Paper Info
Title
An efficient method for dynamic analysis of gene regulatory networks and in silico gene perturbation experiments
Abstract
With the increasing availability of experimental data on gene-gene and protein-protein interactions, modeling of gene regulatory networks has gained a special attention lately. To have a better understanding of these networks it is necessary to capture their dynamical properties, by computing its steady states. Various methods have been proposed to compute steady states but almost all of them suffer from the state space explosion problem with the increasing size of the networks. Hence it becomes difficult to model even moderate sized networks using these techniques. In this paper, we present a new representation of gene regulatory networks, which facilitates the steady state computation of networks as large as 1200 nodes and 5000 edges. We benchmarked and validated our algorithm on the T helper model from [8] and performed in silico knock out experiments: showing both a reduction in computation time and correct steady state identification.
Year
DOI
Venue
2007
10.1007/978-3-540-71681-5_5
RECOMB
Keywords
Field
DocType
state space explosion problem,dynamic analysis,increasing availability,correct steady state identification,better understanding,computation time,gene regulatory network,helper model,efficient method,steady state,increasing size,steady state computation,silico gene perturbation experiment,protein protein interaction
Boolean function,Computer science,Binary decision diagram,Steady state,Bioinformatics,Gene regulatory network,State space,Perturbation (astronomy),Computation,In silico
Conference
Volume
ISSN
Citations 
4453
0302-9743
38
PageRank 
References 
Authors
2.79
9
4
Name
Order
Citations
PageRank
Abhishek Garg118711.66
Ioannis Xenarios22301293.04
luis mendoza327125.94
Giovanni De Micheli4102451018.13