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Network Structure and Biological Function: Reconstruction, Modelling, and Statistical Approaches

Guest Editors: Joachim Selbig, Matthias Steinfath, and Dirk Repsilber

  1. Research Article

    Reverse Engineering of Gene Regulatory Networks: A Comparative Study

    Reverse engineering of gene regulatory networks has been an intensively studied topic in bioinformatics since it constitutes an intermediate step from explorative to causative gene expression analysis. Many me...

    Hendrik Hache, Hans Lehrach and Ralf Herwig

    EURASIP Journal on Bioinformatics and Systems Biology 2009 2009:617281

    Published on: 22 April 2009

  2. Research Article

    Adaptive Dynamics of Regulatory Networks: Size Matters

    To accomplish adaptability, all living organisms are constructed of regulatory networks on different levels which are capable to differentially respond to a variety of environmental inputs. Structure of regula...

    Dirk Repsilber, Thomas Martinetz and Mats Björklund

    EURASIP Journal on Bioinformatics and Systems Biology 2009 2009:618502

    Published on: 3 February 2009

  3. Research Article

    Reconstructing Generalized Logical Networks of Transcriptional Regulation in Mouse Brain from Temporal Gene Expression Data

    Gene expression time course data can be used not only to detect differentially expressed genes but also to find temporal associations among genes. The problem of reconstructing generalized logical networks to ...

    Mingzhou(Joe) Song, Chris K. Lewis, Eric R. Lance, Elissa J. Chesler, Roumyana Kirova Yordanova, Michael A. Langston, Kerrie H. Lodowski and Susan E. Bergeson

    EURASIP Journal on Bioinformatics and Systems Biology 2009 2009:545176

    Published on: 27 January 2009

  4. Research Article

    Functional Classification of Genome-Scale Metabolic Networks

    We propose two strategies to characterize organisms with respect to their metabolic capabilities. The first, investigative, strategy describes metabolic networks in terms of their capability to utilize differe...

    Oliver Ebenhöh and Thomas Handorf

    EURASIP Journal on Bioinformatics and Systems Biology 2009 2009:570456

    Published on: 19 January 2009

  5. Research Article

    Stability from Structure: Metabolic Networks Are Unlike Other Biological Networks

    In recent work, attempts have been made to link the structure of biochemical networks to their complex dynamics. It was shown that structurally stable network motifs are enriched in such networks. In this work...

    P. van Nes, D. Bellomo, M.J.T. Reinders and D. de Ridder

    EURASIP Journal on Bioinformatics and Systems Biology 2008 2009:630695

    Published on: 17 December 2008

  6. Research Article

    On the Impact of Entropy Estimation on Transcriptional Regulatory Network Inference Based on Mutual Information

    The reverse engineering of transcription regulatory networks from expression data is gaining large interest in the bioinformatics community. An important family of inference techniques is represented by algori...

    Catharina Olsen, Patrick E Meyer and Gianluca Bontempi

    EURASIP Journal on Bioinformatics and Systems Biology 2008 2009:308959

    Published on: 26 November 2008

  7. Research Article

    A Bayesian Network View on Nested Effects Models

    Nested effects models (NEMs) are a class of probabilistic models that were designed to reconstruct a hidden signalling structure from a large set of observable effects caused by active interventions into the s...

    Cordula Zeller, Holger Fröhlich and Achim Tresch

    EURASIP Journal on Bioinformatics and Systems Biology 2008 2009:195272

    Published on: 12 November 2008

  8. Research Article

    Assessing the Exceptionality of Coloured Motifs in Networks

    Various methods have been recently employed to characterise the structure of biological networks. In particular, the concept of network motif and the related one of coloured motif have proven useful to model t...

    Sophie Schbath, Vincent Lacroix and Marie-France Sagot

    EURASIP Journal on Bioinformatics and Systems Biology 2008 2009:616234

    Published on: 26 October 2008

  9. Research Article

    Towards Systems Biology of Heterosis: A Hypothesis about Molecular Network Structure Applied for the Arabidopsis Metabolome

    We propose a network structure-based model for heterosis, and investigate it relying on metabolite profiles from Arabidopsis. A simple feed-forward two-layer network model (the Steinbuch matrix) is used in our...

    Sandra Andorf, Tanja Gärtner, Matthias Steinfath, Hanna Witucka-Wall, Thomas Altmann and Dirk Repsilber

    EURASIP Journal on Bioinformatics and Systems Biology 2008 2009:147157

    Published on: 27 August 2008