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

PLoS computational biology, 2018-10, Vol.14 (10), p.e1006541-e1006541

2018

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

Molecular systems biology, 2017-08, Vol.13 (8), p.935-n/a

2017

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

Nature communications, 2019-08, Vol.10 (1), p.3586-13, Article 3586

2019

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

Nature communications, 2022-06, Vol.13 (1), p.3766-3766, Article 3766

2022

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

Nature communications, 2022-05, Vol.13 (1), p.2969-2969, Article 2969

2022

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

International journal of molecular sciences, 2022-08, Vol.23 (15), p.8517

2022

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

Nature communications, 2023-12, Vol.14 (1), p.8171-8171, Article 8171

2023

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

PLoS computational biology, 2023-04, Vol.19 (4), p.e1011009-e1011009

2023

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

International journal of molecular sciences, 2024-04, Vol.25 (7), p.4053

2024

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Probing the metabolic network in bloodstream-form Trypanosoma brucei using untargeted metabolomics with stable isotope labelled glucose

PLoS pathogens, 2015-03, Vol.11 (3), p.e1004689-e1004689

2015

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Nitrogen as the major factor influencing gene expression in Yarrowia lipolytica

Biotechnology reports (Amsterdam, Netherlands), 2020-09, Vol.27, p.e00521-e00521, Article e00521

2020

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

Microbial cell factories, 2023-11, Vol.22 (1), p.1-243, Article 243

2023

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

Biotechnology and Bioprocess Engineering, 2024, 29(1), , pp.35-67

2024

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

Current opinion in microbiology, 2022-08, Vol.68, p.102168-102168, Article 102168

Kerkhoven, Eduard J

2022

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

Biomolecules (Basel, Switzerland), 2022-11, Vol.12 (11), p.1632

2022

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

G3 : genes - genomes - genetics, 2019-12, Vol.9 (12), p.4059-4071

2019

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

iScience, 2022-12, Vol.25 (12), p.105703-105703, Article 105703

2022

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

Biotechnology and bioengineering, 2021-10, Vol.118 (10), p.3640-3654

2021

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

iScience, 2021-11, Vol.24 (11), p.103294-103294, Article 103294

2021

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Rewiring Saccharomyces cerevisiae metabolism for optimised Taxol® precursors production

Metabolic engineering communications, 2024-06, Vol.18, p.e00229-e00229, Article e00229

2024

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

Trends in biotechnology (Regular ed.), 2022-03, Vol.40 (3), p.291-305

2022

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

Proceedings of the National Academy of Sciences - PNAS, 2021-12, Vol.118 (51)

2021

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

Nature communications, 2020-10, Vol.11 (1), p.5443-5443, Article 5443

2020

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

iScience, 2020-09, Vol.23 (9), p.101525-101525, Article 101525

2020

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

Metabolites, 2021-05, Vol.11 (5), p.304

2021

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Biotechnology & Applied Microbiology
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Biochemistry & Molecular Biology
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Metabolic Engineering
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RAVEN 2.0: A versatile toolbox for metabolic network reconstruction and a case study on Streptomyces coelicolor

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

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

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

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

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

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

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

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

Probing the metabolic network in bloodstream-form Trypanosoma brucei using untargeted metabolomics with stable isotope labelled glucose

Nitrogen as the major factor influencing gene expression in Yarrowia lipolytica

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

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

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

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

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

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

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

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

Rewiring Saccharomyces cerevisiae metabolism for optimised Taxol® precursors production

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

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

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

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

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

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