TY - JOUR AU - Pavlidis, N. AU - Pentheroudakis, G. PY - 2012 DA - 2012// TI - Cancer of unknown primary site JO - Lancet VL - 379 UR - https://doi.org/10.1016/S0140-6736(11)61178-1 DO - 10.1016/S0140-6736(11)61178-1 ID - Pavlidis2012 ER - TY - JOUR AU - Vogelstein, B. AU - Kinzler, K. W. PY - 2004 DA - 2004// TI - Cancer genes and the pathways they control JO - Nat Med VL - 10 UR - https://doi.org/10.1038/nm1087 DO - 10.1038/nm1087 ID - Vogelstein2004 ER - TY - JOUR AU - Vogelstein, B. AU - Papadopoulos, N. AU - Velculescu, V. E. AU - Zhou, S. AU - Diaz, L. A. AU - Kinzler, K. W. PY - 2013 DA - 2013// TI - Cancer genome landscapes JO - Science VL - 339 UR - https://doi.org/10.1126/science.1235122 DO - 10.1126/science.1235122 ID - Vogelstein2013 ER - TY - JOUR AU - Golub, T. AU - Slonim, D. AU - Tamayo, P. AU - Huard, C. AU - Gaasenbeek, M. AU - Mesirov, J. PY - 1999 DA - 1999// TI - Molecular classification of cancer: class discovery and class prediction by gene expression monitoring JO - Science VL - 286 UR - https://doi.org/10.1126/science.286.5439.531 DO - 10.1126/science.286.5439.531 ID - Golub1999 ER - TY - JOUR AU - Khan, J. AU - Wei, J. AU - Ringnér, M. AU - Saal, L. AU - Ladanyi, M. AU - Westermann, F. PY - 2001 DA - 2001// TI - Classification and diagnostic prediction of cancers using gene expression profiling and artificial neural networks JO - Nat Med VL - 7 UR - https://doi.org/10.1038/89044 DO - 10.1038/89044 ID - Khan2001 ER - TY - JOUR AU - Ramaswamy, S. AU - Tamayo, P. AU - Rifkin, R. AU - Mukherjee, S. AU - Yeang, C. AU - Angelo, M. PY - 2001 DA - 2001// TI - Multiclass cancer diagnosis using tumor gene expression signatures JO - Proc Natl Acad Sci USA VL - 98 UR - https://doi.org/10.1073/pnas.211566398 DO - 10.1073/pnas.211566398 ID - Ramaswamy2001 ER - TY - JOUR AU - Tibshirani, R. AU - Hastie, T. AU - Narasimhan, B. AU - Chu, G. PY - 2002 DA - 2002// TI - Diagnosis of multiple cancer types by shrunken centroids of gene expression JO - Proc Natl Acad Sci USA VL - 99 UR - https://doi.org/10.1073/pnas.082099299 DO - 10.1073/pnas.082099299 ID - Tibshirani2002 ER - TY - JOUR AU - Kang, S. AU - Li, Q. AU - Chen, Q. AU - Zhou, Y. AU - Park, S. AU - Lee, G. PY - 2017 DA - 2017// TI - CancerLocator: non-invasive cancer diagnosis and tissue-of-origin prediction using methylation profiles of cell-free DNA JO - Genome Biol VL - 18 UR - https://doi.org/10.1186/s13059-017-1191-5 DO - 10.1186/s13059-017-1191-5 ID - Kang2017 ER - TY - JOUR AU - Hao, X. AU - Luo, H. AU - Krawczyk, M. AU - Wei, W. AU - Wang, W. AU - Wang, J. PY - 2017 DA - 2017// TI - DNA methylation markers for diagnosis and prognosis of common cancers JO - Proc Natl Acad Sci USA VL - 114 UR - https://doi.org/10.1073/pnas.1703577114 DO - 10.1073/pnas.1703577114 ID - Hao2017 ER - TY - JOUR AU - Ciriello, G. AU - Miller, M. L. AU - Aksoy, B. A. AU - Senbabaoglu, Y. AU - Schultz, N. AU - Sander, C. PY - 2013 DA - 2013// TI - Emerging landscape of oncogenic signatures across human cancers JO - Nat Genet VL - 45 UR - https://doi.org/10.1038/ng.2762 DO - 10.1038/ng.2762 ID - Ciriello2013 ER - TY - JOUR AU - Polak, P. AU - Karlić, R. AU - Koren, A. AU - Thurman, R. AU - Sandstrom, R. AU - Lawrence, M. S. PY - 2015 DA - 2015// TI - Cell-of-origin chromatin organization shapes the mutational landscape of cancer JO - Nature VL - 518 UR - https://doi.org/10.1038/nature14221 DO - 10.1038/nature14221 ID - Polak2015 ER - TY - JOUR AU - Amar, D. AU - Izraeli, S. AU - Shamir, R. PY - 2017 DA - 2017// TI - Utilizing somatic mutation data from numerous studies for cancer research: proof of concept and applications JO - Oncogene VL - 36 UR - https://doi.org/10.1038/onc.2016.489 DO - 10.1038/onc.2016.489 ID - Amar2017 ER - TY - JOUR AU - Kirkizlar, E. AU - Zimmermann, B. AU - Constantin, T. AU - Swenerton, R. AU - Hoang, B. AU - Wayham, N. PY - 2015 DA - 2015// TI - Detection of clonal and subclonal copy-number variants in cell-free DNA from patients with breast cancer using a massively multiplexed PCR methodology JO - Transl Oncol VL - 8 UR - https://doi.org/10.1016/j.tranon.2015.08.004 DO - 10.1016/j.tranon.2015.08.004 ID - Kirkizlar2015 ER - TY - STD TI - cBioPortal for Cancer Genomics. http://www.cbioportal.org/. Accessed Feb 2016. UR - http://www.cbioportal.org/ ID - ref14 ER - TY - JOUR AU - Cerami, E. AU - Gao, J. AU - Dogrusoz, U. AU - Gross, B. E. AU - Sumer, S. O. AU - Aksoy, B. A. PY - 2012 DA - 2012// TI - The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data JO - Cancer Discov VL - 2 UR - https://doi.org/10.1158/2159-8290.CD-12-0095 DO - 10.1158/2159-8290.CD-12-0095 ID - Cerami2012 ER - TY - JOUR AU - Gao, J. AU - Aksoy, B. A. AU - Dogrusoz, U. AU - Dresdner, G. AU - Gross, B. AU - Sumer, S. O. PY - 2013 DA - 2013// TI - Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal JO - Sci Signal VL - 6 UR - https://doi.org/10.1126/scisignal.2004088 DO - 10.1126/scisignal.2004088 ID - Gao2013 ER - TY - JOUR AU - Lawrence, M. S. AU - Stojanov, P. AU - Polak, P. AU - Kryukov, G. V. AU - Cibulskis, K. AU - Sivachenko, A. PY - 2013 DA - 2013// TI - Mutational heterogeneity in cancer and the search for new cancer-associated genes JO - Nature VL - 499 UR - https://doi.org/10.1038/nature12213 DO - 10.1038/nature12213 ID - Lawrence2013 ER - TY - JOUR AU - Mermel, C. H. AU - Schumacher, S. E. AU - Hill, B. AU - Meyerson, M. L. AU - Beroukhim, R. AU - Getz, G. PY - 2011 DA - 2011// TI - GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers JO - Genome Biol VL - 12 UR - https://doi.org/10.1186/gb-2011-12-4-r41 DO - 10.1186/gb-2011-12-4-r41 ID - Mermel2011 ER - TY - JOUR AU - Futreal, P. A. AU - Coin, L. AU - Marshall, M. AU - Down, T. AU - Hubbard, T. AU - Wooster, R. PY - 2004 DA - 2004// TI - A census of human cancer genes JO - Nat Rev Cancer VL - 4 UR - https://doi.org/10.1038/nrc1299 DO - 10.1038/nrc1299 ID - Futreal2004 ER - TY - JOUR AU - Forbes, S. A. AU - Beare, D. AU - Gunasekaran, P. AU - Leung, K. AU - Bindal, N. AU - Boutselakis, H. PY - 2015 DA - 2015// TI - COSMIC: exploring the world’s knowledge of somatic mutations in human cancer JO - Nucleic Acids Res VL - 43 UR - https://doi.org/10.1093/nar/gku1075 DO - 10.1093/nar/gku1075 ID - Forbes2015 ER - TY - STD TI - HUGO Gene Nomenclature Committee (HGNC). HGNC Database. EMBL Outstation – Hinxton. www.genenames.org. Accessed June 2017. UR - http://www.genenames.org ID - ref21 ER - TY - JOUR AU - Cortes, C. AU - Vapnik, V. PY - 1995 DA - 1995// TI - Support-vector networks JO - Mach Learn VL - 20 ID - Cortes1995 ER - TY - BOOK AU - Hastie, T. AU - Tibshirani, R. AU - Friedman, J. PY - 2009 DA - 2009// TI - The elements of statistical learning: data mining, inference, and prediction, 2nd ed PB - Springer CY - New York UR - https://doi.org/10.1007/978-0-387-84858-7 DO - 10.1007/978-0-387-84858-7 ID - Hastie2009 ER - TY - JOUR AU - Breiman, L. PY - 2001 DA - 2001// TI - Random forests JO - Mach Learn VL - 45 UR - https://doi.org/10.1023/A:1010933404324 DO - 10.1023/A:1010933404324 ID - Breiman2001 ER - TY - CHAP AU - Caruana, R. AU - Niculescu-Mizil, A. PY - 2006 DA - 2006// TI - An empirical comparison of supervised learning algorithms BT - Proceedings of the 23rd International Conference on Machine Learning. ICML ’06 PB - ACM CY - New York ID - Caruana2006 ER - TY - JOUR AU - Guyon, I. AU - Weston, J. AU - Barnhill, S. AU - Vapnik, V. PY - 2002 DA - 2002// TI - Gene selection for cancer classification using support vector machines JO - Mach Learn VL - 46 UR - https://doi.org/10.1023/A:1012487302797 DO - 10.1023/A:1012487302797 ID - Guyon2002 ER - TY - JOUR AU - Zhou, X. AU - Tuck, D. P. PY - 2007 DA - 2007// TI - MSVM-RFE: extensions of SVM-RFE for multiclass gene selection on DNA microarray data JO - Bioinformatics VL - 23 UR - https://doi.org/10.1093/bioinformatics/btm036 DO - 10.1093/bioinformatics/btm036 ID - Zhou2007 ER - TY - STD TI - Helleputte T. LiblineaR: Linear predictive models based on the LIBLINEAR C/C++ library. 2015. R package version 1.94-2. http://cran.r-project.org/web/packages/LiblineaR/index.html. UR - http://cran.r-project.org/web/packages/LiblineaR/index.html ID - ref28 ER - TY - BOOK PY - 2015 DA - 2015// TI - R: a language and environment for statistical computing PB - R Foundation for Statistical Computing CY - Vienna, Austria ID - ref29 ER - TY - JOUR AU - Friedman, J. AU - Hastie, T. AU - Tibshirani, R. PY - 2010 DA - 2010// TI - Regularization paths for generalized linear models via coordinate descent JO - J Stat Softw VL - 33 UR - https://doi.org/10.18637/jss.v033.i01 DO - 10.18637/jss.v033.i01 ID - Friedman2010 ER - TY - JOUR AU - Zhu, J. AU - Hastie, T. PY - 2004 DA - 2004// TI - Classification of gene microarrays by penalized logistic regression JO - Biostatistics VL - 5 UR - https://doi.org/10.1093/biostatistics/kxg046 DO - 10.1093/biostatistics/kxg046 ID - Zhu2004 ER - TY - JOUR AU - Díaz-Uriarte, R. AU - Alvarez de Andrés, S. PY - 2006 DA - 2006// TI - Gene selection and classification of microarray data using random forest JO - BMC Bioinformatics VL - 7 UR - https://doi.org/10.1186/1471-2105-7-3 DO - 10.1186/1471-2105-7-3 ID - Díaz-Uriarte2006 ER - TY - JOUR AU - Wright, M. N. AU - Ziegler, A. PY - 2017 DA - 2017// TI - Ranger: A fast implementation of random forests for high dimensional data in C++ and R JO - J Stat Softw VL - 77 UR - https://doi.org/10.18637/jss.v077.i01 DO - 10.18637/jss.v077.i01 ID - Wright2017 ER - TY - JOUR AU - Ein-Dor, L. AU - Kela, I. AU - Getz, G. AU - Givol, D. AU - Domany, E. PY - 2005 DA - 2005// TI - Outcome signature genes in breast cancer: is there a unique set? JO - Bioinformatics VL - 21 UR - https://doi.org/10.1093/bioinformatics/bth469 DO - 10.1093/bioinformatics/bth469 ID - Ein-Dor2005 ER - TY - JOUR AU - Meinshausen, N. AU - Bühlmann, P. PY - 2010 DA - 2010// TI - Stability selection JO - J R Stat Soc Series B Stat Methodol VL - 72 UR - https://doi.org/10.1111/j.1467-9868.2010.00740.x DO - 10.1111/j.1467-9868.2010.00740.x ID - Meinshausen2010 ER - TY - JOUR AU - Rubio-Perez, C. AU - Tamborero, D. AU - Schroeder, M. P. AU - Antolín, A. A. AU - Deu-Pons, J. AU - Perez-Llamas, C. PY - 2015 DA - 2015// TI - In silico prescription of anticancer drugs to cohorts of 28 tumor types reveals targeting opportunities JO - Cancer Cell VL - 27 UR - https://doi.org/10.1016/j.ccell.2015.02.007 DO - 10.1016/j.ccell.2015.02.007 ID - Rubio-Perez2015 ER - TY - JOUR AU - Gonzalez-Perez, A. AU - Perez-Llamas, C. AU - Deu-Pons, J. AU - Tamborero, D. AU - Schroeder, M. P. AU - Jene-Sanz, A. PY - 2013 DA - 2013// TI - IntOGen-mutations identifies cancer drivers across tumor types JO - Nat Methods VL - 10 UR - https://doi.org/10.1038/nmeth.2642 DO - 10.1038/nmeth.2642 ID - Gonzalez-Perez2013 ER - TY - JOUR AU - O’Leary, N. A. AU - Wright, M. W. AU - Brister, J. R. AU - Ciufo, S. AU - Haddad, D. AU - McVeigh, R. PY - 2016 DA - 2016// TI - Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation JO - Nucleic Acids Res VL - 44 UR - https://doi.org/10.1093/nar/gkv1189 DO - 10.1093/nar/gkv1189 ID - O’Leary2016 ER - TY - JOUR AU - Fabregat, A. AU - Sidiropoulos, K. AU - Garapati, P. AU - Gillespie, M. AU - Hausmann, K. AU - Haw, R. PY - 2016 DA - 2016// TI - The reactome pathway knowledgebase JO - Nucleic Acids Res VL - 44 UR - https://doi.org/10.1093/nar/gkv1351 DO - 10.1093/nar/gkv1351 ID - Fabregat2016 ER - TY - JOUR AU - Milacic, M. AU - Haw, R. AU - Rothfels, K. AU - Wu, G. AU - Croft, D. AU - Hermjakob, H. PY - 2012 DA - 2012// TI - Annotating cancer variants and anti-cancer therapeutics in reactome JO - Cancers (Basel) VL - 4 UR - https://doi.org/10.3390/cancers4041180 DO - 10.3390/cancers4041180 ID - Milacic2012 ER - TY - JOUR AU - Martinez, P. AU - McGranahan, N. AU - Birkbak, N. J. AU - Gerlinger, M. AU - Swanton, C. PY - 2013 DA - 2013// TI - Computational optimisation of targeted DNA sequencing for cancer detection JO - Sci Rep VL - 3 UR - https://doi.org/10.1038/srep03309 DO - 10.1038/srep03309 ID - Martinez2013 ER - TY - JOUR AU - Rubio-Perez, C. AU - Deu-Pons, J. AU - Tamborero, D. AU - Lopez-Bigas, N. AU - Gonzalez-Perez, A. PY - 2016 DA - 2016// TI - Rational design of cancer gene panels with OncoPaD JO - Genome Med VL - 8 UR - https://doi.org/10.1186/s13073-016-0349-1 DO - 10.1186/s13073-016-0349-1 ID - Rubio-Perez2016 ER - TY - JOUR AU - Haber, D. A. AU - Velculescu, V. E. PY - 2014 DA - 2014// TI - Blood-based analyses of cancer: circulating tumor cells and circulating tumor DNA JO - Cancer Discov VL - 4 UR - https://doi.org/10.1158/2159-8290.CD-13-1014 DO - 10.1158/2159-8290.CD-13-1014 ID - Haber2014 ER - TY - JOUR AU - Khurana, E. AU - Fu, Y. AU - Chakravarty, D. AU - Demichelis, F. AU - Rubin, M. A. AU - Gerstein, M. PY - 2016 DA - 2016// TI - Role of non-coding sequence variants in cancer JO - Nat Rev Genet VL - 17 UR - https://doi.org/10.1038/nrg.2015.17 DO - 10.1038/nrg.2015.17 ID - Khurana2016 ER - TY - JOUR AU - Diaz, L. A. J. AU - Bardelli, A. PY - 2014 DA - 2014// TI - Liquid biopsies: genotyping circulating tumor DNA JO - J Clin Oncol VL - 32 UR - https://doi.org/10.1200/JCO.2012.45.2011 DO - 10.1200/JCO.2012.45.2011 ID - Diaz2014 ER - TY - JOUR AU - Bettegowda, C. AU - Sausen, M. AU - Leary, R. J. AU - Kinde, I. AU - Wang, Y. AU - Agrawal, N. PY - 2014 DA - 2014// TI - Detection of circulating tumor DNA in early- and late-stage human malignancies JO - Sci Transl Med VL - 6 UR - https://doi.org/10.1126/scitranslmed.3007094 DO - 10.1126/scitranslmed.3007094 ID - Bettegowda2014 ER - TY - JOUR PY - 2014 DA - 2014// TI - Comprehensive molecular characterization of urothelial bladder carcinoma JO - Nature VL - 507 UR - https://doi.org/10.1038/nature12965 DO - 10.1038/nature12965 ID - ref47 ER - TY - JOUR AU - Ciriello, G. AU - Gatza, M. L. AU - Beck, A. H. AU - Wilkerson, M. D. AU - Rhie, S. K. AU - Pastore, A. PY - 2015 DA - 2015// TI - Comprehensive molecular portraits of invasive lobular breast cancer JO - Cell VL - 163 UR - https://doi.org/10.1016/j.cell.2015.09.033 DO - 10.1016/j.cell.2015.09.033 ID - Ciriello2015 ER - TY - JOUR PY - 2012 DA - 2012// TI - Comprehensive molecular characterization of human colon and rectal cancer JO - Nature VL - 487 UR - https://doi.org/10.1038/nature11252 DO - 10.1038/nature11252 ID - ref49 ER - TY - JOUR AU - Brennan, C. W. AU - Verhaak, R. G. AU - McKenna, A. AU - Campos, B. AU - Noushmehr, H. AU - Salama, S. R. PY - 2013 DA - 2013// TI - The somatic genomic landscape of glioblastoma JO - Cell VL - 155 UR - https://doi.org/10.1016/j.cell.2013.09.034 DO - 10.1016/j.cell.2013.09.034 ID - Brennan2013 ER - TY - JOUR PY - 2015 DA - 2015// TI - Comprehensive genomic characterization of head and neck squamous cell carcinomas JO - Nature VL - 517 UR - https://doi.org/10.1038/nature14129 DO - 10.1038/nature14129 ID - ref51 ER - TY - JOUR PY - 2013 DA - 2013// TI - Comprehensive molecular characterization of clear cell renal cell carcinoma JO - Nature VL - 499 UR - https://doi.org/10.1038/nature12222 DO - 10.1038/nature12222 ID - ref52 ER - TY - JOUR PY - 2013 DA - 2013// TI - Genomic and epigenomic landscapes of adult de novo acute myeloid leukemia JO - N Engl J Med VL - 368 UR - https://doi.org/10.1056/NEJMoa1301689 DO - 10.1056/NEJMoa1301689 ID - ref53 ER - TY - JOUR PY - 2014 DA - 2014// TI - Comprehensive molecular profiling of lung adenocarcinoma JO - Nature VL - 511 UR - https://doi.org/10.1038/nature13385 DO - 10.1038/nature13385 ID - ref54 ER - TY - JOUR PY - 2012 DA - 2012// TI - Comprehensive genomic characterization of squamous cell lung cancers JO - Nature VL - 489 ID - ref55 ER - TY - JOUR PY - 2011 DA - 2011// TI - Integrated genomic analyses of ovarian carcinoma JO - Nature VL - 474 UR - https://doi.org/10.1038/nature10166 DO - 10.1038/nature10166 ID - ref56 ER - TY - JOUR AU - Kandoth, C. AU - Schultz, N. AU - Cherniack, A. D. AU - Akbani, R. AU - Liu, Y. PY - 2013 DA - 2013// TI - Integrated genomic characterization of endometrial carcinoma JO - Nature VL - 497 UR - https://doi.org/10.1038/nature12113 DO - 10.1038/nature12113 ID - Kandoth2013 ER - TY - JOUR AU - Ho, A. S. AU - Kannan, K. AU - Roy, D. M. AU - Morris, L. G. AU - Ganly, I. AU - Katabi, N. PY - 2013 DA - 2013// TI - The mutational landscape of adenoid cystic carcinoma JO - Nat Genet VL - 45 UR - https://doi.org/10.1038/ng.2643 DO - 10.1038/ng.2643 ID - Ho2013 ER - TY - JOUR AU - Ahn, S. M. AU - Jang, S. J. AU - Shim, J. H. AU - Kim, D. AU - Hong, S. M. AU - Sung, C. O. PY - 2014 DA - 2014// TI - Genomic portrait of resectable hepatocellular carcinomas: implications of RB1 and FGF19 aberrations for patient stratification JO - Hepatology VL - 60 UR - https://doi.org/10.1002/hep.27198 DO - 10.1002/hep.27198 ID - Ahn2014 ER - TY - JOUR PY - 2015 DA - 2015// TI - The molecular taxonomy of primary prostate cancer JO - Cell VL - 163 UR - https://doi.org/10.1016/j.cell.2015.10.025 DO - 10.1016/j.cell.2015.10.025 ID - ref60 ER - TY - JOUR PY - 2014 DA - 2014// TI - Comprehensive molecular characterization of gastric adenocarcinoma JO - Nature VL - 513 UR - https://doi.org/10.1038/nature13480 DO - 10.1038/nature13480 ID - ref61 ER - TY - JOUR PY - 2014 DA - 2014// TI - Integrated genomic characterization of papillary thyroid carcinoma JO - Cell VL - 159 UR - https://doi.org/10.1016/j.cell.2014.09.050 DO - 10.1016/j.cell.2014.09.050 ID - ref62 ER - TY - JOUR AU - Davis, C. F. AU - Ricketts, C. J. AU - Wang, M. AU - Yang, L. AU - Cherniack, A. D. AU - Shen, H. PY - 2014 DA - 2014// TI - The somatic genomic landscape of chromophobe renal cell carcinoma JO - Cancer Cell VL - 26 UR - https://doi.org/10.1016/j.ccr.2014.07.014 DO - 10.1016/j.ccr.2014.07.014 ID - Davis2014 ER -