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Items: 1 to 20 of 35

1.

JBrowse: a next-generation genome browser.

Skinner ME, Uzilov AV, Stein LD, Mungall CJ, Holmes IH.

Genome Res. 2009 Sep;19(9):1630-8. doi: 10.1101/gr.094607.109. Epub 2009 Jul 1.

2.

NCBI GEO: archive for high-throughput functional genomic data.

Barrett T, Troup DB, Wilhite SE, Ledoux P, Rudnev D, Evangelista C, Kim IF, Soboleva A, Tomashevsky M, Marshall KA, Phillippy KH, Sherman PM, Muertter RN, Edgar R.

Nucleic Acids Res. 2009 Jan;37(Database issue):D885-90. doi: 10.1093/nar/gkn764. Epub 2008 Oct 21.

3.

Is there a code embedded in proteins that is based on post-translational modifications?

Sims RJ 3rd, Reinberg D.

Nat Rev Mol Cell Biol. 2008 Oct;9(10):815-20. doi: 10.1038/nrm2502. Epub 2008 Sep 11. Review.

PMID:
18784729
4.

Stability and dynamics of polycomb target sites in Drosophila development.

Kwong C, Adryan B, Bell I, Meadows L, Russell S, Manak JR, White R.

PLoS Genet. 2008 Sep 5;4(9):e1000178. doi: 10.1371/journal.pgen.1000178.

5.

xMAN: extreme MApping of OligoNucleotides.

Li W, Carroll JS, Brown M, Liu xS.

BMC Genomics. 2008;9 Suppl 1:S20. doi: 10.1186/1471-2164-9-S1-S20.

6.

NELF and GAGA factor are linked to promoter-proximal pausing at many genes in Drosophila.

Lee C, Li X, Hechmer A, Eisen M, Biggin MD, Venters BJ, Jiang C, Li J, Pugh BF, Gilmour DS.

Mol Cell Biol. 2008 May;28(10):3290-300. doi: 10.1128/MCB.02224-07. Epub 2008 Mar 10.

7.

Transcription factors bind thousands of active and inactive regions in the Drosophila blastoderm.

Li XY, MacArthur S, Bourgon R, Nix D, Pollard DA, Iyer VN, Hechmer A, Simirenko L, Stapleton M, Luengo Hendriks CL, Chu HC, Ogawa N, Inwood W, Sementchenko V, Beaton A, Weiszmann R, Celniker SE, Knowles DW, Gingeras T, Speed TP, Eisen MB, Biggin MD.

PLoS Biol. 2008 Feb;6(2):e27. doi: 10.1371/journal.pbio.0060027.

8.

Efficient and accurate P-value computation for Position Weight Matrices.

Touzet H, Varré JS.

Algorithms Mol Biol. 2007 Dec 11;2:15.

9.

REDfly 2.0: an integrated database of cis-regulatory modules and transcription factor binding sites in Drosophila.

Halfon MS, Gallo SM, Bergman CM.

Nucleic Acids Res. 2008 Jan;36(Database issue):D594-8. Epub 2007 Nov 26.

10.

Reliable prediction of regulator targets using 12 Drosophila genomes.

Kheradpour P, Stark A, Roy S, Kellis M.

Genome Res. 2007 Dec;17(12):1919-31. Epub 2007 Nov 7.

11.

Genomic profiling and expression studies reveal both positive and negative activities for the Drosophila Myb MuvB/dREAM complex in proliferating cells.

Georlette D, Ahn S, MacAlpine DM, Cheung E, Lewis PW, Beall EL, Bell SP, Speed T, Manak JR, Botchan MR.

Genes Dev. 2007 Nov 15;21(22):2880-96. Epub 2007 Oct 31.

12.

Association of cohesin and Nipped-B with transcriptionally active regions of the Drosophila melanogaster genome.

Misulovin Z, Schwartz YB, Li XY, Kahn TG, Gause M, MacArthur S, Fay JC, Eisen MB, Pirrotta V, Biggin MD, Dorsett D.

Chromosoma. 2008 Feb;117(1):89-102. Epub 2007 Oct 27.

13.

FlyMine: an integrated database for Drosophila and Anopheles genomics.

Lyne R, Smith R, Rutherford K, Wakeling M, Varley A, Guillier F, Janssens H, Ji W, Mclaren P, North P, Rana D, Riley T, Sullivan J, Watkins X, Woodbridge M, Lilley K, Russell S, Ashburner M, Mizuguchi K, Micklem G.

Genome Biol. 2007;8(7):R129.

14.

A functional genomics strategy reveals clockwork orange as a transcriptional regulator in the Drosophila circadian clock.

Matsumoto A, Ukai-Tadenuma M, Yamada RG, Houl J, Uno KD, Kasukawa T, Dauwalder B, Itoh TQ, Takahashi K, Ueda R, Hardin PE, Tanimura T, Ueda HR.

Genes Dev. 2007 Jul 1;21(13):1687-700. Epub 2007 Jun 19.

15.

Unravelling the world of cis-regulatory elements.

Wang Z, Wei GH, Liu DP, Liang CC.

Med Biol Eng Comput. 2007 Aug;45(8):709-18. Epub 2007 May 31. Review.

PMID:
17541666
16.

Genome-wide mapping of in vivo protein-DNA interactions.

Johnson DS, Mortazavi A, Myers RM, Wold B.

Science. 2007 Jun 8;316(5830):1497-502. Epub 2007 May 31.

17.
18.

Mixture modeling for genome-wide localization of transcription factors.

Keleş S.

Biometrics. 2007 Mar;63(1):10-21.

PMID:
17447925
19.

Novel TRF1/BRF target genes revealed by genome-wide analysis of Drosophila Pol III transcription.

Isogai Y, Takada S, Tjian R, Keleş S.

EMBO J. 2007 Jan 10;26(1):79-89. Epub 2006 Dec 14.

20.

ArrayExpress--a public database of microarray experiments and gene expression profiles.

Parkinson H, Kapushesky M, Shojatalab M, Abeygunawardena N, Coulson R, Farne A, Holloway E, Kolesnykov N, Lilja P, Lukk M, Mani R, Rayner T, Sharma A, William E, Sarkans U, Brazma A.

Nucleic Acids Res. 2007 Jan;35(Database issue):D747-50. Epub 2006 Nov 28.

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