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Items: 1 to 20 of 100

1.

Variable locus length in the human genome leads to ascertainment bias in functional inference for non-coding elements.

Taher L, Ovcharenko I.

Bioinformatics. 2009 Mar 1;25(5):578-84. doi: 10.1093/bioinformatics/btp043. Epub 2009 Jan 25.

3.

Integrative annotation of 21,037 human genes validated by full-length cDNA clones.

Imanishi T, Itoh T, Suzuki Y, O'Donovan C, Fukuchi S, Koyanagi KO, Barrero RA, Tamura T, Yamaguchi-Kabata Y, Tanino M, Yura K, Miyazaki S, Ikeo K, Homma K, Kasprzyk A, Nishikawa T, Hirakawa M, Thierry-Mieg J, Thierry-Mieg D, Ashurst J, Jia L, Nakao M, Thomas MA, Mulder N, Karavidopoulou Y, Jin L, Kim S, Yasuda T, Lenhard B, Eveno E, Suzuki Y, Yamasaki C, Takeda J, Gough C, Hilton P, Fujii Y, Sakai H, Tanaka S, Amid C, Bellgard M, Bonaldo Mde F, Bono H, Bromberg SK, Brookes AJ, Bruford E, Carninci P, Chelala C, Couillault C, de Souza SJ, Debily MA, Devignes MD, Dubchak I, Endo T, Estreicher A, Eyras E, Fukami-Kobayashi K, Gopinath GR, Graudens E, Hahn Y, Han M, Han ZG, Hanada K, Hanaoka H, Harada E, Hashimoto K, Hinz U, Hirai M, Hishiki T, Hopkinson I, Imbeaud S, Inoko H, Kanapin A, Kaneko Y, Kasukawa T, Kelso J, Kersey P, Kikuno R, Kimura K, Korn B, Kuryshev V, Makalowska I, Makino T, Mano S, Mariage-Samson R, Mashima J, Matsuda H, Mewes HW, Minoshima S, Nagai K, Nagasaki H, Nagata N, Nigam R, Ogasawara O, Ohara O, Ohtsubo M, Okada N, Okido T, Oota S, Ota M, Ota T, Otsuki T, Piatier-Tonneau D, Poustka A, Ren SX, Saitou N, Sakai K, Sakamoto S, Sakate R, Schupp I, Servant F, Sherry S, Shiba R, Shimizu N, Shimoyama M, Simpson AJ, Soares B, Steward C, Suwa M, Suzuki M, Takahashi A, Tamiya G, Tanaka H, Taylor T, Terwilliger JD, Unneberg P, Veeramachaneni V, Watanabe S, Wilming L, Yasuda N, Yoo HS, Stodolsky M, Makalowski W, Go M, Nakai K, Takagi T, Kanehisa M, Sakaki Y, Quackenbush J, Okazaki Y, Hayashizaki Y, Hide W, Chakraborty R, Nishikawa K, Sugawara H, Tateno Y, Chen Z, Oishi M, Tonellato P, Apweiler R, Okubo K, Wagner L, Wiemann S, Strausberg RL, Isogai T, Auffray C, Nomura N, Gojobori T, Sugano S.

PLoS Biol. 2004 Jun;2(6):e162. Epub 2004 Apr 20. Erratum in: PLoS Biol. 2004 Jul;2(7):e256.

4.

Properties of non-coding DNA and identification of putative cis-regulatory elements in Theileria parva.

Guo X, Silva JC.

BMC Genomics. 2008 Dec 3;9:582. doi: 10.1186/1471-2164-9-582.

5.

On the Use of Gene Ontology Annotations to Assess Functional Similarity among Orthologs and Paralogs: A Short Report.

Thomas PD, Wood V, Mungall CJ, Lewis SE, Blake JA; Gene Ontology Consortium.

PLoS Comput Biol. 2012;8(2):e1002386. doi: 10.1371/journal.pcbi.1002386. Epub 2012 Feb 16.

6.

Genomic sequence around butterfly wing development genes: annotation and comparative analysis.

Conceição IC, Long AD, Gruber JD, Beldade P.

PLoS One. 2011;6(8):e23778. doi: 10.1371/journal.pone.0023778. Epub 2011 Aug 31.

7.

GENCODE: producing a reference annotation for ENCODE.

Harrow J, Denoeud F, Frankish A, Reymond A, Chen CK, Chrast J, Lagarde J, Gilbert JG, Storey R, Swarbreck D, Rossier C, Ucla C, Hubbard T, Antonarakis SE, Guigo R.

Genome Biol. 2006;7 Suppl 1:S4.1-9. Epub 2006 Aug 7.

8.

Structural and functional-annotation of an equine whole genome oligoarray.

Bright LA, Burgess SC, Chowdhary B, Swiderski CE, McCarthy FM.

BMC Bioinformatics. 2009 Oct 8;10 Suppl 11:S8. doi: 10.1186/1471-2105-10-S11-S8.

9.

A procedure for assessing GO annotation consistency.

Dolan ME, Ni L, Camon E, Blake JA.

Bioinformatics. 2005 Jun;21 Suppl 1:i136-43.

10.

Coding DNA repeated throughout intergenic regions of the Arabidopsis thaliana genome: evolutionary footprints of RNA silencing.

Feng J, Naiman DQ, Cooper B.

Mol Biosyst. 2009 Dec;5(12):1679-87. doi: 10.1039/b903031j. Epub 2009 Apr 30.

PMID:
19452047
11.

Comparing gene annotation enrichment tools for functional modeling of agricultural microarray data.

van den Berg BH, Thanthiriwatte C, Manda P, Bridges SM.

BMC Bioinformatics. 2009 Oct 8;10 Suppl 11:S9. doi: 10.1186/1471-2105-10-S11-S9.

12.

Large-scale protein annotation through gene ontology.

Xie H, Wasserman A, Levine Z, Novik A, Grebinskiy V, Shoshan A, Mintz L.

Genome Res. 2002 May;12(5):785-94.

13.

GIFtS: annotation landscape analysis with GeneCards.

Harel A, Inger A, Stelzer G, Strichman-Almashanu L, Dalah I, Safran M, Lancet D.

BMC Bioinformatics. 2009 Oct 23;10:348. doi: 10.1186/1471-2105-10-348.

14.

Automatic extraction of gene ontology annotation and its correlation with clusters in protein networks.

Daraselia N, Yuryev A, Egorov S, Mazo I, Ispolatov I.

BMC Bioinformatics. 2007 Jul 10;8:243.

16.

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.

17.
18.

Analysis of genomic variation in non-coding elements using population-scale sequencing data from the 1000 Genomes Project.

Mu XJ, Lu ZJ, Kong Y, Lam HY, Gerstein MB.

Nucleic Acids Res. 2011 Sep 1;39(16):7058-76. doi: 10.1093/nar/gkr342. Epub 2011 May 19.

19.
20.

The Gene Ontology Annotation (GOA) Database: sharing knowledge in Uniprot with Gene Ontology.

Camon E, Magrane M, Barrell D, Lee V, Dimmer E, Maslen J, Binns D, Harte N, Lopez R, Apweiler R.

Nucleic Acids Res. 2004 Jan 1;32(Database issue):D262-6.

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