Biblio

Found 231 results

2018

M. Seiler, Peng, S., Agrawal, A. A., Palacino, J., Teng, T., Zhu, P., Smith, P. G., Caesar-Johnson, S. J., Demchok, J. A., Felau, I., and , “Somatic mutational landscape of splicing factor genes and their functional consequences across 33 cancer types”, Cell reports, vol. 23, pp. 282–296, 2018.

J. Saltz, Gupta, R., Hou, L., Kurc, T., Singh, P., Nguyen, V., Samaras, D., Shroyer, K. R., Zhao, T., Batiste, R., and , “Spatial organization and molecular correlation of tumor-infiltrating lymphocytes using deep learning on pathology images”, Cell reports, vol. 23, p. 181, 2018.

R. G. Jayasinghe, Cao, S., Gao, Q., Wendl, M. C., Vo, N. Sy, Reynolds, S. M., Zhao, Y., Climente-González, H., Chai, S., Wang, F., and , “Systematic analysis of splice-site-creating mutations in cancer”, Cell reports, vol. 23, pp. 270–281, 2018.

A. C. Berger, Korkut, A., Kanchi, R. S., Hegde, A. M., Lenoir, W., Liu, W., Liu, Y., Fan, H., Shen, H., Ravikumar, V., and , “A comprehensive Pan-Cancer molecular study of gynecologic and breast cancers”, Cancer Cell, vol. 33, pp. 690–705, 2018.

V. Thorsson, Gibbs, D. L., Brown, S. D., Wolf, D., Bortone, D. S., Yang, T. - H. Ou, Porta-Pardo, E., Gao, G. F., Plaisier, C. L., Eddy, J. A., and , “The immune landscape of cancer”, Immunity, vol. 48, pp. 812–830, 2018.

Z. Wang, Yang, B., Zhang, M., Guo, W., Wu, Z., Wang, Y., Jia, L., Li, S., Caesar-Johnson, S. J., Demchok, J. A., and , “lncRNA Epigenetic Landscape Analysis Identifies EPIC1 as an Oncogenic lncRNA that Interacts with MYC and Promotes Cell-Cycle Progression in Cancer”, Cancer Cell, vol. 33, pp. 706–720, 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.

M. Gönen, Weir, B. A., Cowley, G. S., Vazquez, F., Guan, Y., Jaiswal, A., Karasuyama, M., Uzunangelov, V., Wang, T., Tsherniak, A., and , “A Community Challenge for Inferring Genetic Predictors of Gene Essentialities through Analysis of a Functional Screen of Cancer Cell Lines”, Cell systems, vol. 5, pp. 485–497, 2017.

A. Ally, Balasundaram, M., Carlsen, R., Chuah, E., Clarke, A., Dhalla, N., Holt, R. A., Jones, S. J. M., Lee, D., Ma, Y., and , “Comprehensive and integrative genomic characterization of hepatocellular carcinoma”, Cell, vol. 169, pp. 1327–1341, 2017.

L. Fishbein, Leshchiner, I., Walter, V., Danilova, L., A Robertson, G., Johnson, A. R., Lichtenberg, T. M., Murray, B. A., Ghayee, H. K., Else, T., and , “Comprehensive molecular characterization of pheochromocytoma and paraganglioma”, Cancer Cell, vol. 31, pp. 181–193, 2017.

E. Rheinbay, Nielsen, M. Muhlig, Abascal, F., Tiao, G., Hornshøj, H., Hess, J. M., Pedersen, R. Istrup Ist, Feuerbach, L., Sabarinathan, R., Madsen, H. Tobias, and , “Discovery and characterization of coding and non-coding driver mutations in more than 2,500 whole cancer genomes”, BioRxiv, p. 237313, 2017.

H. Beale, Lam, D. Linh, Vivian, J., Newton, Y., Shah, A. Tayi, Bjork, I., Goldstein, T., Brooks, A. N., Stuart, J., Salama, S., and , “Identifying confidently measured genes in single pediatric cancer patient samples using RNA sequencing”. American Association for Cancer Research, 2017.

C. Genome Atl Network and , “Integrated genomic and molecular characterization of cervical cancer”, Nature, vol. 543, p. 378, 2017.

G. A Robertson, Shih, J., Yau, C., Gibb, E. A., Oba, J., Mungall, K. L., Hess, J. M., Uzunangelov, V., Walter, V., Danilova, L., and , “Integrative analysis identifies four molecular and clinical subsets in uveal melanoma”, Cancer cell, vol. 32, pp. 204–220, 2017.

F. Farshidfar, Zheng, S., Gingras, M. - C., Newton, Y., Shih, J., A Robertson, G., Hinoue, T., Hoadley, K. A., Gibb, E. A., Roszik, J., and , “Integrative genomic analysis of cholangiocarcinoma identifies distinct IDH-mutant molecular profiles”, Cell reports, vol. 18, pp. 2780–2794, 2017.

J. Guinney, Wang, T., Laajala, T. D., Winner, K. Kanigel, J Bare, C., Neto, E. Chaibub, Khan, S. A., Peddinti, G., Airola, A., Pahikkala, T., and , “Prediction of overall survival for patients with metastatic castration-resistant prostate cancer: development of a prognostic model through a crowdsourced challenge with open clinical trial data”, The Lancet Oncology, vol. 18, pp. 132–142, 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.

Y. Newton, Novak, A. M., Swatloski, T., McColl, D. C., Chopra, S., Graim, K., Weinstein, A. S., Baertsch, R., Salama, S. R., Ellrott, K., and , “TumorMap: exploring the molecular similarities of cancer samples in an interactive portal”, Cancer research, vol. 77, pp. e111–e114, 2017.

O. Morozova, Newton, Y., Shah, A. Tayi, Beale, H., Lam, D. Linh, Vivian, J., Bjork, I., Goldstein, T., Stuart, J., Salama, S., and , “A pan-cancer analysis framework for incorporating gene expression information into clinical interpretation of pediatric cancer genomic data”. American Association for Cancer Research, 2017.

2016

E. Jay Small, Aggarwal, R. Raj, Huang, J., Sokolov, A., Zhang, L., Alumkal, J. J., Youngren, J., Ryan, C. J., Foye, A., Reiter, R. Evan, and , “Clinical and genomic characterization of metastatic small cell/neuroendocrine prostate cancer (SCNC) and intermediate atypical prostate cancer (IAC): Results from the SU2C/PCF/AACRWest Coast Prostate Cancer Dream Team (WCDT).”. American Society of Clinical Oncology, 2016.

H. A. Al-Ahmadie, Lerner, S., Kim, J., Getz, G., Kwiatkowski, D. J., Weinstein, J., Cherniack, A., Guo, G., Akbani, R., Hoadley, K. A., and , “Comprehensive molecular characterization of 412 muscle invasive urothelial carcinomas of the bladder-final analysis of the cancer genome atlas (TCGA) project”, in LABORATORY INVESTIGATION, 2016, vol. 96, p. 213A–214A.

J. N. Weinstein, Lerner, S. P., Kwiatkowski, D. J., Getz, G., Kim, J., Al-ahmadie, H. A., Cherniack, A. D., Guo, G., Akbani, R., Hoadley, K. A., and , “Comprehensive molecular characterization of 412 muscle-invasive urothelial bladder carcinomas: final analysis of The Cancer Genome Atlas (TCGA) project”. American Association for Cancer Research, 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.

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