TY - JOUR AU - Prasad, V. AU - Fojo, T. AU - Brada, M. PY - 2016 DA - 2016// TI - Precision oncology: origins, optimism, and potential JO - Lancet Oncol VL - 17 UR - https://doi.org/10.1016/S1470-2045(15)00620-8 DO - 10.1016/S1470-2045(15)00620-8 ID - Prasad2016 ER - TY - JOUR AU - Ayers, M. PY - 2004 DA - 2004// TI - Gene expression profiles predict complete pathologic response to neoadjuvant paclitaxel and fluorouracil, doxorubicin, and cyclophosphamide chemotherapy in breast cancer JO - J Clin Oncol VL - 22 UR - https://doi.org/10.1200/JCO.2004.05.166 DO - 10.1200/JCO.2004.05.166 ID - Ayers2004 ER - TY - JOUR AU - Barretina, J. PY - 2012 DA - 2012// TI - The cancer cell line encyclopedia enables predictive modelling of anticancer drug sensitivity JO - Nature VL - 483 UR - https://doi.org/10.1038/nature11003 DO - 10.1038/nature11003 ID - Barretina2012 ER - TY - JOUR AU - Collins, I. AU - Workman, P. PY - 2006 DA - 2006// TI - New approaches to molecular cancer therapeutics JO - Nat Chem Biol VL - 2 UR - https://doi.org/10.1038/nchembio840 DO - 10.1038/nchembio840 ID - Collins2006 ER - TY - JOUR AU - Ross, J. S. AU - Fletcher, J. A. PY - 1998 DA - 1998// TI - The HER-2/neu oncogene in breast cancer: prognostic factor, predictive factor, and target for therapy JO - Stem Cells VL - 16 UR - https://doi.org/10.1002/stem.160413 DO - 10.1002/stem.160413 ID - Ross1998 ER - TY - JOUR AU - Tu, S. -. M. AU - Bilen, M. A. AU - Tannir, N. M. PY - 2016 DA - 2016// TI - Personalised cancer care: promises and challenges of targeted therapy JO - J R Soc Med VL - 109 UR - https://doi.org/10.1177/0141076816631154 DO - 10.1177/0141076816631154 ID - Tu2016 ER - TY - JOUR AU - Barretina, J. PY - 2012 DA - 2012// TI - The cancer cell line encyclopedia enables predictive modelling of anticancer drug sensitivity JO - Nature VL - 483 UR - https://doi.org/10.1038/nature11003 DO - 10.1038/nature11003 ID - Barretina2012 ER - TY - JOUR AU - Chang, Y. PY - 2018 DA - 2018// TI - Cancer drug response profile scan (CDRscan): a deep learning model that predicts drug effectiveness from cancer genomic signature JO - Sci Rep VL - 8 UR - https://doi.org/10.1038/s41598-018-27214-6 DO - 10.1038/s41598-018-27214-6 ID - Chang2018 ER - TY - JOUR AU - Chiu, Y. -. C. PY - 2019 DA - 2019// TI - Predicting drug response of tumors from integrated genomic profiles by deep neural networks JO - BMC Med Genet VL - 12 ID - Chiu2019 ER - TY - JOUR AU - Costello, J. C. PY - 2014 DA - 2014// TI - A community effort to assess and improve drug sensitivity prediction algorithms JO - Nat Biotechnol VL - 32 UR - https://doi.org/10.1038/nbt.2877 DO - 10.1038/nbt.2877 ID - Costello2014 ER - TY - JOUR AU - Geeleher, P. AU - Cox, N. J. AU - Huang, R. S. PY - 2014 DA - 2014// TI - Clinical drug response can be predicted using baseline gene expression levels and in vitro drug sensitivity in cell lines JO - Genome Biol VL - 15 UR - https://doi.org/10.1186/gb-2014-15-3-r47 DO - 10.1186/gb-2014-15-3-r47 ID - Geeleher2014 ER - TY - JOUR AU - Guan, N. -. N. PY - 2019 DA - 2019// TI - Anticancer drug response prediction in cell lines using weighted graph regularized matrix factorization JO - Mol Therapy-Nucleic Acids VL - 17 UR - https://doi.org/10.1016/j.omtn.2019.05.017 DO - 10.1016/j.omtn.2019.05.017 ID - Guan2019 ER - TY - JOUR AU - Hejase, H. AU - Chan, C. PY - 2015 DA - 2015// TI - Improving drug sensitivity prediction using different types of data JO - CPT Pharmacometrics Syst Pharmacol VL - 4 UR - https://doi.org/10.1002/psp4.2 DO - 10.1002/psp4.2 ID - Hejase2015 ER - TY - JOUR AU - Huang, C. PY - 2017 DA - 2017// TI - Open source machine-learning algorithms for the prediction of optimal cancer drug therapies JO - PLoS One VL - 12 UR - https://doi.org/10.1371/journal.pone.0186906 DO - 10.1371/journal.pone.0186906 ID - Huang2017 ER - TY - JOUR AU - Liu, H. PY - 2018 DA - 2018// TI - Anti-cancer drug response prediction using neighbor-based collaborative filtering with global effect removal JO - Mol Therapy-Nucleic Acids VL - 13 UR - https://doi.org/10.1016/j.omtn.2018.09.011 DO - 10.1016/j.omtn.2018.09.011 ID - Liu2018 ER - TY - JOUR AU - Suphavilai, C. AU - Bertrand, D. AU - Nagarajan, N. PY - 2018 DA - 2018// TI - Predicting cancer drug response using a recommender system JO - Bioinformatics VL - 34 UR - https://doi.org/10.1093/bioinformatics/bty452 DO - 10.1093/bioinformatics/bty452 ID - Suphavilai2018 ER - TY - JOUR AU - Wei, D. PY - 2019 DA - 2019// TI - Comprehensive anticancer drug response prediction based on a simple cell line-drug complex network model JO - BMC Bioinformatics VL - 20 UR - https://doi.org/10.1186/s12859-019-2608-9 DO - 10.1186/s12859-019-2608-9 ID - Wei2019 ER - TY - JOUR AU - Yang, J. PY - 2019 DA - 2019// TI - A novel approach for drug response prediction in cancer cell lines via network representation learning JO - Bioinformatics VL - 35 UR - https://doi.org/10.1093/bioinformatics/bty848 DO - 10.1093/bioinformatics/bty848 ID - Yang2019 ER - TY - JOUR AU - Azuaje, F. PY - 2016 DA - 2016// TI - Computational models for predicting drug responses in cancer research JO - Brief Bioinform VL - 18 ID - Azuaje2016 ER - TY - JOUR AU - Vidyasagar, M. PY - 2015 DA - 2015// TI - Identifying predictive features in drug response using machine learning: opportunities and challenges JO - Annu Rev Pharmacol Toxicol VL - 55 UR - https://doi.org/10.1146/annurev-pharmtox-010814-124502 DO - 10.1146/annurev-pharmtox-010814-124502 ID - Vidyasagar2015 ER - TY - BOOK AU - Sekula, M. N. PY - 2015 DA - 2015// TI - OptCluster: an R package for determining the optimal clustering algorithm and optimal number of clusters ID - Sekula2015 ER - TY - JOUR AU - Liaw, A. AU - Wiener, M. PY - 2002 DA - 2002// TI - Classification and regression by randomForest JO - R news VL - 2 ID - Liaw2002 ER - TY - STD TI - Cutler A, Cutler DR, Stevens JR. Random Forests. In C. Zhang & Y. Ma (Eds.). Ensemble machine learning: methods and applications. Boston: Springer US; 2012. p. 157–75. ID - ref23 ER - TY - JOUR AU - Weinstein, J. N. PY - 2013 DA - 2013// TI - The cancer genome atlas pan-cancer analysis project JO - Nat Genet VL - 45 UR - https://doi.org/10.1038/ng.2764 DO - 10.1038/ng.2764 ID - Weinstein2013 ER - TY - JOUR AU - Mi, H. PY - 2013 DA - 2013// TI - Large-scale gene function analysis with the PANTHER classification system JO - Nat Protoc VL - 8 UR - https://doi.org/10.1038/nprot.2013.092 DO - 10.1038/nprot.2013.092 ID - Mi2013 ER - TY - JOUR AU - Hoadley, K. A. PY - 2018 DA - 2018// TI - Cell-of-origin patterns dominate the molecular classification of 10,000 tumors from 33 types of cancer JO - Cell VL - 173 UR - https://doi.org/10.1016/j.cell.2018.03.022 DO - 10.1016/j.cell.2018.03.022 ID - Hoadley2018 ER - TY - JOUR AU - Lee, E. PY - 2008 DA - 2008// TI - Inferring pathway activity toward precise disease classification JO - PLoS Comput Biol VL - 4 UR - https://doi.org/10.1371/journal.pcbi.1000217 DO - 10.1371/journal.pcbi.1000217 ID - Lee2008 ER - TY - BOOK AU - Chen, J. AU - Schwarz, E. PY - 2017 DA - 2017// TI - BioMM: biologically-informed multi-stage machine learning for identification of epigenetic fingerprints ID - Chen2017 ER - TY - JOUR AU - Fong, R. C. AU - Scheirer, W. J. AU - Cox, D. D. PY - 2018 DA - 2018// TI - Using human brain activity to guide machine learning JO - Sci Rep VL - 8 UR - https://doi.org/10.1038/s41598-018-23618-6 DO - 10.1038/s41598-018-23618-6 ID - Fong2018 ER - TY - JOUR AU - O'Reilly, R. C. PY - 1998 DA - 1998// TI - Six principles for biologically based computational models of cortical cognition JO - Trends Cogn Sci VL - 2 UR - https://doi.org/10.1016/S1364-6613(98)01241-8 DO - 10.1016/S1364-6613(98)01241-8 ID - O'Reilly1998 ER - TY - STD TI - Moreno-Layseca P, Icha J, Hamidi H, Ivaska J. Integrin trafficking in cells and tissues. Nat Cell Biol. 2019;21(2):122–32. https://doi.org/10.1038/s41556-018-0223-z. ID - ref31 ER - TY - JOUR AU - Seguin, L. PY - 2015 DA - 2015// TI - Integrins and cancer: regulators of cancer stemness, metastasis, and drug resistance JO - Trends Cell Biol VL - 25 UR - https://doi.org/10.1016/j.tcb.2014.12.006 DO - 10.1016/j.tcb.2014.12.006 ID - Seguin2015 ER - TY - JOUR AU - Komiya, Y. AU - Habas, R. PY - 2008 DA - 2008// TI - Wnt signal transduction pathways JO - Organogenesis VL - 4 UR - https://doi.org/10.4161/org.4.2.5851 DO - 10.4161/org.4.2.5851 ID - Komiya2008 ER - TY - JOUR AU - Chiurillo, M. A. PY - 2015 DA - 2015// TI - Role of the Wnt/β-catenin pathway in gastric cancer: an in-depth literature review JO - World J Experimental Med VL - 5 UR - https://doi.org/10.5493/wjem.v5.i2.84 DO - 10.5493/wjem.v5.i2.84 ID - Chiurillo2015 ER - TY - JOUR AU - Turner, M. D. PY - 2014 DA - 2014// TI - Cytokines and chemokines: at the crossroads of cell signalling and inflammatory disease JO - Biochimica et Biophysica Acta (BBA) - Mol Cell Res VL - 1843 UR - https://doi.org/10.1016/j.bbamcr.2014.05.014 DO - 10.1016/j.bbamcr.2014.05.014 ID - Turner2014 ER - TY - CHAP AU - Hutson, M. PY - 2018 DA - 2018// TI - Artificial intelligence faces reproducibility crisis BT - American Association for the Advancement of Science ID - Hutson2018 ER - TY - STD TI - Banfield J, Raftery A. Model-based gaussian and non-gaussian clustering. Biometrics. 1993;49(3):803–21. https://doi.org/10.2307/2532201. ID - ref37 ER - TY - JOUR AU - Johnson, S. C. PY - 1967 DA - 1967// TI - Hierarchical clustering schemes JO - Psychometrika VL - 32 UR - https://doi.org/10.1007/BF02289588 DO - 10.1007/BF02289588 ID - Johnson1967 ER - TY - STD TI - Lloyd, S., Least square quantization in PCM. Bell telephone laboratories paper. Published in journal much later: Lloyd, SP: Least squares quantization in PCM. IEEE trans. Inform. Theor. (1957/1982) Google Scholar, 1957. ID - ref39 ER - TY - JOUR AU - Rousseeuw, P. J. AU - Kaufman, L. PY - 1990 DA - 1990// TI - Finding groups in data JO - Ser Probability Mathematical Stat 1990 VL - 34 ID - Rousseeuw1990 ER - TY - JOUR AU - Tamayo, P. PY - 1999 DA - 1999// TI - Interpreting patterns of gene expression with self-organizing maps: methods and application to hematopoietic differentiation JO - Proc Natl Acad Sci VL - 96 UR - https://doi.org/10.1073/pnas.96.6.2907 DO - 10.1073/pnas.96.6.2907 ID - Tamayo1999 ER - TY - CHAP AU - Liu, H. PY - 2018 DA - 2018// TI - Weighted Gini index feature selection method for imbalanced data BT - 2018 IEEE 15th international conference on networking, sensing and control (ICNSC) ID - Liu2018 ER -