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Page 1
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,… See abstract for full author list ➔ Yue F, et al. Nature. 2014 Nov 20;515(7527):355-64. doi: 10.1038/nature13992. Nature. 2014. PMID: 25409824 Free PMC article.
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. 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.
Replication timing maintains the global epigenetic state in human cells.
Klein KN, Zhao PA, Lyu X, Sasaki T, Bartlett DA, Singh AM, Tasan I, Zhang M, Watts LP, Hiraga SI, Natsume T, Zhou X, Baslan T, Leung D, Kanemaki MT, Donaldson AD, Zhao H, Dalton S, Corces VG, Gilbert DM. Klein KN, et al. Science. 2021 Apr 23;372(6540):371-378. doi: 10.1126/science.aba5545. Epub 2021 Apr 22. Science. 2021. PMID: 33888635 Free PMC article.
Strand-resolved mutagenicity of DNA damage and repair.
Anderson CJ, Talmane L, Luft J, Connelly J, Nicholson MD, Verburg JC, Pich O, Campbell S, Giaisi M, Wei PC, Sundaram V, Connor F, Ginno PA, Sasaki T, Gilbert DM; Liver Cancer Evolution Consortium; López-Bigas N, Semple CA, Odom DT, Aitken SJ, Taylor MS. Anderson CJ, et al. Nature. 2024 Jun;630(8017):744-751. doi: 10.1038/s41586-024-07490-1. Epub 2024 Jun 12. Nature. 2024. PMID: 38867042 Free PMC article.
DNA replication timing.
Rhind N, Gilbert DM. Rhind N, et al. Cold Spring Harb Perspect Biol. 2013 Aug 1;5(8):a010132. doi: 10.1101/cshperspect.a010132. Cold Spring Harb Perspect Biol. 2013. PMID: 23838440 Free PMC article. Review.
Emergence of replication timing during early mammalian development.
Nakatani T, Schauer T, Altamirano-Pacheco L, Klein KN, Ettinger A, Pal M, Gilbert DM, Torres-Padilla ME. Nakatani T, et al. Nature. 2024 Jan;625(7994):401-409. doi: 10.1038/s41586-023-06872-1. Epub 2023 Dec 20. Nature. 2024. PMID: 38123678 Free PMC article.
Mammalian DNA Replication Timing.
Vouzas AE, Gilbert DM. Vouzas AE, et al. Cold Spring Harb Perspect Biol. 2021 Jul 1;13(7):a040162. doi: 10.1101/cshperspect.a040162. Cold Spring Harb Perspect Biol. 2021. PMID: 33558366 Free PMC article. Review.
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.
RIF1 regulates early replication timing in murine B cells.
Malzl D, Peycheva M, Rahjouei A, Gnan S, Klein KN, Nazarova M, Schoeberl UE, Gilbert DM, Buonomo SCB, Di Virgilio M, Neumann T, Pavri R. Malzl D, et al. Nat Commun. 2023 Dec 11;14(1):8049. doi: 10.1038/s41467-023-43778-y. Nat Commun. 2023. PMID: 38081811 Free PMC article.
SARS-CoV-2 restructures host chromatin architecture.
Wang R, Lee JH, Kim J, Xiong F, Hasani LA, Shi Y, Simpson EN, Zhu X, Chen YT, Shivshankar P, Krakowiak J, Wang Y, Gilbert DM, Yuan X, Eltzschig HK, Li W. Wang R, et al. Nat Microbiol. 2023 Apr;8(4):679-694. doi: 10.1038/s41564-023-01344-8. Epub 2023 Mar 23. Nat Microbiol. 2023. PMID: 36959507 Free PMC article.
86 results