Display Settings:

Format
Items per page
Sort by

Send to:

Choose Destination

Results: 1 to 20 of 69

1.

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.

PMID:
24985915
[PubMed - in process]
Free PMC Article
2.

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.

PMID:
24985912
[PubMed - in process]
Free PMC Article
3.

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.

PMID:
24688849
[PubMed]
Free PMC Article
4.

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 Mar 16. doi: 10.1038/nature12962. [Epub ahead of print]

PMID:
24670639
[PubMed - as supplied by publisher]
5.

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.

PMID:
24636835
[PubMed - in process]
6.

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.

PMID:
24633242
[PubMed - in process]
7.

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.

PMID:
23954908
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

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.

PMID:
23954907
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

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.

PMID:
23236164
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

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.

PMID:
22959976
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

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.

PMID:
22955991
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

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.

PMID:
22955977
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

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.

PMID:
22950945
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

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.

PMID:
22522655
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

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
[PubMed - indexed for MEDLINE]
16.

[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
[PubMed - indexed for MEDLINE]
17.

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.

PMID:
22135461
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

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.

PMID:
22127648
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

Skeletal muscle triglycerides, diacylglycerols, and ceramides in insulin resistance: another paradox in endurance-trained athletes?

Amati F, Dubé JJ, Alvarez-Carnero E, Edreira MM, Chomentowski P, Coen PM, Switzer GE, Bickel PE, Stefanovic-Racic M, Toledo FG, Goodpaster BH.

Diabetes. 2011 Oct;60(10):2588-97. doi: 10.2337/db10-1221. Epub 2011 Aug 26.

PMID:
21873552
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

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.

Nature. 2011 Mar 24;471(7339):473-9. doi: 10.1038/nature09715. Epub 2010 Dec 22.

PMID:
21179090
[PubMed - indexed for MEDLINE]
Free PMC Article

Display Settings:

Format
Items per page
Sort by

Send to:

Choose Destination

Supplemental Content

Loading ...
Write to the Help Desk