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    BMCBI
    2007
    112views more  BMCBI 2007»
    Inferring biological functions and associated transcriptional regulators using gene set expression coherence analysis
    14 years 14 days ago
    Inferring biological functions and associated transcriptional regulators using gene set expression coherence analysis
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    Background: Gene clustering has been widely used to group genes with similar expression pattern in microarray data analysis. Subsequent enrichment analysis using predefined gene s...
    Tae-Min Kim, Yeun-Jun Chung, Mun-Gan Rhyu, Myeong ...
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    BMCBI
    2007
    182views more  BMCBI 2007»
    Identifying regulatory targets of cell cycle transcription factors using gene expression and ChIP-chip data
    14 years 14 days ago
    Identifying regulatory targets of cell cycle transcription factors using gene expression and ChIP-chip data
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    Background: ChIP-chip data, which indicate binding of transcription factors (TFs) to DNA regions in vivo, are widely used to reconstruct transcriptional regulatory networks. Howev...
    Wei-Sheng Wu, Wen-Hsiung Li, Bor-Sen Chen
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    BMCBI
    2007
    163views more  BMCBI 2007»
    Use of genomic DNA control features and predicted operon structure in microarray data analysis: ArrayLeaRNA - a Bayesian approac
    14 years 14 days ago
    Use of genomic DNA control features and predicted operon structure in microarray data analysis: ArrayLeaRNA - a Bayesian approac
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    Background: Microarrays are widely used for the study of gene expression; however deciding on whether observed differences in expression are significant remains a challenge. Resul...
    Carmen Pin, Mark Reuter
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    BMCBI
    2007
    128views more  BMCBI 2007»
    Combining classifiers to predict gene function in Arabidopsis thaliana using large-scale gene expression measurements
    14 years 14 days ago
    Combining classifiers to predict gene function in Arabidopsis thaliana using large-scale gene expression measurements
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    Background: Arabidopsis thaliana is the model species of current plant genomic research with a genome size of 125 Mb and approximately 28,000 genes. The function of half of these ...
    Hui Lan, Rachel Carson, Nicholas J. Provart, Antho...
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    BMCBI
    2007
    216views more  BMCBI 2007»
    A replica exchange Monte Carlo algorithm for protein folding in the HP model
    14 years 14 days ago
    A replica exchange Monte Carlo algorithm for protein folding in the HP model
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    Background: The ab initio protein folding problem consists of predicting protein tertiary structure from a given amino acid sequence by minimizing an energy function; it is one of...
    Chris Thachuk, Alena Shmygelska, Holger H. Hoos
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    BMCBI
    2007
    127views more  BMCBI 2007»
    Predicting the phenotypic effects of non-synonymous single nucleotide polymorphisms based on support vector machines
    14 years 14 days ago
    Predicting the phenotypic effects of non-synonymous single nucleotide polymorphisms based on support vector machines
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    Background: Human genetic variations primarily result from single nucleotide polymorphisms (SNPs) that occur approximately every 1000 bases in the overall human population. The no...
    Jian Tian, Ningfeng Wu, Xuexia Guo, Jun Guo, Juhua...
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    BMCBI
    2007
    166views more  BMCBI 2007»
    How to decide which are the most pertinent overly-represented features during gene set enrichment analysis
    14 years 14 days ago
    How to decide which are the most pertinent overly-represented features during gene set enrichment analysis
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    Background: The search for enriched features has become widely used to characterize a set of genes or proteins. A key aspect of this technique is its ability to identify correlati...
    Roland Barriot, David J. Sherman, Isabelle Dutour
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    BMCBI
    2007
    142views more  BMCBI 2007»
    Support Vector Machine-based method for predicting subcellular localization of mycobacterial proteins using evolutionary informa
    14 years 14 days ago
    Support Vector Machine-based method for predicting subcellular localization of mycobacterial proteins using evolutionary informa
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    Background: In past number of methods have been developed for predicting subcellular location of eukaryotic, prokaryotic (Gram-negative and Gram-positive bacteria) and human prote...
    Mamoon Rashid, Sudipto Saha, Gajendra P. S. Raghav...
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    BMCBI
    2007
    149views more  BMCBI 2007»
    Identification of tissue-specific cis-regulatory modules based on interactions between transcription factors
    14 years 14 days ago
    Identification of tissue-specific cis-regulatory modules based on interactions between transcription factors
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    Background: Evolutionary conservation has been used successfully to help identify cis-acting DNA regions that are important in regulating tissue-specific gene expression. Motivate...
    Xueping Yu, Jimmy J. Lin, Donald J. Zack, Jiang Qi...
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    BMCBI
    2007
    140views more  BMCBI 2007»
    Accurate prediction of protein secondary structure and solvent accessibility by consensus combiners of sequence and structure in
    14 years 14 days ago
    Accurate prediction of protein secondary structure and solvent accessibility by consensus combiners of sequence and structure in
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    Background: Structural properties of proteins such as secondary structure and solvent accessibility contribute to three-dimensional structure prediction, not only in the ab initio...
    Gianluca Pollastri, Alberto J. M. Martin, Catherin...
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