Bibliografía

Ashburner, M., Ball, C. A., Blake, J. A., Botstein, D., Butler, H., Cherry, J. M., … others. (2000). Gene ontology: Tool for the unification of biology. Nature Genetics, 25(1), 25.

Atchley, D. P., Albarracin, C. T., Lopez, A., Valero, V., Amos, C. I., Gonzalez-Angulo, A. M., … Arun, B. K. (2008). Clinical and pathologic characteristics of patients with brca-positive and brca-negative breast cancer. Journal of Clinical Oncology, 26(26), 4282–4288.

Aure, M. R., Vitelli, V., Jernström, S., Kumar, S., Krohn, M., Due, E. U., … others. (2017). Integrative clustering reveals a novel split in the luminal a subtype of breast cancer with impact on outcome. Breast Cancer Research, 19(1), 44.

Barrett, T., Wilhite, S. E., Ledoux, P., Evangelista, C., Kim, I. F., Tomashevsky, M., … others. (2012). NCBI geo: Archive for functional genomics data sets—update. Nucleic Acids Research, 41(D1), D991–D995.

Bastien, R. R., Rodrı'guez-Lescure, Á., Ebbert, M. T., Prat, A., Munárriz, B., Rowe, L., … others. (2012). PAM50 breast cancer subtyping by rt-qPCR and concordance with standard clinical molecular markers. BMC Medical Genomics, 5(1), 1.

Berkeley, C. (2004). Linear models and empirical bayes methods for assessing differential expression in microarray experiments. E-Book Available at Http://Www. Bepress. Com/Sagmb/Vol3/Iss1/Art3.[PubMed].

Bittner, M. (2005). Expression project for oncology (expo). National Center for Biotechnology Information. Available at: Http://Www. Ncbi. Nlm. Nih. Gov/Geo.

Bonnefoi, H., Potti, A., Delorenzi, M., Mauriac, L., Campone, M., Tubiana-Hulin, M., … others. (2007). RETRACTED: Validation of gene signatures that predict the response of breast cancer to neoadjuvant chemotherapy: A substudy of the eortc 10994/big 00-01 clinical trial. Elsevier.

Bos, P. D., Zhang, X. H.-F., Nadal, C., Shu, W., Gomis, R. R., Nguyen, D. X., … others. (2009). Genes that mediate breast cancer metastasis to the brain. Nature, 459(7249), 1005.

Burns, P. (2011). The r inferno. Lulu. com.

Cantor, S. B., Bell, D. W., Ganesan, S., Kass, E. M., Drapkin, R., Grossman, S., … others. (2001). BACH1, a novel helicase-like protein, interacts directly with brca1 and contributes to its dna repair function. Cell, 105(1), 149–160.

Canuel, V., Rance, B., Avillach, P., Degoulet, P., & Burgun, A. (2014). Translational research platforms integrating clinical and omics data: A review of publicly available solutions. Briefings in Bioinformatics, 16(2), 280–290.

Carlson, M., Falcon, S., Pages, H., & Li, N. (2013). Org. Hs. Eg. Db: Genome wide annotation for human. R package version.

Cheang, M. C., Chia, S. K., Voduc, D., Gao, D., Leung, S., Snider, J., … others. (2009). Ki67 index, her2 status, and prognosis of patients with luminal b breast cancer. JNCI: Journal of the National Cancer Institute, 101(10), 736–750.

Chen, R., & Snyder, M. (2013). Promise of personalized omics to precision medicine. Wiley Interdisciplinary Reviews: Systems Biology and Medicine, 5(1), 73–82.

Chin, K., DeVries, S., Fridlyand, J., Spellman, P. T., Roydasgupta, R., Kuo, W.-L., … others. (2006). Genomic and transcriptional aberrations linked to breast cancer pathophysiologies. Cancer Cell, 10(6), 529–541.

Cleveland, W. S. (2001). Data science: An action plan for expanding the technical areas of the field of statistics. International Statistical Review, 69(1), 21–26.

Consortium, G. O. (2016). Expansion of the gene ontology knowledgebase and resources. Nucleic Acids Research, 45(D1), D331–D338.

Cooper, K., & Torczon, L. (2011). Engineering a compiler. Elsevier.

Creighton, C. J., Chen, F., Zhang, Y., Gibbons, D. L., Deneen, B., Kwiatkowski, D., & Ittmann, M. (2018). Pan-cancer molecular classes transcending tumor lineage across 32 cancer types, multiple data platforms, and over 10,000 cases. Clinical Cancer Research, clincanres–3378.

Curtis, C., Shah, S. P., Chin, S.-F., Turashvili, G., Rueda, O. M., Dunning, M. J., … others. (2012). The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups. Nature, 486(7403), 346.

Dai, X., Li, T., Bai, Z., Yang, Y., Liu, X., Zhan, J., & Shi, B. (2015). Breast cancer intrinsic subtype classification, clinical use and future trends. American Journal of Cancer Research, 5(10), 2929.

Davis, A. P., Grondin, C. J., Lennon-Hopkins, K., Saraceni-Richards, C., Sciaky, D., King, B. L., … Mattingly, C. J. (2014). The comparative toxicogenomics database’s 10th year anniversary: Update 2015. Nucleic Acids Research, gku935.

Dedeurwaerder, S., Desmedt, C., Calonne, E., Singhal, S. K., Haibe-Kains, B., Defrance, M., … others. (2011). DNA methylation profiling reveals a predominant immune component in breast cancers. EMBO Molecular Medicine, 3(12), 726–741.

Edelman, E., Porrello, A., Guinney, J., Balakumaran, B., Bild, A., Febbo, P. G., & Mukherjee, S. (2006). Analysis of sample set enrichment scores: Assaying the enrichment of sets of genes for individual samples in genome-wide expression profiles. Bioinformatics, 22(14), e108–e116.

Ein-Dor, L., Kela, I., Getz, G., Givol, D., & Domany, E. (2005). Outcome signature genes in breast cancer: Is there a unique set? Bioinformatics, 21(2), 171–178.

Ein-Dor, L., Zuk, O., & Domany, E. (2006). Thousands of samples are needed to generate a robust gene list for predicting outcome in cancer. Proceedings of the National Academy of Sciences, 103(15), 5923–5928.

Falcon, S., & Gentleman, R. (2006). Using gostats to test gene lists for go term association. Bioinformatics, 23(2), 257–258.

Fang, H., & Gough, J. (2014). Thednet’approach promotes emerging research on cancer patient survival. Genome Medicine, 6(8), 64.

Farmer, P., Bonnefoi, H., Becette, V., Tubiana-Hulin, M., Fumoleau, P., Larsimont, D., … others. (2005). Identification of molecular apocrine breast tumours by microarray analysis. Breast Cancer Research, 7(2), P2–11.

Fernandez, E. A., & Casares, F. M. (2018). Current challenges for big omics data analytics and precision medicine. Med Sci Tech, 59, 1–3.

Fernández, E., Alvarez, M., Podhajcer, O., & Stolovitzky, G. (2007). Genomica funcional: En busca de la función de los genes. National Academy of Science, Argentine, 13, 63–76.

Fresno, C., & Fernández, E. A. (2013). RDAVIDWebService: A versatile r interface to david. Bioinformatics, 29(21), 2810–2811.

Fresno, C., González, G. A., Merino, G. A., Flesia, A. G., Podhajcer, O. L., Llera, A. S., & Fernández, E. A. (2016). A novel non-parametric method for uncertainty evaluation of correlation-based molecular signatures: Its application on pam50 algorithm. Bioinformatics, 33(5), 693–700.

Fresno, C., González, G. A., Merino, G. A., Rodriguez, J. C., Balzarini, M. G., & Fernández, E. A. (2014). Control de calidad de microarreglos de adn mediante descomposición anova-pca/pls. XIX Reunión Científica Del Grupo Argentino de Biometría.

Fresno, C., Llera, A. S., Girotti, M. R., Valacco, M. P., López, J. A., Podhajcer, O. L., … Fernández, E. A. (2012). The multi-reference contrast method: Facilitating set enrichment analysis. Computers in Biology and Medicine, 42(2), 188–194.

Gendoo, D. M., Ratanasirigulchai, N., Schröder, M. S., Paré, L., Parker, J. S., Prat, A., & Haibe-Kains, B. (2015). Genefu: An r/bioconductor package for computation of gene expression-based signatures in breast cancer. Bioinformatics, 32(7), 1097–1099.

Gillespie, C., & Lovelace, R. (2016). Efficient r programming: A practical guide to smarter programming. " O’Reilly Media, Inc.".

Goeman, J. J., & Bühlmann, P. (2007). Analyzing gene expression data in terms of gene sets: Methodological issues. Bioinformatics, 23(8), 980–987.

Goldhirsch, A., Winer, E. P., Coates, A., Gelber, R., Piccart-Gebhart, M., Thürlimann, B., … others. (2013). Personalizing the treatment of women with early breast cancer: Highlights of the st gallen international expert consensus on the primary therapy of early breast cancer 2013. Annals of Oncology, 24(9), 2206–2223.

Grasso, C. S., Wu, Y.-M., Robinson, D. R., Cao, X., Dhanasekaran, S. M., Khan, A. P., … others. (2012). The mutational landscape of lethal castration-resistant prostate cancer. Nature, 487(7406), 239.

Gromova, I., Gromov, P., Honma, N., Kumar, S., Rimm, D., Talman, M.-L. M., … Moreira, J. (2015). High level phgdh expression in breast is predominantly associated with keratin 5-positive cell lineage independently of malignancy. Molecular Oncology, 9(8), 1636–1654.

Guen, V. J., Chavarria, T. E., Kröger, C., Ye, X., Weinberg, R. A., & Lees, J. A. (2017). EMT programs promote basal mammary stem cell and tumor-initiating cell stemness by inducing primary ciliogenesis and hedgehog signaling. Proceedings of the National Academy of Sciences, 201711534.

Haibe-Kains, B., Desmedt, C., Loi, S., Culhane, A. C., Bontempi, G., Quackenbush, J., & Sotiriou, C. (2012). A three-gene model to robustly identify breast cancer molecular subtypes. Journal of the National Cancer Institute, 104(4), 311–325.

Hanahan, D., & Weinberg, R. A. (2000). The hallmarks of cancer. Cell, 100(1), 57–70.

Hess, K. R., Anderson, K., Symmans, W. F., Valero, V., Ibrahim, N., Mejia, J. A., … others. (2006). Pharmacogenomic predictor of sensitivity to preoperative chemotherapy with paclitaxel and fluorouracil, doxorubicin, and cyclophosphamide in breast cancer. Journal of Clinical Oncology, 24(26), 4236–4244.

Hoadley, K. A., Yau, C., Wolf, D. M., Cherniack, A. D., Tamborero, D., Ng, S., … others. (2014). Multiplatform analysis of 12 cancer types reveals molecular classification within and across tissues of origin. Cell, 158(4), 929–944.

Huang, D. W., Sherman, B. T., & Lempicki, R. A. (2008a). Bioinformatics enrichment tools: Paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Research, 37(1), 1–13.

Huang, D. W., Sherman, B. T., & Lempicki, R. A. (2008b). Systematic and integrative analysis of large gene lists using david bioinformatics resources. Nature Protocols, 4(1), 44.

Joshi-Tope, G., Gillespie, M., Vastrik, I., D’Eustachio, P., Schmidt, E., Bono, B. de, … others. (2005). Reactome: A knowledgebase of biological pathways. Nucleic Acids Research, 33(suppl_1), D428–D432.

Kanehisa, M., & Goto, S. (2000). KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Research, 28(1), 27–30.

Kedaigle, A., & Fraenkel, E. (2018). Turning omics data into therapeutic insights. Current Opinion in Pharmacology, 42, 95–101.

Khatri, P., Sirota, M., & Butte, A. J. (2012). Ten years of pathway analysis: Current approaches and outstanding challenges. PLoS Computational Biology, 8(2), e1002375.

Kolesnikov, N., Hastings, E., Keays, M., Melnichuk, O., Tang, Y. A., Williams, E., … others. (2014). ArrayExpress update—simplifying data submissions. Nucleic Acids Research, 43(D1), D1113–D1116.

Korkola, J. E., Blaveri, E., DeVries, S., Moore, D. H., Hwang, E. S., Chen, Y.-Y., … Waldman, F. M. (2007). Identification of a robust gene signature that predicts breast cancer outcome in independent data sets. BMC Cancer, 7(1), 61.

Kuleshov, M. V., Jones, M. R., Rouillard, A. D., Fernandez, N. F., Duan, Q., Wang, Z., … others. (2016). Enrichr: A comprehensive gene set enrichment analysis web server 2016 update. Nucleic Acids Research, 44(W1), W90–W97.

Kwa, M., Makris, A., & Esteva, F. J. (2017). Clinical utility of gene-expression signatures in early stage breast cancer. Nature Reviews Clinical Oncology, 14(10), 595.

Law, C. W., Chen, Y., Shi, W., & Smyth, G. K. (2014). Voom: Precision weights unlock linear model analysis tools for rna-seq read counts. Genome Biology, 15(2), R29.

Li, Q., Eklund, A. C., Juul, N., Haibe-Kains, B., Workman, C. T., Richardson, A. L., … Swanton, C. (2010). Minimising immunohistochemical false negative er classification using a complementary 23 gene expression signature of er status. PloS One, 5(12), e15031.

Liberzon, A., Subramanian, A., Pinchback, R., Thorvaldsdóttir, H., Tamayo, P., & Mesirov, J. P. (2011). Molecular signatures database (msigdb) 3.0. Bioinformatics, 27(12), 1739–1740.

Liedtke, C., Mazouni, C., Hess, K. R., André, F., Tordai, A., Mejia, J. A., … others. (2008). Response to neoadjuvant therapy and long-term survival in patients with triple-negative breast cancer. Journal of Clinical Oncology, 26(8), 1275–1281.

Liu, B., Shen, X., & Pan, W. (2016). Integrative and regularized principal component analysis of multiple sources of data. Statistics in Medicine, 35(13), 2235–2250.

Llera, A. S., Podhajcer, O. L., Breitenbach, M., Santini, L., Muller, B., Daneri Navarro, A., … others. (2015). Translational cancer research comes of age in latin america. In American sci transl med (Vol. 7, p. 319). American Association for the Advancement of Science.

Love, M. I., Huber, W., & Anders, S. (2014). Moderated estimation of fold change and dispersion for rna-seq data with deseq2. Genome Biology, 15(12), 550.

Lu, X., Lu, X., Wang, Z. C., Iglehart, J. D., Zhang, X., & Richardson, A. L. (2008). Predicting features of breast cancer with gene expression patterns. Breast Cancer Research and Treatment, 108(2), 191.

Manoli, T., Gretz, N., Gröne, H.-J., Kenzelmann, M., Eils, R., & Brors, B. (2006). Group testing for pathway analysis improves comparability of different microarray datasets. Bioinformatics, 22(20), 2500–2506.

McCarthy, D. J., & Smyth, G. K. (2009). Testing significance relative to a fold-change threshold is a treat. Bioinformatics, 25(6), 765–771.

Meng, C., Kuster, B., Culhane, A. C., & Gholami, A. M. (2014). A multivariate approach to the integration of multi-omics datasets. BMC Bioinformatics, 15(1), 162.

Metzger Filho, O., Ignatiadis, M., & Sotiriou, C. (2011). Genomic grade index: An important tool for assessing breast cancer tumor grade and prognosis. Critical Reviews in Oncology/Hematology, 77(1), 20–29.

Miller, L. D., Smeds, J., George, J., Vega, V. B., Vergara, L., Ploner, A., … others. (2005). An expression signature for p53 status in human breast cancer predicts mutation status, transcriptional effects, and patient survival. Proceedings of the National Academy of Sciences, 102(38), 13550–13555.

Minn, A. J., Gupta, G. P., Padua, D., Bos, P., Nguyen, D. X., Nuyten, D., … others. (2007). Lung metastasis genes couple breast tumor size and metastatic spread. Proceedings of the National Academy of Sciences, 104(16), 6740–6745.

Minn, A. J., Gupta, G. P., Siegel, P. M., Bos, P. D., Shu, W., Giri, D. D., … Massagué, J. (2005). Genes that mediate breast cancer metastasis to lung. Nature, 436(7050), 518.

Mishra, P., Törönen, P., Leino, Y., & Holm, L. (2014). Gene set analysis: Limitations in popular existing methods and proposed improvements. Bioinformatics, 30(19), 2747–2756.

Natrajan, R., Weigelt, B., Mackay, A., Geyer, F. C., Grigoriadis, A., Tan, D. S., … others. (2010). An integrative genomic and transcriptomic analysis reveals molecular pathways and networks regulated by copy number aberrations in basal-like, her2 and luminal cancers. Breast Cancer Research and Treatment, 121(3), 575–589.

Network, C. G. A., & others. (2012). Comprehensive molecular portraits of human breast tumours. Nature, 490(7418), 61.

Nishimura, D. (2001). BioCarta. Biotech Software & Internet Report: The Computer Software Journal for Scient, 2(3), 117–120.

Parker, J. S., Mullins, M., Cheang, M. C., Leung, S., Voduc, D., Vickery, T., … others. (2009). Supervised risk predictor of breast cancer based on intrinsic subtypes. Journal of Clinical Oncology, 27(8), 1160.

Pavlidis, P., Qin, J., Arango, V., Mann, J. J., & Sibille, E. (2004). Using the gene ontology for microarray data mining: A comparison of methods and application to age effects in human prefrontal cortex. Neurochemical Research, 29(6), 1213–1222.

Pawitan, Y., Bjöhle, J., Amler, L., Borg, A.-L., Egyhazi, S., Hall, P., … others. (2005). Gene expression profiling spares early breast cancer patients from adjuvant therapy: Derived and validated in two population-based cohorts. Breast Cancer Research, 7(6), R953.

Perou, C. M., Sørlie, T., Eisen, M. B., Van De Rijn, M., Jeffrey, S. S., Rees, C. A., … others. (2000). Molecular portraits of human breast tumours. Nature, 406(6797), 747.

Prat, A., Parker, J. S., Karginova, O., Fan, C., Livasy, C., Herschkowitz, J. I., … Perou, C. M. (2010). Phenotypic and molecular characterization of the claudin-low intrinsic subtype of breast cancer. Breast Cancer Research, 12(5), R68.

Prat, A., & Perou, C. M. (2011). Deconstructing the molecular portraits of breast cancer. Molecular Oncology, 5(1), 5–23.

Reis-Filho, J. S., & Pusztai, L. (2011). Gene expression profiling in breast cancer: Classification, prognostication, and prediction. The Lancet, 378(9805), 1812–1823.

Richardson, A. L., Wang, Z. C., De Nicolo, A., Lu, X., Brown, M., Miron, A., … Ganesan, S. (2006). X chromosomal abnormalities in basal-like human breast cancer. Cancer Cell, 9(2), 121–132.

Rivals, I., Personnaz, L., Taing, L., & Potier, M.-C. (2006). Enrichment or depletion of a go category within a class of genes: Which test? Bioinformatics, 23(4), 401–407.

Robinson, M. D., McCarthy, D. J., & Smyth, G. K. (2010). EdgeR: A bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics, 26(1), 139–140.

Rodriguez, J. C., González, G. A., Fresno, C., & Fernández, E. A. (2015). Integrative functional analysis improves information retrieval in breast cancer. Iberoamerican Congress on Pattern Recognition.

Rodriguez, J. C., González, G. A., Fresno, C., Llera, A. S., & Fernández, E. A. (2016a). Improving information retrieval in functional analysis. Computers in Biology and Medicine, 79, 10–20.

Rodriguez, J. C., Merino, G. A., Llera, A. S., & Fernández, E. A. (2019). Massive integrative gene set analysis enables functional characterization of breast cancer subtypes. Journal of Biomedical Informatics, 103157.

Rodriguez, J. C., Merino, G. A., Prato, L., Llera, A. S., & Fernández, E. A. (2016b). The impact of rna-seq differential expression algorithms on over-representation analysis of gene sets. ISCB Latin America 2016.

Rodriguez, J. C., Prato, L., Llera, A. S., & Fernández, E. A. (2017). Effects of rna-seq genes analysis on the over-representation analysis of gene sets. XXI Congreso Argentino de Bioingeniería - SABI 2017.

Rodriguez, J. C., Vargas, C., & Fernández, E. A. (2018). ShinyWYSIWYG: A shiny what you see is what you get editor. Latinamerican Conference About the Use of R in R&D 2018.

Ross-Adams, H., Lamb, A., Dunning, M., Halim, S., Lindberg, J., Massie, C., … others. (2015). Integration of copy number and transcriptomics provides risk stratification in prostate cancer: A discovery and validation cohort study. EBioMedicine, 2(9), 1133–1144.

Saal, L. H., Johansson, P., Holm, K., Gruvberger-Saal, S. K., She, Q.-B., Maurer, M., … others. (2007). Poor prognosis in carcinoma is associated with a gene expression signature of aberrant pten tumor suppressor pathway activity. Proceedings of the National Academy of Sciences, 104(18), 7564–7569.

Santuario-Facio, S. K., Cardona-Huerta, S., Perez-Paramo, Y. X., Trevino, V., Hernandez-Cabrera, F., Rojas-Martinez, A., … others. (2017). A new gene expression signature for triple-negative breast cancer using frozen fresh tissue before neoadjuvant chemotherapy. Molecular Medicine, 23, 101.

Scaltriti, M., Elkabets, M., & Baselga, J. (2016). Molecular pathways: AXL, a membrane receptor mediator of resistance to therapy. Clinical Cancer Research, clincanres–1458.

Schmidt, M., Böhm, D., Von Törne, C., Steiner, E., Puhl, A., Pilch, H., … Gehrmann, M. (2008). The humoral immune system has a key prognostic impact in node-negative breast cancer. Cancer Research, 68(13), 5405–5413.

Sharma, D., Blum, J., Yang, X., Beaulieu, N., Macleod, A. R., & Davidson, N. E. (2005). Release of methyl cpg binding proteins and histone deacetylase 1 from the estrogen receptor \(\alpha\) (er) promoter upon reactivation in er-negative human breast cancer cells. Molecular Endocrinology, 19(7), 1740–1751.

Shen, R., Olshen, A. B., & Ladanyi, M. (2009). Integrative clustering of multiple genomic data types using a joint latent variable model with application to breast and lung cancer subtype analysis. Bioinformatics, 25(22), 2906–2912.

Shi, L., Reid, L. H., Jones, W. D., Shippy, R., Warrington, J. A., Baker, S. C., … others. (2006). The microarray quality control (maqc) project shows inter-and intraplatform reproducibility of gene expression measurements. Nature Biotechnology, 24(9), 1151.

Shi, Q., Zhang, C., Peng, M., Yu, X., Zeng, T., Liu, J., & Chen, L. (2017). Pattern fusion analysis by adaptive alignment of multiple heterogeneous omics data. Bioinformatics, 33(17), 2706–2714.

Silver, D. P., Richardson, A. L., Eklund, A. C., Wang, Z. C., Szallasi, Z., Li, Q., … others. (2010). Efficacy of neoadjuvant cisplatin in triple-negative breast cancer. Journal of Clinical Oncology, 28(7), 1145.

Song, Z., Feng, C., Lu, Y., Lin, Y., & Dong, C. (2018). PHGDH is an independent prognosis marker and contributes cell proliferation, migration and invasion in human pancreatic cancer. Gene, 642, 43–50.

Sotiriou, C., Wirapati, P., Loi, S., Harris, A., Fox, S., Smeds, J., … others. (2006). Gene expression profiling in breast cancer: Understanding the molecular basis of histologic grade to improve prognosis. Journal of the National Cancer Institute, 98(4), 262–272.

Subramanian, A., Tamayo, P., Mootha, V. K., Mukherjee, S., Ebert, B. L., Gillette, M. A., … others. (2005). Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles. Proceedings of the National Academy of Sciences, 102(43), 15545–15550.

Sørlie, T., Borgan, E., Myhre, S., Vollan, H. K., Russnes, H., Zhao, X., … Rødland, E. (2010). The importance of gene-centring microarray data. The Lancet Oncology, 11(8), 719–720.

Taylor, B. S., Schultz, N., Hieronymus, H., Gopalan, A., Xiao, Y., Carver, B. S., … others. (2010). Integrative genomic profiling of human prostate cancer. Cancer Cell, 18(1), 11–22.

Tian, L., Greenberg, S. A., Kong, S. W., Altschuler, J., Kohane, I. S., & Park, P. J. (2005). Discovering statistically significant pathways in expression profiling studies. Proceedings of the National Academy of Sciences, 102(38), 13544–13549.

Valentin, M. D., Da Silva, S. D., Privat, M., Alaoui-Jamali, M., & Bignon, Y.-J. (2012). Molecular insights on basal-like breast cancer. Breast Cancer Research and Treatment, 134(1), 21–30.

Van’t Veer, L. J., Dai, H., Van De Vijver, M. J., He, Y. D., Hart, A. A., Mao, M., … others. (2002). Gene expression profiling predicts clinical outcome of breast cancer. Nature, 415(6871), 530.

Varambally, S., Yu, J., Laxman, B., Rhodes, D. R., Mehra, R., Tomlins, S. A., … others. (2005). Integrative genomic and proteomic analysis of prostate cancer reveals signatures of metastatic progression. Cancer Cell, 8(5), 393–406.

Vaske, C. J., Benz, S. C., Sanborn, J. Z., Earl, D., Szeto, C., Zhu, J., … Stuart, J. M. (2010). Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using paradigm. Bioinformatics, 26(12), i237–i245.

Verhaak, R. G., Hoadley, K. A., Purdom, E., Wang, V., Qi, Y., Wilkerson, M. D., … others. (2010). Integrated genomic analysis identifies clinically relevant subtypes of glioblastoma characterized by abnormalities in pdgfra, idh1, egfr, and nf1. Cancer Cell, 17(1), 98–110.

Waddell, N., Arnold, J., Cocciardi, S., Da Silva, L., Marsh, A., Riley, J., … others. (2010). Subtypes of familial breast tumours revealed by expression and copy number profiling. Breast Cancer Research and Treatment, 123(3), 661–677.

Wang, B., Mezlini, A. M., Demir, F., Fiume, M., Tu, Z., Brudno, M., … Goldenberg, A. (2014). Similarity network fusion for aggregating data types on a genomic scale. Nature Methods, 11(3), 333.

Wang, Y., Klijn, J. G., Zhang, Y., Sieuwerts, A. M., Look, M. P., Yang, F., … others. (2005). Gene-expression profiles to predict distant metastasis of lymph-node-negative primary breast cancer. The Lancet, 365(9460), 671–679.

Weinstein, J. N., Collisson, E. A., Mills, G. B., Shaw, K. R. M., Ozenberger, B. A., Ellrott, K., … others. (2013). The cancer genome atlas pan-cancer analysis project. Nature Genetics, 45(10), 1113.

Wickham, H. (2014). Advanced r. Chapman; Hall/CRC.

Wolfe, M. J. (1996). High performance compilers for parallel computing. Addison-Wesley.

Yersal, O., & Barutca, S. (2014). Biological subtypes of breast cancer: Prognostic and therapeutic implications. World Journal of Clinical Oncology, 5(3), 412.

Yu, K., Ganesan, K., Tan, L. K., Laban, M., Wu, J., Zhao, X. D., … others. (2008). A precisely regulated gene expression cassette potently modulates metastasis and survival in multiple solid cancers. PLoS Genetics, 4(7), e1000129.