DREAM4

DREAM4: Combining genetic and dynamic information to identify biological networks and dynamical models. Conclusion/Significance: Our t-test based method proved powerful at ranking regulatory interactions, tying for first out of An external file that holds a picture, illustration, etc. Object name is pone.0013397.e001.jpg methods in the DREAM4 100-gene in-silico network inference challenge. We demonstrate complementarity between this method and the two methods that take advantage of time-series data by combining the three into a pipeline whose ability to rank regulatory interactions is markedly improved compared to either method alone. Moreover, the pipeline is able to accurately predict the response of the system to new conditions (in this case new double knock-out genetic perturbations). Our evaluation of the performance of multiple methods for network inference suggests avenues for future methods development and provides simple considerations for genomic experimental design. Our code is publicly available at http://err.bio.nyu.edu/inferelator/.