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Identification of All Steady States in Biological Regulatory Networks

Abstract:
Computing the long term behavior of regulatory and signaling networks is critical in understanding how biological functions take place in organisms. Steady states of these networks determine the activity levels of individual entities in the long run. Identifying all the steady states of these networks is diffcult as it suffers from the state space explosion problem. In this paper, we propose a method for identifying all the steady states of boolean regulatory and signaling networks accurately and effciently. We build a mathematical model that allows pruning a large portion of the state space quickly without causing any false dismissals. For the remaining state space, which is typically very small compared to the whole state space, we develop a randomized traversal method that extracts the steady states. We estimate the number of steady states, and the expected behavior of individual genes and gene pairs in steady states in an online fashion. Also, we formulate a stopping criterion that terminates the traversal as soon as user supplied percentage of the results are returned with high confidence. We show that our algorithm can identify all the steady states accurately. Furthermore, our method is scalable to virtually any large scale boolean biological regulatory network. Keywords: steady state identification, genetic regulatory networks, state classification
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Download the software for identification of all steady states in biological regulatory networks
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Tamer Kahveci
Last modified: Tue Sep 22 12:26:37 EDT 2009