Biblio

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2018

C. J. Ricketts, De Cubas, A. A., Fan, H., Smith, C. C., Lang, M., Reznik, E., Bowlby, R., Gibb, E. A., Akbani, R., Beroukhim, R., and , “The Cancer Genome Atlas Comprehensive Molecular Characterization of Renal Cell Carcinoma”, Cell reports, vol. 23, pp. 313–326, 2018.

K. A. Hoadley, Yau, C., Hinoue, T., Wolf, D. M., Lazar, A. J., Drill, E., Shen, R., Taylor, A. M., Cherniack, A. D., Thorsson, V., and , “Cell-of-origin patterns dominate the molecular classification of 10,000 tumors from 33 types of cancer”, Cell, vol. 173, pp. 291–304, 2018.

R. Aggarwal, Huang, J., Alumkal, J. J., Zhang, L., Feng, F. Y., Thomas, G. V., Weinstein, A. S., Friedl, V., Zhang, C., Witte, O. N., and , “Clinical and Genomic Characterization of Treatment-Emergent Small-Cell Neuroendocrine Prostate Cancer: A Multi-institutional Prospective Study.”, 2018.

A. Ying- Wah Lee, Ewing, A. D., Ellrott, K., Hu, Y., Houlahan, K. E., J Bare, C., Espiritu, S. Melijah G., Huang, V., Dang, K., Chong, Z., and , “Combining accurate tumour genome simulation with crowd sourcing to benchmark somatic structural variant detection”, bioRxiv, p. 224733, 2018.

Y. Newton, S Rassekh, R., Deyell, R. J., Shen, Y., Jones, M. R., Dunham, C., Yip, S., Leelakumari, S., Zhu, J., McColl, D., and , “Comparative RNA-Sequencing Analysis Benefits a Pediatric Patient With Relapsed Cancer”, JCO Precision Oncology, vol. 2, pp. 1–16, 2018.

Y. Liu, Sethi, N. S., Hinoue, T., Schneider, B. G., Cherniack, A. D., Sanchez-Vega, F., Seoane, J. A., Farshidfar, F., Bowlby, R., Islam, M., and , “Comparative molecular analysis of gastrointestinal adenocarcinomas”, Cancer Cell, vol. 33, pp. 721–735, 2018.

A. Kahles, Van Lehmann, K. -, Toussaint, N. C., Hüser, M., Stark, S. G., Sachsenberg, T., Stegle, O., Kohlbacher, O., Sander, C., Caesar-Johnson, S. J., and , “Comprehensive analysis of alternative splicing across tumors from 8,705 patients”, Cancer cell, vol. 34, pp. 211–224, 2018.

M. H. Bailey, Tokheim, C., Porta-Pardo, E., Sengupta, S., Bertrand, D., Weerasinghe, A., Colaprico, A., Wendl, M. C., Kim, J., Reardon, B., and , “Comprehensive characterization of cancer driver genes and mutations”, Cell, vol. 173, pp. 371–385, 2018.

R. Raj Aggarwal, Lloyd, P., Huang, J., Beer, T. M., Zhang, L., Thomas, G. V., True, L. D., Alumkal, J. J., Friedl, V., Weinstein, A., and , “DNA repair mutations and treatment-emergent small cell neuroendocrine prostate cancer (t-SCNC) as hallmarks of distinct subgroups of metastatic castration resistant prostate cancer (mCRPC): Data from the West Coast Prostate Cancer Dream Team.”. American Society of Clinical Oncology, 2018.

Q. Gao, Liang, W. - W., Foltz, S. M., Mutharasu, G., Jayasinghe, R. G., Cao, S., Liao, W. - W., Reynolds, S. M., Wyczalkowski, M. A., Yao, L., and , “Driver fusions and their implications in the development and treatment of human cancers”, Cell reports, vol. 23, pp. 227–238, 2018.

A. M. Taylor, Shih, J., Ha, G., Gao, G. F., Zhang, X., Berger, A. C., Schumacher, S. E., Wang, C., Hu, H., Liu, J., and , “Genomic and functional approaches to understanding cancer aneuploidy”, Cancer Cell, vol. 33, pp. 676–689, 2018.

T. A. Knijnenburg, Wang, L., Zimmermann, M. T., Chambwe, N., Gao, G. F., Cherniack, A. D., Fan, H., Shen, H., Way, G. P., Greene, C. S., and , “Genomic and molecular landscape of DNA damage repair deficiency across The Cancer Genome Atlas”, Cell reports, vol. 23, p. 239, 2018.

D. A. Quigley, Dang, H. X., Zhao, S. G., Lloyd, P., Aggarwal, R., Alumkal, J. J., Foye, A., Kothari, V., Perry, M. D., Bailey, A. M., and , “Genomic hallmarks and structural variation in metastatic prostate cancer”, Cell, vol. 174, pp. 758–769, 2018.

J. D. Campbell, Yau, C., Bowlby, R., Liu, Y., Brennan, K., Fan, H., Taylor, A. M., Wang, C., Walter, V., Akbani, R., and , “Genomic, pathway network, and immunologic features distinguishing squamous carcinomas”, Cell reports, vol. 23, p. 194, 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.

Z. Ge, Leighton, J. S., Wang, Y., Peng, X., Chen, Z., Chen, H., Sun, Y., Yao, F., Li, J., Zhang, H., and , “Integrated Genomic Analysis of the Ubiquitin Pathway across Cancer Types”, Cell reports, vol. 23, pp. 213–226, 2018.

H. Shen, Shih, J., Hollern, D. P., Wang, L., Bowlby, R., Tickoo, S. K., Thorsson, V., Mungall, A. J., Newton, Y., Hegde, A. M., and , “Integrated Molecular Characterization of Testicular Germ Cell Tumors”, Cell reports, vol. 23, pp. 3392–3406, 2018.

G. P. Way, Sanchez-Vega, F., La, K., Armenia, J., Chatila, W. K., Luna, A., Sander, C., Cherniack, A. D., Mina, M., Ciriello, G., and , “Machine Learning Detects Pan-cancer Ras Pathway Activation in The Cancer Genome Atlas”, Cell Reports, vol. 23, no. 1, 2018.

T. M. Malta, Sokolov, A., Gentles, A. J., Burzykowski, T., Poisson, L., Weinstein, J. N., Kamińska, B., Huelsken, J., Omberg, L., Gevaert, O., and , “Machine learning identifies stemness features associated with oncogenic dedifferentiation”, Cell, vol. 173, pp. 338–354, 2018.

X. Peng, Chen, Z., Farshidfar, F., Xu, X., Lorenzi, P. L., Wang, Y., Cheng, F., Tan, L., Mojumdar, K., Du, D., and , “Molecular Characterization and Clinical Relevance of Metabolic Expression Subtypes in Human Cancers”, Cell reports, vol. 23, pp. 255–269, 2018.

A. Korkut, Zaidi, S., Kanchi, R. S., Rao, S., Gough, N. R., Schultz, A., Li, X., Lorenzi, P. L., Berger, A. C., Robertson, G., and , “A Pan-Cancer Analysis Reveals High-Frequency Genetic Alterations in Mediators of Signaling by the TGF-$\beta$ Superfamily”, Cell systems, 2018.

H. - S. Chiu, Somvanshi, S., Patel, E., Chen, T. - W., Singh, V. P., Zorman, B., Patil, S. L., Pan, Y., Chatterjee, S. S., Sood, A. K., and , “Pan-Cancer analysis of lncRNA regulation supports their targeting of cancer genes in each tumor context”, Cell reports, vol. 23, p. 297, 2018.

M. A. Reyna, Haan, D., Paczkowska, M., Verbeke, L. P. C., Vazquez, M., Kahraman, A., Tamayo, S. Pulido, Barenboim, J., Wadi, L., Dhingra, P., and , “Pathway and network analysis of more than 2,500 whole cancer genomes”, bioRxiv, p. 385294, 2018.

L. Ding, Bailey, M. H., Porta-Pardo, E., Thorsson, V., Colaprico, A., Bertrand, D., Gibbs, D. L., Weerasinghe, A., Huang, K. -lin, Tokheim, C., and , “Perspective on Oncogenic Processes at the End of the Beginning of Cancer Genomics”, Cell, vol. 173, pp. 305–320, 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.

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