-
Article
Open AccessNonlinear gene cluster analysis with labeling for microarray gene expression data in organ development
The gene networks underlying closure of the optic fissure during vertebrate eye development are not well-understood. We use a novel clustering method based on nonlinear dimension reduction with data labeling t...
-
Article
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...
-
Article
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....
-
Article
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...
-
Article
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...
-
Article
Nova regulates brain-specific splicing to shape the synapse
Alternative RNA splicing greatly increases proteome diversity and may thereby contribute to tissue-specific functions. We carried out genome-wide quantitative analysis of alternative splicing using a custom Af...
-
Article
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...
-
Article
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.
-
Article
Open AccessGoMiner: a resource for biological interpretation of genomic and proteomic data
We have developed GoMiner, a program package that organizes lists of 'interesting' genes (for example, under- and overexpressed genes from a microarray experiment) for biological interpretation in the context ...
-
Article
Theoretical effects of radioligand diffusional gradients and microscopic neuroreceptor distribution inin vivo kinetic studies
A simplified one-dimensional model system was used to test the possibility that physically realistic parameters would lead to the prediction of microscopic heterogeneity of radioligand distribution in the brai...
-
Chapter
A Theoretically-Correct Algorithm to Compensate for a Three-Dimensional Spatially-Variant Point Spread Function in Spect Imaging
Three factors which degrade positional information and the quantitative potential of single photon emission computed tomography (SPECT) are finite detector size, Compton scatter, and the detector point spread ...
-
Article
Analysis of three- and four-compartment models forin vivo radioligand-neuroreceptor interaction
Currently applied three-copartment models for analyzing kinetic data derived fromin vivo positron emission tomographic (PET) studies of radioligand-neuroreceptor interactions require assumptions which may not be ...
