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    BMCBI
    2007
    120views more  BMCBI 2007»
    Transcript-based redefinition of grouped oligonucleotide probe sets using AceView: High-resolution annotation for microarrays
    14 years 14 days ago
    Transcript-based redefinition of grouped oligonucleotide probe sets using AceView: High-resolution annotation for microarrays
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    Background: Extracting biological information from high-density Affymetrix arrays is a multi-step process that begins with the accurate annotation of microarray probes. Shortfalls...
    Jun Lu, Joseph C. Lee, Marc L. Salit, Margaret C. ...
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    BMCBI
    2007
    144views more  BMCBI 2007»
    InPrePPI: an integrated evaluation method based on genomic context for predicting protein-protein interactions in prokaryotic ge
    14 years 14 days ago
    InPrePPI: an integrated evaluation method based on genomic context for predicting protein-protein interactions in prokaryotic ge
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    Background: Although many genomic features have been used in the prediction of proteinprotein interactions (PPIs), frequently only one is used in a computational method. After rea...
    Jingchun Sun, Yan Sun, Guohui Ding, Qi Liu, Chuan ...
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    BMCBI
    2007
    124views more  BMCBI 2007»
    BranchClust: a phylogenetic algorithm for selecting gene families
    14 years 14 days ago
    BranchClust: a phylogenetic algorithm for selecting gene families
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    Background: Automated methods for assembling families of orthologous genes include those based on sequence similarity scores and those based on phylogenetic approaches. The first ...
    Maria S. Poptsova, J. Peter Gogarten
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    BMCBI
    2007
    77views more  BMCBI 2007»
    Estimation of the number of extreme pathways for metabolic networks
    14 years 14 days ago
    Estimation of the number of extreme pathways for metabolic networks
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    Matthew Yeung, Ines Thiele, Bernhard O. Palsson
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    BMCBI
    2007
    77views more  BMCBI 2007»
    The reactive metabolite target protein database (TPDB) - a web-accessible resource
    14 years 14 days ago
    The reactive metabolite target protein database (TPDB) - a web-accessible resource
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    Background: The toxic effects of many simple organic compounds stem from their biotransformation to chemically reactive metabolites which bind covalently to cellular proteins. To ...
    Robert P. Hanzlik, Yakov M. Koen, Bhargav Theertha...
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    BMCBI
    2007
    148views more  BMCBI 2007»
    Computation of significance scores of unweighted Gene Set Enrichment Analyses
    14 years 14 days ago
    Computation of significance scores of unweighted Gene Set Enrichment Analyses
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    Background: Gene Set Enrichment Analysis (GSEA) is a computational method for the statistical evaluation of sorted lists of genes or proteins. Originally GSEA was developed for in...
    Andreas Keller, Christina Backes, Hans-Peter Lenho...
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    BMCBI
    2007
    142views more  BMCBI 2007»
    SABERTOOTH: protein structural alignment based on a vectorial structure representation
    14 years 14 days ago
    SABERTOOTH: protein structural alignment based on a vectorial structure representation
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    Background: The task of computing highly accurate structural alignments of proteins in very short computation time is still challenging. This is partly due to the complexity of pr...
    Florian Teichert, Ugo Bastolla, Markus Porto
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    BMCBI
    2007
    154views more  BMCBI 2007»
    h-Profile plots for the discovery and exploration of patterns in gene expression data with an application to time course data
    14 years 14 days ago
    h-Profile plots for the discovery and exploration of patterns in gene expression data with an application to time course data
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    Background: An ever increasing number of techniques are being used to find genes with similar profiles from microarray studies. Visualization of gene expression profiles can aid t...
    Yvonne E. Pittelkow, Susan R. Wilson
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    BMCBI
    2007
    100views more  BMCBI 2007»
    Discovering structural motifs using a structural alphabet: Application to magnesium-binding sites
    14 years 14 days ago
    Discovering structural motifs using a structural alphabet: Application to magnesium-binding sites
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    Background: For many metalloproteins, sequence motifs characteristic of metal-binding sites have not been found or are so short that they would not be expected to be metal-specifi...
    Minko Dudev, Carmay Lim
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    BMCBI
    2007
    169views more  BMCBI 2007»
    The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats
    14 years 14 days ago
    The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats
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    Background: In Archeae and Bacteria, the repeated elements called CRISPRs for "clustered regularly interspaced short palindromic repeats" are believed to participate in ...
    Ibtissem Grissa, Gilles Vergnaud, Christine Pource...
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