Approaches to modeling gene regulatory networks: a gentle introduction

This chapter is split into two main sections; first, I will present an introduction to gene networks. Second, I will discuss various approaches to gene network modeling which will include some examples for using different data sources. Computational modeling has been used for many different biological systems and many approaches have been developed addressing the different needs posed by the different application fields. The modeling approaches presented here are not limited to gene regulatory networks and occasionally I will present other examples. The material covered here is an update based on several previous publications by Thomas Schlitt and Alvis Brazma (FEBS Lett 579(8),1859-1866, 2005; Philos Trans R Soc Lond B Biol Sci 361(1467), 483-494, 2006; BMC Bioinformatics 8(suppl 6), S9, 2007) that formed the foundation for a lecture on gene regulatory networks at the In Silico Systems Biology workshop series at the European Bioinformatics Institute in Hinxton.