Eduard J Kerkhoven
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Improving the phenotype predictions of a yeast genome‐scale metabolic model by incorporating enzymatic constraints
BJ Sánchez, C Zhang, A Nilsson, PJ Lahtvee, EJ Kerkhoven, J Nielsen
Molecular systems biology 13 (8), 935, 2017
RAVEN 2.0: A versatile toolbox for metabolic network reconstruction and a case study on Streptomyces coelicolor
H Wang, S Marcišauskas, BJ Sánchez, I Domenzain, D Hermansson, ...
PLOS Computational Biology 14 (10), e1006541, 2018
A consensus S. cerevisiae metabolic model Yeast8 and its ecosystem for comprehensively probing cellular metabolism
H Lu, F Li, BJ Sánchez, Z Zhu, G Li, I Domenzain, S Marcišauskas, ...
Nature communications 10 (1), 3586, 2019
An atlas of human metabolism
JL Robinson, P Kocabaş, H Wang, PE Cholley, D Cook, A Nilsson, ...
Science signaling 13 (624), eaaz1482, 2020
Barriers and opportunities in bio-based production of hydrocarbons
YJ Zhou, EJ Kerkhoven, J Nielsen
Nature Energy 3 (11), 925-935, 2018
Regulation of amino-acid metabolism controls flux to lipid accumulation in Yarrowia lipolytica
EJ Kerkhoven, KR Pomraning, SE Baker, J Nielsen
NPJ systems biology and applications 2, 16005, 2016
Probing the metabolic network in bloodstream-form Trypanosoma brucei using untargeted metabolomics with stable isotope labelled glucose
DJ Creek, M Mazet, F Achcar, J Anderson, DH Kim, R Kamour, P Morand, ...
PLoS pathogens 11 (3), e1004689, 2015
Deep learning-based kcat prediction enables improved enzyme-constrained model reconstruction
F Li, L Yuan, H Lu, G Li, Y Chen, MKM Engqvist, EJ Kerkhoven, J Nielsen
Nature Catalysis 5 (8), 662-672, 2022
C/N ratio and carbon source-dependent lipid production profiling in Rhodotorula toruloides
HJS Lopes, N Bonturi, EJ Kerkhoven, EA Miranda, PJ Lahtvee
Applied microbiology and biotechnology 104 (6), 2639-2649, 2020
Reconstruction of a catalogue of genome-scale metabolic models with enzymatic constraints using GECKO 2.0
I Domenzain, B Sánchez, M Anton, EJ Kerkhoven, A Millán-Oropeza, ...
Nature Communications 13, 2022
Proteome analysis of xylose metabolism in Rhodotorula toruloides during lipid production
IA Tiukova, J Brandenburg, J Blomqvist, S Sampels, N Mikkelsen, ...
Biotechnology for Biofuels 12 (1), 137, 2019
A molecular genetic toolbox for Yarrowia lipolytica
EL Bredeweg, KR Pomraning, Z Dai, J Nielsen, EJ Kerkhoven, SE Baker
Biotechnology for biofuels 10 (1), 2, 2017
Applications of computational modeling in metabolic engineering of yeast
EJ Kerkhoven, PJ Lahtvee, J Nielsen
FEMS Yeast Res 15 (1), 1-13, 2015
Advancing metabolic engineering of Yarrowia lipolytica using the CRISPR/Cas system
TQ Shi, H Huang, EJ Kerkhoven, XJ Ji
Applied microbiology and biotechnology 102, 9541-9548, 2018
A domino effect in drug action: from metabolic assault towards parasite differentiation
JR Haanstra, EJ Kerkhoven, A Van Tuijl, M Blits, M Wurst, R Van Nuland, ...
Molecular microbiology 79 (1), 94-108, 2011
Genome‐scale metabolic model of Pichia pastoris with native and humanized glycosylation of recombinant proteins
ZA Irani, EJ Kerkhoven, SA Shojaosadati, J Nielsen
Biotechnology and bioengineering 113 (5), 961-969, 2016
Handling uncertainty in dynamic models: the pentose phosphate pathway in Trypanosoma brucei
EJ Kerkhoven, F Achcar, VP Alibu, RJ Burchmore, IH Gilbert, M Trybiło, ...
PLoS computational biology 9 (12), e1003371, 2013
Genome‐scale model of Rhodotorula toruloides metabolism
IA Tiukova, S Prigent, J Nielsen, M Sandgren, EJ Kerkhoven
Biotechnology and bioengineering 116 (12), 3396-3408, 2019
Genome scale metabolic modeling of the riboflavin overproducer Ashbya gossypii
R Ledesma‐Amaro, EJ Kerkhoven, JL Revuelta, J Nielsen
Biotechnology and bioengineering 111 (6), 1191-1199, 2014
SLIMEr: probing flexibility of lipid metabolism in yeast with an improved constraint-based modeling framework
BJ Sánchez, F Li, EJ Kerkhoven, J Nielsen
BMC Systems Biology 13 (1), 4, 2019
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