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)

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)

TrypanoCyc: a community-led biochemical pathways database for Trypanosoma brucei. - Sanu Shameer; Flora J. Logan-Klumpler; Florence Vinson; Ludovic Cottret; Benjamin Merlet; Fiona Achcar; Michael Boshart; Matthew Berriman; Rainer Breitling; Frédéric Bringaud; Peter Bütikofer; Amy M. Cattanach; et al. (Nucleic Acids Res., 2015)

RAVEN 2.0: A versatile toolbox for metabolic network reconstruction and a case study on Streptomyces coelicolor. - Hao Wang 078; Simonas Marcisauskas; Benjamín J. Sánchez; Iván Domenzain; Daniel Hermansson; Rasmus Agren; Jens Nielsen; Eduard J. Kerkhoven (PLoS Comput. Biol., 2018)

SLIMEr: probing flexibility of lipid metabolism in yeast with an improved constraint-based modeling framework. - Benjamín J. Sánchez; Feiran Li; Eduard J. Kerkhoven; Jens Nielsen (BMC Syst. Biol., 2019)

Genome-scale metabolic modeling reveals metabolic trade-offs associated with lipid production in Rhodotorula toruloides. - Alina Rekena; Marina J. Pinheiro; Nemailla Bonturi; Isma Belouah; Eliise Tammekivi; Koit Herodes; Eduard J. Kerkhoven; Petri-Jaan Lahtvee (PLoS Comput. Biol., 2023)

HGTphyloDetect: facilitating the identification and phylogenetic analysis of horizontal gene transfer. - Le Yuan; Hongzhong Lu; Feiran Li; Jens Nielsen; Eduard J. Kerkhoven (Briefings Bioinform., 2023)