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Items: 1 to 20 of 187

1.

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.

2.

The ortholog conjecture is untestable by the current gene ontology but is supported by RNA sequencing data.

Chen X, Zhang J.

PLoS Comput Biol. 2012;8(11):e1002784. doi: 10.1371/journal.pcbi.1002784. Epub 2012 Nov 29. Erratum in: PLoS Comput Biol. 2013 Jan;9(1). doi:10.1371/annotation/6b5adbad-8944-4ab4-acd9-ac6f0d3e624e.

3.

Interspecies gene function prediction using semantic similarity.

Yu G, Luo W, Fu G, Wang J.

BMC Syst Biol. 2016 Dec 23;10(Suppl 4):121. doi: 10.1186/s12918-016-0361-5.

4.

A procedure for assessing GO annotation consistency.

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

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

PMID:
15961450
5.

Gene family level comparative analysis of gene expression in mammals validates the ortholog conjecture.

Rogozin IB, Managadze D, Shabalina SA, Koonin EV.

Genome Biol Evol. 2014 Apr;6(4):754-62. doi: 10.1093/gbe/evu051.

6.

Automatic clustering of orthologs and in-paralogs from pairwise species comparisons.

Remm M, Storm CE, Sonnhammer EL.

J Mol Biol. 2001 Dec 14;314(5):1041-52.

PMID:
11743721
7.

DODO: an efficient orthologous genes assignment tool based on domain architectures. Domain based ortholog detection.

Chen TW, Wu TH, Ng WV, Lin WC.

BMC Bioinformatics. 2010 Oct 15;11 Suppl 7:S6. doi: 10.1186/1471-2105-11-S7-S6.

8.

Measuring semantic similarities by combining gene ontology annotations and gene co-function networks.

Peng J, Uygun S, Kim T, Wang Y, Rhee SY, Chen J.

BMC Bioinformatics. 2015 Feb 14;16:44. doi: 10.1186/s12859-015-0474-7.

9.

GASS: genome structural annotation for Eukaryotes based on species similarity.

Wang Y, Chen L, Song N, Lei X.

BMC Genomics. 2015 Mar 4;16:150. doi: 10.1186/s12864-015-1353-3.

10.

Cross-organism learning method to discover new gene functionalities.

Domeniconi G, Masseroli M, Moro G, Pinoli P.

Comput Methods Programs Biomed. 2016 Apr;126:20-34. doi: 10.1016/j.cmpb.2015.12.002. Epub 2015 Dec 17.

PMID:
26724853
11.

CvManGO, a method for leveraging computational predictions to improve literature-based Gene Ontology annotations.

Park J, Costanzo MC, Balakrishnan R, Cherry JM, Hong EL.

Database (Oxford). 2012 Mar 20;2012:bas001. doi: 10.1093/database/bas001. Print 2012.

12.

Improving the measurement of semantic similarity between gene ontology terms and gene products: insights from an edge- and IC-based hybrid method.

Wu X, Pang E, Lin K, Pei ZM.

PLoS One. 2013 May 31;8(5):e66745. doi: 10.1371/journal.pone.0066745. Print 2013.

13.

Resolving the ortholog conjecture: orthologs tend to be weakly, but significantly, more similar in function than paralogs.

Altenhoff AM, Studer RA, Robinson-Rechavi M, Dessimoz C.

PLoS Comput Biol. 2012;8(5):e1002514. doi: 10.1371/journal.pcbi.1002514. Epub 2012 May 17.

14.
15.

Using computational predictions to improve literature-based Gene Ontology annotations: a feasibility study.

Costanzo MC, Park J, Balakrishnan R, Cherry JM, Hong EL.

Database (Oxford). 2011 Mar 15;2011:bar004. doi: 10.1093/database/bar004. Print 2011.

16.

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.

17.

Large-scale inference of gene function through phylogenetic annotation of Gene Ontology terms: case study of the apoptosis and autophagy cellular processes.

Feuermann M, Gaudet P, Mi H, Lewis SE, Thomas PD.

Database (Oxford). 2016 Dec 26;2016. pii: baw155. doi: 10.1093/database/baw155. Print 2016.

18.

Comparison of RefSeq protein-coding regions in human and vertebrate genomes.

Fong JH, Murphy TD, Pruitt KD.

BMC Genomics. 2013 Sep 25;14:654. doi: 10.1186/1471-2164-14-654.

19.

Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium.

Gaudet P, Livstone MS, Lewis SE, Thomas PD.

Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.

20.

A relation based measure of semantic similarity for Gene Ontology annotations.

Sheehan B, Quigley A, Gaudin B, Dobson S.

BMC Bioinformatics. 2008 Nov 4;9:468. doi: 10.1186/1471-2105-9-468.

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