Salient characteristics of the three core methods.

Here we present the characteristics of the three core network inference methods, combinations of which constituted network inference pipelines. Median corrected z-score (MCZ) uses the t-statistic on solely the steady state genetic knock-out data, and can predict the topology of the network. Time-lagged Context Liklihood of Relatedness (tlCLR) is a mutual information based method that uses both time-series and steady state data to predict the topology of the network. The Inferelator 1.0 (Inf) is an ordinary differential equation (ODE) based method that uses both time-series and steady-state and can predict not only the topology of the network but also the kinetic parameters of regulation, allowing for the prediction of the response of the system to new conditions.