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47 results

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Page 1
Extensive cross-regulation of post-transcriptional regulatory networks in Drosophila.
Stoiber MH, Olson S, May GE, Duff MO, Manent J, Obar R, Guruharsha KG, Bickel PJ, Artavanis-Tsakonas S, Brown JB, Graveley BR, Celniker SE. Stoiber MH, et al. Among authors: bickel pj. Genome Res. 2015 Nov;25(11):1692-702. doi: 10.1101/gr.182675.114. Epub 2015 Aug 20. Genome Res. 2015. PMID: 26294687 Free PMC article.
Comparative validation of the D. melanogaster modENCODE transcriptome annotation.
Chen ZX, Sturgill D, Qu J, Jiang H, Park S, Boley N, Suzuki AM, Fletcher AR, Plachetzki DC, FitzGerald PC, Artieri CG, Atallah J, Barmina O, Brown JB, Blankenburg KP, Clough E, Dasgupta A, Gubbala S, Han Y, Jayaseelan JC, Kalra D, Kim YA, Kovar CL, Lee SL, Li M, Malley JD, Malone JH, Mathew T, Mattiuzzo NR, Munidasa M, Muzny DM, Ongeri F, Perales L, Przytycka TM, Pu LL, Robinson G, Thornton RL, Saada N, Scherer SE, Smith HE, Vinson C, Warner CB, Worley KC, Wu YQ, Zou X, Cherbas P, Kellis M, Eisen MB, Piano F, Kionte K, Fitch DH, Sternberg PW, Cutter AD, Duff MO, Hoskins RA, Graveley BR, Gibbs RA, Bickel PJ, Kopp A, Carninci P, Celniker SE, Oliver B, Richards S. Chen ZX, et al. Among authors: bickel pj. Genome Res. 2014 Jul;24(7):1209-23. doi: 10.1101/gr.159384.113. Genome Res. 2014. PMID: 24985915 Free PMC article.
Genome-wide analysis of promoter architecture in Drosophila melanogaster.
Hoskins RA, Landolin JM, Brown JB, Sandler JE, Takahashi H, Lassmann T, Yu C, Booth BW, Zhang D, Wan KH, Yang L, Boley N, Andrews J, Kaufman TC, Graveley BR, Bickel PJ, Carninci P, Carlson JW, Celniker SE. Hoskins RA, et al. Among authors: bickel pj. Genome Res. 2011 Feb;21(2):182-92. doi: 10.1101/gr.112466.110. Epub 2010 Dec 22. Genome Res. 2011. PMID: 21177961 Free PMC article.
Long noncoding RNAs are rarely translated in two human cell lines.
Bánfai B, Jia H, Khatun J, Wood E, Risk B, Gundling WE Jr, Kundaje A, Gunawardena HP, Yu Y, Xie L, Krajewski K, Strahl BD, Chen X, Bickel P, Giddings MC, Brown JB, Lipovich L. Bánfai B, et al. Genome Res. 2012 Sep;22(9):1646-57. doi: 10.1101/gr.134767.111. Genome Res. 2012. PMID: 22955977 Free PMC article.
DNA regions bound at low occupancy by transcription factors do not drive patterned reporter gene expression in Drosophila.
Fisher WW, Li JJ, Hammonds AS, Brown JB, Pfeiffer BD, Weiszmann R, MacArthur S, Thomas S, Stamatoyannopoulos JA, Eisen MB, Bickel PJ, Biggin MD, Celniker SE. Fisher WW, et al. Among authors: bickel pj. Proc Natl Acad Sci U S A. 2012 Dec 26;109(52):21330-5. doi: 10.1073/pnas.1209589110. Epub 2012 Dec 10. Proc Natl Acad Sci U S A. 2012. PMID: 23236164 Free PMC article.
Navigating and mining modENCODE data.
Boley N, Wan KH, Bickel PJ, Celniker SE. Boley N, et al. Among authors: bickel pj. Methods. 2014 Jun 15;68(1):38-47. doi: 10.1016/j.ymeth.2014.03.007. Epub 2014 Mar 15. Methods. 2014. PMID: 24636835 Free PMC article. Review.
Diversity and dynamics of the Drosophila transcriptome.
Brown JB, Boley N, Eisman R, May GE, Stoiber MH, Duff MO, Booth BW, Wen J, Park S, Suzuki AM, Wan KH, Yu C, Zhang D, Carlson JW, Cherbas L, Eads BD, Miller D, Mockaitis K, Roberts J, Davis CA, Frise E, Hammonds AS, Olson S, Shenker S, Sturgill D, Samsonova AA, Weiszmann R, Robinson G, Hernandez J, Andrews J, Bickel PJ, Carninci P, Cherbas P, Gingeras TR, Hoskins RA, Kaufman TC, Lai EC, Oliver B, Perrimon N, Graveley BR, Celniker SE. Brown JB, et al. Among authors: bickel pj. Nature. 2014 Aug 28;512(7515):393-9. doi: 10.1038/nature12962. Nature. 2014. PMID: 24670639 Free PMC article.
Comparative analysis of the transcriptome across distant species.
Gerstein MB, Rozowsky J, Yan KK, Wang D, Cheng C, Brown JB, Davis CA, Hillier L, Sisu C, Li JJ, Pei B, Harmanci AO, Duff MO, Djebali S, Alexander RP, Alver BH, Auerbach R, Bell K, Bickel PJ, Boeck ME, Boley NP, Booth BW, Cherbas L, Cherbas P, Di C, Dobin A, Drenkow J, Ewing B, Fang G, Fastuca M, Feingold EA, Frankish A, Gao G, Good PJ, Guigó R, Hammonds A, Harrow J, Hoskins RA, Howald C, Hu L, Huang H, Hubbard TJ, Huynh C, Jha S, Kasper D, Kato M, Kaufman TC, Kitchen RR, Ladewig E, Lagarde J, Lai E, Leng J, Lu Z, MacCoss M, May G, McWhirter R, Merrihew G, Miller DM, Mortazavi A, Murad R, Oliver B, Olson S, Park PJ, Pazin MJ, Perrimon N, Pervouchine D, Reinke V, Reymond A, Robinson G, Samsonova A, Saunders GI, Schlesinger F, Sethi A, Slack FJ, Spencer WC, Stoiber MH, Strasbourger P, Tanzer A, Thompson OA, Wan KH, Wang G, Wang H, Watkins KL, Wen J, Wen K, Xue C, Yang L, Yip K, Zaleski C, Zhang Y, Zheng H, Brenner SE, Graveley BR, Celniker SE, Gingeras TR, Waterston R. Gerstein MB, et al. Among authors: bickel pj. Nature. 2014 Aug 28;512(7515):445-8. doi: 10.1038/nature13424. Nature. 2014. PMID: 25164755 Free PMC article.
The developmental transcriptome of Drosophila melanogaster.
Graveley BR, Brooks AN, Carlson JW, Duff MO, Landolin JM, Yang L, Artieri CG, van Baren MJ, Boley N, Booth BW, Brown JB, Cherbas L, Davis CA, Dobin A, Li R, Lin W, Malone JH, Mattiuzzo NR, Miller D, Sturgill D, Tuch BB, Zaleski C, Zhang D, Blanchette M, Dudoit S, Eads B, Green RE, Hammonds A, Jiang L, Kapranov P, Langton L, Perrimon N, Sandler JE, Wan KH, Willingham A, Zhang Y, Zou Y, Andrews J, Bickel PJ, Brenner SE, Brent MR, Cherbas P, Gingeras TR, Hoskins RA, Kaufman TC, Oliver B, Celniker SE. Graveley BR, et al. Among authors: bickel pj. Nature. 2011 Mar 24;471(7339):473-9. doi: 10.1038/nature09715. Epub 2010 Dec 22. Nature. 2011. PMID: 21179090 Free PMC article.
47 results