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Items: 19

1.

Automatic genome-wide reconstruction of phylogenetic gene trees.

Wapinski I, Pfeffer A, Friedman N, Regev A.

Bioinformatics. 2007 Jul 1;23(13):i549-58.

PMID:
17646342
2.

Orthology prediction at scalable resolution by phylogenetic tree analysis.

van der Heijden RT, Snel B, van Noort V, Huynen MA.

BMC Bioinformatics. 2007 Mar 8;8:83.

3.

Ensembl 2007.

Hubbard TJ, Aken BL, Beal K, Ballester B, Caccamo M, Chen Y, Clarke L, Coates G, Cunningham F, Cutts T, Down T, Dyer SC, Fitzgerald S, Fernandez-Banet J, Graf S, Haider S, Hammond M, Herrero J, Holland R, Howe K, Howe K, Johnson N, Kahari A, Keefe D, Kokocinski F, Kulesha E, Lawson D, Longden I, Melsopp C, Megy K, Meidl P, Ouverdin B, Parker A, Prlic A, Rice S, Rios D, Schuster M, Sealy I, Severin J, Slater G, Smedley D, Spudich G, Trevanion S, Vilella A, Vogel J, White S, Wood M, Cox T, Curwen V, Durbin R, Fernandez-Suarez XM, Flicek P, Kasprzyk A, Proctor G, Searle S, Smith J, Ureta-Vidal A, Birney E.

Nucleic Acids Res. 2007 Jan;35(Database issue):D610-7. Epub 2006 Dec 5.

4.

STRING 7--recent developments in the integration and prediction of protein interactions.

von Mering C, Jensen LJ, Kuhn M, Chaffron S, Doerks T, Krüger B, Snel B, Bork P.

Nucleic Acids Res. 2007 Jan;35(Database issue):D358-62. Epub 2006 Nov 10.

5.

Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation.

Letunic I, Bork P.

Bioinformatics. 2007 Jan 1;23(1):127-8. Epub 2006 Oct 18.

PMID:
17050570
6.

Automatic clustering of orthologs and inparalogs shared by multiple proteomes.

Alexeyenko A, Tamas I, Liu G, Sonnhammer EL.

Bioinformatics. 2006 Jul 15;22(14):e9-15.

PMID:
16873526
7.

TreeFam: a curated database of phylogenetic trees of animal gene families.

Li H, Coghlan A, Ruan J, Coin LJ, Hériché JK, Osmotherly L, Li R, Liu T, Zhang Z, Bolund L, Wong GK, Zheng W, Dehal P, Wang J, Durbin R.

Nucleic Acids Res. 2006 Jan 1;34(Database issue):D572-80.

8.

From genomics to chemical genomics: new developments in KEGG.

Kanehisa M, Goto S, Hattori M, Aoki-Kinoshita KF, Itoh M, Kawashima S, Katayama T, Araki M, Hirakawa M.

Nucleic Acids Res. 2006 Jan 1;34(Database issue):D354-7.

9.

Pfam: clans, web tools and services.

Finn RD, Mistry J, Schuster-Böckler B, Griffiths-Jones S, Hollich V, Lassmann T, Moxon S, Marshall M, Khanna A, Durbin R, Eddy SR, Sonnhammer EL, Bateman A.

Nucleic Acids Res. 2006 Jan 1;34(Database issue):D247-51.

10.

Orthologs, paralogs, and evolutionary genomics.

Koonin EV.

Annu Rev Genet. 2005;39:309-38. Review.

PMID:
16285863
11.

Inparanoid: a comprehensive database of eukaryotic orthologs.

O'Brien KP, Remm M, Sonnhammer EL.

Nucleic Acids Res. 2005 Jan 1;33(Database issue):D476-80.

12.

SMART 4.0: towards genomic data integration.

Letunic I, Copley RR, Schmidt S, Ciccarelli FD, Doerks T, Schultz J, Ponting CP, Bork P.

Nucleic Acids Res. 2004 Jan 1;32(Database issue):D142-4.

13.

The COG database: an updated version includes eukaryotes.

Tatusov RL, Fedorova ND, Jackson JD, Jacobs AR, Kiryutin B, Koonin EV, Krylov DM, Mazumder R, Mekhedov SL, Nikolskaya AN, Rao BS, Smirnov S, Sverdlov AV, Vasudevan S, Wolf YI, Yin JJ, Natale DA.

BMC Bioinformatics. 2003 Sep 11;4:41. Epub 2003 Sep 11.

14.

OrthoMCL: identification of ortholog groups for eukaryotic genomes.

Li L, Stoeckert CJ Jr, Roos DS.

Genome Res. 2003 Sep;13(9):2178-89.

15.

Orthology, paralogy and proposed classification for paralog subtypes.

Sonnhammer EL, Koonin EV.

Trends Genet. 2002 Dec;18(12):619-20. No abstract available.

PMID:
12446146
16.

Cross-referencing eukaryotic genomes: TIGR Orthologous Gene Alignments (TOGA).

Lee Y, Sultana R, Pertea G, Cho J, Karamycheva S, Tsai J, Parvizi B, Cheung F, Antonescu V, White J, Holt I, Liang F, Quackenbush J.

Genome Res. 2002 Mar;12(3):493-502.

17.

Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.

Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G.

Nat Genet. 2000 May;25(1):25-9. No abstract available.

18.

A genomic perspective on protein families.

Tatusov RL, Koonin EV, Lipman DJ.

Science. 1997 Oct 24;278(5338):631-7. Review.

PMID:
9381173
19.

Distinguishing homologous from analogous proteins.

Fitch WM.

Syst Zool. 1970 Jun;19(2):99-113. No abstract available.

PMID:
5449325

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