title: Gene regulatory network inference: data integration in dynamic models-a review.
abstract: Systems biology aims to develop mathematical models of biological systems by integrating experimental and theoretical techniques. During the last decade, many systems biological approaches that base on genome-wide data have been developed to unravel the complexity of gene regulation. This review deals with the reconstruction of gene regulatory networks (GRNs) from experimental data through computational methods. Standard GRN inference methods primarily use gene expression data derived from microarrays. However, the incorporation of additional information from heterogeneous data sources, e.g. genome sequence and protein-DNA interaction data, clearly supports the network inference process. This review focuses on promising modelling approaches that use such diverse types of molecular biological information. In particular, approaches are discussed that enable the modelling of the dynamics of gene regulatory systems. The review provides an overview of common modelling schemes and learning algorithms and outlines current challenges in GRN modelling.
authors.affiliation: Leibniz Institute for Natural Product Research and Infection Biology - Hans Knoell Institute, Jena, Germany.
authors.forename: Michael
authors.initials: M
authors.lastname: Hecker
authors.forename: Sandro
authors.initials: S
authors.lastname: Lambeck
authors.forename: Susanne
authors.initials: S
authors.lastname: Toepfer
authors.forename: Eugene
authors.initials: E
authors.lastname: van Someren
authors.forename: Reinhard
authors.initials: R
authors.lastname: Guthke
mesh_terms: D003198:Computer Simulation; D003628:Database Management Systems; D030562:Databases, Protein; D020869:Gene Expression Profiling / Q000379:methods*; D005786:Gene Expression Regulation / Q000502:physiology*; D008954:Models, Biological; D020543:Proteome / Q000378:metabolism*; D015398:Signal Transduction / Q000502:physiology*; D049490:Systems Biology / Q000379:methods*; D018511:Systems Integration
chemical_list: D020543:Proteome