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  1. Watson, E.V., Lee, J.-K., Gulhan, D.C., Melloni, G.E.M., Venev, S.V., Magesh, R.Y., Frederick, A., Chiba, K., Wooten, E.C., Naxerova, K., Dekker, J., Park, P.J., Elledge, S.J. (2024). Chromosome evolution screens recapitulate tissue-specific tumor aneuploidy patterns. Nat. Genet., 56 (5): 900-912. Highlighted in News&Views: Guscott and MeClelland (2024). Experimental evolution of cancer chromosomal changes. Nat. Genet. 56 (5): 743-745.
  2. Hildebrand, E.M.*, Polovnikov, K.*, Dekker, B., Liu, Y., Lafontaine, D.L., Fox, A.N., Li, Y., Venev, S.V., Mirny, L.A.#., Dekker, J.#. (2024). Mitotic chromosomes are self-entangled and disentangle through a Topoisomerase II-dependent two stage exit from mitosis. Mol. Cell, 84 (8): 1421-1441. *: co-first authors; #: co-corresponding authors. Highlighted in this preview: Baxter, J (2024). Entangling and disentangling mitotic chromosomes. Mol. Cell 84 (8): 1398-1400.
  3. Pourmorady, A.D., Bashkirova, E.V., Chiariello, A.M., Belagzhal, H., Kodra, A., Duffié, R., Kahiapo, J., Monahan, K., Pulupa, J., Schieren, I., Osterhoudt, A., Dekker, J., Nicodemi, M., Lomvardas, S. (2024). A symmetry breaking process proposes non-coding functions for olfactory receptor RNAs. Nature, 625 (7993): 181-188.
  4. Kocanova, S., Raynal, F., Goiffon, I., Akgol Oksuz, B., Baú, D., Kamgoué, A., Cantaloube, S., Zhan, Y., Lajoie, B.R., Marti-Renom, M.A.#, Dekker, J.#, Bystricky, K.# (2024). Enhancer-driven local 3D chromatin domain folding modulates transcription in human mammary tumor cells. Life Science Alliance, 7 (2): 7 (2): e202302154. #: co-corresponding authors.
  5. Yin, Q., Yang, C-H., Strelkova, O.S., Sun, Y., Gopalan, S., Yang, L., Dekker, J., Fazzio, T.G., Li, X.Z., Gibcus, J., Rando, O.J. (2023). Revisiting chromatin packaging in mouse sperm. Genome Res., 33 (12), 2079-2093.
  6. Gentien, D., Saberi-Ansari, E., Servant, N., Jolly, A., de la Grange, P., Nemati, F., Liot, G., Saule, S., Teissandier, A., Bourchis, D., Girard, E., Wong, J., Masliah Planchon, J., Rodrigues, M., Villoing Gaudé, L., Reyes, C., Henry, E., Baulande, S., M’kacher, R., Jeandidier, E., Nicolas, A., Decaudin, D., Cassoux, N., Piperno-Neumann, S., Stern, M.-H., Gibcus, J.H., Dekker, J., Heard, E., Roman-Roman, S., Waterfall, J.J. (2023). Multi-omics comparison of malignant and normal uveal melanocytes reveals novel molecular features of uveal melanoma. Cell Reports, 42: 113132.
  7. Cavalli, G., Dekker, J. (2023). Multiscale regulation of genome folding in space, time, and across the tree of life. Curr. Opin. Genet. Dev., 82:102095.
  8. Dekker, J., Alber, F., Aufmkolk, S., Beliveau, B.J., Bruneau, B.G., Belmont, A.S., Bintu, L., Boettiger, A., Calandrelli, R., Disteche, C.M., Gilbert, D.M., Gregor, T., Hansen, A.S., Huang, B., Huangfu, D., Kalhor, R., Leslie, C.S., Li, W. Li, Y., Ma, J., Noble, W.S., Park, P.J., Phillips-Cremins, J.E., Pollard, K.S., Rafelski, S.M., Ren, B., Ruan, Y., Shav-Tal, Y., Shen, Y., Shendure, J., Shu, X., Strambio-De-Castillia, C., Vertii, A., Zhang, H., Zhong, S. (2023). Spatial and temporal organization of the genome: current state and future aims of the 4D Nucleome Project. Mol. Cell, 83: 2624-2640.
  9. Min, J., Zhao, J., Zagelbaum, J., Takahashi, S., Cummins, P., Schooley, A., Dekker, J., Gottesman, M., Rabadan, R., Gautier, J. Mechanisms of insertions at a DNA double-strand break. Mol. Cell, 83:2434-2448.
  10. Zhou, C.Y., Dekker, B., Liu, Z., Cabrera, H., Ryan, J., Dekker, J., Heald, R. (2023). Mitotic chromosomes scale to nuclear-cytoplasmic ratio and cell size in Xenopus. eLife, 12: e84360.
  11. Marlétaz, F., de la Calle-Mustienes, E., Acemel, R.D., Paliou, C., Naranjo, S., Martínez-García, P.M., Cases, I., Sleight, V.A., Hirschberger, C., Marcet-Houben, M., Navon, D., Andrescavage, A., Skvortsova, K., Duckett, P.E., González-Rajal, A., Bogdanovic, O., Gibcus, J.H., Yang, L., Gallardo-Fuentes, L., Sospedra, I., Lopez-Rios, J., Darbellay, F., Visel, A., Dekker, J., Shubin, N., Gabaldón, T., Nakamura, T., Tena, J.J., Lupiáñez, D.G., Rokhsar, D.S., Gómez-Skarmeta, J.L. The little skate genome and the evolutionary emergence of wing-like fin appendages. Nature, 616 (7957): 495–503. Highlighted in News & Views by Amemiya, C. Genome reveals how the skate got its wings. Nature. 616 (7957): 440-441.
  12. Spracklin, G., Yang, L., Pradhan, S., Dekker, J. (2023). Measuring inaccessible chromatin genome-wide using Protect-seq. In: Marinov, G.K., Greenleaf, W.J. (eds) Chromatin Accessibility. Methods in Molecular Biology, vol 2611. Humana, New York, NY.
  13. Yang, L., Akgol Oksuz, B., Dekker, J., Gibcus, J.H. (2023). Capturing chromosome conformation across length scales. J. Vis. Exp., 191, e64001. doi: 10.3791/64001.
  14. Zagelbaum, J., Schooley, A., Zhao, J., Schrank, B.R., Callen, E., Zha, S., Gottesman, M.E., Nussenzweig, A., Rabadan, R., Dekker, J., Gautier, J. (2023). Multiscale reorganization of the genome following DNA damage facilitates chromosome translocations via nuclear actin polymerization. Nat. Struct. Mol. Biol., 30 (1): 99-106.
  15. Spracklin, G., Abdennur, N., Imakaev, M., Chowdhury, N., Pradhan, S., Mirny, L., Dekker, J. (2023). Heterochromatin diversity modulates genome compartmentalization and loop extrusion barriers. Nat. Struct. Mol. Biol., 30 (1): 38-51.
  16. Valton, A-L., Venev, S.V., Mair, B., Khokhar, E., Tong, A.H.Y., Usaj, M., Cham, K.S.K., Pai, A.A., Moffat, J., Dekker, J. (2022). A cohesin traffic pattern genetically linked to gene regulation. Nat. Struct. Mol. Biol., 29 (12): 1239-1251.
  17. Dekker, B., Dekker, J. Regulation of the mitotic chromosome folding machines. Biochem. J. 479: 2153-2173.
  18. Liu, Y., Dekker, J. (2022). CTCF-CTCF loops and intra-TAD interactions show differential dependence on cohesin ring integrity. Nature Cell Biol. 24 (10): 1516-1527.
  19. Emerson, D., Zhao, P.A., Cook, A.L., Barnett, R.J., Klein, K.N., Saulebekova, D., Ge, C., Zhou, L., Simandi, Z., Minsk, M.K., Titus, K.R., Wang, W., Gong, W., Zhang, D., Yang, L., Venev, S.V., Gibcus, J.H., Yang, H., Sasaki, T.,Kanemaki, M.T., Yue, F., Dekker, J., Chen, C-L., Gilbert, D.M., Phillips-Cremins, J.E. (2022). Cohesin-mediated loop anchors confine the locations of human replication origins. Nature 606: 812-819.
  20. 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 20, 103 (2022).
  21. 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.10 (4): 14evac042. PMCID: PMC9011032.
  22. Sanders JT, Golloshi R, Das P, Terry PH, Nash DG, Xu Y, Dekker J, McCord RP. (2022). Loops, TADs, compartments and territories are elastic and robust to dramatic nuclear volume swelling.Sci. Reports, 12 (1): 4721. doi: 10.1038/s41598-022-08602-5
  23. Leidescher S, Ribisel J, Ullrich S, Feodorova Y, Hildebrand E, Bultmann S, Link S, Thanisch K, Mulholland C, Dekker J, Leonhardt H, Mirny LA, Solovei I. Spatial organization of transcribed eukaryotic genes. Nature Cell Biol.24 (3): 327-339.
  24. Voolstra, C.R., Aranda, M., Zhan, Y., Dekker, J. (2021). Genome of the month: Symbiodidinium microadriaticum (coral microalgal endosymbiont). Trends in Genetics, 11: 1044-1045. doi: 10.1016/j.tig.2021.08.008. Epub ahead of print. PMID: 34518054
  25. Cha HJ, Uyan O, Yan Kai Y, Liu T, Zhu Q, Tothova Z, Botten GA, Xu J, Yuan G-C, Dekker J, Orkin SH. (2021). “Inner nuclear protein Matrin-3 coordinates cell differentiation by stabilizing chromatin architecture”.Nature Comms, 12:6241.
  26. Akgol Oksuz, B.*, Yang, L.*, Abraham, S., Venev, S.V., Krietenstein, N., Parsi, K.M., Ozadam, H., Oomen, M.E., Nand, A., Mao, H., Genga, R.M.J., Maehr, R., Rando, O.J., Mirny, L.A., Gibcus, J.H.#, Dekker, J.#(2021). Systematic evaluation of chromosome conformation capture assays.Nat. Methods18:1046-1055. *: co-first authors; #: co-corresponding authors.
  27. Lafontaine, D.L., Yang, L., Dekker, J., Gibcus, J.H. Hi-C 3.0: Improved genome-wide chromosome conformation capture protocol. Current Protocols, 1 (7): e198. doi: 10.1002/cpz1.198.
  28. Choppakatla, P., Dekker, B., Cutts, E.E., Vannini, A., Dekker, J., Funabiki, H. (2021). Linker histone H1.8 inhibits chromatin-binding of condensins and DNA topoisomerase II to tune chromosome compaction and individualization. Elife10: e68918.
  29. Tigano, A., Jacobs, A., Wylder, A.P., Nand, A., Zhan, Y., Dekker, J., Therkildsen, N.O. (2021). Chromosome-level assembly of the Atlantic silverside genome reveals extreme levels of sequence diversity and structural genetic variation. Genome Biol. Evol.13 (6): evab098.doi: 10.1093/gbe/evab098. PMCID: PMC8214408.
  30. Nand, A.*, Zhan, Y.*, Salazar, O.R.*, Aranda, M.#, Voolstra, C.R.#, Dekker, J.#. (2021). Genetic and spatial organization of the unusual chromosomes of the dinoflagellate Symbiodinium microadriaticum. Nat. Genet., 53 (5): 618-629.*: co-first authors; #: co-corresponding authors. PMCID: PMC8110479.
  31. Belaghzal, H.*, Borrman, T.*, Stephens, A.D., Lafontaine, D.L., Venev, S.V., Weng, Z., Marko, J.F., Dekker, J.(2021).Liquid chromatin Hi-C characterizes compartment-dependent chromatin interaction dynamics. Nat. Genet., 53 (3): 367–378. *: co-first authors. PMCID: PMC7946813.
  32. Tothova, Z., Valton, A, Gorelov, R., Vallurupalli, M., Krill-Burger, J.M., Holmes, A., Landers, C.C., Haydu, J.E., Malolepsza, E., Hartigan, C.R., Donahue, M., Popova, K.D., Koochaki, S.H.J., Venev, S.V., Rivera, J.F., Chen, E., Lage, K., Schenone, M., D’Andrea, A.D., Carr, S.A., Morgan, E.A., Dekker, J., Ebert, B.L. (2021). Cohesin mutations alter DNA damage repair and chromatin structure and create therapeutic vulnerabilities in MDS/AML. JCI Insight,6(3): e142149. PMCID:PMC7934867.
  33. Zhang, B.N., Liu, Y., Yang, Q., Leung, P.Y., Wang, C., Wong, T.C.B., Tham, C.C., Chan, S.O., Pang, C.P., Chen, L.J., Dekker, J., Zhao, Z., Chu, W.K. Rad21 is involved in corneal stroma development by regulating neural crest migration. Int. J. Mol. Sci., 21 (20): 7807.
  34. Brossas, C., Valton, A., Venev, S.V., Chilaka, S., Counillon, A., Laurent, M., Goncalves, C., Duriez, B., Picard, F., Dekker, J., Prioleau, M. (2020). Clustering of strong replicators associated with active promoter is sufficient to establish an early-replicating domain. EMBO J., 39:e99520.
  35. Tavares-Cadete, F.*, Norouzi, D.*, Dekker, B., Liu , Y., Dekker, J.(2020). Multi-contact 3C reveals that the human genome during interphase is largely not entangled. Nat. Struct. Mol. Biol., 27: 1105-114. *: co-first authors.
  36. Oomen, M.E., Hedger, A.K., Watts, J.K, Dekker, J. (2020). Detecting chromatin interactions between and along sister chromatids with SisterC. Nature Methods, 17:1002-1009.
  37. Fitz-James, M.H, Tong, P., Pidoux, A.L., Ozadam, H., Yang, L., White, S.A., Dekker, J., Allshire, R.C. (2020). Large domains of heterochromatin direct the formation of short mitotic chromosome loops. Elife, 9:e57212. 
  38. ENCODE Project Consortium, Snyder, M.P., Gingeras, T.R., Moore, J.E., Weng, Z., Gerstein, M.B., Ren, B., Hardison, R.C., Stamatoyannopoulos, J.A., Graveley, B.R., Feingold, E.A., Pazin, M.J., Pagan, M., Gilchrist, D.A., Hitz, B.C., Cherry, J.M., Bernstein, B.E., Mendenhall, E.M., Zerbino, D.R., Frankish, A., Flicek, P., Myers, R.M. (2020). Perspectives on ENCODE. Nature, 583 (7818): 693-698.
  39. ENCODE Project Consortium, Moore, J.E., Purcaro, M.J., Pratt, H.E., Epstein, C.B., Shoresh, N., Adrian, J., Kawli, T., Davis, C.A., Dobin, A., Kaul, R., Halow, J., Van Nostrand, E.L., Freese, P., Gorkin, D.U., Shen, Y., He, Y., Mackiewicz, M., Pauli-Behn, F., Williams, B.A., Mortazavi, A., Keller, C.A., Zhang, X.O., Elhajjajy, S.I., Huey, J., Dickel, D.E., Snetkova, V., Wei, X., Wang, X., Rivera-Mulia, J.C., Rozowsky, J., Zhang, J., Chhetri, S.B., Zhang, J., Victorsen, A., White, K.P., Visel, A., Yeo, G.W., Burge, C.B., Lécuyer, E., Gilbert, D.M., Dekker, J., Rinn, J., Mendenhall, E.M., Ecker, J.R., Kellis, M., Klein, R.J., Noble, W.S., Kundaje, A., Guigó, R., Farnham, P.J., Cherry, J.M., Myers, R.M., Ren, B., Graveley, B.R., Gerstein, M.B., Pennacchio, L.A., Snyder, M.P., Bernstein, B.E., Wold, B., Hardison, R.C., Gingeras, T.R., Stamatoyannopoulos, J.A., Weng, Z. (2020). Expanded encyclopaedias of DNA elements in the human and mouse genomes. Nature, 583 (7818): 699-710.
  40. Hildebrand E., Dekker, J. (2020). Mechanisms and functions of chromosome compartmentalization. Trends Biochem. Sci., 45(5): 385-396.
  41. Krietenstein, N., Abraham, S., Venev, S.V., Abdennur, N., Gibcus, J., Hsieh, T-H.S., Parsi, K.M., Yang, L., Maehr, R., Mirny, L.A., Dekker, J., Rando, O.J. (2020). Ultrastructural details of mammalian chromosome architecture. Mol. Cell, 78 (3): 554-565. PMCID: PMC7222625.
  42. Dossin, F., Pinheiro, I., Żylicz, J.J., 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. (2020). SPEN is a molecular integrator that bridges Xist with transcriptional and epigenetic control of X-chromosome inactivation. Nature, 578: 455-460.
  43. Gisselbrecht, S.S., Palagi, A., Kurland, J.V., Rogers, J.M., Ozadam, H., Zhan, Y., Dekker, J., Bulyk, M.L. (2020). Transcriptional silencers in Drosophila serve a dual role as transcriptional enhancers in alternate cellular contexts. Mol. Cell, 77: 324-337.
  44. Abramo K, Valton A, Venev SV, Ozadam H, Fox AN, Dekker J. (2019). A chromosome folding intermediate at the condensin-to-cohesin transition during telophase. Nat. Cell Biol., 21: 1393-1402. Highlighted in Liu, N.Q. and De Wit, E. (2019). A transient absence of SMC-mediated loops after mitosis. Nat. Cell Biol. 21: 1303-1304.
  45. 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 (2019). Rapid irreversible transcriptional reprogramming in human stem cells accompanied by discordance between replication timing and chromatin compartment. Stem Cell Reports 13 (1): 193-206.
  46. 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 Oct 3;10(1):4485. doi: 10.1038/s41467-019-12208-3.PMID: 31582763
  47. 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 Oct 3;10(1):4486. doi: 10.1038/s41467-019-12211-8. PMID: 31582744
  48. 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;570(7761):395-399. doi: 10.1038/s41586-019-1275-3. PMID: 31168090
  49. Yardimci, G.G, Ozadam, H., Sauria, M.E.G., Ursu, O., Yan, K., Yang, T., Chakraborty, A., Kaul, A., Lajoie, B.R., Song, F., Zhan, Y., Ay, F., Gerstein, M., Kundaje, A., Li, Q., Taylor, J., Yue, F., Dekker, J.#. Noble, W.S.# (2019). Measuring the reproducibility and quality of Hi-C data. Genome Biol. 20: 57. #: co-corresponding authors.
  50. Dekker, J. (2019). Chromosome Folding: Contributions of chromosome conformation capture and polymer physics. In: “Modeling the 3D conformation of genomes”, Chapter 1: 1-17. Series in computational biophysics, Dokholyan N.V. Edited by Tiana. G. and Giorgetti, L. CRC Press. Boca Raton, USA.
  51. Finn, E.H., Pegoraro, G., Brandão, H.B., Valton, A, Oomen, M.E., Dekker, J., Mirny, L.A., Misteli, T. (2019). Extensive heterogeneity and intrinsic variation in spatial genome organization. Cell, 176, 1502-1515.
  52. Oomen, M.E., Anders S. Hansen, A.S., Liu, Y., Darzacq, X., Dekker, J. (2019). CTCF sites display cell cycle dependent dynamics in factor binding and nucleosome positioning. Genome Res., 29: 236-249.
  53. Gdula, M.R., Nesterova, T.B., Pintacuda, G., Godwin, J., Zhan, Y., Ozadam, H., McClellan, M., Moralli, D., Krueger, F., Green, C.M., Reik, W., Kriaucionis, S., Heard, E., Dekker, J., Brockdorff, N. (2019). The non-canonical SMC protein SmcHD1 antagonises TAD formation and compartmentalisation on the inactive X chromosome. Nat. Commun., 10 (1): 30.
  54. Oudelaar, A.M, Davies, J.O.J., Hanssen, L.L.P., Telenius, J.M., Schwessinger, R., Liu, Y., Brown, J.M., Downes, D.J., Chiariello, A.M., Bianco, S., Nicodemi, M., Buckle, V.J., Dekker, J., Higgs, D.R., Hughes, J.R. (2018). Single-allele chromatin interactions reveal regulatory hubs in dynamic compartmentalized domains. Nature Genet. 50: 1744–1751.
  55. Metkar, M., Ozadam, H., Lajoie, B.R., Imakaev, M., Mirny, L.A., Dekker, J.#, Moore, M.J.# (2018). Higher-order organization principles of re-translational mRNPs. Mol. Cell, 72 (4): 715-726. PMCID: PMC6239896. #: co-corresponding authors. (Highlighted in Pierron and Weil (2018). Re-viewing the 3D organization of mRNPs. Mol. Cell 72 (4): 603-605).
  56. 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. #: co-corresponding authors.
  57. 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.
  58. 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.
  59. 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.
  60. 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. *: equal contribution. #: co-corresponding authors.
  61. 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.
  62. 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.
  63. 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.
  64. 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.
  65. 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.
  66. 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.
  67. 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.
  68. 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.
  69. 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.
  70. 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.
  71. 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.
  72. 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.
  73. 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.
  74. 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.
  75. 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.
  76. 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.
  77. 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.
  78. 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.
  79. 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.
  80. 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.
  81. 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.
  82. 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.
  83. 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.
  84. 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.
  85. 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.
  86. 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.
  87. 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.
  88. 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.
  89. 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.
  90. 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.
  91. 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.
  92. 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.
  93. 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.
  94. 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.
  95. 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.
  96. 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.
  97. 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.
  98. 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.
  99. 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.
  100. 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.
  101. 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.
  102. 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.
  103. 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.
  104. 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.
  105. 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.
  106. 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.
  107. 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.
  108. 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.
  109. 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.
  110. 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.
  111. 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.
  112. 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.
  113. 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.
  114. 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.
  115. 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.
  116. 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.
  117. 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.
  118. 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.
  119. 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.
  120. 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.
  121. 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.
  122. 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.
  123. 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.
  124. 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.
  125. 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.
  126. 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.
  127. 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. doi: 10.1073/pnas.1206195109. Epub 2012 May 21. PubMed PMID: 22615386; PubMed Central PMCID: PMC3384181.
  128. 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. doi: 10.1126/science.1221472. Epub 2012 May 3. PubMed PMID: 22555433; PubMed Central PMCID: PMC3376212.
  129. Gibcus JH, Dekker J. The context of gene expression regulation. F1000 Biol Rep. 2012;4:8. doi: 10.3410/B4-8. Epub 2012 Apr 2. PubMed PMID: 22500194; PubMed Central PMCID: PMC3318259.
  130. 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. doi: 10.1038/nature11049. PubMed PMID: 22495304; PubMed Central PMCID: PMC3555144.
  131. Felsenfeld G, Dekker J. Genome architecture and expression. Curr Opin Genet Dev. 2012 Apr;22(2):59-61. doi: 10.1016/j.gde.2012.03.003. Epub 2012 Apr 6. PubMed PMID: 22483506.
  132. 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. doi: 10.1016/j.cell.2012.02.002. Epub 2012 Feb 16. PubMed PMID: 22341456; PubMed Central PMCID: PMC3320767.
  133. 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. doi: 10.1371/journal.pone.0028213. Epub 2012 Jan 4. PubMed PMID: 22238572; PubMed Central PMCID: PMC3251577.
  134. Noble WS, Blau CA, Dekker J, Duan ZJ, Mao Y. The structure and function of chromatin and chromosomes. Pac Symp Biocomput. 2012:434-40. PubMed PMID: 22174298.
  135. 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. doi: 10.1038/nmeth.1748. PubMed PMID: 22037705; PubMed Central PMCID: PMC3235803.
  136. 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. doi: 10.1038/nmeth.1764. PubMed PMID: 22037702; PubMed Central PMCID: PMC3263363.
  137. 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. doi: 10.1016/j.molcel.2011.09.010. PubMed PMID: 22017872; PubMed Central PMCID: PMC3874842.
  138. McCord RP, Dekker J. Translocation mapping exposes the risky lifestyle of B cells. Cell. 2011 Sep 30;147(1):20-2. doi: 10.1016/j.cell.2011.09.005. PubMed PMID: 21962501.
  139. ENCODE Project Consortium. A user’s guide to the encyclopedia of DNA elements (ENCODE). PLoS Biol. 2011 Apr;9(4):e1001046. doi: 10.1371/journal.pbio.1001046. Epub 2011 Apr 19. PubMed PMID: 21526222; PubMed Central PMCID: PMC3079585.
  140. 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. doi: 10.1016/ Epub 2011 Apr 12. Review. PubMed PMID: 21489772; PubMed Central PMCID: PMC3109114.
  141. 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. doi: 10.1038/nature09819. Epub 2011 Mar 20. PubMed PMID: 21423168; PubMed Central PMCID: PMC3670758.
  142. 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. doi: 10.1016/j.cell.2010.11.015. PubMed PMID: 21145459; PubMed Central PMCID: PMC3033573.
  143. Baù D, Sanyal A, Lajoie BR, Capriotti E, Byron M, Lawrence JB, Dekker J, Marti-Renom MA. The three-dimensional folding of the α-globin gene domain reveals formation of chromatin globules. Nat Struct Mol Biol. 2011 Jan;18(1):107-14. doi: 10.1038/nsmb.1936. Epub 2010 Dec 5. PubMed PMID: 21131981; PubMed Central PMCID: PMC3056208.
  144. van Steensel B, Dekker J. Genomics tools for unraveling chromosome architecture. Nat Biotechnol. 2010 Oct;28(10):1089-95. doi: 10.1038/nbt.1680. PubMed PMID: 20944601; PubMed Central PMCID: PMC3023824.
  145. 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. doi: 10.1038/nature09380. Epub 2010 Aug 18. Erratum in: Nature. 2011 Apr 14;472(7342):247. PubMed PMID: 20720539; PubMed Central PMCID: PMC2953795.
  146. 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. doi: 10.1073/pnas.1006774107. Epub 2010 Jun 28. PubMed PMID: 20616024; PubMed Central PMCID: PMC2906581.
  147. Naumova N, Dekker J. Integrating one-dimensional and three-dimensional maps of genomes. J Cell Sci. 2010 Jun 15;123(Pt 12):1979-88. doi: 10.1242/jcs.051631. PubMed PMID: 20519580; PubMed Central PMCID: PMC2880011.
  148. 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 6;(39). pii: 1869. doi: 10.3791/1869. PubMed PMID: 20461051; PubMed Central PMCID: PMC3149993.
  149. 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. doi: 10.1093/nar/gkq175. Epub 2010 Mar 31. PubMed PMID: 20360044; PubMed Central PMCID: PMC2910055.
  150. 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. doi: 10.1126/science.1181369. PubMed PMID: 19815776; PubMed Central PMCID: PMC2858594.
  151. 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. doi: 10.1038/nmeth1009-690. PubMed PMID: 19789528; PubMed Central PMCID: PMC2859197.
  152. van Berkum NL, Dekker J. Determining spatial chromatin organization of large genomic regions using 5C technology. Methods Mol Biol. 2009;567:189-213. doi: 10.1007/978-1-60327-414-2_13. Review. PubMed PMID: 19588094; PubMed Central PMCID: PMC3880132.
  153. 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. doi: 10.1371/journal.pgen.1000522. Epub 2009 Jun 19. PubMed PMID: 19543368; PubMed Central PMCID: PMC2689649.
  154. 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. doi: 10.1038/embor.2009.136. Epub 2009 Jun 12. PubMed PMID: 19525922; PubMed Central PMCID: PMC2727444.
  155. 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. doi: 10.1371/journal.pgen.1000478. Epub 2009 May 8. PubMed PMID: 19424429; PubMed Central PMCID: PMC2673037.
  156. 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. doi: 10.1101/gad.1782209. PubMed PMID: 19390086; PubMed Central PMCID: PMC2675867.
  157. Miele A, Dekker J. Mapping cis- and trans- chromatin interaction networks using chromosome conformation capture (3C). Methods Mol Biol. 2009;464:105-21. doi: 10.1007/978-1-60327-461-6_7. PubMed PMID: 18951182; PubMed Central PMCID: PMC3874836.
  158. Miele A, Dekker J. Long-range chromosomal interactions and gene regulation. Mol Biosyst. 2008 Nov;4(11):1046-57. doi: 10.1039/b803580f. Epub 2008 Aug 13. Review. PubMed PMID: 18931780; PubMed Central PMCID: PMC2653627.
  159. 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. doi: 10.1074/jbc.M806479200. Epub 2008 Oct 16. PubMed PMID: 18930918; PubMed Central PMCID: PMC2596406.
  160. Dekker J. Gene regulation in the third dimension. Science. 2008 Mar 28;319(5871):1793-4. doi: 10.1126/science.1152850. PubMed PMID: 18369139; PubMed Central PMCID: PMC2666883.
  161. 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. doi: 10.1111/j.1365-2141.2008.07065.x. Epub 2008 Mar 3. PubMed PMID: 18318763.
  162. Dostie J, Zhan Y, Dekker J. Chromosome conformation capture carbon copy technology. Curr Protoc Mol Biol. 2007 Oct;Chapter 21:Unit 21.14. doi: 10.1002/0471142727.mb2114s80. PubMed PMID: 18265398.
  163. 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. doi: 10.1002/0471142727.mb2111s74. PubMed PMID: 18265379.
  164. 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. Epub 2007 Sep 9. PubMed PMID: 17828248.
  165. 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. PubMed PMID: 17641637.
  166. 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. PubMed PMID: 17577398; PubMed Central PMCID: PMC2394764.
  167. ENCODE Project Consortium, 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. PubMed PMID: 17571346; PubMed Central PMCID: PMC2212820.
  168. Dostie J, Dekker J. Mapping networks of physical interactions between genomic elements using 5C technology. Nat Protoc. 2007;2(4):988-1002. PubMed PMID: 17446898.
  169. 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. Epub 2006 Sep 5. PubMed PMID: 16954542; PubMed Central PMCID: PMC1581439.
  170. 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. Epub 2006 Aug 4. PubMed PMID: 16891414; PubMed Central PMCID: PMC1567902.
  171. Dekker J. The three ‘C’ s of chromosome conformation capture: controls, controls, controls. Nat Methods. 2006 Jan;3(1):17-21. PubMed PMID: 16369547.
  172. 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. PubMed PMID: 15694345.
  173. 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. Epub 2004 Aug 6. PubMed PMID: 15299144; PubMed Central PMCID: PMC515102.
  174. Dekker J. A closer look at long-range chromosomal interactions. Trends Biochem Sci. 2003 Jun;28(6):277-80. Review. PubMed PMID: 12826398.
  175. Dekker J, Rippe K, Dekker M, Kleckner N. Capturing chromosome conformation. Science. 2002 Feb 15;295(5558):1306-11. PubMed PMID: 11847345.
  176. Cha, R.S., Weiner, B.M., Keeney, S., Dekker, J., Kleckner, N. (2000). Progression of meiotic DNA replication is modulated by interchromosomal interaction proteins, negatively by Spo11p and positively by Rec8p.  Genes Dev. 14 (4): 493-503.
  177. Dekker, J., Kanellopoulos, P.N., van Oosterhout, J.A., Stier, G., Tucker, P.A., van der Vliet, P.C. (1 ATP-independent DNA unwinding by the adenovirus single-stranded DNA binding protein requires a flexible DNA binding loop. (1998). J Mol Biol. 10;277 (4): 825-838. PMID: 9545375
  178. Dekker, J. Kanellopoulos, P.N., Loonstra, A.K., van Oosterhout, J.A., Leonard, K., Tucker, P.A., van der Vliet, P.C. (1997). Multimerization of the adenovirus DNA-binding protein is the driving force for ATP-independent DNA unwinding during strand displacement synthesis. EMBO J. 16 (6): 1455-1463. PMID: 9135160; PMCID: PMC1169742
  179. Dekker, J., van Oosterhout, J.A., van der Vliet, P.C. (1996). Two regions within the DNA binding domain of nuclear factor I interact with DNA and stimulate adenovirus DNA replication independently. Mol Cell Biol. 16 (8): 4073-4080. PMID: 8754805; PMCID: PMC231403
  180. Dekker, J., Coenjaerts, F.E.J., van der Vliet, P.C. (1996). Reconstitution of Adenovirus DNA replication with purified replication proteins. In: Viral Genome Methods. KW Adolph, ed. Pp. 269-282. CRC Press, Boca Raton.