Guest Editors: Edward R. Dougherty, Tatsuya Akutsu, Paul Dan Cristea, and Ahmed H. Tewfik
Genetic Regulatory Networks
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Citation: EURASIP Journal on Bioinformatics and Systems Biology 2007 2007:17321
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Gene Systems Network Inferred from Expression Profiles in Hepatocellular Carcinogenesis by Graphical Gaussian Model
Hepatocellular carcinoma (HCC) in a liver with advanced-stage chronic hepatitis C (CHC) is induced by hepatitis C virus, which chronically infects about 170 million people worldwide. To elucidate the associati...
Citation: EURASIP Journal on Bioinformatics and Systems Biology 2007 2007:47214 -
Uncovering Gene Regulatory Networks from Time-Series Microarray Data with Variational Bayesian Structural Expectation Maximization
We investigate in this paper reverse engineering of gene regulatory networks from time-series microarray data. We apply dynamic Bayesian networks (DBNs) for modeling cell cycle regulations. In developing a net...
Citation: EURASIP Journal on Bioinformatics and Systems Biology 2007 2007:71312 -
Comparison of Gene Regulatory Networks via Steady-State Trajectories
The modeling of genetic regulatory networks is becoming increasingly widespread in the study of biological systems. In the abstract, one would prefer quantitatively comprehensive models, such as a differential...
Citation: EURASIP Journal on Bioinformatics and Systems Biology 2007 2007:82702 -
A Robust Structural PGN Model for Control of Cell-Cycle Progression Stabilized by Negative Feedbacks
The cell division cycle comprises a sequence of phenomena controlled by a stable and robust genetic network. We applied a probabilistic genetic network (PGN) to construct a hypothetical model with a dynamical ...
Citation: EURASIP Journal on Bioinformatics and Systems Biology 2007 2007:73109 -
Inference of a Probabilistic Boolean Network from a Single Observed Temporal Sequence
The inference of gene regulatory networks is a key issue for genomic signal processing. This paper addresses the inference of probabilistic Boolean networks (PBNs) from observed temporal sequences of network s...
Citation: EURASIP Journal on Bioinformatics and Systems Biology 2007 2007:32454 -
Fixed Points in Discrete Models for Regulatory Genetic Networks
It is desirable to have efficient mathematical methods to extract information about regulatory iterations between genes from repeated measurements of gene transcript concentrations. One piece of information is...
Citation: EURASIP Journal on Bioinformatics and Systems Biology 2007 2007:97356 -
Inferring Time-Varying Network Topologies from Gene Expression Data
Most current methods for gene regulatory network identification lead to the inference of steady-state networks, that is, networks prevalent over all times, a hypothesis which has been challenged. There has bee...
Citation: EURASIP Journal on Bioinformatics and Systems Biology 2007 2007:51947 -
Algorithms for Finding Small Attractors in Boolean Networks
A Boolean network is a model used to study the interactions between different genes in genetic regulatory networks. In this paper, we present several algorithms using gene ordering and feedback vertex sets to ...
Citation: EURASIP Journal on Bioinformatics and Systems Biology 2007 2007:20180 -
Analysis of Gene Coexpression by B-Spline Based CoD Estimation
The gene coexpression study has emerged as a novel holistic approach for microarray data analysis. Different indices have been used in exploring coexpression relationship, but each is associated with certain p...
Citation: EURASIP Journal on Bioinformatics and Systems Biology 2007 2007:49478