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Items: 12

1.

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.

2.

Lessons from modENCODE.

Brown JB, Celniker SE.

Annu Rev Genomics Hum Genet. 2015;16:31-53. doi: 10.1146/annurev-genom-090413-025448. Epub 2015 Jun 26. Review.

PMID:
26133010
3.

Anything else but GAGA: a nonhistone protein complex reshapes chromatin structure.

Lehmann M.

Trends Genet. 2004 Jan;20(1):15-22. Review.

PMID:
14698615
4.

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.

5.

Polycomb silencing mechanisms and genomic programming.

Pirrotta V.

Ernst Schering Res Found Workshop. 2006;(57):97-113. Review.

PMID:
16568951
6.

Drosophila melanogaster: a case study of a model genomic sequence and its consequences.

Ashburner M, Bergman CM.

Genome Res. 2005 Dec;15(12):1661-7. Review.

7.

Annotation of the Drosophila melanogaster euchromatic genome: a systematic review.

Misra S, Crosby MA, Mungall CJ, Matthews BB, Campbell KS, Hradecky P, Huang Y, Kaminker JS, Millburn GH, Prochnik SE, Smith CD, Tupy JL, Whitfied EJ, Bayraktaroglu L, Berman BP, Bettencourt BR, Celniker SE, de Grey AD, Drysdale RA, Harris NL, Richter J, Russo S, Schroeder AJ, Shu SQ, Stapleton M, Yamada C, Ashburner M, Gelbart WM, Rubin GM, Lewis SE.

Genome Biol. 2002;3(12):RESEARCH0083. Epub 2002 Dec 31. Review.

8.

Metazoan promoters: emerging characteristics and insights into transcriptional regulation.

Lenhard B, Sandelin A, Carninci P.

Nat Rev Genet. 2012 Mar 6;13(4):233-45. doi: 10.1038/nrg3163. Review.

PMID:
22392219
9.

The gap gene network.

Jaeger J.

Cell Mol Life Sci. 2011 Jan;68(2):243-74. doi: 10.1007/s00018-010-0536-y. Epub 2010 Oct 8. Review.

10.

How do you find transcription factors? Computational approaches to compile and annotate repertoires of regulators for any genome.

Vaquerizas JM, Teichmann SA, Luscombe NM.

Methods Mol Biol. 2012;786:3-19. doi: 10.1007/978-1-61779-292-2_1. Review.

PMID:
21938617
11.

Resources for functional genomics studies in Drosophila melanogaster.

Mohr SE, Hu Y, Kim K, Housden BE, Perrimon N.

Genetics. 2014 May;197(1):1-18. doi: 10.1534/genetics.113.154344. Epub 2014 Mar 20. Review.

12.

Drosophila and experimental neurology in the post-genomic era.

Shulman JM.

Exp Neurol. 2015 Dec;274(Pt A):4-13. doi: 10.1016/j.expneurol.2015.03.016. Epub 2015 Mar 24. Review.

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