Awesome

Jump3

Hybrid machine learning/model-based approach for the inference of gene regulatory networks from time series of expression data.

The Jump3 method is described in the following paper (available here):

Combining tree-based and dynamical systems for the inference of gene regulatory networks 
Huynh-Thu, V. A. and Sanguinetti, G.
Bioinformatics, 31(10):1614-1622, 2015. 

Jump3 is implemented in MATLAB. jump3_doc.pdf contains a step-by-step tutorial showing how to run the code.