TIde: a software for the systematic scanning of drug targets in kinetic network models. - Marvin Schulz; Barbara M. Bakker; Edda Klipp (BMC Bioinform., 2009)

Dynamic Modelling under Uncertainty: The Case of Trypanosoma brucei Energy Metabolism. - Fiona Achcar; Eduard J. Kerkhoven; Barbara M. Bakker; Michael P. Barrett; Rainer Breitling (PLoS Comput. Biol., 2012)

Testing Biochemistry Revisited: How In Vivo Metabolism Can Be Understood from In Vitro Enzyme Kinetics. - Karen van Eunen; José A. L. Kiewiet; Hans V. Westerhoff; Barbara M. Bakker (PLoS Comput. Biol., 2012)

Model-order reduction of biochemical reaction networks. - Shodhan Rao; Arjan van der Schaft; Karen van Eunen; Barbara M. Bakker; Bayu Jayawardhana (ECC, 2013)

Biochemical Competition Makes Fatty-Acid β-Oxidation Vulnerable to Substrate Overload. - Karen van Eunen; Sereh M. J. Simons; Albert Gerding; Aycha Bleeker; Gijs den Besten; Catharina M. L. Touw; Sander M. Houten; Bert K. Groen; Klaas Krab; Dirk-Jan Reijngoud; Barbara M. Bakker (PLoS Comput. Biol., 2013)

Handling Uncertainty in Dynamic Models: The Pentose Phosphate Pathway in Trypanosoma brucei. - Eduard J. Kerkhoven; Fiona Achcar; Vincent P. Alibu; Richard J. Burchmore; Ian H. Gilbert; Maciej Trybilo; Nicole N. Driessen; David R. Gilbert; Rainer Breitling; Barbara M. Bakker; Michael P. Barrett (PLoS Comput. Biol., 2013)

A model reduction method for biochemical reaction networks. - Shodhan Rao; Arjan van der Schaft; Karen van Eunen; Barbara M. Bakker; Bayu Jayawardhana (BMC Syst. Biol., 2014)

The promiscuous enzyme medium-chain 3-keto-acyl-CoA thiolase triggers a vicious cycle in fatty-acid beta-oxidation. - Anne-Claire M. F. Martines; Karen van Eunen; Dirk-Jan Reijngoud; Barbara M. Bakker (PLoS Comput. Biol., 2017)

Bistability in fatty-acid oxidation resulting from substrate inhibition. - Fentaw Abegaz; Anne-Claire M. F. Martines; Marcel A. Vieira-Lara; Melany Rios-Morales; Dirk-Jan Reijngoud; Ernst C. Wit; Barbara M. Bakker (PLoS Comput. Biol., 2021)

Analyzing postprandial metabolomics data using multiway models: a simulation study. - Lu Li; Shi Yan; Barbara M. Bakker; Huub C. J. Hoefsloot; Bo Chawes; David Horner; Morten A. Rasmussen; Age K. Smilde; Evrim Acar (BMC Bioinform., 2024)