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Items 1 - 20 of 208
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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]

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]

4:

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]

5:

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]

6:

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]

7:

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]

8:

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]

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]

10:

Identification of functional links between genes using phylogenetic profiles.

Wu J, Kasif S, DeLisi C.

Bioinformatics. 2003 Aug 12;19(12):1524-30.

PMID: 12912833 [PubMed - indexed for MEDLINE]

11:

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]

12:

From co-expression to co-regulation: how many microarray experiments do we need?

Yeung KY, Medvedovic M, Bumgarner RE.

Genome Biol. 2004;5(7):R48. Epub 2004 Jun 28.

PMID: 15239833 [PubMed - indexed for MEDLINE]

13:

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]

14:

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]

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]

16:

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]

17:

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]

18:

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]

19:

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]

20:

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]

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