KIMMEN SJOLANDER CURRICULUM VITAE EDUCATION: 1997 Ph.D. in Computer Science, University of California, Santa Cruz Thesis Advisor: David Haussler Thesis Title: A Bayesian-Information Theoretic Method for Evolutionary Inference in Proteins 1993 B.A. in Computer Science, University of California, Santa Cruz; Graduated Highest Honors in the Major, College Honors HONORS AND AWARDS: 1996 Program in Mathematics and Molecular Biology (PMMB) Fellowship 1996 University of California Presidential Dissertation Year Fellowship 1993 NSF Three-Year Graduate Research Fellowship 1993 Elected to Phi Beta Kappa WORK HISTORY: November, 2001 - Present Assistant Professor Dept of Bioengineering University of California, Berkeley December, 1999 - November, 2001 Principal Scientist Celera Genomics, Protein Informatics Foster City, CA October, 1997 - December, 1999 Chief Scientist Molecular Applications Group Palo Alto, CA January, 1997 - October 1997 Senior Scientist Pangea Systems Oakland, CA SELECTED TALKS AND TUTORIALS: "The role of phylogenetic inference in proteomics", Plant Proteomes: Structure, Changes, Interactions and Function (Symposium), Iowa State University, June 20-23, 2002 (Invited plenary session talk) "High-throughput Functional Classification of Proteins", Gordon Conference, Bioinformatics, From Inference to Predictive Models, Tilton, NH, August 2001 (Invited talk) "Automated domain identification in proteins using HMMs" Genome Sequencing and Analysis Conference (TIGR) Miami, FL, September 1999 "Issues in Target Identification and Prioritization" Computational Genomics Conference (TIGR) Baltimore, MD, November 1999 "A Bayesian Information-Theoretic Method for Phylogenetic Inference in Proteins" Neyman Seminars, Dept of Statistics, University of California, Berkeley Berkeley, CA, February, 1999 Tutorial: "Remote homolog prediction using HMMs and Threading" Understanding the Genome: Technological and Mathematical Challenges (Mathematical Sciences Research Institute) Berkeley, CA, May 1998 "Bayesian Evolutionary Tree Estimation" Center for Molecular Biotechnology Seattle, WA September 1997 "Recognizing protein folds using Hidden Markov Models: A Behind-the-Scenes look at the UCSC method" Center for Molecular Biotechnology Seattle, WA September 1997 "Large-Scale Protein Function and Structure Prediction using Hidden Markov Models" Beyond the Human Genome Project Cambridge Healthech San Francisco, CA June 1997 "Inferring a protein fold using Hidden Markov models" The Second Asilomar Meeting for the Critical Assessment of Structure Prediction (CASP2), Asilomar, CA. December, 1996 Tutorial: "Stochastic Modeling and Hidden Markov Models" Intelligent Systems in Molecular Biology (ISMB) '96, St. Louis, MO. June, 1996. "Hidden Markov Models for Protein Sequence Analysis" LAFORIA, Universite de Pierre et Marie Curie, Paris, France, July, 1995 "Dirichlet Mixture Priors for Improved Remote Homolog Recognition" European Molecular Biology Laboratory, Heidelberg, Germany, August, 1995 "Research Opportunities in Computational Biology" Windows of Opportunity Symposium, George Washington University, May, 1993. "Dirichlet Mixture Priors for Hidden Markov Models and Stochastic Context-Free Grammars" Workshop on Machine Learning and Computational Biology, Conference on Learning Theory, Rutgers, New Jersey, July, 1994. SELECTED PAPERS: J. Craig Venter et al (2001) "The Sequence of the Human Genome", Science, 2001 Feb 16; Vol 291, No. 5507 Sjolander, K. (1998) "Phylogenetic inference in protein superfamilies: Analysis of SH2 domains" Proceedings of 1998 Intelligent Systems for Molecular Biology Conference (ISMB) Montreal, Canada, June 1998 Karplus, K, Sjolander K, Barrett C, Cline M, Haussler D, Hughey R, Holm L, Sander C. (1997) "Predicting protein structure using hidden Markov models" Proteins, 1997; Suppl 1:134-9 Sjolander, K. (1997) "Bayesian Evolutionary Tree Estimation" Proceedings of Computing in the Genome Era conference, Washington, DC, March, 1997 Sjolander, K., Karplus, K., Brown, M.P., Hughey, R., Krogh, A., Mian, I.S., Haussler D. (1996) ``Dirichlet Mixtures: A Method for Improved Detection of Weak but Significant Protein Sequence Homology,'' Comput Appli Biosci 1996 Aug; 12(4):327-45 Krogh, A., Brown, M., Mian, S., Sjolander, K. and Haussler, D. (1994) ``Hidden Markov Models in Computational Biology: Applications to Protein Modeling,'' Journal of Molecular Biology. 1994 Feb 4; 235(5):1501-31 Sakakibara, Y, Brown, M., Hughey, R., Mian, S., Sjolander, K., Underwood, R., Haussler, D. (1994) ``Recent Methods for RNA Modeling Using Stochastic Context-Free Grammars,'' Proc. of the Asilomar Conference on Combinatorial Pattern Matching Sakakibara, Y, Brown, M., Hughey, R., Mian, S., Sjolander, K., Underwood, R., Haussler, D. (1994) ``Stochastic Context-Free Grammars for tRNA Modeling,'' Nucleic Acids Research. 1994 Nov 25; 22(23):5112-20. Haussler, D., Krogh, A., Mian, I.S., Sjolander, K. (1993) "Protein Modeling using Hidden Markov Models: Analysis of Globins", Proceedings of the Hawaii International Conference on System Sciences, January, 1993. Voted best in the category AI Technologies for Molecular Biology Analysis. Brown, M.P., Hughey, R., Krogh, A., Mian, I.S., Sjolander, K., Haussler, D. (1993) ``Using Dirichlet mixture priors to derive hidden Markov models for protein families,'' Proc. First International Conference on Intelligent Systems for Molecular Biology, Washington D.C., July, 1993. EXTERNAL ADVISORY BOARD MEMBER: University of Texas, Austin Bioengineering Degree Program University of California Santa Cruz Extension Bioinformatics Degree Program PERSONAL AND MISCELLANEOUS: Programming languages: C, C++, Perl URL: http://alumni.cse.ucsc.edu/~kimmen/ email: kimmen@alumni.cse.ucsc.edu U.S. Citizen Languages (fluent): English, French U.S. Patent No. 6,128,587: Method and apparatus using Bayesian subfamily identification for sequence analysis. (Issued Oct. 3, 2000.) Referee, Journal of Molecular Biology Referee, Bioinformatics Program Committee, Genome Informatics 1999 Program Committee, ISMB 2002 Session chair, at NAS Proteomics Symposium "Defining the Mandate of Proteomics in the Post Genomics Era", to be held at the National Academy of Sciences in Washington D.C. on Monday, February 25, 2002