Biblio

Found 231 results

2012

S. Ng, Collisson, E. A., Sokolov, A., Goldstein, T., Gonzalez-Perez, A., Lopez-Bigas, N., Benz, C., Haussler, D., and Stuart, J. M., “PARADIGM-SHIFT predicts the function of mutations in multiple cancers using pathway impact analysis”, Bioinformatics, vol. 28, pp. i640-i646, 2012.

S. Ng, Collisson, E. A., Sokolov, A., Goldstein, T., Gonzalez-Perez, A., Lopez-Bigas, N., Benz, C., Haussler, D., and Stuart, J. M., “PARADIGM-SHIFT predicts the function of mutations in multiple cancers using pathway impact analysis”, Bioinformatics, vol. 28, pp. i640–i646, 2012.

E. Collisson, Ng, S., Collisson, E. A., Sokolov, A., Goldstein, T., Lopez-Bigas, N., Benz, C., Haussler, D., Stuart, J. M., and , “PARADIGM-SHIFT predicts the function of mutations in multiple cancers using pathway impact analysis”, 2012.

C. J. Vaske, Benz, S. C., Stuart, J. M., and Haussler, D., “Pathway recognition algorithm using data integration on genomic models (PARADIGM)”. 2012.

C. J. Vaske, Benz, S. C., Stuart, J. M., and Haussler, D., “Pathway recognition algorithm using data integration on genomic models (PARADIGM)”. 2012.

J. Stuart, “Pathway-based analysis of mutation impact”, in BMC proceedings, 2012, vol. 6, p. O3.

S. Ng, Thusberg, J., Benz, S., Vaske, C., Ellrott, K., Zhu, J., Yau, C., Collisson, E., Mooney, S., Benz, C., and , “Predicting the impact of mutations in cancer using an integrated pathway approach”. American Association for Cancer Research, 2012.

L. M. Heiser, Sadanandam, A., Kuo, W. - L., Benz, S. C., Goldstein, T. C., Ng, S., Gibb, W. J., Wang, N. J., Ziyad, S., Tong, F., Bayani, N., Hu, Z., Billig, J. I., Dueregger, A., Lewis, S., Jakkula, L., Korkola, J. E., Durinck, S., Pepin, F., Guan, Y., Purdom, E., Neuvial, P., Bengtsson, H., Wood, K. W., Smith, P. G., Vassilev, L. T., Hennessy, B. T., Greshock, J., Bachman, K. E., Hardwicke, M. A., Park, J. W., Marton, L. J., Wolf, D. M., Collisson, E. A., Neve, R. M., Mills, G. B., Speed, T. P., Feiler, H. S., Wooster, R. F., Haussler, D., Stuart, J. M., Gray, J. W., and Spellman, P. T., “Subtype and pathway specific responses to anticancer compounds in breast cancer”, Proceedings of the National Academy of Sciences, vol. 109, pp. 2724-2729, 2012.

L. M. Heiser, Sadanandam, A., Kuo, W. - L., Benz, S. C., Goldstein, T. C., Ng, S., Gibb, W. J., Wang, N. J., Ziyad, S., Tong, F., and , “Subtype and pathway specific responses to anticancer compounds in breast cancer”, Proceedings of the National Academy of Sciences, vol. 109, pp. 2724–2729, 2012.

M. Goldman, Craft, B., Swatloski, T., Ellrott, K., Cline, M., Diekhans, M., Wilks, C., Stuart, J., Haussler, D., and Zhu, J., “The UCSC cancer genomics browser: update 2013”, Nucleic acids research, vol. 41, pp. D949–D954, 2012.

M. James Ellis, Ding, L., Shen, D., Luo, J., Suman, V. J., Goiffon, R. J., Wallis, J. W., Goldstein, T. C., Chen, K., Allred, D. Craig, and , “Whole genome sequencing to characterize luminal-type breast cancer.”. American Society of Clinical Oncology, 2012.

M. J. Ellis, Ding, L., Shen, D., Luo, J., Suman, V. J., Wallis, J. W., Van Tine, B. A., Hoog, J., Goiffon, R. J., Goldstein, T. C., Ng, S., Lin, L., Crowder, R., Snider, J., Ballman, K., Weber, J., Chen, K., Koboldt, D. C., Kandoth, C., Schierding, W. S., McMichael, J. F., Miller, C. A., Lu, C., Harris, C. C., McLellan, M. D., Wendl, M. C., DeSchryver, K., Allred, C. D., Esserman, L., Unzeitig, G., Margenthaler, J., Babiera, G. V., Marcom, K. P., Guenther, J. M., Leitch, M., Hunt, K., Olson, J., Tao, Y., Maher, C. A., Fulton, L. L., Fulton, R. S., Harrison, M., Oberkfell, B., Du, F., Demeter, R., Vickery, T. L., Elhammali, A., Piwnica-Worms, H., McDonald, S., Watson, M., Dooling, D. J., Ota, D., Chang, L. - W., Bose, R., Ley, T. J., Piwnica-Worms, D., Stuart, J. M., Wilson, R. K., and Mardis, E. R., “Whole-genome analysis informs breast cancer response to aromatase inhibition”, Nature, vol. 486, pp. 353–360, 2012.

M. J. Ellis, Ding, L., Shen, D., Luo, J., Suman, V. J., Wallis, J. W., Van Tine, B. A., Hoog, J., Goiffon, R. J., Goldstein, T. C., and , “Whole-genome analysis informs breast cancer response to aromatase inhibition”, Nature, vol. 486, p. 353, 2012.

2011

B. Craft, Ellrott, K., Goldman, M., Wilks, C., Szeto, C., Ma, S., Stuart, J., Zhu, J., and Haussler, D., “Abstract A39: The UCSC Cancer Genomics Browser”. American Association for Cancer Research, 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, Forsberg, C. E., and Stuart, J. M., “Computational Integration of Homolog and Pathway Gene Module Expression Reveals General Stemness Signatures”, PLoS ONE, vol. 6, p. e18968, 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.

S. Ng, Vaske, C., Benz, S., Durbin, J., Szeto, C., Heiser, L., Wang, N., Korkola, J., Bayani, N., Spellman, P., and , “Constructing pathway based predictors of cancer clinical outcome”. American Association for Cancer Research, 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.

P. Spellman and The Cancer Genome Atlas, “Integrated genomic analyses of ovarian carcinoma”, Nature, vol. 474, pp. 609–615, 2011.

C. Genome Atl Network and , “Integrated genomic analyses of ovarian carcinoma”, Nature, vol. 474, p. 609, 2011.

J. H. Tripp, Hewson, I., Boyarsky, S., Stuart, J. M., and Zehr, J. P., “Misannotations of rRNA can now generate 90% false positive protein matches in metatranscriptomic studies”, Nucleic Acids Research, vol. 39, pp. 8792-8802, 2011.

D. M. Wolf, Yau, C., Benz, S., Vaske, C., Stuart, J., Roy, R., Olshen, A., Boudreau, A., Haussler, D., Gray, J., and , “P1-06-09: Patient-Specific Integrative Pathway Analysis Using PARADIGM Identifies Key Activities in I-SPY 1 Breast Cancer Patients (CALGB 150007/150012; ACRIN 6657).”. American Association for Cancer Research, 2011.

S. C. Benz, Vaske, C., Ng, S., Sanborn, J. Zachary, Zhu, J., Haussler, D., and Stuart, J., “Patient-specific pathway analysis using PARADIGM identifies key activities in multiple cancers”. American Association for Cancer Research, 2011.

C. D. House, “Role of Voltage-gated Sodium Ion Channels in the Metastatic Potential of Colon Cancer Cells”, The George Washington University, 2011.

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