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Results: 1 to 20 of 71

1.

Comparative analysis of regulatory information and circuits across distant species.

Boyle AP, Araya CL, Brdlik C, Cayting P, Cheng C, Cheng Y, Gardner K, Hillier LW, Janette J, Jiang L, Kasper D, Kawli T, Kheradpour P, Kundaje A, Li JJ, Ma L, Niu W, Rehm EJ, Rozowsky J, Slattery M, Spokony R, Terrell R, Vafeados D, Wang D, Weisdepp P, Wu YC, Xie D, Yan KK, Feingold EA, Good PJ, Pazin MJ, Huang H, Bickel PJ, Brenner SE, Reinke V, Waterston RH, Gerstein M, White KP, Kellis M, Snyder M.

Nature. 2014 Aug 28;512(7515):453-6. doi: 10.1038/nature13668.

2.

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.

Nature. 2014 Aug 28;512(7515):445-8. doi: 10.1038/nature13424.

3.

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.

Genome Res. 2014 Jul;24(7):1209-23. doi: 10.1101/gr.159384.113.

4.

Comparison of D. melanogaster and C. elegans developmental stages, tissues, and cells by modENCODE RNA-seq data.

Li JJ, Huang H, Bickel PJ, Brenner SE.

Genome Res. 2014 Jul;24(7):1086-101. doi: 10.1101/gr.170100.113.

5.

System wide analyses have underestimated protein abundances and the importance of transcription in mammals.

Li JJ, Bickel PJ, Biggin MD.

PeerJ. 2014 Feb 27;2:e270. doi: 10.7717/peerj.270. eCollection 2014.

6.

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.

Nature. 2014 Aug 28;512(7515):393-9.

7.

Navigating and mining modENCODE data.

Boley N, Wan KH, Bickel PJ, Celniker SE.

Methods. 2014 Jun 15;68(1):38-47. doi: 10.1016/j.ymeth.2014.03.007. Epub 2014 Mar 15. Review.

PMID:
24636835
8.

Genome-guided transcript assembly by integrative analysis of RNA sequence data.

Boley N, Stoiber MH, Booth BW, Wan KH, Hoskins RA, Bickel PJ, Celniker SE, Brown JB.

Nat Biotechnol. 2014 Apr;32(4):341-6. doi: 10.1038/nbt.2850. Epub 2014 Mar 16.

9.

On robust regression with high-dimensional predictors.

El Karoui N, Bean D, Bickel PJ, Lim C, Yu B.

Proc Natl Acad Sci U S A. 2013 Sep 3;110(36):14557-62. doi: 10.1073/pnas.1307842110. Epub 2013 Aug 16.

10.

Optimal M-estimation in high-dimensional regression.

Bean D, Bickel PJ, El Karoui N, Yu B.

Proc Natl Acad Sci U S A. 2013 Sep 3;110(36):14563-8. doi: 10.1073/pnas.1307845110. Epub 2013 Aug 16.

11.

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.

Proc Natl Acad Sci U S A. 2012 Dec 26;109(52):21330-5. doi: 10.1073/pnas.1209589110. Epub 2012 Dec 10.

12.

Population-based risk factors for elevated alanine aminotransferase in a South Texas Mexican-American population.

Qu HQ, Li Q, Grove ML, Lu Y, Pan JJ, Rentfro AR, Bickel PE, Fallon MB, Hanis CL, Boerwinkle E, McCormick JB, Fisher-Hoch SP.

Arch Med Res. 2012 Aug;43(6):482-8. doi: 10.1016/j.arcmed.2012.08.005. Epub 2012 Sep 5.

13.

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia.

Landt SG, Marinov GK, Kundaje A, Kheradpour P, Pauli F, Batzoglou S, Bernstein BE, Bickel P, Brown JB, Cayting P, Chen Y, DeSalvo G, Epstein C, Fisher-Aylor KI, Euskirchen G, Gerstein M, Gertz J, Hartemink AJ, Hoffman MM, Iyer VR, Jung YL, Karmakar S, Kellis M, Kharchenko PV, Li Q, Liu T, Liu XS, Ma L, Milosavljevic A, Myers RM, Park PJ, Pazin MJ, Perry MD, Raha D, Reddy TE, Rozowsky J, Shoresh N, Sidow A, Slattery M, Stamatoyannopoulos JA, Tolstorukov MY, White KP, Xi S, Farnham PJ, Lieb JD, Wold BJ, Snyder M.

Genome Res. 2012 Sep;22(9):1813-31. doi: 10.1101/gr.136184.111.

14.

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.

Genome Res. 2012 Sep;22(9):1646-57. doi: 10.1101/gr.134767.111.

15.

Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors.

Yip KY, Cheng C, Bhardwaj N, Brown JB, Leng J, Kundaje A, Rozowsky J, Birney E, Bickel P, Snyder M, Gerstein M.

Genome Biol. 2012 Sep 26;13(9):R48. doi: 10.1186/gb-2012-13-9-r48.

16.

Systematic evaluation of factors influencing ChIP-seq fidelity.

Chen Y, Negre N, Li Q, Mieczkowska JO, Slattery M, Liu T, Zhang Y, Kim TK, He HH, Zieba J, Ruan Y, Bickel PJ, Myers RM, Wold BJ, White KP, Lieb JD, Liu XS.

Nat Methods. 2012 Jun;9(6):609-14. doi: 10.1038/nmeth.1985. Epub 2012 Apr 22.

17.

Nonparametric variable selection and modeling for spatial and temporal regulatory networks.

Aswani A, Biggin MD, Bickel P, Tomlin C.

Methods Cell Biol. 2012;110:243-61. doi: 10.1016/B978-0-12-388403-9.00010-2.

PMID:
22482952
18.

[Splice sites are overrepresented in Pasilla binding motif clusters in D. melanogaster genes].

Polishchuk MS, Brown JB, Favorov AV, Bickel PJ, Tumanian VG.

Biofizika. 2011 Nov-Dec;56(6):1065-70. Russian.

PMID:
22279750
19.

Sparse linear modeling of next-generation mRNA sequencing (RNA-Seq) data for isoform discovery and abundance estimation.

Li JJ, Jiang CR, Brown JB, Huang H, Bickel PJ.

Proc Natl Acad Sci U S A. 2011 Dec 13;108(50):19867-72. doi: 10.1073/pnas.1113972108. Epub 2011 Dec 1.

20.

The lipid droplet coat protein perilipin 5 also localizes to muscle mitochondria.

Bosma M, Minnaard R, Sparks LM, Schaart G, Losen M, de Baets MH, Duimel H, Kersten S, Bickel PE, Schrauwen P, Hesselink MK.

Histochem Cell Biol. 2012 Feb;137(2):205-16. doi: 10.1007/s00418-011-0888-x. Epub 2011 Nov 30.

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