Simulation tools for biochemical networks: evaluation of performance and usability. - Antti Pettinen; Tommi Aho; Olli-Pekka Smolander; Tiina Manninen; Antti Saarinen; Kaisa-Leena Taattola; Olli Yli-Harja; Marja-Leena Linne (Bioinform., 2005)

RMBNToolbox: random models for biochemical networks. - Tommi Aho; Olli-Pekka Smolander; Jari Niemi; Olli Yli-Harja (BMC Syst. Biol., 2007)

Delayed Stochastic Model of Transcription at the Single Nucleotide Level. - Andre S. Ribeiro; Olli-Pekka Smolander; Tiina Rajala; Antti Häkkinen; Olli Yli-Harja (J. Comput. Biol., 2009)

Information propagation within the Genetic Network of Saccharomyces cerevisiae. - Sharif Chowdhury; Jason Lloyd-Price; Olli-Pekka Smolander; Wayne C. V. Baici; Timothy R. Hughes; Olli Yli-Harja; Gordon Chua; Andre S. Ribeiro (BMC Syst. Biol., 2010)

Evolutionary Dynamics of a Population of Cells with a Toxin Suppressor Gene. - Antti Häkkinen; Fred G. Biddle; Olli-Pekka Smolander; Olli Yli-Harja; Andre S. Ribeiro (Trans. Comp. Sys. Biology, 2011)

Transcriptome dynamics-based operon prediction in prokaryotes. - Vittorio Fortino; Olli-Pekka Smolander; Petri Auvinen; Roberto Tagliaferri; Dario Greco (BMC Bioinform., 2014)