Data-driven modelling of signal-transduction networks

By Kevin A. Janes, Michael B. Yaffe. Nature reviews. Molecular cell biology, 2006

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Maximum Entropy Reconstructions of Dynamic Signaling Networks from Quantitative Proteomics Data (2009, background): “networks that govern the behavior of these phosphorylation sites[10].”
Executable cell biology (2007, background): “…for many quantitative relationships between variables, such as molecule concentrations and gene activity levels, have been devised to represent cell signaling pathways in a physically and biologically realistic manner and have been shown repeatedly to generate novel and useful hypotheses 18–27 .”
Sequential Application of Anti-Cancer Drugs Enhances Cell Death by Re-wiring Apoptotic Signaling Networks (2012, methodology): “Data-Driven Modeling Data-driven modeling and the application of partial least-squares to biological data have been described in detail previously (Janes and Yaffe, 2006).”
Calorie restriction and SIRT3 trigger global reprogramming of the mitochondrial protein acetylome. (2013, methodology): “To determine the distribution of experimental groups, an unsupervised principal component analysis (PCA) (Bathe et al., 2011; Janes and Yaffe, 2006) was performed with 31 metabolites that were quantifiable in all samples (Figure 6).”