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  1. Article

    Open Access

    RedundancyMiner: De-replication of redundant GO categories in microarray and proteomics analysis

    The Gene Ontology (GO) Consortium organizes genes into hierarchical categories based on biological process, molecular function and subcellular localization. Tools such as GoMiner can leverage GO to perform ont...

    Barry R Zeeberg, Hongfang Liu, Ari B Kahn, Martin Ehler… in BMC Bioinformatics (2011)

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  2. Article

    Open Access

    SpliceCenter: A suite of web-based bioinformatic applications for evaluating the impact of alternative splicing on RT-PCR, RNAi, microarray, and peptide-based studies

    Over 60% of protein-coding genes in vertebrates express mRNAs that undergo alternative splicing. The resulting collection of transcript isoforms poses significant challenges for contemporary biological assays....

    Michael C Ryan, Barry R Zeeberg, Natasha J Caplen, James A Cleland… in BMC Bioinformatics (2008)

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  3. Article

    Open Access

    VennMaster: Area-proportional Euler diagrams for functional GO analysis of microarrays

    Microarray experiments generate vast amounts of data. The functional context of differentially expressed genes can be assessed by querying the Gene Ontology (GO) database via GoMiner. Directed acyclic graph re...

    Hans A Kestler, André Müller, Johann M Kraus, Malte Buchholz… in BMC Bioinformatics (2008)

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  4. Article

    Open Access

    SpliceMiner: a high-throughput database implementation of the NCBI Evidence Viewer for microarray splice variant analysis

    There are many fewer genes in the human genome than there are expressed transcripts. Alternative splicing is the reason. Alternatively spliced transcripts are often specific to tissue type, developmental stage...

    Ari B Kahn, Michael C Ryan, Hongfang Liu, Barry R Zeeberg… in BMC Bioinformatics (2007)

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  5. Article

    Open Access

    High-Throughput GoMiner, an 'industrial-strength' integrative gene ontology tool for interpretation of multiple-microarray experiments, with application to studies of Common Variable Immune Deficiency (CVID)

    We previously developed GoMiner, an application that organizes lists of 'interesting' genes (for example, under-and overexpressed genes from a microarray experiment) for biological interpretation in the contex...

    Barry R Zeeberg, Haiying Qin, Sudarshan Narasimhan, Margot Sunshine… in BMC Bioinformatics (2005)

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  6. Article

    Open Access

    Mistaken Identifiers: Gene name errors can be introduced inadvertently when using Excel in bioinformatics

    When processing microarray data sets, we recently noticed that some gene names were being changed inadvertently to non-gene names.

    Barry R Zeeberg, Joseph Riss, David W Kane, Kimberly J Bussey… in BMC Bioinformatics (2004)

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