University of Louisville,
Cardiovascular Innovation Institute
Using the bioinformatics tools developed in our lab combined with biological experiments, our research goal is to uncover the functions of lncRNAs. In last few years, we have developed a number of bioinformatics tools:
- “ANGIOGENES” for expression profiles of transcripts in endothelial cells
- “C-It” for evolutionary-conserved, tissue-enriched, uncharacterized genes
- “C-It-Loci” for evolutionary-conserved, tissue-enriched, protein-coding genes and lncRNAs
- “Exon Array Analyzer (EAA)” for analyzing GeneChip Exon 1.0 ST Arrays (Affymetrix, Inc.)
- “Gene Array Analyzer (GAA)” for analyzing GeneChip Gene 1.0 ST Arrays (Affymetrix, Inc.)
- “noncoder” for quantifying the expression changes of lncRNAs and protein-coding genes from GeneChip Exon 1.0 ST Arrays (Affymetrix, Inc.)
- “RenalDB” for in silico screening of enriched/specific transcripts of humans, mice, and zebrafish with respect to nephrotic tissues and cells, developmental stages, and other metadata.
- “RNAEditor” for analyzing RNA editing sites and islands from RNA-seq data
- “SNP4Disease” for disease-related and/or -suspected SNPs
- “UGAHash” for mapping human genomic features among various bioinformatics databases and versions of databases
Bioinformatics, Cardiovascular, Database, Disease, long non-coding RNA, Muscle, RNA Editing, RNA Modification, Stem Cells.
Selected publications on ncRNA and cardiovascular disease
ANGIOGENES: knowledge database for protein-coding and noncoding RNA genes in endothelial cells
Müller R, Weirick T, John D, Militello G, Chen W, Dimmeler S, Uchida S. Sci Rep. 2016, 6:32475.
Identification and Characterization of Hypoxia-Regulated Endothelial Circular RNA
Boeckel JN, Jaé N, Heumüller AW, Chen W, Boon RA, Stellos K, Zeiher AM, John D, Uchida S, Dimmeler S. Circ Res. 2015, 117(10):884-90.
Long noncoding RNA MALAT1 regulates endothelial cell function and vessel growth
Michalik KM, You X, Manavski Y, Doddaballapur A, Zörnig M, Braun T, John D, Ponomareva Y, Chen W, Uchida S, Boon RA, Dimmeler S. Circ Res. 2014, 114(9):1389-97.
Noncoder: a web interface for exon array-based detection of long non-coding RNAs
Gellert P, Ponomareva Y, Braun T, Uchida S. Nucleic Acids Res. 2013, 41(1):e20.