Biblio

Found 51 results

Filters: Author is Stuart, Joshua M [Clear All Filters]

2011

J. M. Stuart, “Abstract CN07-04: Patient-specific pathway analysis using PARADIGM identifies key activities in multiple cancers.”. American Association for Cancer Research, 2011.

M. Koeva, E Forsberg, C., and Stuart, J. M., “Computational integration of homolog and pathway gene module expression reveals general stemness signatures”, PLoS One, vol. 6, p. e18968, 2011.

A. Radenbaugh, Sanborn, J. Z., Zerbino, D., Wilks, C., Stuart, J. M., and Haussler, D., “Identification of RNA editing events in cancer using high-throughput sequencing data”. American Association for Cancer Research, 2011.

N. B. Zuckerman, Quan, T. K., Bray, W. M., Ruybal, J. E., Gassner, N. C., Stuart, J. M., Hartzog, G. A., R Lokey, S., and Konopelski, J. P., “Synthesis of a small molecule drug lead: Tamoxilog”, in ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, 2011, vol. 241.

C. M. Tamble, St Onge, R. P., Giaever, G., Nislow, C., Williams, A. G., Stuart, J. M., and R Lokey, S., “The synthetic genetic interaction network reveals small molecules that target specific pathways in Sacchromyces cerevisiae”, Molecular BioSystems, vol. 7, pp. 2019–2030, 2011.

2010

M. H. Woehrmann, Gassner, N. C., Bray, W. M., Stuart, J. M., and Lokey, S., “HALO384: a halo-based potency prediction algorithm for high-throughput detection of antimicrobial agents”, Journal of biomolecular screening, vol. 15, pp. 196–205, 2010.

C. J. Vaske, Benz, S. C., J Sanborn, Z., Earl, D., Szeto, C., Zhu, J., Haussler, D., and Stuart, J. M., “Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM”, Bioinformatics, vol. 26, pp. i237–i245, 2010.

C. E Forsberg, Passegué, E., Prohaska, S. S., Wagers, A. J., Koeva, M., Stuart, J. M., and Weissman, I. L., “Molecular signatures of quiescent, mobilized and leukemia-initiating hematopoietic stem cells”, PloS one, vol. 5, p. e8785, 2010.

2009

P. N. Kanabar, Vaske, C. J., Yeang, C. - H., Yildiz, F. H., and Stuart, J. M., “Inferring disease-related pathways using a probabilistic epistasis model”, in Biocomputing 2009, 2009, pp. 480–491.

A. E. Cozen, Weirauch, M. T., Pollard, K. S., Bernick, D. L., Stuart, J. M., and Lowe, T. M., “Transcriptional map of respiratory versatility in the hyperthermophilic crenarchaeon Pyrobaculum aerophilum”, Journal of bacteriology, vol. 191, pp. 782–794, 2009.

C. J. Vaske, House, C., Luu, T., Frank, B., Yeang, C. - H., Lee, N. H., and Stuart, J. M., “A factor graph nested effects model to identify networks from genetic perturbations”, PLoS computational biology, vol. 5, p. e1000274, 2009.

2007

J. M. Stuart, Bradley, E., Capps, D., and Luftig, J., “Generating Novel, Stylistically Consonant Variations on Human Movement Sequences”, 2007.

A. Byrne, Weirauch, M., Wong, V., Koeva, M., Dixon, S. J., Stuart, J. M., and Roy, P. J., “Genetic Interactions Bridge Functional Modules on a Global Scale in C. elegans.”, in International Worm Meeting, 2007.

D. M. Ng, Woehrmann, M. H., and Stuart, J. M., “Recommending pathway genes using a compendium of clustering solutions”, in Biocomputing 2007, 2007, pp. 379–390.

Z. Hu, Mellor, J., Wu, J., Kanehisa, M., Stuart, J. M., and DeLisi, C., “Towards zoomable multidimensional maps of the cell”, Nature biotechnology, vol. 25, p. 547, 2007.

Z. Hu, Ng, D. M., Yamada, T., Chen, C., Kawashima, S., Mellor, J., Linghu, B., Kanehisa, M., Stuart, J. M., and DeLisi, C., “VisANT 3.0: new modules for pathway visualization, editing, prediction and construction”, Nucleic acids research, vol. 35, pp. W625–W632, 2007.

A. B. Byrne, Weirauch, M. T., Wong, V., Koeva, M., Dixon, S. J., Stuart, J. M., and Roy, P. J., “A global analysis of genetic interactions in Caenorhabditis elegans”, Journal of biology, vol. 6, p. 8, 2007.

2003

J. M. Stuart, Segal, E., Koller, D., and Kim, S., “Discovering conserved pathways and core molecular machinery on a global scale.”, in International Worm Meeting, 2003.

J. M. Stuart, Segal, E., Koller, D., and Kim, S. K., “A Gene-Coexpression Network for Global Discovery of Conserved Genetic Modules”, Science, vol. 302, no. 5643, 2003.

J. M. Stuart, Segal, E., Koller, D., and Kim, S. K., “A gene-coexpression network for global discovery of conserved genetic modules”, science, vol. 302, pp. 249–255, 2003.

2002

P. J. Roy, Stuart, J. M., Lund, J., and Kim, S. K., “Chromosomal clustering of muscle-expressed genes in Caenorhabditis elegans”, Nature, vol. 418, p. 975, 2002.

2001

D. E. Oliver, Hewett, M., Rubin, D. L., Stuart, J. M., Klein, T. E., and Altman, R. B., “Management of data, knowledge, and metadata on the semantic web: Experience with a pharmacogenetics knowledge base”. Stanford Medical Informatics Research Reports SMI-2001–0901–1, 9th September (URL: http://smiweb. stanford. edu/pubs/SMI\_Reports/SMI-2001–0901–1. pdf), 2001.

D. E. Oliver, Rubin, D. L., Stuart, J. M., Hewett, M., Klein, T. E., and Altman, R. B., “Ontology development for a pharmacogenetics knowledge base”, in Biocomputing 2002, 2001, pp. 65–76.

E. Bradley and Stuart, J. M., “Optimization and human movement”, SIAG/OPT Views-and-News, vol. 12, 2001.

S. K. Kim, Lund, J., Kiraly, M., Duke, K., Jiang, M., Stuart, J. M., Eizinger, A., Wylie, B. N., and Davidson, G. S., “A gene expression map for Caenorhabditis elegans”, Science, vol. 293, pp. 2087–2092, 2001.

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