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

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

  1. 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...

    Authors: Hendrik Hache, Hans Lehrach and Ralf Herwig
    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2009 2009:617281
    Content type: Research Article Published on:

  3. 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...

    Authors: Dirk Repsilber, Thomas Martinetz and Mats Björklund
    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2009 2009:618502
    Content type: Research Article Published on:

  4. 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 ...

    Authors: 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
    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2009 2009:545176
    Content type: Research Article Published on:

  5. 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...

    Authors: Oliver Ebenhöh and Thomas Handorf
    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2009 2009:570456
    Content type: Research Article Published on:

  6. Gene-Gene dependency plays a very important role in system biology as it pertains to the crucial understanding of different biological mechanisms. Time-course microarray data provides a new platform useful to ...

    Authors: Xin Gao, Daniel Q. Pu and Peter X.-K. Song
    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2009 2009:535869
    Content type: Research Article Published on:

  7. 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...

    Authors: P. van Nes, D. Bellomo, M.J.T. Reinders and D. de Ridder
    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2008 2009:630695
    Content type: Research Article Published on:

  8. 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...

    Authors: Catharina Olsen, Patrick E Meyer and Gianluca Bontempi
    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2008 2009:308959
    Content type: Research Article Published on:

  9. 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...

    Authors: Cordula Zeller, Holger Fröhlich and Achim Tresch
    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2008 2009:195272
    Content type: Research Article Published on:

  10. 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...

    Authors: Sophie Schbath, Vincent Lacroix and Marie-France Sagot
    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2008 2009:616234
    Content type: Research Article Published on:

  11. 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...

    Authors: Sandra Andorf, Tanja Gärtner, Matthias Steinfath, Hanna Witucka-Wall, Thomas Altmann and Dirk Repsilber
    Citation: EURASIP Journal on Bioinformatics and Systems Biology 2008 2009:147157
    Content type: Research Article Published on: