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| Refereed Journal Papers
- J.M. Stuart, E. Segal, D. Koller, S.K. Kim. ”A Gene Coexpression Network for Global Discovery of Conserved Genetic Modules.” Science 302(5643):249-55 (2003). [Pubmed] [PDF]
- A.B. Owen, J. Stuart, K. Mach, and S.K. Kim. “A gene recommender algorithm to identify co-expressed genes in C. elegans.” Genome Res. 13(8):1828-37 (2003). [Pubmed] [PDF]
- P.J. Roy, J.M. Stuart, J. Lund, and S.K. Kim. “Chromosomal clustering of muscle-expressed genes in C. elegans.” Nature 418:975-9 (2002). [Pubmed] [PDF]
- S.K. Kim, J.Lund, M. Kiraly, K. Duke, M. Jiang, J.M. Stuart, A. Eizinger, B.N. Wylie, and G.S. Davidson. “A gene expression map for C. elegans.” Science 293:2087-92. [Pubmed] [PDF]
- M. Hewett, D.E. Oliver, D.L. Rubin, K.L. Easton, J.M. Stuart, R.B. Altman, and T.E. Klein. “PharmGKB: The Pharmacogenetics Knowledge Base.” Nucleic Acids Research 30:163-5 (2001). [Pubmed] [PDF]
- T.E. Klein, J.T. Chang, M.K. Cho, K.L. Easton, R. Fergerson, M. Hewett, Z. Lin, S. Yueyi I. Liu, V. Liu, D.E. Oliver, D.L. Rubin, F. Shafa, J.M. Stuart, and R.B. Altman. “Integrating genotype and phenotype information: an overview of the PharmGKB project.” Journal of Pharmacogenomics 1:167-70 (2001). [Pubmed]
- E. Bradley and J.M. Stuart. “Using Chaos to Generate Variations on Movement Sequences.” Chaos 8:800-7 (1998). [PDF]
Refereed Conference Papers
- D.E. Oliver, D.L. Rubin, J.M. Stuart, M. Hewett, T.E. Klein, and R.B. Altman. “Ontology development for a pharmacogenetics knowledge base.” Proceedings of the Pacific Symposium on Biocomputing. Pages 65-76 (2002). [Pubmed] [PDF]
- S. Raychaudhuri, J.M. Stuart, X. Liu, P.M. Small, and R.B. Altman. “Pattern recognition of genomic features with microarrays: Site typing of Mycobacterium tuberculosis strains.” Proceedings of the International Conference on Intelligent Systems for Molecular Biology 8:286-95 (2001). [Pubmed] [PDF]
- S. Raychaudhuri, J.M. Stuart, and R.B. Altman. “Principal components analysis to summarize microarray experiments: Application to sporulation time series” Proceedings of the Pacific Symposium on Biocomputing. 455-66 (2001). [Pubmed] [PDF]
- J.M. Stuart and E. Bradley. “Learning the grammar of dance.” Proceedings of the International Conference on Machine Learning, Madison , Wisconsin , (1998). [PDF]
Invited Book Chapters
- Emerging Molecular and Computational Approaches for Cross-Species Extrapolations , Society of Environmental Toxicology and Chemistry in preparation. A joint SETAC-SOP Pellston Workshop, Portland , OR July 18-22 (2004).
Non-refereed Papers
- S. Raychaudhuri, P.D. Sutphin, J.M. Stuart, and R.B. Altman. “CLEAVER : Analyzing microarray data using known biological categories.” Stanford Medical Informatics Technical Report 2000-0839 (2000). [Tech Report]
- S. Raychaudhuri, P.D. Sutphin, J.M. Stuart, A.J. Giaccia, and R.B. Altman. “Supervised Machine Learning: Analyzing Microarray Data Using Known Biological Categories” Stanford Medical Informatics Technical Report 2000-0853 (2000). [Tech Report]
- E. Bradley and J.M. Stuart. “Using chaos to generate choreographic variations.” Proceedings of the Fourth Experimental Chaos Conference. World Scientific, (1997).
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