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Girke, Thomas
Personal Web Site
thomas.girke@ucr.edu

1207F GENOMICS BUILDING
University of California
Riverside, CA 92521

(951) 905-5232 (Voice)

    Girke, Thomas

    Assoc. Professor of Bioinformatics & Assoc. Bioinformaticist

    College of Natural and Agricultural Sciences
    Botany & Plant Sciences

    Biography

     Academic Coordinator in Bioinformatics - Analysis of genomes, mRNA profiling data, protein families and small molecule libraries for chemical genomics screens

    Degrees

    PHD Plant Biochemistry & Molecular Biology 1998
    University of Hamburg

    Awards

    Doctoral fellowship, German Research Association, DFG (1996-1998) Ph.D. thesis with Honors - University Hamburg (1998) Postdoctoral fellowship, Max Kade Foundation (1998-1999). Best Plant Physiology paper of the year award in 2001 for publication "G

    Research Area

    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

    9.Heilmann I., M. Pidkowich, T. Girke & J. Shanklin. 2004 Switching desaturase enzyme specificity by alternate subcellular targeting. Proc Natl Acad Sci U S A 101: 10266-10271.

    10.Girke T., J. Lauricha, H. Tran, K. Keegstra & N. Raikhel. 2004. The Cell Wall Navigator Database: Organism-Unrestricted Mining of Protein Families Involved in Cell Wall Metabolism. Plant Physiol. 136: 3003-3008.

    11.Carter C., S. Pan, J. Zouhar, E. Avila, T. Girke, and N. Raikhel. 2004. Comprehensive analysis of the Arabidopsis thaliana vegetative vacuole proteome. Plant Cell 16: 3285-303.

    12.Sunkar, R., Girke, T., Kumar Jain, P. & JK. Zhu. 2005. Cloning and characterization of microRNAs from rice. Plant Cell, 17, 1397–1411.

    13.Horan, K., Lauricha, J., Bailey-Serres, J., Raikhel, N. & T. Girke. 2005. Genome Cluster Database: A Sequence Family Analysis Platform for Arabidopsis and rice. Plant Physiol. 138: 47-54.

    14.Girke T., LC. Cheng & N. Raikhel. 2005. ChemMine: A Compound Mining Database for Chemical Genomics. Plant Physiol. 138: 573-577.

    15.Sunkar R., T. Girke & JK. Zhu. 2005. Identification and characterization of endogenous small interfering RNAs from rice. Nucleic Acids Res. 33: 4443-4454.

    16. Gollery, M., Harper, J., Cushman, J., Mittler, T., Girke, T., Zhu, J., Bailey-Serres, J., Mittler, R. 2006. What makes species unique? The contribution of proteins with obscure features. Genome Biology. Vol. 7: 7 p.R57.1-R54.8. 8p. (Refereed)
    Website: http://www.hubmed.org/fulltext.cgi?uids=16859532

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