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Genetic Regulatory Networks

Guest Editors: Edward R. Dougherty, Tatsuya Akutsu, Paul Dan Cristea, and Ahmed H. Tewfik

  1. Editorial

    Genetic Regulatory Networks

    Edward R Dougherty, Tatsuya Akutsu, Paul Dan Cristea and Ahmed H Tewfik

    EURASIP Journal on Bioinformatics and Systems Biology 2007 2007:17321

    Published on: 2 August 2007

  2. Research Article

    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...

    Sachiyo Aburatani, Fuyan Sun, Shigeru Saito, Masao Honda, Shu-ichi Kaneko and Katsuhisa Horimoto

    EURASIP Journal on Bioinformatics and Systems Biology 2007 2007:47214

    Published on: 26 July 2007

  3. Research Article

    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...

    Isabel Tienda Luna, Yufei Huang, Yufang Yin, Diego P Ruiz Padillo and M Carmen Carrion Perez

    EURASIP Journal on Bioinformatics and Systems Biology 2007 2007:71312

    Published on: 27 June 2007

  4. Research Article

    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...

    Marcel Brun, Seungchan Kim, Woonjung Choi and Edward R Dougherty

    EURASIP Journal on Bioinformatics and Systems Biology 2007 2007:82702

    Published on: 22 May 2007

  5. Research Article

    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 ...

    Nestor Walter Trepode, Hugo Aguirre Armelin, Michael Bittner, Junior Barrera, Marco Dimas Gubitoso and Ronaldo Fumio Hashimoto

    EURASIP Journal on Bioinformatics and Systems Biology 2007 2007:73109

    Published on: 17 May 2007

  6. Research Article

    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...

    Stephen Marshall, Le Yu, Yufei Xiao and Edward R Dougherty

    EURASIP Journal on Bioinformatics and Systems Biology 2007 2007:32454

    Published on: 7 May 2007

  7. Research Article

    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...

    Dorothy Bollman, Omar Colón-Reyes and Edusmildo Orozco

    EURASIP Journal on Bioinformatics and Systems Biology 2007 2007:97356

    Published on: 19 April 2007

  8. Research Article

    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 ...

    Shu-Qin Zhang, Morihiro Hayashida, Tatsuya Akutsu, Wai-Ki Ching and Michael K Ng

    EURASIP Journal on Bioinformatics and Systems Biology 2007 2007:20180

    Published on: 12 April 2007

  9. Research Article

    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...

    Arvind Rao, Alfred O Hero III, David J States and James Douglas Engel

    EURASIP Journal on Bioinformatics and Systems Biology 2007 2007:51947

    Published on: 12 April 2007

  10. Research Article

    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...

    Huai Li, Yu Sun and Ming Zhan

    EURASIP Journal on Bioinformatics and Systems Biology 2007 2007:49478

    Published on: 13 March 2007