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Items: 1 to 20 of 113

1.

Identification of mammalian orthologs using local synteny.

Jun J, Mandoiu II, Nelson CE.

BMC Genomics. 2009 Dec 23;10:630. doi: 10.1186/1471-2164-10-630.

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
3.

The other side of comparative genomics: genes with no orthologs between the cow and other mammalian species.

Mazza R, Strozzi F, Caprera A, Ajmone-Marsan P, Williams JL.

BMC Genomics. 2009 Dec 14;10:604. doi: 10.1186/1471-2164-10-604.

4.

Using shared genomic synteny and shared protein functions to enhance the identification of orthologous gene pairs.

Zheng XH, Lu F, Wang ZY, Zhong F, Hoover J, Mural R.

Bioinformatics. 2005 Mar;21(6):703-10. Epub 2004 Sep 30.

PMID:
15458983
5.

Designating eukaryotic orthology via processed transcription units.

Ho MR, Jang WJ, Chen CH, Ch'ang LY, Lin WC.

Nucleic Acids Res. 2008 Jun;36(10):3436-42. doi: 10.1093/nar/gkn227. Epub 2008 Apr 29.

6.

Computational methods for Gene Orthology inference.

Kristensen DM, Wolf YI, Mushegian AR, Koonin EV.

Brief Bioinform. 2011 Sep;12(5):379-91. doi: 10.1093/bib/bbr030. Epub 2011 Jun 19.

7.

Screening synteny blocks in pairwise genome comparisons through integer programming.

Tang H, Lyons E, Pedersen B, Schnable JC, Paterson AH, Freeling M.

BMC Bioinformatics. 2011 Apr 18;12:102. doi: 10.1186/1471-2105-12-102.

8.

The evolution of protostome GATA factors: molecular phylogenetics, synteny, and intron/exon structure reveal orthologous relationships.

Gillis WQ, Bowerman BA, Schneider SQ.

BMC Evol Biol. 2008 Apr 15;8:112. doi: 10.1186/1471-2148-8-112.

9.

Clustering of main orthologs for multiple genomes.

Fu Z, Jiang T.

J Bioinform Comput Biol. 2008 Jun;6(3):573-84.

PMID:
18574863
10.

Whole genome duplications and expansion of the vertebrate GATA transcription factor gene family.

Gillis WQ, St John J, Bowerman B, Schneider SQ.

BMC Evol Biol. 2009 Aug 20;9:207. doi: 10.1186/1471-2148-9-207.

11.

OrthoFocus: program for identification of orthologs in multiple genomes in family-focused studies.

Ivliev AE, Sergeeva MG.

J Bioinform Comput Biol. 2008 Aug;6(4):811-24.

PMID:
18763744
12.

Identification of gene-oriented exon orthology between human and mouse.

Fu GC, Lin WC.

BMC Genomics. 2012;13 Suppl 1:S10. doi: 10.1186/1471-2164-13-S1-S10. Epub 2012 Jan 17.

13.

A universal genomic coordinate translator for comparative genomics.

Zamani N, Sundström G, Meadows JR, Höppner MP, Dainat J, Lantz H, Haas BJ, Grabherr MG.

BMC Bioinformatics. 2014 Jun 30;15:227. doi: 10.1186/1471-2105-15-227.

14.
15.

Revealing mammalian evolutionary relationships by comparative analysis of gene clusters.

Song G, Riemer C, Dickins B, Kim HL, Zhang L, Zhang Y, Hsu CH, Hardison RC, Nisc Comparative Sequencing Program, Green ED, Miller W.

Genome Biol Evol. 2012;4(4):586-601. doi: 10.1093/gbe/evs032. Epub 2012 Mar 27.

16.

MSOAR: a high-throughput ortholog assignment system based on genome rearrangement.

Fu Z, Chen X, Vacic V, Nan P, Zhong Y, Jiang T.

J Comput Biol. 2007 Nov;14(9):1160-75.

PMID:
17990975
17.

Techniques for multi-genome synteny analysis to overcome assembly limitations.

Bhutkar A, Russo S, Smith TF, Gelbart WM.

Genome Inform. 2006;17(2):152-61.

PMID:
17503388
18.

A tight link between orthologs and bidirectional best hits in bacterial and archaeal genomes.

Wolf YI, Koonin EV.

Genome Biol Evol. 2012;4(12):1286-94. doi: 10.1093/gbe/evs100.

19.

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.

20.

OrthologID: automation of genome-scale ortholog identification within a parsimony framework.

Chiu JC, Lee EK, Egan MG, Sarkar IN, Coruzzi GM, DeSalle R.

Bioinformatics. 2006 Mar 15;22(6):699-707. Epub 2006 Jan 12.

PMID:
16410324

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