Job Dekker - Publications

Harvard University, Cambridge, MA, United States 

61 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2018 Dixon JR, Xu J, Dileep V, Zhan Y, Song F, Le VT, Yardımcı GG, Chakraborty A, Bann DV, Wang Y, Clark R, Zhang L, Yang H, Liu T, Iyyanki S, ... ... Dekker J, et al. Integrative detection and analysis of structural variation in cancer genomes. Nature Genetics. PMID 30202056 DOI: 10.1038/s41588-018-0195-8  0.6
2016 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. Biochimica Et Biophysica Acta. PMID 27514584 DOI: 10.1016/j.bbagrm.2016.08.003  0.6
2016 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. PMID 27437574 DOI: 10.1038/nature18589  0.6
2016 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 Research. PMID 27435934 DOI: 10.1101/gr.201624.115  0.6
2016 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. 18: 611-624. PMID 27152443 DOI: 10.1016/j.stem.2016.04.004  0.6
2016 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, et al. Activation of proto-oncogenes by disruption of chromosome neighborhoods. Science (New York, N.Y.). PMID 26940867 DOI: 10.1126/science.aad9024  0.6
2016 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 American Journal of Human Genetics. 98: 185-201. DOI: 10.1016/j.ajhg.2015.12.002  0.6
2015 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 Reports. 13: 1855-67. PMID 26655901 DOI: 10.1016/j.celrep.2015.10.063  0.6
2015 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 Biology. 16: 259. PMID 26619908 DOI: 10.1186/s13059-015-0831-x  0.6
2015 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. Molecular Cell. 60: 146-62. PMID 26431028 DOI: 10.1016/j.molcel.2015.08.024  0.6
2015 Dekker J, Heard E. Structural and functional diversity of Topologically Associating Domains. Febs Letters. 589: 2877-84. PMID 26348399 DOI: 10.1016/j.febslet.2015.08.044  0.6
2015 Belton JM, Dekker J. Measuring Chromatin Structure in Budding Yeast. Cold Spring Harbor Protocols. 2015: pdb.top077552. PMID 26134912 DOI: 10.1101/pdb.top077552  0.6
2015 Belton JM, Dekker J. Hi-C in Budding Yeast. Cold Spring Harbor Protocols. 2015: pdb.prot085209. PMID 26134906 DOI: 10.1101/pdb.prot085209  0.6
2015 Hsieh TH, Weiner A, Lajoie B, Dekker J, Friedman N, Rando OJ. Mapping Nucleosome Resolution Chromosome Folding in Yeast by Micro-C. Cell. 162: 108-19. PMID 26119342 DOI: 10.1016/j.cell.2015.05.048  0.6
2015 Belton JM, Dekker J. Chromosome Conformation Capture Carbon Copy (5C) in Budding Yeast. Cold Spring Harbor Protocols. 2015: pdb.prot085191. PMID 26034306 DOI: 10.1101/pdb.prot085191  0.6
2015 Belton JM, Dekker J. Randomized ligation control for chromosome conformation capture. Cold Spring Harbor Protocols. 2015: pdb.prot085183. PMID 26034305 DOI: 10.1101/pdb.prot085183  0.6
2015 Belton JM, Dekker J. Chromosome Conformation Capture (3C) in Budding Yeast. Cold Spring Harbor Protocols. 2015: pdb.prot085175. PMID 26034304 DOI: 10.1101/pdb.prot085175  0.6
2015 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. PMID 26030525 DOI: 10.1038/nature14450  0.6
2015 Lajoie BR, Dekker J, Kaplan N. The Hitchhiker's guide to Hi-C analysis: practical guidelines. Methods (San Diego, Calif.). 72: 65-75. PMID 25448293 DOI: 10.1016/j.ymeth.2014.10.031  0.6
2015 Kind J, Pagie L, deVries SS, Nahidiazar L, Dey SS, Bienko M, Zhan Y, Lajoie B, deGraaf CA, Amendola M, Fudenberg G, Imakaev M, Mirny LA, Jalink K, Dekker J, et al. Genome-wide Maps of Nuclear Lamina Interactions in Single Human Cells Cell. DOI: 10.1016/j.cell.2015.08.040  0.6
2014 Mizuguchi T, Fudenberg G, Mehta S, Belton JM, Taneja N, Folco HD, FitzGerald P, Dekker J, Mirny L, Barrowman J, Grewal SI. Cohesin-dependent globules and heterochromatin shape 3D genome architecture in S. pombe. Nature. 516: 432-5. PMID 25307058 DOI: 10.1038/nature13833  0.6
2014 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, et al. Reply to Brunet and Doolittle: Both selected effect and causal role elements can influence human biology and disease. Proceedings of the National Academy of Sciences of the United States of America. 111: E3366. PMID 25275169 DOI: 10.1073/pnas.1410434111  0.6
2014 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. 157: 950-63. PMID 24813616 DOI: 10.1016/j.cell.2014.03.025  0.6
2014 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, et al. Defining functional DNA elements in the human genome. Proceedings of the National Academy of Sciences of the United States of America. 111: 6131-8. PMID 24753594 DOI: 10.1073/pnas.1318948111  0.6
2013 Kaplan N, Dekker J. High-throughput genome scaffolding from in vivo DNA interaction frequency. Nature Biotechnology. 31: 1143-7. PMID 24270850 DOI: 10.1038/nbt.2768  0.6
2013 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 & Development. 27: 2439-44. PMID 24240234 DOI: 10.1101/gad.227165.113  0.6
2013 Naumova N, Imakaev M, Fudenberg G, Zhan Y, Lajoie BR, Mirny LA, Dekker J. Organization of the mitotic chromosome. Science (New York, N.Y.). 342: 948-53. PMID 24200812 DOI: 10.1126/science.1236083  0.6
2013 Dekker J, Mirny L. Biological techniques: Chromosomes captured one by one Nature. 502: 45-46. PMID 24067607 DOI: 10.1038/nature12691  0.6
2013 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 Research. 23: 2066-77. PMID 24002784 DOI: 10.1101/gr.161620.113  0.6
2013 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, et al. Architectural protein subclasses shape 3D organization of genomes during lineage commitment. Cell. 153: 1281-95. PMID 23706625 DOI: 10.1016/j.cell.2013.04.053  0.6
2013 Dekker J, Marti-Renom MA, Mirny LA. Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data. Nature Reviews. Genetics. 14: 390-403. PMID 23657480 DOI: 10.1038/nrg3454  0.6
2013 Dekker J, Wysocka J, Mattaj I, Lieberman Aiden E, Pikaard C. Nuclear biology: what's been most surprising? Cell. 152: 1207-8. PMID 23616995  0.6
2012 de Laat W, Dekker J. 3C-based technologies to study the shape of the genome Methods. 58: 189-191. PMID 23199640 DOI: 10.1016/j.ymeth.2012.11.005  0.6
2012 Ferraiuolo MA, Sanyal A, Naumova N, Dekker J, Dostie J. From cells to chromatin: capturing snapshots of genome organization with 5C technology. Methods (San Diego, Calif.). 58: 255-67. PMID 23137922 DOI: 10.1016/j.ymeth.2012.10.011  0.6
2012 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, ... ... Dekker J, et al. The accessible chromatin landscape of the human genome. Nature. 489: 75-82. PMID 22955617 DOI: 10.1038/nature11232  0.6
2012 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. Nature Methods. 9: 999-1003. PMID 22941365 DOI: 10.1038/nmeth.2148  0.6
2012 Stamatoyannopoulos JA, Snyder M, Hardison R, Ren B, Gingeras T, Gilbert DM, Groudine M, Bender M, Kaul R, Canfield T, Giste E, Johnson A, Zhang M, Balasundaram G, ... ... Dekker J, et al. An encyclopedia of mouse DNA elements (Mouse ENCODE). Genome Biology. 13: 418. PMID 22889292 DOI: 10.1186/gb-2012-13-8-418  0.6
2012 Belton JM, McCord RP, Gibcus JH, Naumova N, Zhan Y, Dekker J. Hi-C: a comprehensive technique to capture the conformation of genomes. Methods (San Diego, Calif.). 58: 268-76. PMID 22652625 DOI: 10.1016/j.ymeth.2012.05.001  0.6
2012 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. 485: 381-385. PMID 22495304 DOI: 10.1038/nature11049  0.6
2012 Felsenfeld G, Dekker J. Genome architecture and expression. Current Opinion in Genetics & Development. 22: 59-61. PMID 22483506 DOI: 10.1016/j.gde.2012.03.003  0.6
2012 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. 148: 908-21. PMID 22341456 DOI: 10.1016/j.cell.2012.02.002  0.6
2012 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, ... ... Dekker J, et al. Evidence for transcript networks composed of chimeric RNAs in human cells. Plos One. 7: e28213. PMID 22238572 DOI: 10.1371/journal.pone.0028213  0.6
2011 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. Nature Methods. 8: 1059-64. PMID 22037705 DOI: 10.1038/nmeth.1748  0.6
2011 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. Nature Methods. 8: 1050-2. PMID 22037702 DOI: 10.1038/nmeth.1764  0.6
2011 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. 472: 120-4. PMID 21423168 DOI: 10.1038/nature09819  0.6
2010 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. 143: 924-37. PMID 21145459 DOI: 10.1016/j.cell.2010.11.015  0.6
2010 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. 467: 430-5. PMID 20720539 DOI: 10.1038/nature09380  0.6
2010 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, et al. Chemical genetic strategy identifies histone deacetylase 1 (HDAC1) and HDAC2 as therapeutic targets in sickle cell disease. Proceedings of the National Academy of Sciences of the United States of America. 107: 12617-22. PMID 20616024 DOI: 10.1073/pnas.1006774107  0.6
2010 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. Journal of Visualized Experiments : Jove. PMID 20461051 DOI: 10.3791/1869  0.6
2010 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 Research. 38: 4325-4336. PMID 20360044 DOI: 10.1093/nar/gkq175  0.6
2009 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 & Development. 23: 912-27. PMID 19390086 DOI: 10.1101/gad.1782209  0.6
2007 Dostie J, Zhan Y, Dekker J. Chromosome conformation capture carbon copy technology. Current Protocols in Molecular Biology / Edited by Frederick M. Ausubel ... [Et Al.]. Unit 21.14. PMID 18265398 DOI: 10.1002/0471142727.mb2114s80  0.6
2007 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 Nature Cell Biology. 9: 1167-1174. PMID 17828248 DOI: 10.1038/ncb1637  0.6
2007 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). Nature Protocols. 2: 1722-1733. PMID 17641637 DOI: 10.1038/nprot.2007.243  0.6
2007 Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, Thurman RE, Kuehn MS, Taylor CM, Neph S, Koch CM, ... ... Dekker J, et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature. 447: 799-816. PMID 17571346 DOI: 10.1038/nature05874  0.6
2007 Dostie J, Dekker J. Mapping networks of physical interactions between genomic elements using 5C technology. Nature Protocols. 2: 988-1002. PMID 17446898 DOI: 10.1038/nprot.2007.116  0.6
2006 Miele A, Gheldof N, Tabuchi TM, Dostie J, Dekker J. Mapping chromatin interactions by chromosome conformation capture. Current Protocols in Molecular Biology / Edited by Frederick M. Ausubel ... [Et Al.]. Unit 21.11. PMID 18265379 DOI: 10.1002/0471142727.mb2111s74  0.6
2006 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 Research. 16: 1299-309. PMID 16954542 DOI: 10.1101/gr.5571506  0.6
2005 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. Molecular Cell. 17: 453-62. PMID 15694345 DOI: 10.1016/j.molcel.2004.12.028  0.6
2002 Luo P, Tsang TC, Takeuchi C, Dekker J, Badowski M, Harris DT. High-efficiency cloning system for versatile adaptation of DNA fragments. Biotechniques. 33: 738, 740, 742. PMID 12398178 DOI: 10.2144/02334BM04  0.6
2000 Cha RS, Weiner BM, Keeney S, Dekker J, Kleckner N. Progression of meiotic DNA replication is modulated by interchromosomal interaction proteins, negatively by Spo11p and positively by Rec8p. Genes & Development. 14: 493-503. PMID 10691741  0.6
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