References
Bouhaddou, M. et al. Drug response consistency in CCLE and CGP. Nature 540, http://dx.doi.org/10.1038/nature20580 (2016)
Garnett, M. J. et al. Systematic identification of genomic markers of drug sensitivity in cancer cells. Nature 483, 570–575 (2012)
Barretina, J. et al. The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity. Nature 483, 603–607 (2012)
Pozdeyev, N. et al. Integrating heterogeneous drug sensitivity data from cancer pharmacogenomic studies. Oncotarget http://dx.doi.org/10.18632/oncotarget.10010 (2016)
Mpindi, J. P. et al. Consistency in drug response profiling. Nature 540, http://dx.doi.org/10.1038/nature20171 (2016)
Smirnov, P. et al. PharmacoGx: An R package for analysis of large pharmacogenomic datasets. Bioinformatics 32, 1244–1246 (2015)
Haibe-Kains, B. et al. Inconsistency in large pharmacogenomic studies. Nature 504, 389–393 (2013)
Safikhani, Z. et al. Revisiting inconsistency in large pharmacogenomic studies. F1000Research http://dx.doi.org/10.12688/f1000research.9611.1 (2016)
Matthews, B. W. Comparison of the predicted and observed secondary structure of T4 phage lysozyme. Biochim. Biophys. Acta 405, 442–451 (1975)
Landis, J. R. & Koch, G. G. The measurement of observer agreement for categorical data. Biometrics 33, 159–174 (1977)
Seashore-Ludlow, B. et al. Harnessing connectivity in a large-scale small-molecule sensitivity dataset. Cancer Discov. 5, 1210–1223 (2015)
Iorio, F. et al. A landscape of pharmacogenomic interactions in cancer. Cell 166, 740–754 (2016)
Sandve, G. K., Nekrutenko, A., Taylor, J. & Hovig, E. Ten simple rules for reproducible computational research. PLoS Comput. Biol. 9, e1003285 (2013)
Author information
Authors and Affiliations
Supplementary information
Supplementary Information
This file contains Supplementary Methods, Supplementary Text and Data, Supplementary Figures 1 -6 and additional references. (PDF 1139 kb)
Rights and permissions
About this article
Cite this article
Safikhani, Z., El-Hachem, N., Smirnov, P. et al. Safikhani et al. reply. Nature 540, E11–E12 (2016). https://doi.org/10.1038/nature20581
Published:
Issue Date:
DOI: https://doi.org/10.1038/nature20581
- Springer Nature Limited
This article is cited by
-
Bayesian multi-source regression and monocyte-associated gene expression predict BCL-2 inhibitor resistance in acute myeloid leukemia
npj Precision Oncology (2021)
-
Remember why we work on cancer
Nature (2017)