CEPCEB Members

Thomas Girke Assistant Professor of Bioinformatics/Assistant Bioinformaticist Department of Botany and Plant Sciences University of California Riverside, CA 92521 Phone: (951) 827-2469 Fax: (951) (909) 827-4437
Background Research Interests Publications (Bibliography page) Bioinformatics Core Homepage

Background

Our role is it to provide the Center for Plant Cell Biology in the UCR Genomics Institute with professional bioinformatics support. To deliver practical and user-friendly tools, we establish close interactions with other scientists in the center by offering research collaborations in areas, which can benefit from computational approaches. In addition, as part of the UCR Genomics Institute, we keep the local community informed about internal and external bioinformatics resources by organizing workshops and seminars. Furthermore, we maintain a functional bioinformatics infrastructure by administrating several networked terminals and server(s), which are dedicated to provide the center with state-of-the-art tools for high-throughput sequence analysis, project-specific data mining approaches, construction of relational databases and many other tasks.

Our extensive hands-on experience in plant molecular biology, biochemistry and functional genomics allows us to interpret computational results from modern genomics and proteomics projects in a broad biological context, to communicate the results clearly and efficiently, and to develop future experimental and/or bioinformatics projects from complex data sets. Our experimental expertise spectrum covers molecular cloning, library construction, targeted as well as random insertional mutagenesis in plants, molecular/biochemical gene characterization, microarray fabrication and automation of high-throughput projects with robotic devices. Our computational skills reach from database construction and large-scale sequence analysis to data mining of transcriptional profiling experiments using microarrays and DNA chips. Dr. Thomas Girke a full-time Academic Coordinator, who conducted his graduate and postdoctoral research in the areas of plant lipid metabolism and transcriptional profiling, supervises the Core.

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Research Interests

Due to the collaborative nature of our work, we focus our projects preferentially towards the bioinformatics needs in other groups. In addition to group-specific projects, we are interested in developing data mining tools and databases, which are of general interest to most researchers in the center and represent a discovery resource for future projects. These general applications are tools to mine various functional aspects of partially or entirely sequenced plant genomes as those from Arabidopsis, rice and others. Here we envision user-friendly applications to model/reconstruct metabolic and signaling pathways, to identify common promoter elements of co-regulated genes based on RNA profiling data, to discover signals for RNA or protein stability, to predict subcellular localizations of proteins and to integrate databases from different research disciplines.

Publications (Bibliography page)

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