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    Results: 1 to 20 of 180

    1.

    Detection of evolutionarily stable fragments of cellular pathways by hierarchical clustering of phyletic patterns.

    Glazko GV, Mushegian AR.

    Genome Biol. 2004;5(5):R32. Epub 2004 Apr 27.

    PMID:
    15128446
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    2.

    Quantifying modularity in the evolution of biomolecular systems.

    Snel B, Huynen MA.

    Genome Res. 2004 Mar;14(3):391-7.

    PMID:
    14993205
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    4.

    Detection of biochemical pathways by probabilistic matching of phyletic vectors.

    Li H, Kristensen DM, Coleman MK, Mushegian A.

    PLoS One. 2009;4(4):e5326. Epub 2009 Apr 24.

    PMID:
    19390636
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    5.

    A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes.

    Koonin EV, Fedorova ND, Jackson JD, Jacobs AR, Krylov DM, Makarova KS, Mazumder R, Mekhedov SL, Nikolskaya AN, Rao BS, Rogozin IB, Smirnov S, Sorokin AV, Sverdlov AV, Vasudevan S, Wolf YI, Yin JJ, Natale DA.

    Genome Biol. 2004;5(2):R7. Epub 2004 Jan 15.

    PMID:
    14759257
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    6.

    Evolution of gene fusions: horizontal transfer versus independent events.

    Yanai I, Wolf YI, Koonin EV.

    Genome Biol. 2002;3(5):research0024. Epub 2002 Apr 26.

    PMID:
    12049665
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    7.

    Discovering functional linkages and uncharacterized cellular pathways using phylogenetic profile comparisons: a comprehensive assessment.

    Jothi R, Przytycka TM, Aravind L.

    BMC Bioinformatics. 2007 May 23;8:173.

    PMID:
    17521444
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    8.

    Persistence drives gene clustering in bacterial genomes.

    Fang G, Rocha EP, Danchin A.

    BMC Genomics. 2008 Jan 7;9:4.

    PMID:
    18179692
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    9.

    Automatic detection of conserved gene clusters in multiple genomes by graph comparison and P-quasi grouping.

    Fujibuchi W, Ogata H, Matsuda H, Kanehisa M.

    Nucleic Acids Res. 2000 Oct 15;28(20):4029-36.

    PMID:
    11024184
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    10.

    Comparative analysis of chloroplast genomes: functional annotation, genome-based phylogeny, and deduced evolutionary patterns.

    De Las Rivas J, Lozano JJ, Ortiz AR.

    Genome Res. 2002 Apr;12(4):567-83.

    PMID:
    11932241
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    11.

    Genomic gene clustering analysis of pathways in eukaryotes.

    Lee JM, Sonnhammer EL.

    Genome Res. 2003 May;13(5):875-82. Epub 2003 Apr 14. Erratum in: Genome Res. 2004 Dec;14(12):2510.

    PMID:
    12695325
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    12.

    Integrating genomic data to predict transcription factor binding.

    Holloway DT, Kon M, DeLisi C.

    Genome Inform. 2005;16(1):83-94.

    PMID:
    16362910
    [PubMed - indexed for MEDLINE]
    13.

    COCO-CL: hierarchical clustering of homology relations based on evolutionary correlations.

    Jothi R, Zotenko E, Tasneem A, Przytycka TM.

    Bioinformatics. 2006 Apr 1;22(7):779-88. Epub 2006 Jan 24.

    PMID:
    16434444
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    14.

    Exploring the conditional coregulation of yeast gene expression through fuzzy k-means clustering.

    Gasch AP, Eisen MB.

    Genome Biol. 2002 Oct 10;3(11):RESEARCH0059. Epub 2002 Oct 10.

    PMID:
    12429058
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    15.

    Selection of informative clusters from hierarchical cluster tree with gene classes.

    Toronen P.

    BMC Bioinformatics. 2004 Mar 25;5:32.

    PMID:
    15043761
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    16.

    Judging the quality of gene expression-based clustering methods using gene annotation.

    Gibbons FD, Roth FP.

    Genome Res. 2002 Oct;12(10):1574-81.

    PMID:
    12368250
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    17.

    Influence of microarrays experiments missing values on the stability of gene groups by hierarchical clustering.

    de Brevern AG, Hazout S, Malpertuy A.

    BMC Bioinformatics. 2004 Aug 23;5:114.

    PMID:
    15324460
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    18.

    Clustering gene expression data using adaptive double self-organizing map.

    Ressom H, Wang D, Natarajan P.

    Physiol Genomics. 2003 Jun 24;14(1):35-46.

    PMID:
    12672901
    [PubMed - indexed for MEDLINE]
    19.

    Comparing bacterial genomes through conservation profiles.

    Martin MJ, Herrero J, Mateos A, Dopazo J.

    Genome Res. 2003 May;13(5):991-8. Epub 2003 Apr 14.

    PMID:
    12695324
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    20.

    The balance of driving forces during genome evolution in prokaryotes.

    Kunin V, Ouzounis CA.

    Genome Res. 2003 Jul;13(7):1589-94.

    PMID:
    12840037
    [PubMed - indexed for MEDLINE]
    Free PMC Article

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