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
1999Present
Present
Senior Staff Scientist
San Diego Supercomputer Center
19931999
Adjunct Assistant Professor of Biology
University of California, San Diego
1994Present
UCSD Academic Senate
Campus Committee on Computing
19931996
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
1985
Ph.D. in Molecular Biology
University of Wisconsin-Madison
1979
B.S. with Honors in Biochemistry and Biophysics
Oregon State University
1996-
Education
Professional
Activities
Adjunct Associate Professor of Biology
University of California, San Diego
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 - 9th International
Conference on Intelligent Systems for Molecular
Biology (ISMB)
Professional
Activities
(Continued)
2000
NIH Biophysics Peer Review Panel
2000
NSF EPSCOR Peer Review Panel
2000
Organizing committee co-chairman – 8th International
Conference on Intelligent Systems for Molecular
Biology (ISMB)
1993 1999
Program committee - 1st – 7th International
Conferences on Intelligent Systems for Molecular
Biology (ISMB)
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 Critical Reviews in Biochemistry and Molecular Biology
Reviewer 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., ShepanskiColavito, 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, 38433849, 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 Lasparaginase 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 DistanceBased Approach, H. Bohr and S. Brunak, eds., CRC Press, Boca Raton, pp 7179, 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.
Bailey, T.L. and Gribskov, M., "Combining evidence using p-values: Application to
sequence homology searches", Bioinformatics, 14, 48-54, 1998. .
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.
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.
Harmon,A.C., Gribskov, M., and Harper, J.F., CDPKs A kinase for every Ca2+, Trends in
Plant Science, 5, 154-159, 2000.
Bailey, T.L., Gribskov, M., Concerning the accuracy of MAST E-values, Bioinformatics,
16, 488-489, 2000.
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.
Harmon, A.C., Gribskov, M., Gubrium, E., and Harper, J.F.. The CDPK superfamily of
protein kinases, New Phytologist, 151, 175-183, 2001.
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.
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.
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.
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.
Chien, S., Reiter, L.T., Bier, E., and Gribskov, M., Homophila: human disease genes in
Drosophila, Nucleic Acids Research, 30, 149-151, 2002.
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.
Bailey, T.L.; and Gribskov, M. "Estimating and evaluating the statistics of gapped localalignment scores." Journal of Computational Biology 9, 575-593, 2002.
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, 342344, 2003.
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.
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.
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.
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.
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
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.