An analytic and systematic framework for estimating metabolic flux ratios from 13C tracer experiments. - Ari Rantanen; Juho Rousu; Paula Jouhten; Nicola Zamboni; Hannu Maaheimo; Esko Ukkonen (BMC Bioinform., 2008)

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)

ReMatch: a web-based tool to construct, store and share stoichiometric metabolic models with carbon maps for metabolic flux analysis. - Esa Pitkänen; Arto Åkerlund; Ari Rantanen; Paula Jouhten; Esko Ukkonen (J. Integr. Bioinform., 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)

Inferring branching pathways in genome-scale metabolic networks. - Esa Pitkänen; Paula Jouhten; Juho Rousu (BMC Syst. Biol., 2009)

A multi-level study of recombinant Pichia pastoris in different oxygen conditions. - Kristin Baumann; Marc Carnicer; Martin Dragosits; Alexandra Graf; Johannes Stadlmann; Paula Jouhten; Hannu Maaheimo; Brigitte Gasser; Joan Albiol; Diethard Mattanovich; Pau Ferrer (BMC Syst. Biol., 2010)

Reconstruction of the yeast protein-protein interaction network involved in nutrient sensing and global metabolic regulation. - Subir K. Nandy; Paula Jouhten; Jens Nielsen (BMC Syst. Biol., 2010)

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)

Genome-scale metabolic models reveal determinants of phenotypic differences in non-Saccharomyces yeasts. - Jakob P. Pettersen; Sandra Castillo; Paula Jouhten; Eivind Almaas (BMC Bioinform., 2023)