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Results: 1 to 20 of 81

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 Article
2.

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]
3.

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]
4.

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]
5.

Spatial expression of transcription factors in Drosophila embryonic organ development.

Hammonds AS, Bristow CA, Fisher WW, Weiszmann R, Wu S, Hartenstein V, Kellis M, Yu B, Frise E, Celniker SE.

Genome Biol. 2013 Dec 20;14(12):R140. [Epub ahead of print]

PMID:
24359758
[PubMed - as supplied by publisher]
Free PMC Article
6.

Computational identification of diverse mechanisms underlying transcription factor-DNA occupancy.

Cheng Q, Kazemian M, Pham H, Blatti C, Celniker SE, Wolfe SA, Brodsky MH, Sinha S.

PLoS Genet. 2013;9(8):e1003571. doi: 10.1371/journal.pgen.1003571. Epub 2013 Aug 1.

PMID:
23935523
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

An extracellular interactome of immunoglobulin and LRR proteins reveals receptor-ligand networks.

Özkan E, Carrillo RA, Eastman CL, Weiszmann R, Waghray D, Johnson KG, Zinn K, Celniker SE, Garcia KC.

Cell. 2013 Jul 3;154(1):228-39. doi: 10.1016/j.cell.2013.06.006.

PMID:
23827685
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Global analysis of Drosophila Cys₂-His₂ zinc finger proteins reveals a multitude of novel recognition motifs and binding determinants.

Enuameh MS, Asriyan Y, Richards A, Christensen RG, Hall VL, Kazemian M, Zhu C, Pham H, Cheng Q, Blatti C, Brasefield JA, Basciotta MD, Ou J, McNulty JC, Zhu LJ, Celniker SE, Sinha S, Stormo GD, Brodsky MH, Wolfe SA.

Genome Res. 2013 Jun;23(6):928-40. doi: 10.1101/gr.151472.112. Epub 2013 Mar 7.

PMID:
23471540
[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.

Global patterns of tissue-specific alternative polyadenylation in Drosophila.

Smibert P, Miura P, Westholm JO, Shenker S, May G, Duff MO, Zhang D, Eads BD, Carlson J, Brown JB, Eisman RC, Andrews J, Kaufman T, Cherbas P, Celniker SE, Graveley BR, Lai EC.

Cell Rep. 2012 Mar 29;1(3):277-89. Erratum in: Cell Rep. 2013 Mar 28;3(3):969.

PMID:
22685694
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

Automated protein-DNA interaction screening of Drosophila regulatory elements.

Hens K, Feuz JD, Isakova A, Iagovitina A, Massouras A, Bryois J, Callaerts P, Celniker SE, Deplancke B.

Nat Methods. 2011 Oct 30;8(12):1065-70. doi: 10.1038/nmeth.1763.

PMID:
22037703
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

A protein complex network of Drosophila melanogaster.

Guruharsha KG, Rual JF, Zhai B, Mintseris J, Vaidya P, Vaidya N, Beekman C, Wong C, Rhee DY, Cenaj O, McKillip E, Shah S, Stapleton M, Wan KH, Yu C, Parsa B, Carlson JW, Chen X, Kapadia B, VijayRaghavan K, Gygi SP, Celniker SE, Obar RA, Artavanis-Tsakonas S.

Cell. 2011 Oct 28;147(3):690-703. doi: 10.1016/j.cell.2011.08.047.

PMID:
22036573
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Characterization of MtnE, the fifth metallothionein member in Drosophila.

Atanesyan L, Günther V, Celniker SE, Georgiev O, Schaffner W.

J Biol Inorg Chem. 2011 Oct;16(7):1047-56. doi: 10.1007/s00775-011-0825-4. Epub 2011 Aug 26.

PMID:
21870250
[PubMed - indexed for MEDLINE]
14.

Dynamic reprogramming of chromatin accessibility during Drosophila embryo development.

Thomas S, Li XY, Sabo PJ, Sandstrom R, Thurman RE, Canfield TK, Giste E, Fisher W, Hammonds A, Celniker SE, Biggin MD, Stamatoyannopoulos JA.

Genome Biol. 2011;12(5):R43. doi: 10.1186/gb-2011-12-5-r43. Epub 2011 May 11.

PMID:
21569360
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Development of expression-ready constructs for generation of proteomic libraries.

Yu C, Wan KH, Hammonds AS, Stapleton M, Carlson JW, Celniker SE.

Methods Mol Biol. 2011;723:257-72. doi: 10.1007/978-1-61779-043-0_17.

PMID:
21370071
[PubMed - indexed for MEDLINE]
16.

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
17.

Identification of functional elements and regulatory circuits by Drosophila modENCODE.

modENCODE Consortium, Roy S, Ernst J, Kharchenko PV, Kheradpour P, Negre N, Eaton ML, Landolin JM, Bristow CA, Ma L, Lin MF, Washietl S, Arshinoff BI, Ay F, Meyer PE, Robine N, Washington NL, Di Stefano L, Berezikov E, Brown CD, Candeias R, Carlson JW, Carr A, Jungreis I, Marbach D, Sealfon R, Tolstorukov MY, Will S, Alekseyenko AA, Artieri C, Booth BW, Brooks AN, Dai Q, Davis CA, Duff MO, Feng X, Gorchakov AA, Gu T, Henikoff JG, Kapranov P, Li R, MacAlpine HK, Malone J, Minoda A, Nordman J, Okamura K, Perry M, Powell SK, Riddle NC, Sakai A, Samsonova A, Sandler JE, Schwartz YB, Sher N, Spokony R, Sturgill D, van Baren M, Wan KH, Yang L, Yu C, Feingold E, Good P, Guyer M, Lowdon R, Ahmad K, Andrews J, Berger B, Brenner SE, Brent MR, Cherbas L, Elgin SC, Gingeras TR, Grossman R, Hoskins RA, Kaufman TC, Kent W, Kuroda MI, Orr-Weaver T, Perrimon N, Pirrotta V, Posakony JW, Ren B, Russell S, Cherbas P, Graveley BR, Lewis S, Micklem G, Oliver B, Park PJ, Celniker SE, Henikoff S, Karpen GH, Lai EC, MacAlpine DM, Stein LD, White KP, Kellis M.

Science. 2010 Dec 24;330(6012):1787-97. doi: 10.1126/science.1198374. Epub 2010 Dec 22.

PMID:
21177974
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

The transcriptional diversity of 25 Drosophila cell lines.

Cherbas L, Willingham A, Zhang D, Yang L, Zou Y, Eads BD, Carlson JW, Landolin JM, Kapranov P, Dumais J, Samsonova A, Choi JH, Roberts J, Davis CA, Tang H, van Baren MJ, Ghosh S, Dobin A, Bell K, Lin W, Langton L, Duff MO, Tenney AE, Zaleski C, Brent MR, Hoskins RA, Kaufman TC, Andrews J, Graveley BR, Perrimon N, Celniker SE, Gingeras TR, Cherbas P.

Genome Res. 2011 Feb;21(2):301-14. doi: 10.1101/gr.112961.110. Epub 2010 Dec 22.

PMID:
21177962
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

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.

Genome Res. 2011 Feb;21(2):182-92. doi: 10.1101/gr.112466.110. Epub 2010 Dec 22.

PMID:
21177961
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Competitive repair by naturally dispersed repetitive DNA during non-allelic homologous recombination.

Hoang ML, Tan FJ, Lai DC, Celniker SE, Hoskins RA, Dunham MJ, Zheng Y, Koshland D.

PLoS Genet. 2010 Dec 2;6(12):e1001228. doi: 10.1371/journal.pgen.1001228.

PMID:
21151956
[PubMed - indexed for MEDLINE]
Free PMC Article

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