Eduard Kerkhoven
The research in Kerkhoven lab revolves around metabolic systems biology, where computational model-driven analysis of experimental data is used to understand, predict and engineer biology. With a particular focus on metabolism we bridge the gap between in silico prediction and in vivo validation through data-driven genetic engineering. We are working on a variety of different projects, from developing microbes as cell factories for sustainable production of chemicals, to investigating metabolic aspects in human disease. Computational analysis of metabolism helps us to come up with strategies for metabolic engineering. We reconstruct and curate genome-scale metabolic models (GEMs) for various organisms (yeasts, bacteria, human) using our RAVEN Toolbox. Our model development is tracked on GitHub, and important models are those for S. cerevisiae, Y. lipolytica, S. coelicolor and Homo sapiens. These models are combined with omics analyses (primarily RNAseq and proteomics), either directly or through the use of enzyme-constrained models using our GECKO Toolbox. In addition to biotechnological applications, we have also been using our approaches to investigate for instance evolution of the yeast subphylum, and prediction of kcat values through deep learning. Besides computational research, we also investigate the oleaginous yeast Y. lipolytica as microbial cell factory, for instance to produce itaconic acid. This promising platform chemical can be used as monomer to e.g. aid bioleaching, or as a range of innovative polymers. We perform this through genetic engineering, integrative omics analysis, modeling of metabolism and fermentation optimization.Metabolic systems biology
Computational metabolic engineering
Oleaginous yeasts as biocatalysts
Showing 60 publications
Rewiring Saccharomyces cerevisiae metabolism for optimised Taxol® precursors production
Single-cell omics analysis with genome-scale metabolic modeling
Advances in genome-scale metabolic models of industrially important fungi
Resin acids play key roles in shaping microbial communities during degradation of spruce bark
Abolishing storage lipids induces protein misfolding and stress responses in Yarrowia lipolytica
Deep learning-based k(cat) prediction enables improved enzyme-constrained model reconstruction
Multiscale models quantifying yeast physiology: towards a whole-cell model
Genome-scale metabolic model of oleaginous yeast Papiliotrema laurentii
Urea is a drop-in nitrogen source alternative to ammonium sulphate in Yarrowia lipolytica
A Pan-Draft Metabolic Model Reflects Evolutionary Diversity across 332 Yeast Species
Reconstruction of Genome-Scale Metabolic Model for Hansenula polymorpha Using RAVEN
Validated Growth Rate-Dependent Regulation of Lipid Metabolism in Yarrowia lipolytica
Proteome Constraints in Genome-Scale Models
Adaptations in metabolism and protein translation give rise to the Crabtree effect in yeast
The yeastGemMap: A process diagram to assist yeast systems-metabolic studies
Editorial: Multi-Omics Technologies for Optimizing Synthetic Biomanufacturing
Yeast metabolic innovations emerged via expanded metabolic network and gene positive selection
C/N ratio and carbon source-dependent lipid production profiling in Rhodotorula toruloides
Extracting novel hypotheses and findings from RNA-seq data
Nitrogen as the major factor influencing gene expression in Yarrowia lipolytica
Proteome analysis of xylose metabolism in Rhodotorula toruloides during lipid production
Genome-scale model of Rhodotorula toruloides metabolism
Regulation of yeast-to-hyphae transition in Yarrowia lipolytica
Barriers and opportunities in bio-based production of hydrocarbons
Advancing metabolic engineering of Yarrowia lipolytica using the CRISPR/Cas system
A molecular genetic toolbox for Yarrowia lipolytica
Leucine Biosynthesis Is Involved in Regulating High Lipid Accumulation in Yarrowia lipolytica
Regulation of amino-acid metabolism controls flux to lipid accumulation in yarrowia lipolytica
Applications of computational modeling in metabolic engineering of yeast
TrypanoCyc: a community-led biochemical pathways database for Trypanosoma brucei
Genome Scale Metabolic Modeling of the Riboflavin Overproducer Ashbya gossypii
Trypanosoma brucei: meet the system
The Silicon Trypanosome: A Test Case of Iterative Model Extension in Systems Biology
Handling Uncertainty in Dynamic Models: The Pentose Phosphate Pathway in Trypanosoma brucei
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Showing 7 research projects
Sustainable biometallurgical battery recycling
Awakening of cryptic biosynthetic gene clusters using obese red yeast
Optimera mikrobiell tillverkning av itakonat för hållbar plast och tvättmedel
Engineering a robust biocatalyst for sustainable biofuel production
From electricity towards biodiesel production in yeast
Systematic Rebuilding of Actinomycetes for Natural Product Formation (ERASysAPP - SYSTERACT)