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The majority of primate-specific regulatory sequences are derived from transposable elements.
Jacques PÉ, Jeyakani J, Bourque G. Jacques PÉ, et al. Among authors: bourque g. PLoS Genet. 2013 May;9(5):e1003504. doi: 10.1371/journal.pgen.1003504. Epub 2013 May 9. PLoS Genet. 2013. PMID: 23675311 Free PMC article.
Genome-wide microhomologies enable precise template-free editing of biologically relevant deletion mutations.
Grajcarek J, Monlong J, Nishinaka-Arai Y, Nakamura M, Nagai M, Matsuo S, Lougheed D, Sakurai H, Saito MK, Bourque G, Woltjen K. Grajcarek J, et al. Among authors: bourque g. Nat Commun. 2019 Oct 24;10(1):4856. doi: 10.1038/s41467-019-12829-8. Nat Commun. 2019. PMID: 31649251 Free PMC article.
Benefits and barriers in the design of harmonized access agreements for international data sharing.
Saulnier KM, Bujold D, Dyke SOM, Dupras C, Beck S, Bourque G, Joly Y. Saulnier KM, et al. Among authors: bourque g. Sci Data. 2019 Dec 2;6(1):297. doi: 10.1038/s41597-019-0310-4. Sci Data. 2019. PMID: 31792275 Free PMC article.
Genome sequence of the Brown Norway rat yields insights into mammalian evolution.
Gibbs RA, Weinstock GM, Metzker ML, Muzny DM, Sodergren EJ, Scherer S, Scott G, Steffen D, Worley KC, Burch PE, Okwuonu G, Hines S, Lewis L, DeRamo C, Delgado O, Dugan-Rocha S, Miner G, Morgan M, Hawes A, Gill R, Celera, Holt RA, Adams MD, Amanatides PG, Baden-Tillson H, Barnstead M, Chin S, Evans CA, Ferriera S, Fosler C, Glodek A, Gu Z, Jennings D, Kraft CL, Nguyen T, Pfannkoch CM, Sitter C, Sutton GG, Venter JC, Woodage T, Smith D, Lee HM, Gustafson E, Cahill P, Kana A, Doucette-Stamm L, Weinstock K, Fechtel K, Weiss RB, Dunn DM, Green ED, Blakesley RW, Bouffard GG, De Jong PJ, Osoegawa K, Zhu B, Marra M, Schein J, Bosdet I, Fjell C, Jones S, Krzywinski M, Mathewson C, Siddiqui A, Wye N, McPherson J, Zhao S, Fraser CM, Shetty J, Shatsman S, Geer K, Chen Y, Abramzon S, Nierman WC, Havlak PH, Chen R, Durbin KJ, Egan A, Ren Y, Song XZ, Li B, Liu Y, Qin X, Cawley S, Worley KC, Cooney AJ, D'Souza LM, Martin K, Wu JQ, Gonzalez-Garay ML, Jackson AR, Kalafus KJ, McLeod MP, Milosavljevic A, Virk D, Volkov A, Wheeler DA, Zhang Z, Bailey JA, Eichler EE, Tuzun E, Birney E, Mongin E, Ureta-Vidal A, Woodwark C, Zdobnov E, Bork P, Suyama M, Torrents D, Alexandersson M, Trask BJ, Young JM, Huang H, Wang H, Xing H, Daniels S, Gietzen D, Schmidt J, Stevens K, Vitt U, Wingrove J, Camara F, Mar Albà M, Abril JF, Guigo R, Smit A, Dubchak I, Rubin EM, Couronne O, Poliakov A, Hübner N, Ganten D, Goesele C, Hummel O, Kreitler T, Lee YA, Monti J, Schulz H, Zimdahl H, Himmelbauer H, Lehrach H, Jacob HJ, Bromberg S, Gullings-Handley J, Jensen-Seaman MI, Kwitek AE, Lazar J, Pasko D, Tonellato PJ, Twigger S, Ponting CP, Duarte JM, Rice S, Goodstadt L, Beatson SA, Emes RD, Winter EE, Webber C, Brandt P, Nyakatura G, Adetobi M, Chiaromonte F, Elnitski L, Eswara P, Hardison RC, Hou M, Kolbe D, Makova K, Miller W, Nekrutenko A, Riemer C, Schwartz S, Taylor J, Yang S, Zhang Y, Lindpaintner K, Andrews TD, Caccamo M, Clamp M, Clarke L, Curwen V, Durbin R, Eyras E, Searle SM, Cooper GM, Batzoglou S, Brudno M, Sidow A, Stone EA, Venter JC, Payseur BA, Bourque G, López-Otín C, Puente XS, Chakrabarti K, Chatterji S, Dewey C, Pachter L, Bray N, Yap VB, Caspi A, Tesler G, Pevzner PA, Haussler D, Roskin KM, Baertsch R, Clawson H, Furey TS, Hinrichs AS, Karolchik D, Kent WJ, Rosenbloom KR, Trumbower H, Weirauch M, Cooper DN, Stenson PD, Ma B, Brent M, Arumugam M, Shteynberg D, Copley RR, Taylor MS, Riethman H, Mudunuri U, Peterson J, Guyer M, Felsenfeld A, Old S, Mockrin S, Collins F; Rat Genome Sequencing Project Consortium. Gibbs RA, et al. Among authors: bourque g. Nature. 2004 Apr 1;428(6982):493-521. doi: 10.1038/nature02426. Nature. 2004. PMID: 15057822
Comparative architectures of mammalian and chicken genomes reveal highly variable rates of genomic rearrangements across different lineages.
Bourque G, Zdobnov EM, Bork P, Pevzner PA, Tesler G. Bourque G, et al. Genome Res. 2005 Jan;15(1):98-110. doi: 10.1101/gr.3002305. Epub 2004 Dec 8. Genome Res. 2005. PMID: 15590940 Free PMC article.
The Oct4 and Nanog transcription network regulates pluripotency in mouse embryonic stem cells.
Loh YH, Wu Q, Chew JL, Vega VB, Zhang W, Chen X, Bourque G, George J, Leong B, Liu J, Wong KY, Sung KW, Lee CW, Zhao XD, Chiu KP, Lipovich L, Kuznetsov VA, Robson P, Stanton LW, Wei CL, Ruan Y, Lim B, Ng HH. Loh YH, et al. Among authors: bourque g. Nat Genet. 2006 Apr;38(4):431-40. doi: 10.1038/ng1760. Epub 2006 Mar 5. Nat Genet. 2006. PMID: 16518401
Genomewide expression profiling in the zebrafish embryo identifies target genes regulated by Hedgehog signaling during vertebrate development.
Xu J, Srinivas BP, Tay SY, Mak A, Yu X, Lee SG, Yang H, Govindarajan KR, Leong B, Bourque G, Mathavan S, Roy S. Xu J, et al. Among authors: bourque g. Genetics. 2006 Oct;174(2):735-52. doi: 10.1534/genetics.106.061523. Epub 2006 Aug 3. Genetics. 2006. PMID: 16888327 Free PMC article.
Multiplatform genome-wide identification and modeling of functional human estrogen receptor binding sites.
Vega VB, Lin CY, Lai KS, Kong SL, Xie M, Su X, Teh HF, Thomsen JS, Yeo AL, Sung WK, Bourque G, Liu ET. Vega VB, et al. Among authors: bourque g. Genome Biol. 2006;7(9):R82. doi: 10.1186/gb-2006-7-9-r82. Genome Biol. 2006. PMID: 16961928 Free PMC article.
Whole-genome cartography of estrogen receptor alpha binding sites.
Lin CY, Vega VB, Thomsen JS, Zhang T, Kong SL, Xie M, Chiu KP, Lipovich L, Barnett DH, Stossi F, Yeo A, George J, Kuznetsov VA, Lee YK, Charn TH, Palanisamy N, Miller LD, Cheung E, Katzenellenbogen BS, Ruan Y, Bourque G, Wei CL, Liu ET. Lin CY, et al. Among authors: bourque g. PLoS Genet. 2007 Jun;3(6):e87. doi: 10.1371/journal.pgen.0030087. Epub 2007 Apr 17. PLoS Genet. 2007. PMID: 17542648 Free PMC article.
Fusion transcripts and transcribed retrotransposed loci discovered through comprehensive transcriptome analysis using Paired-End diTags (PETs).
Ruan Y, Ooi HS, Choo SW, Chiu KP, Zhao XD, Srinivasan KG, Yao F, Choo CY, Liu J, Ariyaratne P, Bin WG, Kuznetsov VA, Shahab A, Sung WK, Bourque G, Palanisamy N, Wei CL. Ruan Y, et al. Among authors: bourque g. Genome Res. 2007 Jun;17(6):828-38. doi: 10.1101/gr.6018607. Genome Res. 2007. PMID: 17568001 Free PMC article.
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