9 Result(s)
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Article
John N Weinstein
Life Sciences
Computer Appl. in Life Sciences
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Article
Open AccessElemCor: accurate data analysis and enrichment calculation for high-resolution LC-MS stable isotope labeling experiments
The investigation of intracellular metabolism is the mainstay in the biotechnology and physiology settings. Intracellular metabolic rates are commonly evaluated using labeling pattern of the identified metabol...
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Open AccessRedundancyMiner: 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...
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Open AccessSpliceCenter: 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....
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Open AccessVennMaster: 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...
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Open AccessSpliceMiner: 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...
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Open AccessAbMiner: A bioinformatic resource on available monoclonal antibodies and corresponding gene identifiers for genomic, proteomic, and immunologic studies
Monoclonal antibodies are used extensively throughout the biomedical sciences for detection of antigens, either in vitro or in vivo. We, for example, have used them for quantitation of proteins on "reverse-phase"...
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Open AccessHigh-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...
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Open AccessQuality assessment of microarrays: Visualization of spatial artifacts and quantitation of regional biases
Quality-control is an important issue in the analysis of gene expression microarrays. One type of problem is regional bias, in which one region of a chip shows artifactually high or low intensities (or ratios ...
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Open AccessMistaken 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.
