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    Results: 15

    1.

    CycADS: an annotation database system to ease the development and update of BioCyc databases.

    Vellozo AF, Véron AS, Baa-Puyoulet P, Huerta-Cepas J, Cottret L, Febvay G, Calevro F, Rahbé Y, Douglas AE, Gabaldón T, Sagot MF, Charles H, Colella S.

    Database (Oxford). 2011 Apr 7;2011:bar008. Print 2011.

    PMID:
    21474551
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    2.

    Phylemon 2.0: a suite of web-tools for molecular evolution, phylogenetics, phylogenomics and hypotheses testing.

    Sánchez R, Serra F, Tárraga J, Medina I, Carbonell J, Pulido L, de María A, Capella-Gutíerrez S, Huerta-Cepas J, Gabaldón T, Dopazo J, Dopazo H.

    Nucleic Acids Res. 2011 Jul;39(Web Server issue):W470-4. Epub 2011 Jun 6.

    PMID:
    21646336
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    3.

    Evidence for short-time divergence and long-time conservation of tissue-specific expression after gene duplication.

    Huerta-Cepas J, Dopazo J, Huynen MA, Gabaldón T.

    Brief Bioinform. 2011 Sep;12(5):442-8. Epub 2011 Apr 22.

    PMID:
    21515902
    [PubMed - indexed for MEDLINE]
    4.

    Assigning duplication events to relative temporal scales in genome-wide studies.

    Huerta-Cepas J, Gabaldón T.

    Bioinformatics. 2011 Jan 1;27(1):38-45. Epub 2010 Nov 11.

    PMID:
    21075746
    [PubMed - indexed for MEDLINE]
    Free Article
    5.

    PhylomeDB v3.0: an expanding repository of genome-wide collections of trees, alignments and phylogeny-based orthology and paralogy predictions.

    Huerta-Cepas J, Capella-Gutierrez S, Pryszcz LP, Denisov I, Kormes D, Marcet-Houben M, Gabaldón T.

    Nucleic Acids Res. 2011 Jan;39(Database issue):D556-60. Epub 2010 Nov 12.

    PMID:
    21075798
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    6.

    MetaPhOrs: orthology and paralogy predictions from multiple phylogenetic evidence using a consistency-based confidence score.

    Pryszcz LP, Huerta-Cepas J, Gabaldón T.

    Nucleic Acids Res. 2011 Mar;39(5):e32. Epub 2010 Dec 11.

    PMID:
    21149260
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    7.

    The pea aphid phylome: a complete catalogue of evolutionary histories and arthropod orthology and paralogy relationships for Acyrthosiphon pisum genes.

    Huerta-Cepas J, Marcet-Houben M, Pignatelli M, Moya A, Gabaldón T.

    Insect Mol Biol. 2010 Mar;19 Suppl 2:13-21.

    PMID:
    20482636
    [PubMed - indexed for MEDLINE]
    8.

    Fine-scale evolution: genomic, phenotypic and ecological differentiation in two coexisting Salinibacter ruber strains.

    Peña A, Teeling H, Huerta-Cepas J, Santos F, Yarza P, Brito-Echeverría J, Lucio M, Schmitt-Kopplin P, Meseguer I, Schenowitz C, Dossat C, Barbe V, Dopazo J, Rosselló-Mora R, Schüler M, Glöckner FO, Amann R, Gabaldón T, Antón J.

    ISME J. 2010 Jul;4(7):882-95. Epub 2010 Feb 18.

    PMID:
    20164864
    [PubMed - indexed for MEDLINE]
    9.

    ETE: a python Environment for Tree Exploration.

    Huerta-Cepas J, Dopazo J, Gabaldón T.

    BMC Bioinformatics. 2010 Jan 13;11:24.

    PMID:
    20070885
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    10.

    PhylomeDB: a database for genome-wide collections of gene phylogenies.

    Huerta-Cepas J, Bueno A, Dopazo J, Gabaldón T.

    Nucleic Acids Res. 2008 Jan;36(Database issue):D491-6. Epub 2007 Oct 25.

    PMID:
    17962297
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    11.

    Interoperability with Moby 1.0--it's better than sharing your toothbrush!

    BioMoby Consortium, Wilkinson MD, Senger M, Kawas E, Bruskiewich R, Gouzy J, Noirot C, Bardou P, Ng A, Haase D, Saiz Ede A, Wang D, Gibbons F, Gordon PM, Sensen CW, Carrasco JM, Fernández JM, Shen L, Links M, Ng M, Opushneva N, Neerincx PB, Leunissen JA, Ernst R, Twigger S, Usadel B, Good B, Wong Y, Stein L, Crosby W, Karlsson J, Royo R, Párraga I, Ramírez S, Gelpi JL, Trelles O, Pisano DG, Jimenez N, Kerhornou A, Rosset R, Zamacola L, Tarraga J, Huerta-Cepas J, Carazo JM, Dopazo J, Guigo R, Navarro A, Orozco M, Valencia A, Claros MG, Pérez AJ, Aldana J, Rojano MM, Fernandez-Santa Cruz R, Navas I, Schiltz G, Farmer A, Gessler D, Schoof H, Groscurth A.

    Brief Bioinform. 2008 May;9(3):220-31. Epub 2008 Jan 31. Review.

    PMID:
    18238804
    [PubMed - indexed for MEDLINE]
    Free Article
    12.

    PhylomeDB: a database for genome-wide collections of gene phylogenies.

    Huerta-Cepas J, Bueno A, Dopazo J, Gabaldón T.

    Nucleic Acids Res. 2008 Jan;36(Database issue):D491-6. Epub 2007 Oct 25.

    PMID:
    17962297
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    13.

    PeroxisomeDB: a database for the peroxisomal proteome, functional genomics and disease.

    Schlüter A, Fourcade S, Domènech-Estévez E, Gabaldón T, Huerta-Cepas J, Berthommier G, Ripp R, Wanders RJ, Poch O, Pujol A.

    Nucleic Acids Res. 2007 Jan;35(Database issue):D815-22. Epub 2006 Nov 28.

    PMID:
    17135190
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    14.

    The human phylome.

    Huerta-Cepas J, Dopazo H, Dopazo J, Gabaldón T.

    Genome Biol. 2007;8(6):R109.

    PMID:
    17567924
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    15.

    Phylemon: a suite of web tools for molecular evolution, phylogenetics and phylogenomics.

    Tárraga J, Medina I, Arbiza L, Huerta-Cepas J, Gabaldón T, Dopazo J, Dopazo H.

    Nucleic Acids Res. 2007 Jul;35(Web Server issue):W38-42. Epub 2007 Apr 22.

    PMID:
    17452346
    [PubMed - indexed for MEDLINE]
    Free PMC Article

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