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Job Dekker PhD

TitleProfessor
InstitutionUniversity of Massachusetts Medical School
DepartmentBiochemistry and Molecular Pharmacology
AddressUniversity of Massachusetts Medical School
368 Plantation Street, AS5-1049
Worcester MA 01605
Phone508-856-4371
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    Other Positions
    InstitutionUMMS - School of Medicine
    DepartmentBiochemistry and Molecular Pharmacology

    InstitutionUMMS - Graduate School of Biomedical Sciences
    DepartmentBiochemistry and Molecular Pharmacology

    InstitutionUMMS - Graduate School of Biomedical Sciences
    DepartmentBioinformatics and Computational Biology

    InstitutionUMMS - Graduate School of Biomedical Sciences
    DepartmentInterdisciplinary Graduate Program

    InstitutionUMMS - Programs, Centers and Institutes
    DepartmentBioinformatics and Integrative Biology

    InstitutionUMMS - Programs, Centers and Institutes
    DepartmentSystems Biology


    Collapse ORNG Applications 
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    Collapse Biography 
    Collapse education and training
    Utrecht University, Utrecht, , NetherlandsMSBiology
    Utrecht University, Utrecht, , NetherlandsPHDPhysiological Chemistry
    Collapse awards and honors
    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
    2018Novitski Prize of the Genetics Society of America
    2018International Award of the Biochemical Society

    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.
    List All   |   Timeline
    1. 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 Jun 12. PMID: 31231024.
      View in: PubMed
    2. 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 Jun 05. PMID: 31168090.
      View in: PubMed
    3. 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.
      View in: PubMed
    4. 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 Mar 07; 176(6):1502-1515.e10. PMID: 30799036.
      View in: PubMed
    5. 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 Jan 17. PMID: 30655336.
      View in: PubMed
    6. 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 Jan 03; 10(1):30. PMID: 30604745.
      View in: PubMed
    7. 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 Nov 15; 72(4):715-726.e3. PMID: 30415953.
      View in: PubMed
    8. 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.
      View in: PubMed
    9. 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 Sep 10. PMID: 30202056.
      View in: PubMed
    10. Kim TH, Dekker J. 5C Analysis of 3C, ChIP-Loop, and Control Libraries. Cold Spring Harb Protoc. 2018 Sep 04; 2018(9):pdb.prot097899. PMID: 30181223.
      View in: PubMed
    11. Kim TH, Dekker J. 4C Analysis of 3C, ChIP-Loop, and Control Libraries. Cold Spring Harb Protoc. 2018 Sep 04; 2018(9):pdb.prot097881. PMID: 30181222.
      View in: PubMed
    12. 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 Sep 04; 2018(9):pdb.prot097873. PMID: 30181221.
      View in: PubMed
    13. Kim TH, Dekker J. 3C-Based Chromatin Interaction Analyses. Cold Spring Harb Protoc. 2018 Sep 04; 2018(9):pdb.top097832. PMID: 30181229.
      View in: PubMed
    14. 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. CBFß-SMMHC Inhibition Triggers Apoptosis by Disrupting MYC Chromatin Dynamics in Acute Myeloid Leukemia. Cell. 2018 Aug 23; 174(5):1325. PMID: 30142347.
      View in: PubMed
    15. Kim TH, Dekker J. Generation of ChIP-Loop Libraries. Cold Spring Harb Protoc. 2018 Aug 01; 2018(8):pdb.prot097857. PMID: 30068591.
      View in: PubMed
    16. Kim TH, Dekker J. Generation of 3C Libraries from Cross-Linked Cells. Cold Spring Harb Protoc. 2018 Aug 01; 2018(8):pdb.prot097840. PMID: 30068590.
      View in: PubMed
    17. Kim TH, Dekker J. Generation of Control Ligation Product Libraries for 3C Analyses. Cold Spring Harb Protoc. 2018 Aug 01; 2018(8):pdb.prot097865. PMID: 30068592.
      View in: PubMed
    18. 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 Jul 05; 71(1):191. PMID: 29979966.
      View in: PubMed
    19. 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. CBFß-SMMHC Inhibition Triggers Apoptosis by Disrupting MYC Chromatin Dynamics in Acute Myeloid Leukemia. Cell. 2018 Jun 28; 174(1):172-186.e21. PMID: 29958106.
      View in: PubMed
    20. 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 May 07. PMID: 29735996.
      View in: PubMed
    21. Kim TH, Dekker J. Chromatin Immunoprecipitation (ChIP) Analysis of Protein-DNA Interactions. Cold Spring Harb Protoc. 2018 May 01; 2018(5):pdb.top082586. PMID: 29717056.
      View in: PubMed
    22. Kim TH, Dekker J. ChIP-chip. Cold Spring Harb Protoc. 2018 May 01; 2018(5):pdb.prot082636. PMID: 29717045.
      View in: PubMed
    23. Kim TH, Dekker J. ChIP-seq. Cold Spring Harb Protoc. 2018 May 01; 2018(5):pdb.prot082644. PMID: 29717046.
      View in: PubMed
    24. Kim TH, Dekker J. ChIP-Quantitative Polymerase Chain Reaction (ChIP-qPCR). Cold Spring Harb Protoc. 2018 May 01; 2018(5):pdb.prot082628. PMID: 29717044.
      View in: PubMed
    25. Kim TH, Dekker J. ChIP. Cold Spring Harb Protoc. 2018 Apr 02; 2018(4):pdb.prot082610. PMID: 29610359.
      View in: PubMed
    26. Kim TH, Dekker J. Preparation of Cross-Linked Chromatin for ChIP. Cold Spring Harb Protoc. 2018 Apr 02; 2018(4):pdb.prot082602. PMID: 29610358.
      View in: PubMed
    27. Kim TH, Dekker J. Formaldehyde Cross-Linking. Cold Spring Harb Protoc. 2018 Apr 02; 2018(4):pdb.prot082594. PMID: 29610357.
      View in: PubMed
    28. 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.
      View in: PubMed
    29. 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.
      View in: PubMed
    30. 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.
      View in: PubMed
    31. 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.
      View in: PubMed
    32. 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.
      View in: PubMed
    33. 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.
      View in: PubMed
    34. 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.
      View in: PubMed
    35. 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 May 10. PMID: 28490498.
      View in: PubMed
    36. 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 Apr 18. PMID: 28435001.
      View in: PubMed
    37. 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.
      View in: PubMed
    38. 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.
      View in: PubMed
    39. 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 Dec 15; 194(12):1465-1474. PMID: 27367781.
      View in: PubMed
    40. Narendra V, Bulajic M, Dekker J, Mazzoni EO, Reinberg D. CTCF-mediated topological boundaries during development foster appropriate gene regulation. Genes Dev. 2016 Dec 15; 30(24):2657-2662. PMID: 28087711.
      View in: PubMed
    41. Dekker J. Mapping the 3D genome: Aiming for consilience. Nat Rev Mol Cell Biol. 2016 Nov 21; 17(12):741-742. PMID: 27869158.
      View in: PubMed
    42. 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 Oct 25; 113(43):E6572-E6581. PMID: 27791029.
      View in: PubMed
    43. 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 Nov; 1859(11):1389-1397. PMID: 27514584.
      View in: PubMed
    44. 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 Jul 28; 535(7613):575-9. PMID: 27437574.
      View in: PubMed
    45. 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 Sep; 26(9):1188-201. PMID: 27435934.
      View in: PubMed
    46. 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 May 5; 18(5):611-24. PMID: 27152443.
      View in: PubMed
    47. Valton AL, Dekker J. TAD disruption as oncogenic driver. Curr Opin Genet Dev. 2016 Feb; 36:34-40. PMID: 27111891.
      View in: PubMed
    48. Dekker J, Guttman M, Lomvardas S. A Guide to Packing Your DNA. Cell. 2016 Apr 7; 165(2):259-61. PMID: 27058655.
      View in: PubMed
    49. Dekker J, Mirny L. The 3D Genome as Moderator of Chromosomal Communication. Cell. 2016 Mar 10; 164(6):1110-21. PMID: 26967279.
      View in: PubMed
    50. 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):1454-8. PMID: 26940867.
      View in: PubMed
    51. 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.
      View in: PubMed
    52. 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 7; 98(1):185-201. PMID: 26748519.
      View in: PubMed
    53. 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.
      View in: PubMed
    54. 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.
      View in: PubMed
    55. 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 1; 60(1):146-62. PMID: 26431028.
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    56. Dekker J, Misteli T. Long-Range Chromatin Interactions. Cold Spring Harb Perspect Biol. 2015 Oct; 7(10):a019356. PMID: 26430217.
      View in: PubMed
    57. 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.
      View in: PubMed
    58. 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.
      View in: PubMed
    59. 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.
      View in: PubMed
    60. 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 1; 29(15):1661-75. PMID: 26253537.
      View in: PubMed
    61. 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.
      View in: PubMed
    62. Belton JM, Dekker J. Measuring Chromatin Structure in Budding Yeast. Cold Spring Harb Protoc. 2015 Jul; 2015(7):614-8. PMID: 26134912.
      View in: PubMed
    63. Belton JM, Dekker J. Hi-C in Budding Yeast. Cold Spring Harb Protoc. 2015 Jul; 2015(7):649-61. PMID: 26134906.
      View in: PubMed
    64. 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 2; 162(1):108-19. PMID: 26119342.
      View in: PubMed
    65. 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.
      View in: PubMed
    66. Belton JM, Dekker J. Chromosome Conformation Capture Carbon Copy (5C) in Budding Yeast. Cold Spring Harb Protoc. 2015 Jun; 2015(6):593-8. PMID: 26034306.
      View in: PubMed
    67. Belton JM, Dekker J. Randomized ligation control for chromosome conformation capture. Cold Spring Harb Protoc. 2015 Jun; 2015(6):587-92. PMID: 26034305.
      View in: PubMed
    68. Belton JM, Dekker J. Chromosome Conformation Capture (3C) in Budding Yeast. Cold Spring Harb Protoc. 2015 Jun; 2015(6):580-6. PMID: 26034304.
      View in: PubMed
    69. 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.
      View in: PubMed
    70. 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.
      View in: PubMed
    71. 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.
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    72. Mizuguchi T, Fudenberg G, Mehta S, Belton JM, Taneja N, Folco HD, FitzGerald P, Dekker J, Mirny L, Barrowman J, Grewal SI. Cohesin-dependent globules and heterochromatin shape 3D genome architecture in S. pombe. Nature. 2014 Dec 18; 516(7531):432-5. PMID: 25307058.
      View in: PubMed
    73. 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 8; 157(4):950-63. PMID: 24813616.
      View in: PubMed
    74. 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.
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    75. Kaplan N, Dekker J. High-throughput genome scaffolding from in vivo DNA interaction frequency. Nat Biotechnol. 2013 Dec; 31(12):1143-7. PMID: 24270850.
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    76. 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.
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    77. 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.
      View in: PubMed
    78. Dekker J, Mirny L. Biological techniques: Chromosomes captured one by one. Nature. 2013 Oct 3; 502(7469):45-6. PMID: 24067607.
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    79. 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.
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    80. 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.
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    81. 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 6; 153(6):1281-95. PMID: 23706625.
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    82. 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.
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    83. 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.
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    84. Gibcus JH, Dekker J. The hierarchy of the 3D genome. Mol Cell. 2013 Mar 7; 49(5):773-82. PMID: 23473598.
      View in: PubMed
    85. 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.
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    86. 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.
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    87. de Laat W, Dekker J. 3C-based technologies to study the shape of the genome. Methods. 2012 Nov; 58(3):189-91. PMID: 23199640.
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    88. An integrated encyclopedia of DNA elements in the human genome. Nature. 2012 Sep 06; 489(7414):57-74. PMID: 22955616.
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    89. 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 6; 489(7414):75-82. PMID: 22955617.
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    90. 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.
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    91. 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.
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    92. 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 1; 28(21):2843-4. PMID: 22923296.
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    93. 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.
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    94. An encyclopedia of mouse DNA elements (Mouse ENCODE). Genome Biol. 2012 Aug 13; 13(8):418. PMID: 22889292.
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    95. 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.
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    96. Dekker J. CTCF and cohesin help neurons raise their self-awareness. Proc Natl Acad Sci U S A. 2012 Jun 5; 109(23):8799-800. PMID: 22615386.
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    97. 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.
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    98. 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.
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    99. Felsenfeld G, Dekker J. Genome architecture and expression. Curr Opin Genet Dev. 2012 Apr; 22(2):59-61. PMID: 22483506.
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    100. Gibcus JH, Dekker J. The context of gene expression regulation. F1000 Biol Rep. 2012; 4:8. PMID: 22500194.
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    101. 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 2; 148(5):908-21. PMID: 22341456.
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    102. 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.
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    103. 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.
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    104. 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.
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    105. 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.
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    106. 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.
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    107. McCord RP, Dekker J. Translocation mapping exposes the risky lifestyle of B cells. Cell. 2011 Sep 30; 147(1):20-2. PMID: 21962501.
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    108. A user's guide to the encyclopedia of DNA elements (ENCODE). PLoS Biol. 2011 Apr; 9(4):e1001046. PMID: 21526222.
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    109. 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.
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    110. 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 7; 472(7341):120-4. PMID: 21423168.
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    111. 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.
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    112. Baù 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.
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    113. van Steensel B, Dekker J. Genomics tools for unraveling chromosome architecture. Nat Biotechnol. 2010 Oct; 28(10):1089-95. PMID: 20944601.
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    114. 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.
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    115. 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.
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    116. 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.
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    117. 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.
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    118. 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.
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    119. 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 9; 326(5950):289-93. PMID: 19815776.
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    120. 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.
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    121. 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.
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    122. 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.
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    123. 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.
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    124. 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.
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    125. 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.
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    126. 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.
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    127. 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.
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    128. Miele A, Dekker J. Long-range chromosomal interactions and gene regulation. Mol Biosyst. 2008 Nov; 4(11):1046-57. PMID: 18931780.
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    129. Dekker J. Gene regulation in the third dimension. Science. 2008 Mar 28; 319(5871):1793-4. PMID: 18369139.
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    130. 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.
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    131. 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.
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    132. 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.
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    133. 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.
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    134. Dostie J, Dekker J. Mapping networks of physical interactions between genomic elements using 5C technology. Nat Protoc. 2007; 2(4):988-1002. PMID: 17446898.
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    135. 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.
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    136. 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.
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    137. 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.
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    138. 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.
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    139. 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.
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    140. Dekker J. The three 'C' s of chromosome conformation capture: controls, controls, controls. Nat Methods. 2006 Jan; 3(1):17-21. PMID: 16369547.
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    141. 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 4; 17(3):453-62. PMID: 15694345.
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    142. 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.
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    143. Dekker J. A closer look at long-range chromosomal interactions. Trends Biochem Sci. 2003 Jun; 28(6):277-80. PMID: 12826398.
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    144. Dekker J, Rippe K, Dekker M, Kleckner N. Capturing chromosome conformation. Science. 2002 Feb 15; 295(5558):1306-11. PMID: 11847345.
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    145. 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.
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    146. 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.
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    147. 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.
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    148. 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.
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