Eduard Kerkhoven

Senior Researcher at Systems and Synthetic Biology

Contact Details ORCID

Publications (68)
Projects (8)

Showing 68 publications

2025

Flux in the field: genome-scale modelling reveals changes in soybean (Glycine max) seed reserve metabolism under drought stress

Christina Cleo Vinson, Erica Mangaravite, Humberto Nasser Louro Lopes et al

Plant Physiology and Biochemistry. Vol. 224

Journal article

2024

A unique metabolic gene cluster regulates lactose and galactose metabolism in the yeast Candida intermedia

Kameshwara Venkata Ramana Peri, Le Yuan, Fábio Luis Da Silva Faria Oliveira et al

Applied and Environmental Microbiology. Vol. 90 (10)

Journal article

2024

Rewiring Saccharomyces cerevisiae metabolism for optimised Taxol® precursors production

Behnaz Nowrouzi, Pablo Torres-Montero, Eduard Kerkhoven et al

Metabolic Engineering Communications. Vol. 18

Journal article

2024

Biosynthesis of Hesperetin, Homoeriodictyol, and Homohesperetin in a Transcriptomics-Driven Engineered Strain of Streptomyces albidoflavus

Álvaro Pérez-Valero, Juan Serna-Diestro, Albert Tafur Rangel et al

International Journal of Molecular Sciences. Vol. 25 (7)

Journal article

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2024

Engineering of Saccharomyces cerevisiae for enhanced metabolic robustness and L-lactic acid production from lignocellulosic biomass

BoHyun Choi, Albert Tafur Rangel, Eduard Kerkhoven et al

Metabolic Engineering. Vol. 84, p. 23-33

Journal article

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2024

Single-cell omics analysis with genome-scale metabolic modeling

Yu Chen, Johan Gustafsson, Jingyu Yang et al

Current Opinion in Biotechnology. Vol. 86

Review article

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2024

Reconstruction, simulation and analysis of enzyme-constrained metabolic models using GECKO Toolbox 3.0

Yu Chen, Johan Gustafsson, Albert Tafur Rangel et al

Nature Protocols. Vol. 19 (3), p. 629-667

Journal article

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2024

Yeast9: a consensus genome-scale metabolic model for S. cerevisiae curated by the community

Chengyu Zhang, Benjamín José Sánchez, Feiran Li et al

Molecular Systems Biology. Vol. 20 (10), p. 1134-1150

Journal article

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2024

Reprogramming Yarrowia lipolytica metabolism for efficient synthesis of itaconic acid from flask to semipilot scale

Jing Fu, Simone Zaghen, Hongzhong Lu et al

Science advances. Vol. 10 (32), p. eadn0414-

Journal article

2024

Reconstruction of genome-scale metabolic models of non-conventional yeasts: current state, challenges, and perspectives

Eduardo Luís Menezes de Almeida, Eduard Kerkhoven, Wendel Batista da Silveira

Biotechnology and Bioprocess Engineering. Vol. 29 (1), p. 35-67

Review article

2024

Streptomyces castrisilvae sp. nov. and Streptomyces glycanivorans sp. nov., novel soil streptomycetes metabolizing mutan and alternan

Tove Widén, Albert Tafur Rangel, Vincent Lombard et al

International Journal of Systematic and Evolutionary Microbiology. Vol. 74 (9)

Journal article

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2023

HGTphyloDetect: facilitating the identification and phylogenetic analysis of horizontal gene transfer

Le Yuan, Hongzhong Lu, Feiran Li et al

Briefings in Bioinformatics. Vol. 24 (2)

Journal article

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2023

Abolishing storage lipids induces protein misfolding and stress responses in Yarrowia lipolytica

Simone Zaghen, Oliver Konzock, Jing Fu et al

Journal of Industrial Microbiology and Biotechnology. Vol. 50 (1)

Journal article

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2023

Generation and analysis of context-specific genome-scale metabolic models derived from single-cell RNA-Seq data

Johan Gustafsson, Petre Mihail Anton, Fariba Roshanzamir et al

Proceedings of the National Academy of Sciences of the United States of America. Vol. 120 (6)

Journal article

2023

Advances in genome-scale metabolic models of industrially important fungi

Yichao Han, Albert Enrique Tafur Rangel, Kyle R. Pomraning et al

Current Opinion in Biotechnology. Vol. 84

Review article

2023

Improved production of Taxol<sup>®</sup> precursors in S. cerevisiae using combinatorial in silico design and metabolic engineering

Koray Malcı, Rodrigo Santibáñez, Nestor Jonguitud-Borrego et al

Microbial Cell Factories. Vol. 22 (1)

Journal article

2023

Genome-scale metabolic modeling reveals metabolic trade-offs associated with lipid production in Rhodotorula toruloides

Alina J. Rekena, Marina Pinheiro, Nemailla Bonturi et al

PLoS Computational Biology. Vol. 19 (4)

Journal article

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2023

Regulation of lactose and galactose growth: Insights from a unique metabolic gene cluster in Candida intermedia

Kameshwara Venkata Ramana Peri, Le Yuan, Fábio Luis Da Silva Faria Oliveira et al

Preprint

2023

Resin acids play key roles in shaping microbial communities during degradation of spruce bark

Amanda Sörensen Ristinmaa, Albert Tafur Rangel, Eduard Kerkhoven et al

Nature Communications. Vol. 14

Journal article

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2022

Validated Growth Rate-Dependent Regulation of Lipid Metabolism in Yarrowia lipolytica

Naghmeh Poorinmohammad, Jing Fu, Bob Wabeke et al

International Journal of Molecular Sciences. Vol. 23 (15)

Journal article

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2022

Multiscale models quantifying yeast physiology: towards a whole-cell model

Hongzhong Lu, Eduard Kerkhoven, Jens B Nielsen

Trends in Biotechnology. Vol. 40 (3), p. 291-305

Review article

2022

Improving recombinant protein production by yeast through genome-scale modeling using proteome constraints

Feiran Li, Yu Chen, Qi Qi et al

Nature Communications. Vol. 13 (1)

Journal article

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2022

Advances in constraint-based models: methods for improved predictive power based on resource allocation constraints

Eduard Kerkhoven

Current Opinion in Microbiology. Vol. 68

Review article

2022

Reconstruction of Genome-Scale Metabolic Model for Hansenula polymorpha Using RAVEN

Francisco Zorrilla, Eduard Kerkhoven

Methods in Molecular Biology. Vol. 2513, p. 271-290

Book chapter

2022

Genome-scale metabolic model of oleaginous yeast Papiliotrema laurentii

Rafaela Zandonade Ventorim, Maurício Alexander de Moura Ferreira, Eduardo Luís Menezes de Almeida et al

Biochemical Engineering Journal. Vol. 180

Journal article

2022

Deep learning-based k(cat) prediction enables improved enzyme-constrained model reconstruction

Feiran Li, Le Yuan, Hongzhong Lu et al

Nature Catalysis. Vol. 5 (8), p. 662-672

Journal article

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2022

Urea is a drop-in nitrogen source alternative to ammonium sulphate in Yarrowia lipolytica

Oliver Konzock, Simone Zaghen, Jing Fu et al

iScience. Vol. 25 (12)

Journal article

2022

A Pan-Draft Metabolic Model Reflects Evolutionary Diversity across 332 Yeast Species

Hongzhong Lu, Eduard Kerkhoven, Jens B Nielsen

Biomolecules. Vol. 12 (11)

Journal article

2022

Generation and analysis of context-specific genome-scale metabolic models derived from single-cell RNA-Seq data

Johan Gustafsson, Jonathan Robinson, Fariba Roshanzamir et al

Preprint

2022

Reconstruction of a catalogue of genome-scale metabolic models with enzymatic constraints using GECKO 2.0

Iván Domenzain Del Castillo Cerecer, Benjamín José Sánchez, Petre Mihail Anton et al

Nature Communications. Vol. 13 (1)

Journal article

2021

Kinetic Models of Metabolism

Hongzhong Lu, Yu Chen, Jens B Nielsen et al

Metabolic Engineering: Concepts and Applications: Volume 13a and 13b. Vol. 13, p. 153-170

Book chapter

2021

Yeast metabolic innovations emerged via expanded metabolic network and gene positive selection

Hongzhong Lu, Feiran Li, Le Yuan et al

Molecular Systems Biology. Vol. 17 (10)

Journal article

2021

Constraint-based modeling of yeast mitochondria reveals the dynamics of protein import and iron-sulfur cluster biogenesis

Carl Malina, Francesca Di Bartolomeo, Eduard Kerkhoven et al

iScience. Vol. 24 (11)

Journal article

2021

Systems-level approaches for understanding and engineering of the oleaginous cell factory Yarrowia lipolytica

Naghmeh Poorinmohammad, Eduard Kerkhoven

Biotechnology and Bioengineering. Vol. 118 (10), p. 3640-3654

Review article

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2021

Editorial: Multi-Omics Technologies for Optimizing Synthetic Biomanufacturing

Young Mo Kim, Christopher J. Petzold, Eduard Kerkhoven et al

Frontiers in Bioengineering and Biotechnology. Vol. 9

Other text in scientific journal

2021

The yeastGemMap: A process diagram to assist yeast systems-metabolic studies

Luis Caspeta-Guadarrama, Eduard Kerkhoven, Alfredo Martinez et al

Biotechnology and Bioengineering. Vol. 118 (12), p. 4800-4814

Journal article

2021

Proteome Constraints in Genome-Scale Models

Yu Chen, Jens B Nielsen, Eduard Kerkhoven

Metabolic Engineering: Concepts and Applications: Volume 13a and 13b. Vol. 13, p. 137-152

Book chapter

2021

Adaptations in metabolism and protein translation give rise to the Crabtree effect in yeast

Carl Malina, Rosemary Brown, Johan Björkeroth et al

Proceedings of the National Academy of Sciences of the United States of America. Vol. 118 (51)

Journal article

2021

Reconstruction of a Genome-Scale Metabolic Model of Streptomyces albus J1074: Improved Engineering Strategies in Natural Product Synthesis

Cheewin Kittikunapong, Suhui Ye, Patricia Magadan-Corpas et al

Metabolites. Vol. 11 (5)

Journal article

2021

Evaluating accessibility, usability and interoperability of genome-scale metabolic models for diverse yeasts species

Iván Domenzain Del Castillo Cerecer, Feiran Li, Eduard Kerkhoven et al

FEMS Yeast Research. Vol. 21 (1)

Review article

2020

C/N ratio and carbon source-dependent lipid production profiling in Rhodotorula toruloides

Helberth Júnnior Santos Lopes, Nemailla Bonturi, Eduard Kerkhoven et al

Applied Microbiology and Biotechnology. Vol. 104 (6), p. 2639-2649

Journal article

2020

Enzyme-Constrained Models and Omics Analysis of Streptomyces coelicolor Reveal Metabolic Changes that Enhance Heterologous Production

Snorre Sulheim, Tjaša Kumelj, Dino van Dissel et al

iScience. Vol. 23 (9)

Journal article

2020

Nitrogen as the major factor influencing gene expression in Yarrowia lipolytica

Piotr Hapeta, Eduard Kerkhoven, Zbigniew Lazar

Biotechnology Reports. Vol. 27

Journal article

2020

An atlas of human metabolism

Jonathan Robinson, Pinar Kocabas, Hao Wang et al

Science signaling. Vol. 13 (624)

Journal article

2020

Extracting novel hypotheses and findings from RNA-seq data

Tyler Doughty, Eduard Kerkhoven

FEMS Yeast Research. Vol. 20 (2)

Review article

2019

SLIMEr: Probing flexibility of lipid metabolism in yeast with an improved constraint-based modeling framework

Benjamín José Sánchez, Feiran Li, Eduard Kerkhoven et al

BMC Systems Biology. Vol. 13 (1)

Journal article

2019

A consensus S. cerevisiae metabolic model Yeast8 and its ecosystem for comprehensively probing cellular metabolism

Hongzhong Lu, Feiran Li, Benjamín José Sánchez et al

Nature Communications. Vol. 10 (1)

Journal article

2019

Genome-scale model of Rhodotorula toruloides metabolism

Ievgeniia Tiukova, Sylvain Prigent, Jens B Nielsen et al

Biotechnology and Bioengineering. Vol. 116 (12), p. 3396-3408

Journal article

2019

Proteome analysis of xylose metabolism in Rhodotorula toruloides during lipid production

Ievgeniia Tiukova, Jule Brandenburg, Johanna Blomqvist et al

Biotechnology for Biofuels. Vol. 12 (1)

Journal article

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2019

Mapping the metabolism of five amino acids in bloodstream form Trypanosoma brucei using U- 13C-labelled substrates and LC–MS

Katharina Johnston, D. H. Kim, Eduard Kerkhoven et al

Bioscience Reports. Vol. 39 (5)

Journal article

2019

Investigating the Influence of Glycerol on the Utilization of Glucose in Yarrowia lipolytica Using RNA-Seq-Based Transcriptomics

Patrice Lubuta, M. Workman, Eduard Kerkhoven et al

G3: Genes, Genomes, Genetics. Vol. 9 (12), p. 4059-4071

Journal article

2018

Barriers and opportunities in bio-based production of hydrocarbons

Yongjin Zhou, Eduard Kerkhoven, Jens B Nielsen

Nature Energy. Vol. 3 (11), p. 925-935

Review article

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2018

Advancing metabolic engineering of Yarrowia lipolytica using the CRISPR/Cas system

Tian Qiong Shi, He Huang, Eduard Kerkhoven et al

Applied Microbiology and Biotechnology. Vol. 102 (22), p. 9541-9548

Review article

2018

Regulation of yeast-to-hyphae transition in Yarrowia lipolytica

Kyle R. Pomraning, Erin L. Bredeweg, Eduard Kerkhoven et al

mSphere. Vol. 3 (6)

Journal article

2018

RAVEN 2.0: A versatile toolbox for metabolic network reconstruction and a case study on Streptomyces coelicolor

Hao Wang, Simonas Marcisauskas, Benjamin José Sanchez Barja et al

PLoS Computational Biology. Vol. 14 (10), p. e1006541-

Journal article

2017

Leucine Biosynthesis Is Involved in Regulating High Lipid Accumulation in Yarrowia lipolytica

Eduard Kerkhoven, Y. M. Kim, S. W. Wei et al

mBio. Vol. 8 (3), p. Article no. e00857-17

Journal article

2017

A molecular genetic toolbox for Yarrowia lipolytica

Erin L. Bredeweg, Kyle R. Pomraning, Ziyu Dai et al

Biotechnology for Biofuels. Vol. 10 (1)

Journal article

2017

Improving the phenotype predictions of a yeast genome-scale metabolic model by incorporating enzymatic constraints

Benjamin José Sanchez Barja, C. Zhang, Avlant Nilsson et al

Molecular Systems Biology. Vol. 13 (8), p. Article no 935 -

Journal article

2016

Regulation of amino-acid metabolism controls flux to lipid accumulation in yarrowia lipolytica

Eduard Kerkhoven, Kyle R. Pomraning, S. E. Baker et al

npj Systems Biology and Applications. Vol. 2

Journal article

2016

Genome-scale metabolic model of Pichia pastoris with native and humanized glycosylation of recombinant proteins

Z. A. Irani, Eduard Kerkhoven, S. A. Shojaosadati et al

Biotechnology and Bioengineering. Vol. 113 (5), p. 961-969

Journal article

2015

TrypanoCyc: a community-led biochemical pathways database for Trypanosoma brucei

S. Shameer, F. J. Logan-Klumpler, F. Vinson et al

Nucleic Acids Research. Vol. 43 (D1), p. D637-D644

Journal article

2015

Crystal Structure of an Arginase-like Protein from Trypanosoma brucei That Evolved without a Binuclear Manganese Cluster

Y. Hai, Eduard Kerkhoven, M. P. Barrett et al

Biochemistry. Vol. 54 (2), p. 458-471

Journal article

2015

Probing the Metabolic Network in Bloodstream-Form Trypanosoma brucei Using Untargeted Metabolomics with Stable Isotope Labelled Glucose

D. J. Creek, M. Mazet, F. Achcar et al

PLoS Pathogens. Vol. 11 (3), p. 1-25

Journal article

2015

Applications of computational modeling in metabolic engineering of yeast

Eduard Kerkhoven, Petri-Jaan Lahtvee, Jens B Nielsen

FEMS Yeast Research. Vol. 15 (1)

Journal article

2014

Trypanosoma brucei: meet the system

F. Achcar, Eduard Kerkhoven, M. P. Barrett

Current Opinion in Microbiology. Vol. 20, p. 162-169

Review article

2014

Genome Scale Metabolic Modeling of the Riboflavin Overproducer Ashbya gossypii

R. Ledesma-Amaro, Eduard Kerkhoven, J. L. Revuelta et al

Biotechnology and Bioengineering. Vol. 111 (6), p. 1191-1199

Journal article

2014

The Silicon Trypanosome: A Test Case of Iterative Model Extension in Systems Biology

F. Achcar, A. Fadda, J. R. Haanstra et al

Advances in Microbial Physiology. Vol. 64, p. 115-143

Book chapter

2013

Handling Uncertainty in Dynamic Models: The Pentose Phosphate Pathway in Trypanosoma brucei

Eduard Kerkhoven, F. Achcar, V. P. Alibu et al

PLoS Computational Biology. Vol. 9 (12), p. Art. no. e1003371-

Journal article

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Showing 8 research projects

2024–2028

BIONEER SCALED-UP PRODUCTION OF NEXT-GENERATION CARBOHYDRATE-DERIVED BUILDING BLOCKS TO ENHANCE THE COMPETITIVENESS OF A SUSTAINABLE EUROPEAN CHEMICALS INDUSTRY