Paper Info
Title
Efficient parameter search for qualitative models of regulatory networks using symbolic model checking.
Abstract
Investigating the relation between the structure and behavior of complex biological networks often involves posing the question if the hypothesized structure of a regulatory network is consistent with the observed behavior, or if a proposed structure can generate a desired behavior.The above questions can be cast into a parameter search problem for qualitative models of regulatory networks. We develop a method based on symbolic model checking that avoids enumerating all possible parametrizations, and show that this method performs well on real biological problems, using the IRMA synthetic network and benchmark datasets. We test the consistency between IRMA and time-series expression profiles, and search for parameter modifications that would make the external control of the system behavior more robust.GNA and the IRMA model are available at http://ibis.inrialpes.fr/.
Year
DOI
Venue
2010
10.1093/bioinformatics/btq387
Bioinformatics
Keywords
Field
DocType
parameter search problem,system behavior,parameter modification,irma synthetic network,fr supplementary information,symbolic model checking,irma model,efficient parameter search,qualitative model,proposed structure,complex biological network,regulatory network,observed behavior,computer simulation,time series data,gene regulatory networks,benchmarking,biological network,differential equation,quantitative method,systems biology
Data mining,Model checking,Biological network,Computer science,Systems biology,Theoretical computer science,Software,Bioinformatics,Search problem,Gene regulatory network,Benchmarking,Ibis
Journal
Volume
Issue
ISSN
26
18
1367-4811
Citations 
PageRank 
References 
14
0.71
11
Authors
6
Name
Order
Citations
PageRank
Gregory Batt1924.78
Michel Page231025.93
Irene Cantone3140.71
Gregor Goessler4664.25
Pedro Monteiro5140.71
Hidde de Jong61328132.83