Symbolic approaches for finding control strategies in boolean networks Conference

Langmead, CJ, Jha, SK. (2009). Symbolic approaches for finding control strategies in boolean networks . Journal of Bioinformatics and Computational Biology, 7(2), 323-338. 10.1142/S0219720009004084

cited authors

  • Langmead, CJ; Jha, SK

abstract

  • We present an exact algorithm, based on techniques from the field of Model Checking , for finding control policies for Boolean Networks (BN) with control nodes. Given a BN, a set of starting states, I, a set of goal states, F, and a target time, t , our algorithm automatically finds a sequence of control signals that deterministically drives the BN from I to F at, or before time t, or else guarantees that no such policy exists. Despite recent hardness-results for finding control policies for BNs, we show that, in practice, our algorithm runs in seconds to minutes on over 13,400 BNs of varying sizes and topologies, including a BN model of embryogenesis in Drosophila melanogaster with 15,360 Boolean variables. We then extend our method to automatically identify a set of Boolean transfer functions that reproduce the qualitative behavior of gene regulatory networks. Specifically, we automatically learn a BN model of D. melanogaster embryogenesis in 5.3 seconds, from a space containing 6.9 × 1010 possible models. © 2009 Imperial College Press.

authors

publication date

  • May 15, 2009

published in

Digital Object Identifier (DOI)

start page

  • 323

end page

  • 338

volume

  • 7

issue

  • 2