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A comparative encyclopedia of DNA elements in the mouse genome.
Nature. 2014 Nov 20;515(7527):355-64. doi: 10.1038/nature13992.
Nature. 2014.
PMID: 25409824
Free PMC article.
An encyclopedia of mouse DNA elements (Mouse ENCODE).
Mouse ENCODE Consortium; 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, Byron R, Roach V, Sabo PJ, Sandstrom R, Stehling AS, Thurman RE, Weissman SM, Cayting P, Hariharan M, Lian J, Cheng Y, Landt SG, Ma Z, Wold BJ, Dekker J, Crawford GE, Keller CA, Wu W, Morrissey C, Kumar SA, Mishra T, Jain D, Byrska-Bishop M, Blankenberg D, Lajoie BR, Jain G, Sanyal A, Chen KB, Denas O, Taylor J, Blobel GA, Weiss MJ, Pimkin M, Deng W, Marinov GK, Williams BA, Fisher-Aylor KI, Desalvo G, Kiralusha A, Trout D, Amrhein H, Mortazavi A, Edsall L, McCleary D, Kuan S, Shen Y, Yue F, Ye Z, Davis CA, Zaleski C, Jha S, Xue C, Dobin A, Lin W, Fastuca M, Wang H, Guigo R, Djebali S, Lagarde J, Ryba T, Sasaki T, Malladi VS, Cline MS, Kirkup VM, Learned K, Rosenbloom KR, Kent WJ, Feingold EA, Good PJ, Pazin M, Lowdon RF, Adams LB.
Mouse ENCODE Consortium, et al. Among authors: denas o.
Genome Biol. 2012 Aug 13;13(8):418. doi: 10.1186/gb-2012-13-8-418.
Genome Biol. 2012.
PMID: 22889292
Free PMC article.
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Principles of regulatory information conservation between mouse and human.
Cheng Y, Ma Z, Kim BH, Wu W, Cayting P, Boyle AP, Sundaram V, Xing X, Dogan N, Li J, Euskirchen G, Lin S, Lin Y, Visel A, Kawli T, Yang X, Patacsil D, Keller CA, Giardine B; mouse ENCODE Consortium; Kundaje A, Wang T, Pennacchio LA, Weng Z, Hardison RC, Snyder MP.
Cheng Y, et al.
Nature. 2014 Nov 20;515(7527):371-375. doi: 10.1038/nature13985.
Nature. 2014.
PMID: 25409826
Free PMC article.
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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: denas o.
Nature. 2014 Nov 20;515(7527):402-5. doi: 10.1038/nature13986.
Nature. 2014.
PMID: 25409831
Free PMC article.
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Genome-wide comparative analysis reveals human-mouse regulatory landscape and evolution.
Denas O, Sandstrom R, Cheng Y, Beal K, Herrero J, Hardison RC, Taylor J.
Denas O, et al.
BMC Genomics. 2015 Feb 14;16(1):87. doi: 10.1186/s12864-015-1245-6.
BMC Genomics. 2015.
PMID: 25765714
Free PMC article.
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The genome sequence of the leaf-cutter ant Atta cephalotes reveals insights into its obligate symbiotic lifestyle.
Suen G, Teiling C, Li L, Holt C, Abouheif E, Bornberg-Bauer E, Bouffard P, Caldera EJ, Cash E, Cavanaugh A, Denas O, Elhaik E, Favé MJ, Gadau J, Gibson JD, Graur D, Grubbs KJ, Hagen DE, Harkins TT, Helmkampf M, Hu H, Johnson BR, Kim J, Marsh SE, Moeller JA, Muñoz-Torres MC, Murphy MC, Naughton MC, Nigam S, Overson R, Rajakumar R, Reese JT, Scott JJ, Smith CR, Tao S, Tsutsui ND, Viljakainen L, Wissler L, Yandell MD, Zimmer F, Taylor J, Slater SC, Clifton SW, Warren WC, Elsik CG, Smith CD, Weinstock GM, Gerardo NM, Currie CR.
Suen G, et al. Among authors: denas o.
PLoS Genet. 2011 Feb 10;7(2):e1002007. doi: 10.1371/journal.pgen.1002007.
PLoS Genet. 2011.
PMID: 21347285
Free PMC article.
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Fast and compact matching statistics analytics.
Cunial F, Denas O, Belazzougui D.
Cunial F, et al. Among authors: denas o.
Bioinformatics. 2022 Mar 28;38(7):1838-1845. doi: 10.1093/bioinformatics/btac064.
Bioinformatics. 2022.
PMID: 35134833
Free PMC article.
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Efficient tools for comparative substring analysis.
Apostolico A, Denas O, Dress A.
Apostolico A, et al. Among authors: denas o.
J Biotechnol. 2010 Sep 1;149(3):120-6. doi: 10.1016/j.jbiotec.2010.05.006. Epub 2010 Jun 2.
J Biotechnol. 2010.
PMID: 20682467
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Fast algorithms for computing sequence distances by exhaustive substring composition.
Apostolico A, Denas O.
Apostolico A, et al. Among authors: denas o.
Algorithms Mol Biol. 2008 Oct 28;3:13. doi: 10.1186/1748-7188-3-13.
Algorithms Mol Biol. 2008.
PMID: 18957094
Free PMC article.
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