Dr. Michael Gribskov

San Diego Supercomputer Center • UCSD • 9500 Gilman Drive • La Jolla CA 92093-0537
VOICE: 858.534.8312 • gribskov@sdsc.edu • http://www.sdsc.edu/~gribskov • FAX: 858.822.0873

Professional Experience	1999- Present	Adjunct Associate Professor of Biology University of California, San Diego
	1996- Present	Senior Staff Scientist San Diego Supercomputer Center
	1993-1999	Adjunct Assistant Professor of Biology University of California, San Diego
	1994- Present	UCSD Academic Senate Campus Committee on Computing
	1993-1996	Principal Scientist San Diego Supercomputer Center
	1992	Staff Scientist San Diego Supercomputer Center
	1988 - 1992	Scientist Associate National Cancer Institute--FCRDC
	1985 - 1988	American Cancer Society post-doctoral fellowship University of California - Los Angeles
	1979 - 1985	Research assistantship & NIH training grant University of Wisconsin-Madison

Education	1985	Ph.D. in Molecular Biology University of Wisconsin-Madison
	1979	B.S. with Honors in Biochemistry and Biophysics Oregon State University

Professional Activities	Editorial Board - Bioinformatics (formerly CABIOS) Editorial Board - Computers and Chemistry Editorial Board - Journal of Molecular Microbiology & Biotechnology Vice President – International Society for Computational Biology Chairman, Scientific Advisory Board - Protein Information Resource (PIR)
	2001	Organizing committee member - 9^th International Conference on Intelligent Systems for Molecular Biology (ISMB)
	2000	NIH Biophysics Peer Review Panel
	2000	NSF EPSCOR Peer Review Panel
	2000	Organizing committee co-chairman – 8^th International Conference on Intelligent Systems for Molecular Biology (ISMB)
	1993 - 1999	Program committee - 1^st – 7^th International Conferences on Intelligent Systems for Molecular Biology (ISMB)
Professional Activities (Continued)	1999, 1994, 1992	DOE Human Genome Review Panel
	2000, 1999, 1997, 1996	NIH Genome Informatics, Peer Review Panel
	1994	DOE Computational Genome Analysis Chairman, Peer Review panel
	1991	Co-chairman -- Summer School Planning Group NLM-NSF Intelligent Systems in Molecular Biology Workshop
	Manuscript Reviewer	Critical Reviews in Biochemistry and Molecular Biology European Journal of Biochemistry Genomics Hawaiian International Conference on Complex Systems Journal of Computational Biology Journal of Molecular Biology Journal of Supercomputer Applications Nucleic Acids Research Pacific Symposium on Biocomputing Proceedings of the National Academy of Sciences Protein Science Science
	Member	American Association for the Advancement of Science International Society for Computational Biology Protein Society Society for Mathematical Biology

Recent Grants and Awards

• Functional Genomics of Plant Phosphorylation”

  PI: John C. Walker, University of Missouri

  Co-PI: Michael Gribskov (20% effort)

  NSF DBI-9975808 Period: 09/01/99 - 08/31/02

  Isolate genetic knockouts for every kinase and phosphatase genes in Arabidopsis; construct an online database for functional annotation of all phosphorylation related genes.

• National Biomedical Computation Resource”

  PI: Peter Arzberger, UCSD

  Director/Core 2: Michael Gribskov (20% effort)

  NIH P41 RR-08605 Years: 06-10 Period: 04/15/99 - 04/14/04

  Research Resource providing advanced computational support for biomedical researchers.

• Cancer Classification Based On RNA Isoforms”

  PI: Fu, Xiang-Dong, UCSD

  Co-Investigator: Michael Gribskov (10% effort)

  NIH, proposed Period: 07/01/00-06/30/04

  Initial Budget Period: $125,976 TDC, Entire Period of Support: $2,520,356

  Development of experimental and computational techniques for the analysis of alternative RNA splicing, and use of splicing isoforms in diagnosis, classification, and treatment of cancer.

• Network Support for NSF Plant Genome Project”

  PI: Michael Gribskov

  NSF: DBI, Period: 07/01/00 – 06/30/02

  Budget for Entire Period: $65,602 (Direct)

Publications

Gross, C., Burton, Z., Gribskov, M., Grossman, A., Liebke, H., Taylor, W., Walter, W., and Burgess, R.R., Genetic, functional and structural analysis of E. coli RNA polymerase sigma subunit: A heat shock protein, in Promoters - Structure and Function, Rodriguez, R.L., and Chamberlin, M.J. eds., New York, Praeger, 1983.

Burgess, R.R., Burton, Z., Gross, C., Taylor, W., and Gribskov, M., Structure and regulatory features of a complex operon encoding E. coli ribosomal protein S21, DNA primase, and the RNA polymerase sigma subunit, in Gene Expression, New York, Alan R. Liss, pp 387-401, 1983.

Gribskov, M. and Burgess, R.R., Overexpression and purification of the sigma subunit of E. coli RNA polymerase, Gene 26, 109-118, 1983.

Gribskov, M., Devereux, J., and Burgess, R.R., The codon preference plot: graphic analysis of protein coding sequences and prediction of gene expression, Nucleic Acids Research 12, 359-549, 1984.

Gribskov, M., Burgess, R.R., and Devereux, J., PEPPLOT, a protein secondary structure analysis program for the UWGCG sequence analysis software package., Nucleic Acids Research 14, 327-334, 1986.

Gribskov, M., and Burgess, R.R., Sigma factors from E. coli, B. subtilis, phage SPO1, and phage T4 are homologous proteins., Nucleic Acids Research 14, 6745-6763, 1986.

Burgess, R.R., Erickson, B., Gentry, D., Gribskov, M., Hager, D., Lesley, S., Strickland, M., Thompson, N., Bacterial RNA polymerase subunits and genes, in Steenbock Symposium, University of Wisconsin, Madison, WI, 1986.

Gribskov, M., McLachlan, A.D., and Eisenberg, D., Profile analysis: detection of distantly related proteins, Proceedings of the National Academy of Sciences
84, 4355-4358, 1987.

Eisenberg, D., Wesson, M., Goodsell, D, Wilcox, W., Gribskov, M., Altschuh, D., Richmond, T.J., and Rees, D.C. Binding energies estimated from atomic solvation parameters. in Protein Structure, Folding, and Design, Oxender, D.L., ed., Alan R. Liss, New York, pp 203-214, 1987.

Gribskov, M., Homyak, M., Edenfield, J., and Eisenberg, D., Profile scanning for three--dimensional structural patterns in protein sequences, CABIOS 4, 61-66, 1988.

Gribskov, M., and Eisenberg D. Detection of protein structural features with profile analysis, in Techniques in Protein Chemistry, T.E. Hugli, ed., Academic Press, San Diego, pp 108-117, 1989.

Mullen, J.R., Kayne, P.S., Moerschell, R.P., Tsunasawa, S., Gribskov, M., Shepanski-Colavito, M., Grunstein, M., Sherman, F., and Sternglanz, R. Identification and characterization of genes and mutants for an N-terminal acetyltransferase from yeast, EMBO Journal 8, 2067-2075, 1989.

Gribskov, M., Luethy, R., and Eisenberg, D., Profile analysis, in Methods in Enzymology, vol 183, R.F. Doolittle, ed., Academic Press, San Diego,
pp 146-159, 1990.

Gribskov, M., and Devereux, J., eds., Sequence Analysis Primer, Stockton Press, New York, 279 pages, 1991.

Rice, P.M., Elliston, K., and Gribskov, M., DNA, Chapter 1, in Sequence Analysis Primer, Gribskov, M., and Devereux, J., eds., Stockton Press, New York,
pp 1-59, 1991.

Gribskov, M., The language metaphor in sequence analysis, Computers and Chemistry 16, 85-88, 1992.

Lonetto, M, Gribskov, M, and Gross, C.A., Minireview: The s70 family: sequence conservation and evolutionary relationships Journal of Bacteriology 174, 3843-3849, 1992.

Gribskov, M., Translational initiation factors IF-1 and eIF-2a share an RNA-binding motif with prokaryotic ribosomal protein S1 and polynucleotide phosphorylase, Gene 119, 107-111, 1993.

Miller, M., Rao, J.K.M. Wlodawer, A., and Gribskov, M.R. A left-handed crossover involved in amidohydrolase catalysis: crystal structure of Erwinia chrysanthemi L-asparaginase with bound L-aspartate, FEBS Letters 328, 275-279, 1993.

Gribskov, M. A mechanistic view of proteins and their sequences, Computers and Chemistry 7, 113-116 (1993).

Gribskov, M. Chapter 22: Profile analysis, in Computer Analysis of Sequence Data, Part II, Methods in Molecular Biology Vol. 25, A.M. Griffin and H.G. Griffin Eds., pp 247-266, 1994.

Gribskov, M., and Alvarado, A.A., NIH approves $3.2 million grant for National Biomedical Computation Resource at SDSC, Gather/Scatter July-Sept. 1994.

Gribskov, M., Sequence matching in homology modeling, in Protein Folds, A Distance-Based Approach, H. Bohr and S. Brunak, eds., CRC Press, Boca Raton, pp 71-79, 1995.

Gribskov, M., and Robinson, N.L., The use of receiver operating characteristic (ROC) analysis to evaluate sequence matching, Computers and Chemistry 20, 25-34, 1996.

Jorgenson, J., Buskirk, S.F., Gribskov, M., and Smith D.W. SEARCH: locating and identifying genes and intron-exon junctions in large genomic sequences using parallel computers, in Proceedings of the Third International Conference on Bioinformatics and Genome Research, Lim, H. A., and Cantor, C. R., Eds, World Scientific Publishing Co., Ltd., Singapore. pp. 143-158, 1995

Gribskov, M. and Veretnik, S. Identification of Sequence Patterns with Profile Analysis, Methods in Enzymology 266, 198-212, 1996.

Bailey, T.L., and Gribskov, M., The megaprior heuristic for discovering protein sequence patterns, in Proceedings of the Fourth International Conference on Intelligent Systems for Molecular Biology, pp 15-24, 1996.

Rao, J.K.M., Gribskov, M., Lubkowski, J., Miller, M., Swain, A.L., and Wlodawer, A., A comparison of the crystal structures of bacterial L-asparaginases, in Techniques in Protein Chemistry VII, Marshak, D.R., ed., Academic Press, San Diego CA, pp 373-381, 1996.

Bailey, T.L. and Gribskov, M., Score distributions for simultaneous matching to multiple motifs, Journal of Computational Biology 4, 45-59, 1997.

Miller, M., Geller, M., Gribskov, M., and Kent, S.B.H., Analysis of the structure of chemically synthesized HIV-1 protease complexed with a hexapeptide inhibitor. Part I: crystallographic refinement of 2 Angstrom data, Proteins 27, 184-194, 1997.

Smith, C.M., Shindyalov, I.N., Veretnik, S., Gribskov, M., Taylor, S.S., Ten Eyck, L.F., and Bourne, P.E., The protein kinase resource, Trends in Biochemical Sciences 22, 444-446, 1997.

Bourne, P.E., Gribskov, M., Johnson, G., Moreland, J., and Weissig, H., “A Prototype Molecular Interactive Collaborative Environment (MICE),in Proceedings of the Pacific Symposium on Biocomputing, R Altman, R., Dunker, K., Hunter, L., and Klein T., eds., pp.118-129, 1998. [PDF]

Bailey, T.L. and Gribskov, M., "Combining evidence using p-values: Application to sequence homology searches", Bioinformatics, 14, 48-54, 1998. [PDF].

Bailey, T.L. and Gribskov, M.,"Methods and statistics for combining motif match scores", Journal of Computational Biology, 5, 211-221, 1998.

Veretnik, S., and Gribskov, M., RNA binding domain of HDV is homologous to the HMG box of SRY, Arch. Virol. 144, 1-20, 1999.

Gribskov, M., The new biological literature. Bioinformatics, 15, 347, 1999. [PDF]

Gribskov, M., Sequence comparison, in Genetics Databases, M. Bishop, ed., Academic Press, 105-120, 1999.

Gribskov, M., Bourne, P., and Smith, C.M., Integrated data resource for protein kinases, in Genetics Databases, M. Bishop, ed., Academic Press, pp 241-246, 1999.

Bourne, P.E., and Gribskov, M. ISMB-2000: Bioinformatics enters a new millenium, Bioinformatics 16, 749, 2000. [PDF]

Harmon,A.C., Gribskov, M., and Harper, J.F., CDPKs A kinase for every Ca2+, Trends in Plant Science, 5, 154-159, 2000. [PDF]

Bailey, T.L., Gribskov, M., Concerning the accuracy of MAST E-values, Bioinformatics, 16, 488-489, 2000. [PDF]

Gribskov, M., Fana, F., Harper, J., Hope, D.A., Harmon, A.C., Smith, D.W., Tax, F.E., and Zhang, G.F., PlantsP: a functional genomics database for plant phosphorylation, Nucleic Acids Research, 29, 111-113, 2001. [PDF]

Harmon, A.C., Gribskov, M., Gubrium, E., and Harper, J.F.. The CDPK superfamily of protein kinases, New Phytologist, 151, 175-183, 2001. [PDF]

Masys, D.R., Welsh, J.B., Fink, J.L., Gribskov, M., Klacansky, I., and Corbeil, J., Use of keyword hierarchies to interpret gene expression patterns, Bioinformatics, 17, 319-326, 2001. [PDF]

Reiter, L.T., Potocki, L., Chien, S., Gribskov, M., and Bier, E., A systematic analysis of human disease-associated gene sequences in Drosophila melanogaster, Genome Research, 11, 1114-1125, 2001. [PDF]

Maser, P., Thomine, S., Schroeder, J.I., Ward, J.M., Hirschi, K., Sze, H., Talke, I.N., Amtmann, A., Maathuis, F.J.M., Sanders, D., Harper, J.F., Tchieu, J., Gribskov, M., Persans, M.W., Salt, D.E., Kim, S.A., Guerinot, M.L., Phylogenetic relationships within cation transporter families of Arabidopsis, Plant Physiology, 126, 1646-1667, 2001. [PDF]

Ghassemian, M., Waner, D., Tchieu, J., Gribskov, M., Schroeder, J.I., An integrated Arabidopsis annotation database for Affymetrix Genechip (R) data analysis, and tools for regulatory motif searches, Trends In Plant Science 6, 448-449, 2001. [PDF]

Chien, S., Reiter, L.T., Bier, E., and Gribskov, M., Homophila: human disease genes in Drosophila, Nucleic Acids Research, 30, 149-151, 2002. [PDF]

Kerk, D., Bulgrien, J., Smith, D.W., Barsam, B., Veretnik, S., and Gribskov, M. “The complement of protein phosphatase catalytic subunits encoded in the genome of arabidopsis.” Plant Physiology 129 908-925, 2002. [PDF]

Bailey, T.L.; and Gribskov, M. "Estimating and evaluating the statistics of gapped local-alignment scores." Journal of Computational Biology 9, 575-593, 2002. [PDF]

Tchieu, J.H., Fana, F., Fink J.L., Harper, J., Nair, T.M., Neidner, R.H., Smith, D.W., Steube, K., Tam, T.M., Veretnik, S., Wang, D.; and Gribskov, M., "The PlantsP and PlantsT Functional genomics Databases", Nucleic Acids research 31, 342-344, 2003. [PDF]

Kerk, D., Bulgrien, J., Smith, D.W., and Gribskov, M., "Arabidopsis proteins containing similarity to the universal stress protein domain of bacteria", Plant Physiology 131, 1290-1219, 2003. [PDF]

Hrabak, E.M., Chan, C.W.M., Harmon, A.C., Harper, J.F., Choi, J.H., Halford, N., Kudla, J., Luan, S., Nimmo, H.G., Sussman, M.R., Thomas, M., Welker-Simmons, K., Zhu, J.K., and Gribskov, M., "The CDPK-SnRK superfamily of protein kinases", Plant Physiology 132, 666-680, 2003. [PDF]

Zheng, C.L., Fana, F., Udupi, P.V., and Gribskov, M., "Modulewriter: A program for automatic generation of database interfaces:, Computational biology and chemistry 27, 135-139, 2003. [PDF]

Baxter, I., Tchieu, J., Sussman, M.R., Boutry, M., Palmgren, M., Gribskov, M., Harper, J.F., and Axelsen, K.B., "Genomic comparison of P-Type ATPase ion pumps in Arabidopsis and Rice", Plant Physiology 132, 618-628, 2003. [PDF]

Fink, J.L., Drewes, S., Patel, H., Welsh, J.B., Masys, D.R., Corbeil, J., and Gribskov, M.R., "2HAPI: A web-based microarray data analysis system", Bioinformatics 19, 1443-1445 2003 [PDF]

Gribskov, M. Challenges in data management for functional genomics. OMICS. 2003 Spring;7(1):3-5.

Wang D, Harper JF, Gribskov M. Systematic trans-genomic comparison of protein kinases between Arabidopsis and Saccharomyces cerevisiae. Plant Physiol. 2003 Aug;132(4):2152-65. [PDF]