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Items: 1 to 20 of 94


A tutorial on protein ontology resources for proteomic studies.

Arighi CN.

Methods Mol Biol. 2011;694:77-90. doi: 10.1007/978-1-60761-977-2_6.


TGF-beta signaling proteins and the Protein Ontology.

Arighi CN, Liu H, Natale DA, Barker WC, Drabkin H, Blake JA, Smith B, Wu CH.

BMC Bioinformatics. 2009 May 6;10 Suppl 5:S3. doi: 10.1186/1471-2105-10-S5-S3.


Framework for a protein ontology.

Natale DA, Arighi CN, Barker WC, Blake J, Chang TC, Hu Z, Liu H, Smith B, Wu CH.

BMC Bioinformatics. 2007 Nov 27;8 Suppl 9:S1.


The representation of protein complexes in the Protein Ontology (PRO).

Bult CJ, Drabkin HJ, Evsikov A, Natale D, Arighi C, Roberts N, Ruttenberg A, D'Eustachio P, Smith B, Blake JA, Wu C.

BMC Bioinformatics. 2011 Sep 19;12:371. doi: 10.1186/1471-2105-12-371.


The Protein Ontology: a structured representation of protein forms and complexes.

Natale DA, Arighi CN, Barker WC, Blake JA, Bult CJ, Caudy M, Drabkin HJ, D'Eustachio P, Evsikov AV, Huang H, Nchoutmboube J, Roberts NV, Smith B, Zhang J, Wu CH.

Nucleic Acids Res. 2011 Jan;39(Database issue):D539-45. doi: 10.1093/nar/gkq907. Epub 2010 Oct 8.


Protein Ontology: a controlled structured network of protein entities.

Natale DA, Arighi CN, Blake JA, Bult CJ, Christie KR, Cowart J, D'Eustachio P, Diehl AD, Drabkin HJ, Helfer O, Huang H, Masci AM, Ren J, Roberts NV, Ross K, Ruttenberg A, Shamovsky V, Smith B, Yerramalla MS, Zhang J, AlJanahi A, Çelen I, Gan C, Lv M, Schuster-Lezell E, Wu CH.

Nucleic Acids Res. 2014 Jan;42(Database issue):D415-21. doi: 10.1093/nar/gkt1173. Epub 2013 Nov 21.


Use of the protein ontology for multi-faceted analysis of biological processes: a case study of the spindle checkpoint.

Ross KE, Arighi CN, Ren J, Natale DA, Huang H, Wu CH.

Front Genet. 2013 Apr 26;4:62. doi: 10.3389/fgene.2013.00062. eCollection 2013.


Standardized description of scientific evidence using the Evidence Ontology (ECO).

Chibucos MC, Mungall CJ, Balakrishnan R, Christie KR, Huntley RP, White O, Blake JA, Lewis SE, Giglio M.

Database (Oxford). 2014 Jul 22;2014. pii: bau075. doi: 10.1093/database/bau075. Print 2014.


Discovery of novel genes and gene isoforms by integrating transcriptomic and proteomic profiling from mouse liver.

Wu P, Zhang H, Lin W, Hao Y, Ren L, Zhang C, Li N, Wei H, Jiang Y, He F.

J Proteome Res. 2014 May 2;13(5):2409-19. doi: 10.1021/pr4012206. Epub 2014 Apr 18.


Comparative proteomics reveals a significant bias toward alternative protein isoforms with conserved structure and function.

Ezkurdia I, del Pozo A, Frankish A, Rodriguez JM, Harrow J, Ashman K, Valencia A, Tress ML.

Mol Biol Evol. 2012 Sep;29(9):2265-83. doi: 10.1093/molbev/mss100. Epub 2012 Mar 22.


Large-scale gene function analysis with the PANTHER classification system.

Mi H, Muruganujan A, Casagrande JT, Thomas PD.

Nat Protoc. 2013 Aug;8(8):1551-66. doi: 10.1038/nprot.2013.092. Epub 2013 Jul 18.


Characterization of native protein complexes and protein isoform variation using size-fractionation-based quantitative proteomics.

Kirkwood KJ, Ahmad Y, Larance M, Lamond AI.

Mol Cell Proteomics. 2013 Dec;12(12):3851-73. doi: 10.1074/mcp.M113.032367. Epub 2013 Sep 16.


SysPTM: a systematic resource for proteomic research on post-translational modifications.

Li H, Xing X, Ding G, Li Q, Wang C, Xie L, Zeng R, Li Y.

Mol Cell Proteomics. 2009 Aug;8(8):1839-49. doi: 10.1074/mcp.M900030-MCP200. Epub 2009 Apr 14.


PEPPI: a peptidomic database of human protein isoforms for proteomics experiments.

Zhou A, Zhang F, Chen JY.

BMC Bioinformatics. 2010 Oct 7;11 Suppl 6:S7. doi: 10.1186/1471-2105-11-S6-S7.


Construction of protein phosphorylation networks by data mining, text mining and ontology integration: analysis of the spindle checkpoint.

Ross KE, Arighi CN, Ren J, Huang H, Wu CH.

Database (Oxford). 2013 Jun 7;2013:bat038. doi: 10.1093/database/bat038. Print 2013.


KEGG orthology-based annotation of the predicted proteome of Acropora digitifera: ZoophyteBase - an open access and searchable database of a coral genome.

Dunlap WC, Starcevic A, Baranasic D, Diminic J, Zucko J, Gacesa R, van Oppen MJ, Hranueli D, Cullum J, Long PF.

BMC Genomics. 2013 Jul 26;14:509. doi: 10.1186/1471-2164-14-509.


How to link ontologies and protein-protein interactions to literature: text-mining approaches and the BioCreative experience.

Krallinger M, Leitner F, Vazquez M, Salgado D, Marcelle C, Tyers M, Valencia A, Chatr-aryamontri A.

Database (Oxford). 2012 Mar 21;2012:bas017. doi: 10.1093/database/bas017. Print 2012.


Gene-oriented ortholog database: a functional comparison platform for orthologous loci.

Ho MR, Chen CH, Lin WC.

Database (Oxford). 2010;2010:baq002. doi: 10.1093/database/baq002. Epub 2010 Feb 10.


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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