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STAR: ultrafast universal RNA-seq aligner.
Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M, Gingeras TR. Dobin A, et al. Among authors: batut p. Bioinformatics. 2013 Jan 1;29(1):15-21. doi: 10.1093/bioinformatics/bts635. Epub 2012 Oct 25. Bioinformatics. 2013. PMID: 23104886 Free PMC article.
RAMPAGE: promoter activity profiling by paired-end sequencing of 5'-complete cDNAs.
Batut P, Gingeras TR. Batut P, et al. Curr Protoc Mol Biol. 2013 Nov 11;104:Unit 25B.11. doi: 10.1002/0471142727.mb25b11s104. Curr Protoc Mol Biol. 2013. PMID: 24510412 Free PMC article.
High-fidelity promoter profiling reveals widespread alternative promoter usage and transposon-driven developmental gene expression.
Batut P, Dobin A, Plessy C, Carninci P, Gingeras TR. Batut P, et al. Genome Res. 2013 Jan;23(1):169-80. doi: 10.1101/gr.139618.112. Epub 2012 Aug 30. Genome Res. 2013. PMID: 22936248 Free PMC article.
Conserved noncoding transcription and core promoter regulatory code in early Drosophila development.
Batut PJ, Gingeras TR. Batut PJ, et al. Elife. 2017 Dec 20;6:e29005. doi: 10.7554/eLife.29005. Elife. 2017. PMID: 29260710 Free PMC article.
Evidence for transcript networks composed of chimeric RNAs in human cells.
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, Lin C, Bell I, Dumais E, Drenkow J, Tress ML, Gelpí JL, Orozco M, Valencia A, van Berkum NL, Lajoie BR, Vidal M, Stamatoyannopoulos J, Batut P, Dobin A, Harrow J, Hubbard T, Dekker J, Frankish A, Salehi-Ashtiani K, Reymond A, Antonarakis SE, Guigó R, Gingeras TR. Djebali S, et al. Among authors: batut p. PLoS One. 2012;7(1):e28213. doi: 10.1371/journal.pone.0028213. Epub 2012 Jan 4. PLoS One. 2012. PMID: 22238572 Free PMC article.
Landscape of transcription in human cells.
Djebali S, Davis CA, Merkel A, Dobin A, Lassmann T, Mortazavi A, Tanzer A, Lagarde J, Lin W, Schlesinger F, Xue C, Marinov GK, Khatun J, Williams BA, Zaleski C, Rozowsky J, Röder M, Kokocinski F, Abdelhamid RF, Alioto T, Antoshechkin I, Baer MT, Bar NS, Batut P, Bell K, Bell I, Chakrabortty S, Chen X, Chrast J, Curado J, Derrien T, Drenkow J, Dumais E, Dumais J, Duttagupta R, Falconnet E, Fastuca M, Fejes-Toth K, Ferreira P, Foissac S, Fullwood MJ, Gao H, Gonzalez D, Gordon A, Gunawardena H, Howald C, Jha S, Johnson R, Kapranov P, King B, Kingswood C, Luo OJ, Park E, Persaud K, Preall JB, Ribeca P, Risk B, Robyr D, Sammeth M, Schaffer L, See LH, Shahab A, Skancke J, Suzuki AM, Takahashi H, Tilgner H, Trout D, Walters N, Wang H, Wrobel J, Yu Y, Ruan X, Hayashizaki Y, Harrow J, Gerstein M, Hubbard T, Reymond A, Antonarakis SE, Hannon G, Giddings MC, Ruan Y, Wold B, Carninci P, Guigó R, Gingeras TR. Djebali S, et al. Among authors: batut p. Nature. 2012 Sep 6;489(7414):101-8. doi: 10.1038/nature11233. Nature. 2012. PMID: 22955620 Free PMC article.
SnapShot: The Regulatory Genome.
Bing XY, Batut PJ, Levo M, Levine M, Raimundo J. Bing XY, et al. Among authors: batut pj. Cell. 2020 Sep 17;182(6):1674-1674.e1. doi: 10.1016/j.cell.2020.07.041. Cell. 2020. PMID: 32946787
An integrated encyclopedia of DNA elements in the human genome.
ENCODE Project Consortium. ENCODE Project Consortium. Nature. 2012 Sep 6;489(7414):57-74. doi: 10.1038/nature11247. Nature. 2012. PMID: 22955616 Free PMC article.
A user's guide to the encyclopedia of DNA elements (ENCODE).
ENCODE Project Consortium. ENCODE Project Consortium. PLoS Biol. 2011 Apr;9(4):e1001046. doi: 10.1371/journal.pbio.1001046. Epub 2011 Apr 19. PLoS Biol. 2011. PMID: 21526222 Free PMC article.
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