It gives me great pleasure to present the Special Issue of LNCS Transactions on Computational Systems Biology devoted to considerably extended versions of selected papers presented at the International Workshop on Bioinformatics Research and Applications (IWBRA 2005). The IWBRA workshop was a part of the International Conference on Computational Science (ICCS 2005) which took place in Emory University, Atlanta, Georgia, USA, May 22 24, 2005. See http: //www.cs.gsu.edu/pan/ iwbra.htm for more details. The 10 papers selected for the special issue cover a wide range of bioinformatics research....