Publications

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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). https://doi.org/10.1186/s12915-022-01306-2
  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.
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