Assigning probes into a small number of pools separable by electrophoresis. - Teemu Kivioja; Mikko Arvas; Kari Kataja; Merja Penttilä; Hans Söderlund; Esko Ukkonen (ISMB, 2002)

Optimization of cDNA-AFLP experiments using genomic sequence data. - Teemu Kivioja; Mikko Arvas; Markku Saloheimo; Merja Penttilä; Esko Ukkonen (Bioinform., 2005)

Oxygen dependence of metabolic fluxes and energy generation of Saccharomyces cerevisiae CEN.PK113-1A. - Paula Jouhten; Eija Rintala; Anne Huuskonen; Anu Tamminen; Mervi Toivari; Marilyn Wiebe; Laura Ruohonen; Merja Penttilä; Hannu Maaheimo (BMC Syst. Biol., 2008)

13C-metabolic flux ratio and novel carbon path analyses confirmed that Trichoderma reesei uses primarily the respirative pathway also on the preferred carbon source glucose. - Paula Jouhten; Esa Pitkänen; Tiina Pakula; Markku Saloheimo; Merja Penttilä; Hannu Maaheimo (BMC Syst. Biol., 2009)

Integration of transcription and flux data reveals molecular paths associated with differences in oxygen-dependent phenotypes of Saccharomyces cerevisiae. - Erno Lindfors; Paula Jouhten; Merja Oja; Eija Rintala; Matej Oresic; Merja Penttilä (BMC Syst. Biol., 2014)

Comparative Genome-Scale Reconstruction of Gapless Metabolic Networks for Present and Ancestral Species. - Esa Pitkänen; Paula Jouhten; Jian Hou 007; Muhammad Fahad Syed; Peter Blomberg; Jana Kludas; Merja Oja; Liisa Holm; Merja Penttilä; Juho Rousu; Mikko Arvas (PLoS Comput. Biol., 2014)

Strain design optimization using reinforcement learning. - Maryam Sabzevari; Sándor Szedmák; Merja Penttilä; Paula Jouhten; Juho Rousu (PLoS Comput. Biol., 2022)