Biblio

Found 231 results

2014

D. M. Wolf, Fan, C., Hoadley, K. A., Yau, C., Sokolov, A., Network, T. C. G. A., Stuart, J., Perou, C., and Veer, Lvan't, “Thousands of published cancer signatures and pathways can be collapsed into a handful of non-redundant gene programs: a TCGA pan-cancer analysis”. American Association for Cancer Research, 2014.

P. C. Boutros, Margolin, A. A., Stuart, J. M., Califano, A., and Stolovitzky, G., “Toward better benchmarking: challenge-based methods assessment in cancer genomics”, Genome biology, vol. 15, p. 462, 2014.

E. Jay Small, Youngren, J., Beer, T. M., Ryan, C. J., Thomas, G., Pourmand, N., Reiter, R. Evan, Alumkal, J. J., Stuart, J. M., Evans, C. P., and , “The molecular and pathway characterization of patients with metastatic castration resistant prostate cancer (mCRPC) refractory to therapy with abiraterone acetate or enzalutamide: Preliminary results from the SU2C/PCF/AACR West Coast Prostate Cancer Dream”. American Society of Clinical Oncology, 2014.

2013

L. M. Heiser, Shaw, C. A., Wang, N. J., Grasso, C., Anur, P., Ng, S., Goldstein, T., Spellman, P. T., Stuart, J., Osborne, K., and , “Acquired therapeutic resistance is mediated by deregulation of multiple pathways.”. American Association for Cancer Research, 2013.

A. Gonzalez-Perez, Mustonen, V., Reva, B., Ritchie, G. R. S., Creixell, P., Karchin, R., Vazquez, M., J Fink, L., Kassahn, K. S., Pearson, J. V., and , “Computational approaches to identify functional genetic variants in cancer genomes”, Nature methods, vol. 10, p. 723, 2013.

E. O. Paull, Carlin, D. E., Niepel, M., Sorger, P. K., Haussler, D., and Stuart, J. M., “Discovering causal pathways linking genomic events to transcriptional states using Tied Diffusion Through Interacting Events (TieDIE)”, Bioinformatics, vol. 29, pp. 2757–2764, 2013.

L. Omberg, Ellrott, K., Yuan, Y., Kandoth, C., Wong, C., Kellen, M. R., Friend, S. H., Stuart, J., Liang, H., and Margolin, A. A., “Enabling transparent and collaborative computational analysis of 12 tumor types within The Cancer Genome Atlas”, Nature genetics, vol. 45, p. 1121, 2013.

C. J. Schulze, Bray, W. M., Woerhmann, M. H., Stuart, J., Lokey, S. R., and Linington, R. G., “"Function-first" lead discovery: mode of action profiling of natural product libraries using image-based screening.”, Chem Biol, vol. 20, pp. 285–295, 2013.

R. Karchin, Ochs, M. F., Stuart, J. M., Ideker, T., and Bader, J. S., “Identification of aberrant pathway and network activity from high-throughput data”, in Biocomputing 2013, 2013, pp. 103–110.

P. G. Febbo, Goldstein, T. C., Baertsch, R., Youngren, J., Newton, Y., Bivol, A., Small, E. Jay, and Stuart, J. M., “Identification of polo-like kinase 1 (PLK1) in aggressive prostate cancer by paradigm analysis.”. American Society of Clinical Oncology, 2013.

D. A. Levine, Network, C. Genome Atl, and , “Integrated genomic characterization of endometrial carcinoma”, Nature, vol. 497, p. 67, 2013.

M. H. Woehrmann, Bray, W. M., Durbin, J. K., Nisam, S. C., Michael, A. K., Glassey, E., Stuart, J. M., and R Lokey, S., “Large-scale cytological profiling for functional analysis of bioactive compounds”, Molecular BioSystems, vol. 9, pp. 2604–2617, 2013.

T. Goldstein, Paull, E. O., Ellis, M. J., and Stuart, J. M., “Molecular Pathways: Extracting Medical Knowledge from High Throughput Genomic Data.”, Clin Cancer Res, 2013.

B. Craft, Swatloski, T., Goldman, M., Ellrott, K., Ma, S., Wilks, C., Stuart, J., Haussler, D., and Zhu, J., “The New UCSC Cancer Genomics Browser”, Nucleic Acids Research, vol. 41, no. D1, 2013.

M. Goldman, Craft, B., Swatloski, T., Ellrott, K., Cline, M., Diekhans, M., Ma, S., Wilks, C., Stuart, J., Haussler, D., and Zhu, J., “The UCSC Cancer Genomics Browser: update 2013.”, Nucleic Acids Res, vol. 41, pp. D949–D954, 2013.

C. K. Wong, Vaske, C. J., Ng, S., J Sanborn, Z., Benz, S. C., Haussler, D., and Stuart, J. M., “The UCSC Interaction Browser: multidimensional data views in pathway context”, Nucleic acids research, vol. 41, pp. W218–W224, 2013.

J. N. Weinstein, Collisson, E. A., Mills, G. B., Shaw, K. R. Mills, Ozenberger, B. A., Ellrott, K., Shmulevich, I., Sander, C., Stuart, J. M., Network, C. Genome Atl, and , “The cancer genome atlas pan-cancer analysis project”, Nature genetics, vol. 45, p. 1113, 2013.

C. W. Brennan, Verhaak, R. G. W., McKenna, A., Campos, B., Noushmehr, H., Salama, S. R., Zheng, S., Chakravarty, D., J Sanborn, Z., Berman, S. H., and , “The somatic genomic landscape of glioblastoma”, Cell, vol. 155, pp. 462–477, 2013.

2012

The Cancer Genome Atlas Research Network, “Comprehensive genomic characterization of squamous cell lung cancers”, Nature, vol. advance online publication, p. –, 2012.

C. Genome Atl Network and , “Comprehensive genomic characterization of squamous cell lung cancers”, Nature, vol. 489, p. 519, 2012.

R. Kucherlapati and The Cancer Genome Atlas, “Comprehensive molecular characterization of human colon and rectal cancer”, Nature, vol. 487, pp. 330–337, 2012.

C. Genome Atl Network and , “Comprehensive molecular characterization of human colon and rectal cancer”, Nature, vol. 487, p. 330, 2012.

TCGA, “Comprehensive molecular portraits of human breast tumours.”, Nature, vol. 490, pp. 61–70, 2012.

C. Genome Atl Network and , “Comprehensive molecular portraits of human breast tumours”, Nature, vol. 490, p. 61, 2012.

R. Karchin, Ochs, M. F., Stuart, J. M., and Bader, J. S., “Identification of Aberrant Pathway and Network Activity from High-Throughput Data”, in Pacific Symposium on Biocomputing, 2012.

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