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Results: 1 to 20 of 114

1.

Benchmarking ortholog identification methods using functional genomics data.

Hulsen T, Huynen MA, de Vlieg J, Groenen PM.

Genome Biol. 2006;7(4):R31. Epub 2006 Apr 13.

PMID:
16613613
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

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
[PubMed - indexed for MEDLINE]
3.

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.

PMID:
20428317
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

Orthology confers intron position conservation.

Henricson A, Forslund K, Sonnhammer EL.

BMC Genomics. 2010 Jul 2;11:412. doi: 10.1186/1471-2164-11-412.

PMID:
20598118
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

MultiMSOAR 2.0: an accurate tool to identify ortholog groups among multiple genomes.

Shi G, Peng MC, Jiang T.

PLoS One. 2011;6(6):e20892. doi: 10.1371/journal.pone.0020892. Epub 2011 Jun 21.

PMID:
21712981
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

Assignment of orthologous genes via genome rearrangement.

Chen X, Zheng J, Fu Z, Nan P, Zhong Y, Lonardi S, Jiang T.

IEEE/ACM Trans Comput Biol Bioinform. 2005 Oct-Dec;2(4):302-15.

PMID:
17044168
[PubMed - indexed for MEDLINE]
7.

Improving the specificity of high-throughput ortholog prediction.

Fulton DL, Li YY, Laird MR, Horsman BG, Roche FM, Brinkman FS.

BMC Bioinformatics. 2006 May 28;7:270.

PMID:
16729895
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

MSOAR 2.0: Incorporating tandem duplications into ortholog assignment based on genome rearrangement.

Shi G, Zhang L, Jiang T.

BMC Bioinformatics. 2010 Jan 6;11:10. doi: 10.1186/1471-2105-11-10.

PMID:
20053291
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

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.

PMID:
21106128
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

Inferring modules of functionally interacting proteins using the Bond Energy Algorithm.

Watanabe RL, Morett E, Vallejo EE.

BMC Bioinformatics. 2008 Jun 17;9:285. doi: 10.1186/1471-2105-9-285.

PMID:
18559112
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

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.

PMID:
23209392
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Experimental-confirmation and functional-annotation of predicted proteins in the chicken genome.

Buza TJ, McCarthy FM, Burgess SC.

BMC Genomics. 2007 Nov 19;8:425.

PMID:
18021451
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

HCOP: the HGNC comparison of orthology predictions search tool.

Wright MW, Eyre TA, Lush MJ, Povey S, Bruford EA.

Mamm Genome. 2005 Nov;16(11):827-8. Epub 2005 Nov 11.

PMID:
16284797
[PubMed - indexed for MEDLINE]
14.

Testing the ortholog conjecture with comparative functional genomic data from mammals.

Nehrt NL, Clark WT, Radivojac P, Hahn MW.

PLoS Comput Biol. 2011 Jun;7(6):e1002073. doi: 10.1371/journal.pcbi.1002073. Epub 2011 Jun 9.

PMID:
21695233
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Phylogenetic and functional assessment of orthologs inference projects and methods.

Altenhoff AM, Dessimoz C.

PLoS Comput Biol. 2009 Jan;5(1):e1000262. doi: 10.1371/journal.pcbi.1000262. Epub 2009 Jan 16.

PMID:
19148271
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

CLUSS: clustering of protein sequences based on a new similarity measure.

Kelil A, Wang S, Brzezinski R, Fleury A.

BMC Bioinformatics. 2007 Aug 4;8:286.

PMID:
17683581
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Clusters of orthologous genes for 41 archaeal genomes and implications for evolutionary genomics of archaea.

Makarova KS, Sorokin AV, Novichkov PS, Wolf YI, Koonin EV.

Biol Direct. 2007 Nov 27;2:33.

PMID:
18042280
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Clustering of main orthologs for multiple genomes.

Fu Z, Jiang T.

Comput Syst Bioinformatics Conf. 2007;6:195-201.

PMID:
17951824
[PubMed - indexed for MEDLINE]
Free Article
19.

Automated ortholog inference from phylogenetic trees and calculation of orthology reliability.

Storm CE, Sonnhammer EL.

Bioinformatics. 2002 Jan;18(1):92-9.

PMID:
11836216
[PubMed - indexed for MEDLINE]
Free Article
20.

Signalogs: orthology-based identification of novel signaling pathway components in three metazoans.

Korcsmáros T, Szalay MS, Rovó P, Palotai R, Fazekas D, Lenti K, Farkas IJ, Csermely P, Vellai T.

PLoS One. 2011 May 3;6(5):e19240. doi: 10.1371/journal.pone.0019240.

PMID:
21559328
[PubMed - indexed for MEDLINE]
Free PMC Article

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