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1986 1
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1997 2
1998 4
1999 4
2000 5
2001 5
2002 6
2003 3
2004 7
2005 5
2006 3
2007 6
2008 3
2009 5
2010 10
2011 8
2012 11
2013 6
2014 9
2015 9
2016 5
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2018 8
2019 7
2020 8
2021 7
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Page 1
Perspectives on ENCODE.
ENCODE Project Consortium, Snyder MP, Gingeras TR, Moore JE, Weng Z, Gerstein MB, Ren B, Hardison RC, Stamatoyannopoulos JA, Graveley BR, Feingold EA, Pazin MJ, Pagan M, Gilchrist DA, Hitz BC, Cherry JM, Bernstein BE, Mendenhall EM, Zerbino DR, Frankish A, Flicek P, Myers RM. ENCODE Project Consortium, et al. Nature. 2020 Jul;583(7818):693-698. doi: 10.1038/s41586-020-2449-8. Epub 2020 Jul 29. Nature. 2020. PMID: 32728248 Free PMC article.
The Encylopedia of DNA Elements (ENCODE) Project launched in 2003 with the long-term goal of developing a comprehensive map of functional elements in the human genome. ...The project has been extended to model organisms, particularly the mouse. In the third phase of …
The Encylopedia of DNA Elements (ENCODE) Project launched in 2003 with the long-term goal of developing a comprehensive map of …
Expanded encyclopaedias of DNA elements in the human and mouse genomes.
ENCODE Project Consortium, Moore JE, Purcaro MJ, Pratt HE, Epstein CB, Shoresh N, Adrian J, Kawli T, Davis CA, Dobin A, Kaul R, Halow J, Van Nostrand EL, Freese P, Gorkin DU, Shen Y, He Y, Mackiewicz M, Pauli-Behn F, Williams BA, Mortazavi A, Keller CA, Zhang XO, Elhajjajy SI, Huey J, Dickel DE, Snetkova V, Wei X, Wang X, Rivera-Mulia JC, Rozowsky J, Zhang J, Chhetri SB, Zhang J, Victorsen A, White KP, Visel A, Yeo GW, Burge CB, Lécuyer E, Gilbert DM, Dekker J, Rinn J, Mendenhall EM, Ecker JR, Kellis M, Klein RJ, Noble WS, Kundaje A, Guigó R, Farnham PJ, Cherry JM, Myers RM, Ren B, Graveley BR, Gerstein MB, Pennacchio LA, Snyder MP, Bernstein BE, Wold B, Hardison RC, Gingeras TR, Stamatoyannopoulos JA, Weng Z. ENCODE Project Consortium, et al. Among authors: gilbert dm. Nature. 2020 Jul;583(7818):699-710. doi: 10.1038/s41586-020-2493-4. Epub 2020 Jul 29. Nature. 2020. PMID: 32728249 Free PMC article.
To better delineate these elements, phase III of the Encyclopedia of DNA Elements (ENCODE) Project has expanded analysis of the cell and tissue repertoires of RNA transcription, chromatin structure and modification, DNA methylation, chromatin lo …
To better delineate these elements, phase III of the Encyclopedia of DNA Elements (ENCODE) Project has expanded analysis of th …
Control of DNA replication timing in the 3D genome.
Marchal C, Sima J, Gilbert DM. Marchal C, et al. Among authors: gilbert dm. Nat Rev Mol Cell Biol. 2019 Dec;20(12):721-737. doi: 10.1038/s41580-019-0162-y. Epub 2019 Sep 2. Nat Rev Mol Cell Biol. 2019. PMID: 31477886 Review.
The 3D organization of mammalian chromatin was described more than 30 years ago by visualizing sites of DNA synthesis at different times during the S phase of the cell cycle. ...But the causal relationship between these features and DNA replication
The 3D organization of mammalian chromatin was described more than 30 years ago by visualizing sites of DNA synthesis at diffe …
4D Genome Rewiring during Oncogene-Induced and Replicative Senescence.
Sati S, Bonev B, Szabo Q, Jost D, Bensadoun P, Serra F, Loubiere V, Papadopoulos GL, Rivera-Mulia JC, Fritsch L, Bouret P, Castillo D, Gelpi JL, Orozco M, Vaillant C, Pellestor F, Bantignies F, Marti-Renom MA, Gilbert DM, Lemaitre JM, Cavalli G. Sati S, et al. Among authors: gilbert dm. Mol Cell. 2020 May 7;78(3):522-538.e9. doi: 10.1016/j.molcel.2020.03.007. Epub 2020 Mar 26. Mol Cell. 2020. PMID: 32220303 Free PMC article.
To understand the role of the extensive senescence-associated 3D genome reorganization, we generated genome-wide chromatin interaction maps, epigenome, replication-timing, whole-genome bisulfite sequencing, and gene expression profiles from cells entering replica
To understand the role of the extensive senescence-associated 3D genome reorganization, we generated genome-wide chromatin interactio …
Integrative detection and analysis of structural variation in cancer genomes.
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, An L, Pool C, Sasaki T, Rivera-Mulia JC, Ozadam H, Lajoie BR, Kaul R, Buckley M, Lee K, Diegel M, Pezic D, Ernst C, Hadjur S, Odom DT, Stamatoyannopoulos JA, Broach JR, Hardison RC, Ay F, Noble WS, Dekker J, Gilbert DM, Yue F. Dixon JR, et al. Among authors: gilbert dm. Nat Genet. 2018 Oct;50(10):1388-1398. doi: 10.1038/s41588-018-0195-8. Epub 2018 Sep 10. Nat Genet. 2018. PMID: 30202056 Free PMC article.
Furthermore, we observe widespread structural variation events affecting the functions of noncoding sequences, including the deletion of distal regulatory sequences, alteration of DNA replication timing, and the creation of novel three-dimensional chromatin s …
Furthermore, we observe widespread structural variation events affecting the functions of noncoding sequences, including the deletion of dis …
A comparative encyclopedia of DNA elements in the mouse genome.
Yue F, Cheng Y, Breschi A, Vierstra J, Wu W, Ryba T, Sandstrom R, Ma Z, Davis C, Pope BD, Shen Y, Pervouchine DD, Djebali S, Thurman RE, Kaul R, Rynes E, Kirilusha A, Marinov GK, Williams BA, Trout D, Amrhein H, Fisher-Aylor K, Antoshechkin I, DeSalvo G, See LH, Fastuca M, Drenkow J, Zaleski C, Dobin A, Prieto P, Lagarde J, Bussotti G, Tanzer A, Denas O, Li K, Bender MA, Zhang M, Byron R, Groudine MT, McCleary D, Pham L, Ye Z, Kuan S, Edsall L, Wu YC, Rasmussen MD, Bansal MS, Kellis M, Keller CA, Morrissey CS, Mishra T, Jain D, Dogan N, Harris RS, Cayting P, Kawli T, Boyle AP, Euskirchen G, Kundaje A, Lin S, Lin Y, Jansen C, Malladi VS, Cline MS, Erickson DT, Kirkup VM, Learned K, Sloan CA, Rosenbloom KR, Lacerda de Sousa B, Beal K, Pignatelli M, Flicek P, Lian J, Kahveci T, Lee D, Kent WJ, Ramalho Santos M, Herrero J, Notredame C, Johnson A, Vong S, Lee K, Bates D, Neri F, Diegel M, Canfield T, Sabo PJ, Wilken MS, Reh TA, Giste E, Shafer A, Kutyavin T, Haugen E, Dunn D, Reynolds AP, Neph S, Humbert R, Hansen RS, De Bruijn M, Selleri L, Rudensky A, Josefowicz S, Samstein R, Eichler EE, Orkin SH, Levasseur D, Papayannopoulou T, Chang KH, Skoultchi A, Gosh S, Disteche C, Treuting P, Wang Y, Weiss MJ, Blobel GA, Cao X, Zhong S, Wang T, Good PJ, Lowdon RF, Adams LB, Zhou XQ, Pazin MJ, Feingold EA, Wold B, Taylor J, Mortazavi A, Weissman SM, Stamatoyannopoulos JA, Snyder MP, Guigo R, Gingeras TR, Gilbert DM, Hardison RC, Beer MA, Ren B; Mouse ENCODE Consortium. Yue F, et al. Among authors: gilbert dm. Nature. 2014 Nov 20;515(7527):355-64. doi: 10.1038/nature13992. Nature. 2014. PMID: 25409824 Free PMC article.
To gain greater insights into both shared and species-specific transcriptional and cellular regulatory programs in the mouse, the Mouse ENCODE Consortium has mapped transcription, DNase I hypersensitivity, transcription factor binding, chromatin modifications and …
To gain greater insights into both shared and species-specific transcriptional and cellular regulatory programs in the mouse, the Mouse E
3D genome organization contributes to genome instability at fragile sites.
Sarni D, Sasaki T, Irony Tur-Sinai M, Miron K, Rivera-Mulia JC, Magnuson B, Ljungman M, Gilbert DM, Kerem B. Sarni D, et al. Among authors: gilbert dm. Nat Commun. 2020 Jul 17;11(1):3613. doi: 10.1038/s41467-020-17448-2. Nat Commun. 2020. PMID: 32680994 Free PMC article.
Therefore, the molecular mechanisms underlying CFS instability remain unclear. Here, we explore the transcriptional profile and DNA replication timing (RT) under mild replication stress in the context of the 3D genome organization. ...This signature enables p …
Therefore, the molecular mechanisms underlying CFS instability remain unclear. Here, we explore the transcriptional profile and DNA
An integrative ENCODE resource for cancer genomics.
Zhang J, Lee D, Dhiman V, Jiang P, Xu J, McGillivray P, Yang H, Liu J, Meyerson W, Clarke D, Gu M, Li S, Lou S, Xu J, Lochovsky L, Ung M, Ma L, Yu S, Cao Q, Harmanci A, Yan KK, Sethi A, Gürsoy G, Schoenberg MR, Rozowsky J, Warrell J, Emani P, Yang YT, Galeev T, Kong X, Liu S, Li X, Krishnan J, Feng Y, Rivera-Mulia JC, Adrian J, Broach JR, Bolt M, Moran J, Fitzgerald D, Dileep V, Liu T, Mei S, Sasaki T, Trevilla-Garcia C, Wang S, Wang Y, Zang C, Wang D, Klein RJ, Snyder M, Gilbert DM, Yip K, Cheng C, Yue F, Liu XS, White KP, Gerstein M. Zhang J, et al. Among authors: gilbert dm. Nat Commun. 2020 Jul 29;11(1):3696. doi: 10.1038/s41467-020-14743-w. Nat Commun. 2020. PMID: 32728046 Free PMC article.
ENCODE comprises thousands of functional genomics datasets, and the encyclopedia covers hundreds of cell types, providing a universal annotation for genome interpretation. ...Targeted validations of the prioritized regulators, elements and variants using siRNA knockdowns,
ENCODE comprises thousands of functional genomics datasets, and the encyclopedia covers hundreds of cell types, providing a universal
Topologically associating domains are stable units of replication-timing regulation.
Pope BD, Ryba T, Dileep V, Yue F, Wu W, Denas O, Vera DL, Wang Y, Hansen RS, Canfield TK, Thurman RE, Cheng Y, Gülsoy G, Dennis JH, Snyder MP, Stamatoyannopoulos JA, Taylor J, Hardison RC, Kahveci T, Ren B, Gilbert DM. Pope BD, et al. Among authors: gilbert dm. Nature. 2014 Nov 20;515(7527):402-5. doi: 10.1038/nature13986. Nature. 2014. PMID: 25409831 Free PMC article.
Eukaryotic chromosomes replicate in a temporal order known as the replication-timing program. ...Moreover, cell-type-specific replication timing of TADs partitions the genome into two large-scale sub-nuclear compartments revealing that replication-timi …
Eukaryotic chromosomes replicate in a temporal order known as the replication-timing program. ...Moreover, cell-type-specific …
Identifying cis Elements for Spatiotemporal Control of Mammalian DNA Replication.
Sima J, Chakraborty A, Dileep V, Michalski M, Klein KN, Holcomb NP, Turner JL, Paulsen MT, Rivera-Mulia JC, Trevilla-Garcia C, Bartlett DA, Zhao PA, Washburn BK, Nora EP, Kraft K, Mundlos S, Bruneau BG, Ljungman M, Fraser P, Ay F, Gilbert DM. Sima J, et al. Among authors: gilbert dm. Cell. 2019 Feb 7;176(4):816-830.e18. doi: 10.1016/j.cell.2018.11.036. Epub 2018 Dec 27. Cell. 2019. PMID: 30595451 Free PMC article.
The temporal order of DNA replication (replication timing [RT]) is highly coupled with genome architecture, but cis-elements regulating either remain elusive. ...The dispensability of TAD boundaries and the necessity of these "early replication control …
The temporal order of DNA replication (replication timing [RT]) is highly coupled with genome architecture, but cis-ele …
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