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Items: 19

1.

A proposed syntax for Minimotif Semantics, version 1.

Vyas J, Nowling RJ, Maciejewski MW, Rajasekaran S, Gryk MR, Schiller MR.

BMC Genomics. 2009 Aug 5;10:360. doi: 10.1186/1471-2164-10-360.

2.

MIMAS 3.0 is a Multiomics Information Management and Annotation System.

Gattiker A, Hermida L, Liechti R, Xenarios I, Collin O, Rougemont J, Primig M.

BMC Bioinformatics. 2009 May 18;10:151. doi: 10.1186/1471-2105-10-151.

3.

Genome and proteome annotation: organization, interpretation and integration.

Reeves GA, Talavera D, Thornton JM.

J R Soc Interface. 2009 Feb 6;6(31):129-47. doi: 10.1098/rsif.2008.0341. Review.

4.

Minimotif miner 2nd release: a database and web system for motif search.

Rajasekaran S, Balla S, Gradie P, Gryk MR, Kadaveru K, Kundeti V, Maciejewski MW, Mi T, Rubino N, Vyas J, Schiller MR.

Nucleic Acids Res. 2009 Jan;37(Database issue):D185-90. doi: 10.1093/nar/gkn865. Epub 2008 Oct 31.

5.

Genome annotation.

Kawaji H, Hayashizaki Y.

Methods Mol Biol. 2008;452:125-39. doi: 10.1007/978-1-60327-159-2_6. Review.

PMID:
18563372
6.

A quantitative study of the recruitment potential of all intracellular tyrosine residues on EGFR, FGFR1 and IGF1R.

Kaushansky A, Gordus A, Chang B, Rush J, MacBeath G.

Mol Biosyst. 2008 Jun;4(6):643-53. doi: 10.1039/b801018h. Epub 2008 Apr 8.

7.

The annotation of both human and mouse kinomes in UniProtKB/Swiss-Prot: one small step in manual annotation, one giant leap for full comprehension of genomes.

Braconi Quintaje S, Orchard S.

Mol Cell Proteomics. 2008 Aug;7(8):1409-19. doi: 10.1074/mcp.R700001-MCP200. Epub 2008 Apr 24. Review.

8.

PepCyber:P~PEP: a database of human protein protein interactions mediated by phosphoprotein-binding domains.

Gong W, Zhou D, Ren Y, Wang Y, Zuo Z, Shen Y, Xiao F, Zhu Q, Hong A, Zhou X, Gao X, Li T.

Nucleic Acids Res. 2008 Jan;36(Database issue):D679-83. Epub 2007 Dec 26.

9.

DAVID Knowledgebase: a gene-centered database integrating heterogeneous gene annotation resources to facilitate high-throughput gene functional analysis.

Sherman BT, Huang da W, Tan Q, Guo Y, Bour S, Liu D, Stephens R, Baseler MW, Lane HC, Lempicki RA.

BMC Bioinformatics. 2007 Nov 2;8:426.

10.

Phospho.ELM: a database of phosphorylation sites--update 2008.

Diella F, Gould CM, Chica C, Via A, Gibson TJ.

Nucleic Acids Res. 2008 Jan;36(Database issue):D240-4. Epub 2007 Oct 25.

11.

Integration of curated databases to identify genotype-phenotype associations.

Goh CS, Gianoulis TA, Liu Y, Li J, Paccanaro A, Lussier YA, Gerstein M.

BMC Genomics. 2006 Oct 12;7:257.

12.

Minimotif Miner: a tool for investigating protein function.

Balla S, Thapar V, Verma S, Luong T, Faghri T, Huang CH, Rajasekaran S, del Campo JJ, Shinn JH, Mohler WA, Maciejewski MW, Gryk MR, Piccirillo B, Schiller SR, Schiller MR.

Nat Methods. 2006 Mar;3(3):175-7.

PMID:
16489333
13.

Towards multidimensional genome annotation.

Reed JL, Famili I, Thiele I, Palsson BO.

Nat Rev Genet. 2006 Feb;7(2):130-41. Review.

PMID:
16418748
14.

Protein variety and functional diversity: Swiss-Prot annotation in its biological context.

Boeckmann B, Blatter MC, Famiglietti L, Hinz U, Lane L, Roechert B, Bairoch A.

C R Biol. 2005 Oct-Nov;328(10-11):882-99. Epub 2005 Jul 28. Review.

PMID:
16286078
15.

A survey of current work in biomedical text mining.

Cohen AM, Hersh WR.

Brief Bioinform. 2005 Mar;6(1):57-71. Review.

PMID:
15826357
16.

Textpresso: an ontology-based information retrieval and extraction system for biological literature.

Müller HM, Kenny EE, Sternberg PW.

PLoS Biol. 2004 Nov;2(11):e309. Epub 2004 Sep 21.

17.

Scansite 2.0: Proteome-wide prediction of cell signaling interactions using short sequence motifs.

Obenauer JC, Cantley LC, Yaffe MB.

Nucleic Acids Res. 2003 Jul 1;31(13):3635-41.

18.

ELM server: A new resource for investigating short functional sites in modular eukaryotic proteins.

Puntervoll P, Linding R, Gemünd C, Chabanis-Davidson S, Mattingsdal M, Cameron S, Martin DM, Ausiello G, Brannetti B, Costantini A, Ferrè F, Maselli V, Via A, Cesareni G, Diella F, Superti-Furga G, Wyrwicz L, Ramu C, McGuigan C, Gudavalli R, Letunic I, Bork P, Rychlewski L, Küster B, Helmer-Citterich M, Hunter WN, Aasland R, Gibson TJ.

Nucleic Acids Res. 2003 Jul 1;31(13):3625-30.

19.

Specific motifs recognized by the SH2 domains of Csk, 3BP2, fps/fes, GRB-2, HCP, SHC, Syk, and Vav.

Songyang Z, Shoelson SE, McGlade J, Olivier P, Pawson T, Bustelo XR, Barbacid M, Sabe H, Hanafusa H, Yi T, et al.

Mol Cell Biol. 1994 Apr;14(4):2777-85.

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