TY - JOUR AU - Majewski, I. J. AU - Bernards, R. PY - 2011 DA - 2011// TI - Taming the dragon: genomic biomarkers to individualize the treatment of cancer JO - Nat Med VL - 17 UR - https://doi.org/10.1038/nm.2311 DO - 10.1038/nm.2311 ID - Majewski2011 ER - TY - STD TI - Slosberg ED, Kang BP, Peguero J, Taylor M, Bauer TM, Berry DA, et al. Signature program: a platform of basket trials. Oncotarget. 2018;9:21383–95. doi:https://doi.org/10.18632/oncotarget.25109. ID - ref2 ER - TY - JOUR AU - Davies, H. AU - Bignell, G. R. AU - Cox, C. AU - Stephens, P. AU - Edkins, S. AU - Clegg, S. PY - 2002 DA - 2002// TI - Mutations of the BRAF gene in human cancer JO - Nature. VL - 417 UR - https://doi.org/10.1038/nature00766 DO - 10.1038/nature00766 ID - Davies2002 ER - TY - JOUR AU - Dhomen, N. AU - Marais, R. PY - 2007 DA - 2007// TI - New insight into BRAF mutations in cancer JO - Curr Opin Genet Dev VL - 17 UR - https://doi.org/10.1016/j.gde.2006.12.005 DO - 10.1016/j.gde.2006.12.005 ID - Dhomen2007 ER - TY - JOUR AU - Chapman, P. B. AU - Hauschild, A. AU - Robert, C. AU - Haanen, J. B. AU - Ascierto, P. AU - Larkin, J. PY - 2011 DA - 2011// TI - Improved survival with Vemurafenib in melanoma with BRAF V600E mutation JO - N Engl J Med VL - 364 UR - https://doi.org/10.1056/NEJMoa1103782 DO - 10.1056/NEJMoa1103782 ID - Chapman2011 ER - TY - JOUR AU - Klauschen, F. r. e. d. e. r. i. c. k. AU - Andreeff, M. i. c. h. a. e. l. AU - Keilholz, U. l. r. i. c. h. AU - Dietel, M. a. n. f. r. e. d. AU - Stenzinger, A. l. b. r. e. c. h. t. PY - 2014 DA - 2014// TI - The combinatorial complexity of cancer precision medicine JO - Oncoscience VL - 1 UR - https://doi.org/10.18632/oncoscience.66 DO - 10.18632/oncoscience.66 ID - Klauschen2014 ER - TY - JOUR AU - Hyman, D. M. AU - Puzanov, I. AU - Subbiah, V. AU - Faris, J. E. AU - Chau, I. AU - Blay, J. -. Y. PY - 2015 DA - 2015// TI - Vemurafenib in multiple nonmelanoma cancers with BRAF V600 mutations JO - N Engl J Med VL - 373 UR - https://doi.org/10.1056/NEJMoa1502309 DO - 10.1056/NEJMoa1502309 ID - Hyman2015 ER - TY - JOUR AU - Ding, M. i. c. h. a. e. l. Q. AU - Chen, L. u. j. i. a. AU - Cooper, G. r. e. g. o. r. y. F. AU - Young, J. o. n. a. t. h. a. n. D. AU - Lu, X. i. n. g. h. u. a. PY - 2017 DA - 2017// TI - Precision Oncology beyond Targeted Therapy: Combining Omics Data with Machine Learning Matches the Majority of Cancer Cells to Effective Therapeutics JO - Molecular Cancer Research VL - 16 UR - https://doi.org/10.1158/1541-7786.MCR-17-0378 DO - 10.1158/1541-7786.MCR-17-0378 ID - Ding2017 ER - TY - STD TI - Kaddi CD, Coulter WH, Wang MD. Developing Robust Predictive Models for Head and Neck Cancer across Microarray and RNA-seq Data. ACM-BCB . . . ACM Conf Bioinformatics, Comput Biol Biomed ACM Conf Bioinformatics, Comput Biol Biomed 2015;2015:393–402. doi:https://doi.org/10.1145/2808719.2808760. ID - ref9 ER - TY - JOUR AU - Prasasya, R. D. AU - Vang, K. Z. AU - Kreeger, P. K. PY - 2012 DA - 2012// TI - A multivariate model of ErbB network composition predicts ovarian cancer cell response to canertinib JO - Biotechnol Bioeng VL - 109 UR - https://doi.org/10.1002/bit.23297 DO - 10.1002/bit.23297 ID - Prasasya2012 ER - TY - JOUR AU - Schoeberl, B. AU - Kudla, A. AU - Masson, K. AU - Kalra, A. AU - Curley, M. AU - Finn, G. PY - 2017 DA - 2017// TI - Systems biology driving drug development: from design to the clinical testing of the anti-ErbB3 antibody seribantumab (MM-121) JO - NPJ Syst Biol Appl VL - 3 UR - https://doi.org/10.1038/npjsba.2016.34 DO - 10.1038/npjsba.2016.34 ID - Schoeberl2017 ER - TY - JOUR AU - Li, J. AU - Zhao, W. AU - Akbani, R. AU - Liu, W. AU - Ju, Z. AU - Ling, S. PY - 2017 DA - 2017// TI - Characterization of human Cancer cell lines by reverse-phase protein arrays JO - Cancer Cell VL - 31 UR - https://doi.org/10.1016/j.ccell.2017.01.005 DO - 10.1016/j.ccell.2017.01.005 ID - Li2017 ER - TY - STD TI - Pozdeyev N, Yoo M, Mackie R, Schweppe RE, Tan AC, Haugen BR. Integrating heterogeneous drug sensitivity data from cancer pharmacogenomic studies. Oncotarget. 2016;7:51619–25. doi:https://doi.org/10.18632/oncotarget.10010. ID - ref13 ER - TY - BOOK AU - Witten, I. H. AU - Frank, E. AU - Hall, M. A. AU - Pal, C. J. PY - 2016 DA - 2016// TI - Data mining, fourth edition: practical machine learning tools and techniques PB - Morgan Kaufmann Publishers Inc. CY - San Francisco, CA, USA ID - Witten2016 ER - TY - STD TI - Babur Ö, Luna A, Korkut A, Durupinar F, Siper MC, Dogrusoz U, et al. Causal interactions from proteomic profiles: molecular data meets pathway knowledge. bioRxiv. 2018. http://biorxiv.org/content/early/2018/05/21/258855.abstract. UR - http://biorxiv.org/content/early/2018/05/21/258855.abstract ID - ref15 ER - TY - JOUR AU - Yadav, B. AU - Wennerberg, K. AU - Aittokallio, T. AU - Tang, J. PY - 2015 DA - 2015// TI - Searching for drug synergy in complex dose–response landscapes using an interaction potency model JO - Comput Struct Biotechnol J VL - 13 UR - https://doi.org/10.1016/j.csbj.2015.09.001 DO - 10.1016/j.csbj.2015.09.001 ID - Yadav2015 ER - TY - JOUR AU - Basu, A. AU - Bodycombe, N. E. AU - Cheah, J. H. AU - Price, E. V. AU - Liu, K. AU - Schaefer, G. I. PY - 2013 DA - 2013// TI - An interactive resource to identify cancer genetic and lineage dependencies targeted by small molecules JO - Cell. VL - 154 UR - https://doi.org/10.1016/j.cell.2013.08.003 DO - 10.1016/j.cell.2013.08.003 ID - Basu2013 ER - TY - JOUR AU - Safikhani, Z. h. a. l. e. h. AU - Smirnov, P. e. t. r. AU - Freeman, M. a. r. k. AU - El-Hachem, N. e. h. m. e. AU - She, A. d. r. i. a. n. AU - Rene, Q. u. e. v. e. d. o. AU - Goldenberg, A. n. n. a. AU - Birkbak, N. i. c. o. l. a. i. J. AU - Hatzis, C. h. r. i. s. t. o. s. AU - Shi, L. e. m. i. n. g. AU - Beck, A. n. d. r. e. w. H. AU - Aerts, H. u. g. o. J. W. L. AU - Quackenbush, J. o. h. n. AU - Haibe-Kains, B. e. n. j. a. m. i. n. PY - 2017 DA - 2017// TI - Revisiting inconsistency in large pharmacogenomic studies JO - F1000Research VL - 5 UR - https://doi.org/10.12688/f1000research.9611.2 DO - 10.12688/f1000research.9611.2 ID - Safikhani2017 ER - TY - JOUR AU - Worley, B. AU - Powers, R. PY - 2013 DA - 2013// TI - Multivariate analysis in metabolomics JO - Curr Metabolomics VL - 1 UR - https://doi.org/10.2174/2213235X11301010092 DO - 10.2174/2213235X11301010092 ID - Worley2013 ER - TY - JOUR AU - Tibshirani, R. PY - 1996 DA - 1996// TI - Regression shrinkage and selection via the Lasso JO - J R Stat Soc Ser B VL - 58 ID - Tibshirani1996 ER - TY - JOUR AU - Breiman, L. PY - 2001 DA - 2001// JO - Random Forests Mach Learn VL - 45 UR - https://doi.org/10.1023/A:1010933404324 DO - 10.1023/A:1010933404324 ID - Breiman2001 ER - TY - JOUR AU - Hall, M. AU - Frank, E. AU - Holmes, G. AU - Pfahringer, B. AU - Reutemann, P. AU - Witten, I. H. PY - 2009 DA - 2009// TI - The WEKA data mining software JO - ACM SIGKDD Explor Newsl VL - 11 UR - https://doi.org/10.1145/1656274.1656278 DO - 10.1145/1656274.1656278 ID - Hall2009 ER - TY - STD TI - Jang INS, Neto EC, Guinney J, Friend SH, Margolin AA. Systematic Assessment Of Analytical Methods For Drug Sensitivity Prediction From Cancer Cell Line Data. In: Biocomputing 2014. WORLD SCIENTIFIC; 2013. p. 63–74. doi:doi:https://doi.org/10.1142/9789814583220_0007. ID - ref23 ER - TY - JOUR AU - Wagle, M. -. C. AU - Kirouac, D. AU - Klijn, C. AU - Liu, B. AU - Mahajan, S. AU - Junttila, M. PY - 2018 DA - 2018// TI - A transcriptional MAPK pathway activity score (MPAS) is a clinically relevant biomarker in multiple cancer types JO - NPJ Precis Oncol VL - 2 UR - https://doi.org/10.1038/s41698-018-0051-4 DO - 10.1038/s41698-018-0051-4 ID - Wagle2018 ER - TY - JOUR AU - Regan, K. E. AU - Payne, P. R. O. AU - Li, F. PY - 2017 DA - 2017// TI - Integrative network and transcriptomics-based approach predicts genotype- specific drug combinations for melanoma JO - AMIA Jt Summits Transl Sci proceedings AMIA Jt Summits Transl Sci VL - 2017 ID - Regan2017 ER - TY - BOOK AU - Dean, L. PY - 2012 DA - 2012// TI - Vemurafenib therapy and BRAF and NRAS genotype ID - Dean2012 ER - TY - JOUR AU - Agarwal, A. AU - Ressler, D. AU - Snyder, G. PY - 2015 DA - 2015// TI - The current and future state of companion diagnostics JO - Pharmgenomics Pers Med VL - 8 UR - https://doi.org/10.2147/PGPM.S49493 DO - 10.2147/PGPM.S49493 ID - Agarwal2015 ER - TY - JOUR AU - Jørgensen, J. a. n. T. r. ø. s. t. AU - Hersom, M. a. r. i. a. PY - 2016 DA - 2016// TI - Companion diagnostics—a tool to improve pharmacotherapy JO - Annals of Translational Medicine VL - 4 UR - https://doi.org/10.21037/atm.2016.12.26 DO - 10.21037/atm.2016.12.26 ID - Jørgensen2016 ER - TY - JOUR AU - Jørgensen, J. T. PY - 2014 DA - 2014// TI - Drug-diagnostics co-development in oncology JO - Front Oncol VL - 4 UR - https://doi.org/10.3389/fonc.2014.00208 DO - 10.3389/fonc.2014.00208 ID - Jørgensen2014 ER - TY - JOUR AU - Timpe, L. C. AU - Li, D. AU - Yen, T. -. Y. AU - Wong, J. AU - Yen, R. AU - Macher, B. A. PY - 2015 DA - 2015// TI - Mining the breast Cancer proteome for predictors of drug sensitivity JO - J Proteomics Bioinform VL - 8 UR - https://doi.org/10.4172/jpb.1000370 DO - 10.4172/jpb.1000370 ID - Timpe2015 ER - TY - JOUR AU - Koplev, S. i. m. o. n. AU - Lin, K. a. t. i. e. AU - Dohlman, A. n. d. e. r. s. B. AU - Ma’ayan, A. v. i. PY - 2018 DA - 2018// TI - Integration of pan-cancer transcriptomics with RPPA proteomics reveals mechanisms of epithelial-mesenchymal transition JO - PLOS Computational Biology VL - 14 UR - https://doi.org/10.1371/journal.pcbi.1005911 DO - 10.1371/journal.pcbi.1005911 ID - Koplev2018 ER - TY - JOUR AU - Mueller, C. AU - Liotta, L. A. AU - Espina, V. PY - 2010 DA - 2010// TI - Reverse phase protein microarrays advance to use in clinical trials JO - Mol Oncol VL - 4 UR - https://doi.org/10.1016/j.molonc.2010.09.003 DO - 10.1016/j.molonc.2010.09.003 ID - Mueller2010 ER - TY - JOUR AU - Eroglu, Z. AU - Ribas, A. PY - 2016 DA - 2016// TI - Combination therapy with BRAF and MEK inhibitors for melanoma: latest evidence and place in therapy JO - Ther Adv Med Oncol VL - 8 UR - https://doi.org/10.1177/1758834015616934 DO - 10.1177/1758834015616934 ID - Eroglu2016 ER - TY - JOUR AU - Broman, K. K. AU - Dossett, L. A. AU - Sun, J. AU - Eroglu, Z. AU - Zager, J. S. PY - 2019 DA - 2019// TI - Update on BRAF and MEK inhibition for treatment of melanoma in metastatic, unresectable, and adjuvant settings JO - Expert Opin Drug Saf VL - 18 UR - https://doi.org/10.1080/14740338.2019.1607289 DO - 10.1080/14740338.2019.1607289 ID - Broman2019 ER - TY - STD TI - Prasetyanti PR, Capone E, Barcaroli D, D’Agostino D, Volpe S, Benfante A, et al. ErbB-3 activation by NRG-1β sustains growth and promotes vemurafenib resistance in BRAF-V600E colon cancer stem cells (CSCs). Oncotarget. 2015;6:16902–11. doi:https://doi.org/10.18632/oncotarget.4642. ID - ref35 ER - TY - JOUR AU - Kwong, L. N. AU - Boland, G. M. AU - Frederick, D. T. AU - Helms, T. L. AU - Akid, A. T. AU - Miller, J. P. PY - 2015 DA - 2015// TI - Co-clinical assessment identifies patterns of BRAF inhibitor resistance in melanoma JO - J Clin Invest VL - 125 UR - https://doi.org/10.1172/JCI78954 DO - 10.1172/JCI78954 ID - Kwong2015 ER - TY - JOUR AU - Jonker, D. J. AU - O’Callaghan, C. J. AU - Karapetis, C. S. AU - Zalcberg, J. R. AU - Tu, D. AU - Au, H. -. J. PY - 2007 DA - 2007// TI - Cetuximab for the treatment of colorectal Cancer JO - N Engl J Med VL - 357 UR - https://doi.org/10.1056/NEJMoa071834 DO - 10.1056/NEJMoa071834 ID - Jonker2007 ER -