Publications

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  1. Dixon, J.R., Xu, J., Dileep, V., Zhan, Y., Song, F., Le, V.T., Yardımcı, G.G., Chakraborty, A., Bann, D.V., Wang, Y., Clark, R., Zhang, L., Yang, H., Liu, T., Iyyanki, S., An, L., Pool, C., Sasaki, T., Rivera-Mulia, J.C., Ozadam, H., Lajoie, B.R., Kaul, R., Buckley, M., Lee, K., Diegel, M., Pezic, D., Ernst, C., Hadjur, S., Odom, D.T., Stamatoyannopoulos, J.A., Broach, J.R., Hardison, R., Ay, F., Noble, W.S., Dekker, J., Gilbert, D.M., Yue, F. (2018). Integrative Detection and Analysis of Structural Variation in Cancer Genomes. Nature Genet., 50:1388–1398.
  2. Pulikkan, J.A., Hegde, M., Belaghzal, H., Illendula, A., Yu, Y., Ahmed, H., O’Hagan, K., Xue, L., Wolfe, S., Zhu L.J., Dekker, J., Bushweller, J.H., Lucio H. Castilla, L.H. (2018). CBFb-SMMHC Inhibition Triggers Apoptosis by Disrupting MYC Chromatin Dynamics in Acute Myeloid Leukemia. Cell, 174:172-186.
  3. Gao, X.D., Tu, L., Mir, A., Rodriguez, T., Ding, Y., Leszyk, J., Dekker, J., Shaffer, S.A., Zhu, L.J., Scot A. Wolfe, S.A., Sontheimer, E.J. (2018). C-BERST: Defining subnuclear proteomic landscapes at genomic elements with dCas9-APEX2.  Nat. Methods, 15, 433–436.
  4. Hedger, A.K., Oomen, M., Liu, V., Moazami, M.P., Rhind, N., Dekker, J., Watts, J.K. (2018). Progress toward an amplifiable metabolic label for DNA: Conversion of 4-thiothymidine (4sT) to 5-methylcytidine and synthesis of a 4sT phosphorodiamidate prodrug. Can. J. Chemistry, 96 (7): 636-645.
  5. 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 Jan 18. pii: eaao6135. doi: 10.1126/science.aao6135. PubMed PMID: 29348367.
  6. 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 Nov 15;31(22):2264-2281. doi: 10.1101/gad.307769.117. Epub 2017 Dec 22. PubMed PMID: 29273679; PubMed Central PMCID: PMC5769770.
  7. 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; 4D Nucleome Network. The 4D nucleome project. Nature. 2017 Sep 13;549(7671):219-226. doi: 10.1038/nature23884. Erratum in: Nature. 2017 Nov 22;:. PubMed PMID: 28905911; PubMed Central PMCID: PMC5617335.
  8. 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. doi: 10.1038/ncb3594. Epub 2017 Aug 21. PubMed PMID: 28825700; PubMed Central PMCID: PMC5640152.
  9. 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. doi: 10.1016/j.cell.2017.05.004. PubMed PMID: 28525758; PubMed Central PMCID: PMC5538188.
  10. 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 23;114(21):5479-5484. doi: 10.1073/pnas.1705527114. Epub 2017 May 10. PubMed PMID: 28490498; PubMed Central PMCID: PMC5448194.
  11. 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 Jul 1;123:56-65. doi: 10.1016/j.ymeth.2017.04.004. Epub 2017 Apr 18. PubMed PMID: 28435001; PubMed Central PMCID: PMC5522765.
  12. 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. doi: 10.1080/10409238.2017.1287160. Epub 2017 Feb 15. Review. PubMed PMID: 28228067; PubMed Central PMCID: PMC5456460.
  13. 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 2;65(3):432-446.e5. doi: 10.1016/j.molcel.2017.01.009. PubMed PMID: 28157505; PubMed Central PMCID: PMC5421375.
  14. Narendra V, Bulajić 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. doi: 10.1101/gad.288324.116. Erratum in: Genes Dev. 2017 Aug 15;31(16):1714. PubMed PMID: 28087711; PubMed Central PMCID: PMC5238725.
  15. Dekker J. Mapping the 3D genome: Aiming for consilience. Nat Rev Mol Cell Biol. 2016 Nov 21;17(12):741-742. doi: 10.1038/nrm.2016.151. PubMed PMID: 27869158.
  16. 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. Epub 2016 Oct 10. PubMed PMID: 27791029; PubMed Central PMCID: PMC5087062.
  17. 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. doi: 10.1016/j.bbagrm.2016.08.003. Epub 2016 Aug 9. PubMed PMID: 27514584; PubMed Central PMCID: PMC5071180.
  18. 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. Epub 2016 Jul 18. PubMed PMID: 27437574; PubMed Central PMCID: PMC5443622.
  19. 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. doi: 10.1101/gr.201624.115. Epub 2016 Jul 19. PubMed PMID: 27435934; PubMed Central PMCID: PMC5052043.
  20. 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; CAMP Research Group. 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. PubMed PMID: 27367781; PubMed Central PMCID: PMC5215031.
  21. 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. doi: 10.1016/j.stem.2016.04.004. PubMed PMID: 27152443; PubMed Central PMCID: PMC4859942.
  22. Valton AL, Dekker J. TAD disruption as oncogenic driver. Curr Opin Genet Dev. 2016 Feb;36:34-40. doi: 10.1016/j.gde.2016.03.008. Epub 2016 Apr 22. Review. PubMed PMID: 27111891; PubMed Central PMCID: PMC4880504.
  23. Dekker J, Guttman M, Lomvardas S. A Guide to Packing Your DNA. Cell. 2016 Apr 7;165(2):259-61. doi: 10.1016/j.cell.2016.03.039. PubMed PMID: 27058655.
  24. Dekker J, Mirny L. The 3D Genome as Moderator of Chromosomal Communication. Cell. 2016 Mar 10;164(6):1110-1121. doi: 10.1016/j.cell.2016.02.007. Review. PubMed PMID: 26967279; PubMed Central PMCID: PMC4788811.
  25. 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. doi: 10.1126/science.aad9024. Epub 2016 Mar 3. PubMed PMID: 26940867; PubMed Central PMCID: PMC4884612.
  26. 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 2;14(4):896-906. doi: 10.1016/j.celrep.2015.12.083. Epub 2016 Jan 21. PubMed PMID: 26804913; PubMed Central PMCID: PMC4975037.
  27. 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. doi: 10.1016/j.ajhg.2015.12.002. PubMed PMID: 26748519; PubMed Central PMCID: PMC4716690.
  28. 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 1;13(9):1855-67. doi: 10.1016/j.celrep.2015.10.063. Epub 2015 Nov 19. PubMed PMID: 26655901; PubMed Central PMCID: PMC4681004.
  29. 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 1;16:259. doi: 10.1186/s13059-015-0831-x. PubMed PMID: 26619908; PubMed Central PMCID: PMC4665391.
  30. 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. doi: 10.1016/j.molcel.2015.08.024. PubMed PMID: 26431028; PubMed Central PMCID: PMC4806858.
  31. Dekker J, Misteli T. Long-Range Chromatin Interactions. Cold Spring Harb Perspect Biol. 2015 Oct 1;7(10):a019356. doi: 10.1101/cshperspect.a019356. Review. PubMed PMID: 26430217; PubMed Central PMCID: PMC4588061.
  32. 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. doi: 10.1186/s13059-015-0768-0. PubMed PMID: 26415882; PubMed Central PMCID: PMC4587679.
  33. 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. doi: 10.1016/j.cell.2015.08.040. Epub 2015 Sep 10. PubMed PMID: 26365489; PubMed Central PMCID: PMC4583798.
  34. Dekker J, Heard E. Structural and functional diversity of Topologically Associating Domains. FEBS Lett. 2015 Oct 7;589(20 Pt A):2877-84. doi: 10.1016/j.febslet.2015.08.044. Epub 2015 Sep 5. Review. PubMed PMID: 26348399; PubMed Central PMCID: PMC4598308.
  35. 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. doi: 10.1101/gad.265876.115. PubMed PMID: 26253537; PubMed Central PMCID: PMC4536313.
  36. 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. doi: 10.1093/nar/gkv723. Epub 2015 Jul 21. PubMed PMID: 26202961; PubMed Central PMCID: PMC4787801.
  37. Belton JM, Dekker J. Measuring Chromatin Structure in Budding Yeast. Cold Spring Harb Protoc. 2015 Jul 1;2015(7):614-8. doi: 10.1101/pdb.top077552. PubMed PMID: 26134912.
  38. Belton JM, Dekker J. Hi-C in Budding Yeast. Cold Spring Harb Protoc. 2015 Jul 1;2015(7):649-61. doi: 10.1101/pdb.prot085209. PubMed PMID: 26134906.
  39. 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. doi: 10.1016/j.cell.2015.05.048. Epub 2015 Jun 25. PubMed PMID: 26119342; PubMed Central PMCID: PMC4509605.
  40. Belton JM, Dekker J. Chromosome Conformation Capture Carbon Copy (5C) in Budding Yeast. Cold Spring Harb Protoc. 2015 Jun 1;2015(6):593-8. doi: 10.1101/pdb.prot085191. PubMed PMID: 26034306.
  41. Belton JM, Dekker J. Randomized ligation control for chromosome conformation capture. Cold Spring Harb Protoc. 2015 Jun 1;2015(6):587-92. doi: 10.1101/pdb.prot085183. PubMed PMID: 26034305.
  42. Belton JM, Dekker J. Chromosome Conformation Capture (3C) in Budding Yeast. Cold Spring Harb Protoc. 2015 Jun 1;2015(6):580-6. doi: 10.1101/pdb.prot085175. PubMed PMID: 26034304.
  43. 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 9;523(7559):240-4. doi: 10.1038/nature14450. Epub 2015 Jun 1. PubMed PMID: 26030525; PubMed Central PMCID: PMC4498965.
  44. 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. doi: 10.1101/gr.184986.114. Epub 2015 Feb 12. PubMed PMID: 25677180; PubMed Central PMCID: PMC4381522.
  45. Lajoie BR, Dekker J, Kaplan N. The Hitchhiker’s guide to Hi-C analysis: practical guidelines. Methods. 2015 Jan 15;72:65-75. doi: 10.1016/j.ymeth.2014.10.031. Epub 2014 Nov 6. PubMed PMID: 25448293; PubMed Central PMCID: PMC4347522.
  46. Dekker J. Two ways to fold the genome during the cell cycle: insights obtained with chromosome conformation capture. Epigenetics Chromatin. 2014 Nov 25;7(1):25. doi: 10.1186/1756-8935-7-25. eCollection 2014. Review. PubMed PMID: 25435919; PubMed Central PMCID: PMC4247682.
  47. 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. doi: 10.1038/nature13833. Epub 2014 Oct 12. PubMed PMID: 25307058; PubMed Central PMCID: PMC4465753.
  48. 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 J, Weng Z, White KP, Hardison RC. Reply to Brunet and Doolittle: Both selected effect and causal role elements can influence human biology and disease. Proc Natl Acad Sci U S A. 2014 Aug 19;111(33):E3366. PubMed PMID: 25275169; PubMed Central PMCID: PMC4143047.
  49. 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. doi: 10.1016/j.cell.2014.03.025. PubMed PMID: 24813616; PubMed Central PMCID: PMC4427251.
  50. 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. doi: 10.1073/pnas.1318948111. Epub 2014 Apr 21. Review. PubMed PMID: 24753594; PubMed Central PMCID: PMC4035993.
  51. Kaplan N, Dekker J. High-throughput genome scaffolding from in vivo DNA interaction frequency. Nat Biotechnol. 2013 Dec;31(12):1143-7. doi: 10.1038/nbt.2768. Epub 2013 Nov 24. PubMed PMID: 24270850; PubMed Central PMCID: PMC3880131.
  52. 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. doi: 10.1101/gad.227165.113. PubMed PMID: 24240234; PubMed Central PMCID: PMC3841733.
  53. 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. doi: 10.1126/science.1236083. Epub 2013 Nov 7. PubMed PMID: 24200812; PubMed Central PMCID: PMC4040465.
  54. Dekker J, Mirny L. Biological techniques: Chromosomes captured one by one. Nature. 2013 Oct 3;502(7469):45-6. doi: 10.1038/nature12691. Epub 2013 Sep 25. PubMed PMID: 24067607.
  55. 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. doi: 10.1101/gr.161620.113. Epub 2013 Sep 3. PubMed PMID: 24002784; PubMed Central PMCID: PMC3847776.
  56. 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. doi: 10.1002/bies.201300040. Epub 2013 Jul 5. PubMed PMID: 23832846; PubMed Central PMCID: PMC3874840.
  57. 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. doi: 10.1016/j.cell.2013.04.053. Epub 2013 May 23. PubMed PMID: 23706625; PubMed Central PMCID: PMC3712340.
  58. 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. doi: 10.1038/nrg3454. Epub 2013 May 9. Review. PubMed PMID: 23657480; PubMed Central PMCID: PMC3874835.
  59. 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. PubMed PMID: 23616995; PubMed Central PMCID: PMC4149748.
  60. Gibcus JH, Dekker J. The hierarchy of the 3D genome. Mol Cell. 2013 Mar 7;49(5):773-82. doi: 10.1016/j.molcel.2013.02.011. Review. PubMed PMID: 23473598; PubMed Central PMCID: PMC3741673.
  61. de Laat W, Dekker J. 3C-based technologies to study the shape of the genome. Methods. 2012 Nov;58(3):189-91. doi: 10.1016/j.ymeth.2012.11.005. PubMed PMID: 23199640; PubMed Central PMCID: PMC3874834.
  62. 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. doi: 10.1101/gr.138032.112. Epub 2012 Nov 14. PubMed PMID: 23152449; PubMed Central PMCID: PMC3561867.
  63. 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. doi: 10.1016/j.ymeth.2012.10.011. Epub 2012 Nov 5. PubMed PMID: 23137922; PubMed Central PMCID: PMC3874844.
  64. Sanyal A, Lajoie BR, Jain G, Dekker J. The long-range interaction landscape of gene promoters. Nature. 2012 Sep 6;489(7414):109-13. doi: 10.1038/nature11279. PubMed PMID: 22955621; PubMed Central PMCID: PMC3555147.
  65. 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. doi: 10.1038/nature11232. PubMed PMID: 22955617; PubMed Central PMCID: PMC3721348.
  66. ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature. 2012 Sep 6;489(7414):57-74. doi: 10.1038/nature11247. PubMed PMID: 22955616; PubMed Central PMCID: PMC3439153.
  67. 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. doi: 10.1038/nmeth.2148. Epub 2012 Sep 2. PubMed PMID: 22941365; PubMed Central PMCID: PMC3816492.
  68. 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. doi: 10.1093/bioinformatics/bts521. Epub 2012 Aug 24. PubMed PMID: 22923296; PubMed Central PMCID: PMC3476334.
  69. 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. doi: 10.1016/j.ymeth.2012.07.022. Epub 2012 Aug 15. PubMed PMID: 22903059; PubMed Central PMCID: PMC3874837.
  70. Mouse ENCODE Consortium, An encyclopedia of mouse DNA elements (Mouse ENCODE). Genome Biol. 2012 Aug 13;13(8):418. doi: 10.1186/gb-2012-13-8-418. PubMed PMID: 22889292; PubMed Central PMCID: PMC3491367.
  71. 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. doi: 10.1016/j.ymeth.2012.05.001. Epub 2012 May 29. PubMed PMID: 22652625; PubMed Central PMCID: PMC3874846.
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