Biblio

Found 51 results

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

Submitted

J. M. Stuart, Segal, E., Koller, D., and Kim, S. K., “Construction of a gene co-expression network”, Submitted.

2018

D. H. Sendorek, Caloian, C., Ellrott, K., J Bare, C., Yamaguchi, T. N., Ewing, A. D., Houlahan, K. E., Norman, T. C., Margolin, A. A., Stuart, J. M., and , “Germline contamination and leakage in whole genome somatic single nucleotide variant detection”, BMC bioinformatics, vol. 19, p. 28, 2018.

2017

M. Niepel, Hafner, M., Duan, Q., Wang, Z., Paull, E. O., Chung, M., Lu, X., Stuart, J. M., Golub, T. R., Subramanian, A., and , “Common and cell-type specific responses to anti-cancer drugs revealed by high throughput transcript profiling”, Nature Communications, vol. 8, p. 1186, 2017.

D. E. Carlin, Paull, E. O., Graim, K., Wong, C. K., Bivol, A., Ryabinin, P., Ellrott, K., Sokolov, A., and Stuart, J. M., “Prophetic Granger Causality to infer gene regulatory networks”, PloS one, vol. 12, p. e0170340, 2017.

K. Graim, Liu, T. Ting, Achrol, A. S., Paull, E. O., Newton, Y., Chang, S. D., Harsh, G. R., Cordero, S. P., Rubin, D. L., and Stuart, J. M., “Revealing cancer subtypes with higher-order correlations applied to imaging and omics data”, BMC medical genomics, vol. 10, p. 20, 2017.

P. Cordero and Stuart, J. M., “Tracing co-regulatory network dynamics in noisy, single-cell transcriptome trajectories”, in PACIFIC SYMPOSIUM ON BIOCOMPUTING 2017, 2017, pp. 576–587.

2016

T. T. Liu, Achrol, A. S., Mitchell, L. A., Du, W. A., Loya, J. J., Rodriguez, S. A., Feroze, A., Westbroek, E. M., Yeom, K. W., Stuart, J. M., and , “Computational identification of tumor anatomic location associated with survival in 2 large cohorts of human primary glioblastomas”, American Journal of Neuroradiology, 2016.

A. Sokolov, Paull, E. O., and Stuart, J. M., “One-class detection of cell states in tumor subtypes”, in Biocomputing 2016: Proceedings of the Pacific Symposium, 2016, pp. 405–416.

A. Sokolov, Carlin, D. E., Paull, E. O., Baertsch, R., and Stuart, J. M., “Pathway-based genomics prediction using generalized elastic net”, PLoS computational biology, vol. 12, p. e1004790, 2016.

R. Aggarwal, Beer, T. M., Gleave, M., Stuart, J. M., Rettig, M., Evans, C. P., Youngren, J., Alumkal, J. J., Huang, J., Thomas, G., and , “Targeting Adaptive Pathways in Metastatic Treatment-Resistant Prostate Cancer: Update on the Stand Up 2 Cancer/Prostate Cancer Foundation–Supported West Coast Prostate Cancer Dream Team”, European urology focus, vol. 2, pp. 469–471, 2016.

2015

E. M. Pietras, Reynaud, D., Kang, Y. - A., Carlin, D., Calero-Nieto, F. J., Leavitt, A. D., Stuart, J. M., Göttgens, B., and Passegué, E., “Functionally distinct subsets of lineage-biased multipotent progenitors control blood production in normal and regenerative conditions”, Cell stem cell, vol. 17, pp. 35–46, 2015.

B. A. Smith, Sokolov, A., Uzunangelov, V., Baertsch, R., Newton, Y., Graim, K., Mathis, C., Cheng, D., Stuart, J. M., and Witte, O. N., “A basal stem cell signature identifies aggressive prostate cancer phenotypes”, Proceedings of the National Academy of Sciences, vol. 112, pp. E6544–E6552, 2015.

2014

S. Brunak, DE LA VEGA, F. R. A. N. C. I. S. C. O. M., Margolin, A., Raphael, B. J., Raetsch, G., and Stuart, J. M., “Cancer Panomics: Computational Methods and Infrastructure for Integrative Analysis of Cancer High-Throughput “Omics” Data”, in Pacific Symposium on Biocomputing Co-Chairs, 2014, pp. 8–9.

A. J. Radenbaugh, Ma, S., Ewing, A., Stuart, J. M., Collisson, E. A., Zhu, J., and Haussler, D., “RADIA: RNA and DNA integrated analysis for somatic mutation detection”, PloS one, vol. 9, p. e111516, 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

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.

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.

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.

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.

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