Dr. Michael Gribskov                                                                            

Department of Biological Sciences • Purdue University • 915 W. State Street • West Lafayette, IN  47907-2054
VOICE: 765.494.6933•  gribskov@purdue.edu  •  FAX: 765.496.1189

 

Professional
Experience

2004 -
Present

Professor of Biological Sciences
Purdue University

 

1999-
Present

Adjunct Associate Professor of Biology
University of California, San Diego

 

1996-
2004

Lead Scientist, Computational Biology
San Diego Supercomputer Center

 

1993-1999

Adjunct Assistant Professor of Biology
University of California, San Diego

 

1994- 2000

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

President – International Society for Computational Biology
Chairman, Scientific Advisory Board - Protein Information Resource (PIR)
Member Idaho BRIN/INBRE Advisory Board
Editorial Board - Bioinformatics
Editorial Board – Computational Biology and Chemistry
Editorial Board - Journal of Molecular Microbiology & Biotechnology

 

2003

Workshop on Data Management for Molecular Biology
Participant and writing panel

 

2002

NIH Genome Informatics Review Panel

 

2001

Organizing committee member - 9th International Conference on Intelligent Systems for Molecular Biology (ISMB)

 

2000

NIH Biophysics Peer Review Panel

 

2000

NSF EPSCOR Peer Review Panel

Professional
Activities (Continued)

2000

Organizing committee co-chairman – 8th International Conference on Intelligent Systems for Molecular Biology (ISMB)

 

1993 -
2004

Program committee - 1st – 12th International Conferences on Intelligent Systems for Molecular Biology (ISMB)

 

1999,
1994,
1992

DOE Human Genome Review Panel

 

2002,
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 (Active funding in bold)

“Functional Genomics of Plant Phosphorylation”

      This project combines experimental efforts to identify knockout mutants in Arabidopsis protein kinases with bioinformatic efforts to infer the function of protein kinases and phosphatases.  Intial funding for PlantsP database.

      PI: John C. Walker, University of Missouri

 “Network Support for NSF Plant Genome Project”

      Pilot project to develop a website for distribution of information and materials related to the NSF Plant Genome Project.

      NSF: DBI, Period: 07/01/2000 – 06/30/2002

“National Biomedical Computation Resource”

      Provides access to advance scientific computing resource to biomedical researchers.

      NIH  P41 RR-08605  Years: 06-10  Period: 04/15/1999 - 04/14/2004

“Cancer Classification Based On RNA Isoforms”

      Experimental analysis of differences in RNA splicing and its correlation with tumor properties.  Funds the establishment of RNA splicing database.

      PI: Fu, Xiang-Dong, UCSD

      Co-Investigator: Michael Gribskov

      NIH  Period: 07/01/2000-06/30/2004

“Gene Discovery in Aid of Plant Nutrition, Human Health and Environmental Remediation”

      Experimental measurement of metal concentrations in yeast and plants as a screen for defects in metal transport systems.  Funds creation of the PlantsT database.

      PI: Mary Lou Guerinot, Dartmouth University

      Co-PI Michael Gribskov

      NSF: Period: 08/01/2000 – 07/31/2004

“Community-based Development of Interoperable Databases”

      Investigates methods and technology for interoperation of scientific database with a focus on plant functional genomics.

      PI: Michael Gribskov

      NSF DBI-0221524, Period - 10/01/2002 – 9/30/2005

“Protein Interaction Map for Rice Kinases”

      Experimental characterization of protein kinases and interacting proteins in Rice.  Continued funding for PlantsT database.

      PI: Michael Fromm, University of Nebraska, Lincoln

      Co-PI: Michael Gribskov

      NSF DBI-0217312, Period: 9/01/02 – 8/31/2006

“Protein Kinase Resource”

      Creation of an integrated data laboratory for the analysis of protein kinases

      PI: Michael Gribskov

      NSF DBI-0217951 Period: 10/1/2002 – 9/30/2005

“Prediction and Validation of Phospho-Regulatory Sites in Crop Proteomes”

      Bioinformatic prediction and experimental validation of protein kinase target sites in crop plant proteomes.

      PI: Jeffrey Harper (The Scripps Research Institute)

      Co-PI: Michael Gribskov

      NSF Period - 09/01/2003 – 08/31/2007

 

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., Lüthy, 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-2 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 Å 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”, Archives of Virology 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 millennium”, 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. [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.

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., and 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., and 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. (2002) 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 local-alignment scores.”  Journal of Computational Biology 9, 575-593, 2002.

Gribskov, M., “Bioinformatic tools for functional Genomics”, in Biology of Plant Microbe Interactions, Leong, S.A., Allen, C., and Triplett, E.W., eds.  International Society for Plant Microbe Interactions, St. Paul  MI, pp 320-324, 2002.

Tchieu J.H., Fana F., Fink J.L., Harper J., Nair T.M., Niedner 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

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, 1209–1219, 2003.

Gribskov, M., “Challenges in data management for functional genomics”, Omics 7, 3-5, 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.

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.

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

Wang, D., Harper,, J.F., and Gribskov,, M., “Systematic trans-genomic comparison of protein kinases between Arabidopsis thaliana and Saccharomyces cerevisiae”, Plant Physiology 132, 2152-2165, 2003.

Nair, T.M., Zheng, C.L., Fink, J.L, Stuart, R.O., Gribskov, M., “Rival penalized competitive learning (RPCL): a topology determining algorithm for analyzing gene-expression data”, Computational Biology and Chemistry, 27, 563-574, 2003.

Zheng, C.L., de Sa, V.R., Gribskov, M., Nair, T.M., “On selecting features from splice junctions: An analysis using information theoretic and machine learning approaches”, Genome Informatics, 14, 73-83, 2003.

Zheng, C.L., Nair, T.M., Gribskov, M., Kwon, Y.S., Li, H.R., and Fu, X-.D., “A Database Designed to Computationally Aid An Experimental Approach to Alternative Splicing”, Pacific Symposium on Biocomputing 2004, Altman, R.B., Dunker, A.K., Hunter, L., Jung, T.A., and Klein T.E., Eds, World Scientific, New Jersey, pp 78-88, 2004.

Podell, S., and Gribskov, M., “Predicting N-terminal myristoylation sites in plant proteins”, BMC Genomics, 5:37 (DOI:10.1186/1471-2164-5-37), 2004.