D, Yang L, Venev SV, Gibcus JH, Yang H, Sasaki T, Kanemaki MT, Yue F, Dekker J, Chen CL, Gilbert DM, Phillips-Cremins JE. Cohesin-mediated loop anchors confine the locations of human replication origins. Nature. 2022 06; 606(7915):812-819. PMID: 35676475.
      Citations: 21     Fields:    Translation:HumansCells
    32. Cui G, Liew YJ, Konciute MK, Zhan Y, Hung SH, Thistle J, Gastoldi L, Schmidt-Roach S, Dekker J, Aranda M. Nutritional control regulates symbiont proliferation and life history in coral-dinoflagellate symbiosis. BMC Biol. 2022 05 13; 20(1):103. PMID: 35549698.
      Citations: 6     Fields:    Translation:Animals
    33. Stevens L, Moya ND, Tanny RE, Gibson SB, Tracey A, Na H, Chitrakar R, Dekker J, Walhout AJM, Baugh LR, Andersen EC. Chromosome-Level Reference Genomes for Two Strains of Caenorhabditis briggsae: An Improved Platform for Comparative Genomics. Genome Biol Evol. 2022 04 10; 14(4). PMID: 35348662.
      Citations: 8     Fields:    Translation:AnimalsCells
    34. 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: 3     Fields:    Translation:Cells
    35. Leidescher S, Ribisel J, Ullrich S, Feodorova Y, Hildebrand E, Galitsyna A, Bultmann S, Link S, Thanisch K, Mulholland C, Dekker J, Leonhardt H, Mirny L, Solovei I. Spatial organization of transcribed eukaryotic genes. Nat Cell Biol. 2022 03; 24(3):327-339. PMID: 35177821.
      Citations: 17     Fields:    Translation:AnimalsCells
    36. Cha HJ, Uyan ?, 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: 11     Fields:    Translation:AnimalsCells
    37. Voolstra CR, Aranda M, Zhan Y, Dekker J. Symbiodinium microadriaticum (coral microalgal endosymbiont). Trends Genet. 2021 11; 37(11):1044-1045. PMID: 34518054.
      Citations: 1     Fields:    Translation:Animals
    38. 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: 45     Fields:    Translation:HumansCells
    39. 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: 15     Fields:    Translation:AnimalsCells
    40. 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:    
    41. 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: 24     Fields:    Translation:AnimalsCells
    42. 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: 7     Fields:    Translation:Animals
    43. 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: 18     Fields:    Translation:AnimalsCells
    44. 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: 47     Fields:    Translation:HumansCells
    45. 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: 23     Fields:    Translation:HumansAnimalsCells
    46. 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: 13     Fields:    Translation:AnimalsCells
    47. 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: 4     Fields:    Translation:HumansCells
    48. 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: 24     Fields:    Translation:HumansCells
    49. 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
    50. 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: 195     Fields:    Translation:HumansAnimalsCells
    51. Hildebrand EM, Dekker J. Mechanisms and Functions of Chromosome Compartmentalization. Trends Biochem Sci. 2020 05; 45(5):385-396. PMID: 32311333.
      Citations: 79     Fields:    Translation:Cells
    52. Dossin F, Pinheiro I, Zylicz 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: 80     Fields:    Translation:AnimalsCells
    53. 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: 45     Fields:    Translation:AnimalsCells
    54. 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: 70     Fields:    Translation:HumansCells
    55. 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: 24     Fields:    Translation:AnimalsCells
    56. 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: 18     Fields:    Translation:AnimalsCells
    57. Viny AD, Bowman RL, Liu Y, Lavall?e 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: 58     Fields:    Translation:HumansAnimalsCells
    58. 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: 1     Fields:    
    59. 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: 9     Fields:    Translation:HumansCells
    60. 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: 228     Fields:    Translation:AnimalsCells
    61. Yardimci 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: 55     Fields:    Translation:HumansCells
    62. Finn EH, Pegoraro G, Brand?o HB, Valton AL, Oomen ME, Dekker J, Mirny L, Misteli T. Extensive Heterogeneity and Intrinsic Variation in Spatial Genome Organization. Cell. 2019 03 07; 176(6):1502-1515.e10. PMID: 30799036.
      Citations: 178     Fields:    Translation:HumansCells
    63. 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: 55     Fields:    Translation:HumansCells
    64. 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: 48     Fields:    Translation:AnimalsCells
    65. 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: 34     Fields:    Translation:HumansCells
    66. 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: 75     Fields:    Translation:AnimalsCells
    67. Dixon JR, Xu J, Dileep V, Zhan Y, Song F, Le VT, Yardimci 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: 143     Fields:    Translation:HumansCells
    68. 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: 1     Fields:    
    69. Kim TH, Dekker J. 3C-Based Chromatin Interaction Analyses. Cold Spring Harb Protoc. 2018 09 04; 2018(9). PMID: 30181229.
      Citations: 6     Fields:    Translation:Cells
    70. 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: 1     Fields:    
    71. 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
    72. 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: 10     Fields:    
    73. 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
    74. 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
    75. Kim TH, Dekker J. Generation of ChIP-Loop Libraries. Cold Spring Harb Protoc. 2018 08 01; 2018(8). PMID: 30068591.
      Citations:    Fields:    Translation:Cells
    76. 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: 13     Fields:    
    77. 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: 35     Fields:    Translation:HumansAnimalsCells
    78. 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: 60     Fields:    Translation:HumansCells
    79. Kim TH, Dekker J. ChIP-chip. Cold Spring Harb Protoc. 2018 05 01; 2018(5). PMID: 29717045.
      Citations: 2     Fields:    Translation:HumansAnimals
    80. Kim TH, Dekker J. ChIP-seq. Cold Spring Harb Protoc. 2018 05 01; 2018(5). PMID: 29717046.
      Citations: 3     Fields:    
    81. 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
    82. Kim TH, Dekker J. ChIP-Quantitative Polymerase Chain Reaction (ChIP-qPCR). Cold Spring Harb Protoc. 2018 05 01; 2018(5). PMID: 29717044.
      Citations: 13     Fields:    
    83. Kim TH, Dekker J. Preparation of Cross-Linked Chromatin for ChIP. Cold Spring Harb Protoc. 2018 04 02; 2018(4). PMID: 29610358.
      Citations: 1     Fields:    Translation:HumansCells
    84. Kim TH, Dekker J. ChIP. Cold Spring Harb Protoc. 2018 04 02; 2018(4). PMID: 29610359.
      Citations: 1     Fields:    Translation:Humans
    85. Kim TH, Dekker J. Formaldehyde Cross-Linking. Cold Spring Harb Protoc. 2018 04 02; 2018(4). PMID: 29610357.
      Citations: 1     Fields:    Translation:HumansCells
    86. 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: 278     Fields:    Translation:AnimalsCells
    87. 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:    
    88. Rodr?guez-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: 72     Fields:    Translation:AnimalsCells
    89. 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: 272     Fields:    Translation:HumansAnimalsCells
    90. 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: 59     Fields:    Translation:AnimalsCells
    91. Narendra V, Bulajic 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:    
    92. 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: 665     Fields:    Translation:AnimalsCells
    93. 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: 10     Fields:    Translation:AnimalsCells
    94. 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: 134     Fields:    Translation:HumansCells
    95. 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: 13     Fields:    Translation:HumansAnimalsCells
    96. 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: 148     Fields:    Translation:HumansAnimalsCells
    97. 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: 11     Fields:    Translation:Humans
    98. Narendra V, Bulajic 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: 73     Fields:    Translation:AnimalsCells
    99. Dekker J. Mapping the 3D genome: Aiming for consilience. Nat Rev Mol Cell Biol. 2016 Nov 21; 17(12):741-742. PMID: 27869158.
      Citations: 33     Fields:    Translation:HumansCells
    100. 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: 11     Fields:    Translation:AnimalsCells
    101. 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: 32     Fields:    Translation:HumansCells
    102. 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: 55     Fields:    Translation:HumansCells
    103. 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: 198     Fields:    Translation:AnimalsCells
    104. 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: 56     Fields:    Translation:AnimalsCells
    105. Valton AL, Dekker J. TAD disruption as oncogenic driver. Curr Opin Genet Dev. 2016 02; 36:34-40. PMID: 27111891.
      Citations: 96     Fields:    Translation:HumansCells
    106. 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
    107. Dekker J, Mirny L. The 3D Genome as Moderator of Chromosomal Communication. Cell. 2016 Mar 10; 164(6):1110-1121. PMID: 26967279.
      Citations: 425     Fields:    Translation:HumansAnimalsCells
    108. 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: 485     Fields:    Translation:HumansCells
    109. 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: 41     Fields:    Translation:AnimalsCells
    110. 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: 81     Fields:    Translation:HumansCells
    111. 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: 891     Fields:    Translation:HumansCells
    112. Belton JM, Lajoie BR, Audibert S, Cantaloube S, Lassadi I, Goiffon I, Ba? 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: 15     Fields:    Translation:AnimalsCells
    113. Ram?rez 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: 46     Fields:    Translation:AnimalsCells
    114. Dekker J, Misteli T. Long-Range Chromatin Interactions. Cold Spring Harb Perspect Biol. 2015 Oct 01; 7(10):a019356. PMID: 26430217.
      Citations: 125     Fields:    Translation:HumansAnimalsCells
    115. 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: 113     Fields:    Translation:HumansCells
    116. 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: 202     Fields:    Translation:HumansCells
    117. 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: 134     Fields:    Translation:HumansAnimalsCells
    118. 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: 111     Fields:    Translation:Cells
    119. 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: 41     Fields:    Translation:AnimalsCells
    120. 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
    121. Belton JM, Dekker J. Hi-C in Budding Yeast. Cold Spring Harb Protoc. 2015 Jul 01; 2015(7):649-61. PMID: 26134906.
      Citations: 9     Fields:    Translation:AnimalsCells
    122. 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: 302     Fields:    Translation:AnimalsCells
    123. 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: 416     Fields:    Translation:AnimalsCells
    124. 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
    125. 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: 2     Fields:    Translation:AnimalsCells
    126. 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: 5     Fields:    Translation:AnimalsCells
    127. 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: 92     Fields:    Translation:AnimalsCells
    128. 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: 40     Fields:    
    129. 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: 162     Fields:    Translation:HumansCells
    130. 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: 134     Fields:    Translation:AnimalsCells
    131. 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: 203     Fields:    Translation:AnimalsCells
    132. 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: 328     Fields:    Translation:HumansCells
    133. 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: 96     Fields:    
    134. 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: 28     Fields:    Translation:AnimalsCells
    135. 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: 450     Fields:    Translation:HumansCells
    136. 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
    137. 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: 181     Fields:    Translation:AnimalsCells
    138. 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: 88     Fields:    Translation:HumansAnimalsCells
    139. 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: 641     Fields:    Translation:AnimalsCells
    140. 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: 528     Fields:    Translation:HumansAnimalsCells
    141. 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
    142. Gibcus JH, Dekker J. The hierarchy of the 3D genome. Mol Cell. 2013 Mar 07; 49(5):773-82. PMID: 23473598.
      Citations: 362     Fields:    Translation:HumansAnimalsCells
    143. 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: 167     Fields:    Translation:HumansCells
    144. 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
    145. 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: 48     Fields:    Translation:HumansCells
    146. An integrated encyclopedia of DNA elements in the human genome. Nature. 2012 Sep 06; 489(7414):57-74. PMID: 22955616.
      Citations: 8471     Fields:    Translation:HumansAnimalsCells
    147. 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: 1489     Fields:    Translation:HumansCells
    148. 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: 819     Fields:    Translation:HumansCells
    149. 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: 638     Fields:    Translation:HumansCells
    150. 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: 100     Fields:    Translation:HumansAnimalsCells
    151. 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: 87     Fields:    Translation:HumansAnimalsCells
    152. 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: 287     Fields:    Translation:HumansAnimals
    153. 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: 436     Fields:    Translation:HumansAnimalsCells
    154. 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
    155. 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: 161     Fields:    Translation:AnimalsCells
    156. 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, Bl?thgen 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: 1407     Fields:    Translation:AnimalsCells
    157. Felsenfeld G, Dekker J. Genome architecture and expression. Curr Opin Genet Dev. 2012 Apr; 22(2):59-61. PMID: 22483506.
      Citations: 6     Fields:    Translation:HumansCells
    158. Gibcus JH, Dekker J. The context of gene expression regulation. F1000 Biol Rep. 2012; 4:8. PMID: 22500194.
      Citations:    
    159. 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: 294     Fields:    Translation:AnimalsCells
    160. 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, Gelp? 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, Guig? R, Gingeras TR. Evidence for transcript networks composed of chimeric RNAs in human cells. PLoS One. 2012; 7(1):e28213. PMID: 22238572.
      Citations: 41     Fields:    Translation:HumansCells
    161. 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
    162. 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: 30     Fields:    Translation:HumansCells
    163. 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: 67     Fields:    Translation:HumansAnimals
    164. Umbarger MA, Toro E, Wright MA, Porreca GJ, Ba? 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: 135     Fields:    Translation:Cells
    165. 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:    
    166. A user's guide to the encyclopedia of DNA elements (ENCODE). PLoS Biol. 2011 Apr; 9(4):e1001046. PMID: 21526222.
      Citations: 863     Fields:    Translation:HumansCells
    167. Sanyal A, Ba? D, Mart?-Renom MA, Dekker J. Chromatin globules: a common motif of higher order chromosome structure? Curr Opin Cell Biol. 2011 Jun; 23(3):325-31. PMID: 21489772.
      Citations: 35     Fields:    Translation:HumansAnimalsCells
    168. 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: 1092     Fields:    Translation:HumansAnimalsCells
    169. 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: 151     Fields:    Translation:AnimalsCells
    170. Ba? D, Sanyal A, Lajoie BR, Capriotti E, Byron M, Lawrence JB, Dekker J, Marti-Renom MA. The three-dimensional folding of the a-globin gene domain reveals formation of chromatin globules. Nat Struct Mol Biol. 2011 Jan; 18(1):107-14. PMID: 21131981.
      Citations: 161     Fields:    Translation:HumansCells
    171. van Steensel B, Dekker J. Genomics tools for unraveling chromosome architecture. Nat Biotechnol. 2010 Oct; 28(10):1089-95. PMID: 20944601.
      Citations: 127     Fields:    Translation:HumansAnimalsCells
    172. 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: 1087     Fields:    Translation:AnimalsCells
    173. 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: 102     Fields:    Translation:Humans
    174. 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: 33     Fields:    Translation:HumansAnimalsCells
    175. 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: 209     Fields:    Translation:Cells
    176. 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: 56     Fields:    Translation:HumansCells
    177. 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: 3706     Fields:    Translation:HumansCells
    178. 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: 47     Fields:    Translation:Cells
    179. 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
    180. 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
    181. 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: 61     Fields:    Translation:AnimalsCells
    182. 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: 172     Fields:    Translation:AnimalsCells
    183. 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: 52     Fields:    Translation:HumansAnimalsCells
    184. 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: 29     Fields:    Translation:HumansAnimalsCells
    185. 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: 75     Fields:    Translation:AnimalsCells
    186. Miele A, Dekker J. Long-range chromosomal interactions and gene regulation. Mol Biosyst. 2008 Nov; 4(11):1046-57. PMID: 18931780.
      Citations: 86     Fields:    Translation:HumansAnimalsCells
    187. Dekker J. Gene regulation in the third dimension. Science. 2008 Mar 28; 319(5871):1793-4. PMID: 18369139.
      Citations: 138     Fields:    Translation:HumansAnimalsCells
    188. 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: 23     Fields:    Translation:HumansAnimalsCells
    189. 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
    190. 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: 150     Fields:    Translation:AnimalsCells
    191. Birney E, Stamatoyannopoulos JA, Dutta A, Guig? 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, Hackerm?ller 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, Kara?z 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, L?ytynoja 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, Hallgr?msd?ttir 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: 2657     Fields:    Translation:HumansCells
    192. 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: 102     Fields:    Translation:Cells
    193. 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: 35     Fields:    Translation:AnimalsCells
    194. Hag?ge H, Klous P, Braem C, Splinter E, Dekker J, Cathala G, de Laat W, Forn? T. Quantitative analysis of chromosome conformation capture assays (3C-qPCR). Nat Protoc. 2007; 2(7):1722-33. PMID: 17641637.
      Citations: 424     Fields:    Translation:AnimalsCells
    195. 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: 573     Fields:    Translation:HumansCells
    196. 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: 37     Fields:    Translation:HumansCells
    197. 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: 55     Fields:    Translation:AnimalsCells
    198. Dekker J. The three 'C' s of chromosome conformation capture: controls, controls, controls. Nat Methods. 2006 Jan; 3(1):17-21. PMID: 16369547.
      Citations: 194     Fields:    Translation:Cells
    199. 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: 267     Fields:    Translation:HumansAnimalsCells
    200. 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: 172     Fields:    Translation:HumansAnimalsCells
    201. 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
    202. Dekker J, Rippe K, Dekker M, Kleckner N. Capturing chromosome conformation. Science. 2002 Feb 15; 295(5558):1306-11. PMID: 11847345.
      Citations: 1608     Fields:    Translation:AnimalsCells
    203. 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: 110     Fields:    Translation:AnimalsCells
    204. 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
    205. 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: 21     Fields:    Translation:AnimalsCells
    206. 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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