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Research
interests
I am interested in computational approaches for predicting how genes
function and discovering how their functions are regulated and modulated to
produce orchestrated cellular responses.
I am particularly interested in approaches that combine genome-wide
functional data across multiple organisms to identify conserved mechanisms
of gene activity and to understand how genetic networks evolve.
- Discovering conserved genetic modules from gene
expression data across multiple organisms. Work with Stuart Kim in the
Developmental Biology and Genetics.
- Discovering new members of genetic pathways.
With Art Owen in
Statistics at Stanford and Stuart
Kim.
- Discovering tissue-specific splice forms in
human and mouse from DNA microarray data. With Manny Ares in Molecular,
Cellular, and Developmental Biology.
- Developing a database for gene expression
studies on alternative splicing. With Manny Ares in Molecular,
Cellular, and Developmental Biology.
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Recent
publications
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A Gene Coexpression Network for Global Discovery of
Conserved Genetic Modules JM
Stuart, E Segal, D Koller,
SK Kim. Science 302:249-55.
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A gene recommender
algorithm to identify co-expressed genes in C. elegans AB Owen, J Stuart, K Mach, AM Villeneuve, S Kim. Genome Research 2003 13:1828-37.
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Chromosomal
clustering of muscle-expressed genes in C. elegans. PJ Roy, JM Stuart, J Lund,
SK Kim. Nature 2002 418:975-9.
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A Gene Expression
Map for Caenorhabditis elegans.
SK Kim, J Lund, M Kiraly, K Duke, M Jiang, JM Stuart, A Eizinger,
BN Wylie, GS Davidson. Science 2001 293:2087-2092.
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Ontology development
for a pharmacogenetics knowledge base. Oliver DE, Rubin DL, Stuart JM, Hewett M, Klein TE, Altman RB. Pac Symp
Biocomput. 2002:65-76.
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PharmGKB:
the Pharmacogenetics Knowledge Base. Hewett M, Oliver DE, Rubin DL, Easton KL, Stuart JM, Altman RB,
Klein TE. Nucleic
Acids Res. 2002 30:163-5.
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Pattern recognition of
genomic features with microarrays: site typing of
Mycobacterium tuberculosis strains. S Raychaudhuri,
JM Stuart, X Liu, PM Small, RB Altman.
Intelligent Systems for Molecular Biology 2000:286-295.
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Principal components
analysis to summarize microarray experiments: application to sporulation time series. S Raychaudhuri,
JM Stuart, RB Altman. Pacific
Symposium on Biocomputing. 2000:455-466.
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