Department of Pharmacology
Department of Neuroscience
College of Medicine
Research Interests: The research interests of the Rotter laboratory center on the application of bioinformatics and computational biology. This application includes the analysis of genome sequences encoding novel molecules related to neural signal transduction, cell adhesion and cell recognition.
Current Research: Data mining activities rely on a variety of computer algorithms used to search public and private databases for homologs and orthologs of ligand-gated ion channels and receptor protein tyrosine phosphatases (RPTPs). Of particular interest is a novel RPTP (RPTPr) that is expressed exclusively in the central nervous system (CNS). This phosphatase is developmentally regulated and its expression delineates a unique anterior-posterior boundary in the cerebellar granule cell layer.
Computational gene-finding programs are used to define functional sites that encode elements of RPTP gene structure (exon/intron organization), regulation and transcription. Comparisons with homology domains catalogued in a number of databases are used to make functional assignments and to predict putative 3-D structure. Alignments of orthologous sequences from a variety of different species (human, mouse, bovine and zebrafish) — using several phylogenetic reconstruction algorithms — are used as the basis for phylogenetic analysis and comparative genomics. The information generated by the approaches described above is used to design experiments aimed at confirming the computational predictions.
Degree: National Institute for Medical Research, Mill Hill, UK
Postdoctoral: National Institutes of Health (NIH), Bethesda, MD