1. S. Kachalo, R. Zhang, E.D. Sontag, R. Albert, and B. Dasgupta. NET-SYNTHESIS: A software for synthesis, inference and simplification of signal transduction networks. Bioinformatics, 24:293 - 295, 2008. [PDF] Keyword(s): systems biology, reaction networks, algorithms, signal transduction networks, graph algorithms. Abstract:

   This paper presents a software tool for inference and simplification of signal transduction networks. The method relies on the representation of observed indirect causal relationships as network paths, using techniques from combinatorial optimization to find the sparsest graph consistent with all experimental observations. We illustrate the biological usability of our software by applying it to a previously published signal transduction network and by using it to synthesize and simplify a novel network corresponding to activation-induced cell death in large granular lymphocyte leukemia.

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