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.




2. R. Albert, B. DasGupta, R. Dondi, S. Kachalo, E.D. Sontag, A. Zelikovsky, and K. Westbrooks. A novel method for signal transduction network inference from indirect experimental evidence. In R. Giancarlo and S. Hannenhalli, editors, 7th Workshop on Algorithms in Bioinformatics (WABI), volume 14, pages 407-419. Springer-Verlag, Berlin, 2007. Note: Conference version of journal paper with same title. Keyword(s): systems biology, reaction networks, algorithms, signal transduction networks, graph algorithms.



3. R. Albert, B. DasGupta, R. Dondi, S. Kachalo, E.D. Sontag, A. Zelikovsky, and K. Westbrooks. A novel method for signal transduction network inference from indirect experimental evidence. Journal of Computational Biology, 14:927-949, 2007. [PDF] Keyword(s): systems biology, reaction networks, algorithms, signal transduction networks, graph algorithms. Abstract:

   This paper introduces a new method of combined synthesis and inference of biological signal transduction networks. The main idea lies in representing observed causal relationships as network paths, and using techniques from combinatorial optimization to find the sparsest graph consistent with all experimental observations. The paper formalizes the approach, studies its computational complexity, proves new results for exact and approximate solutions of the computationally hard transitive reduction substep of the approach, validates the biological applicability by applying it to a previously published signal transduction network by Li et al., and shows that the algorithm for the transitive reduction substep performs well on graphs with a structure similar to those observed in transcriptional regulatory and signal transduction networks.

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