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

Molecular systems biology, 2021-10, Vol.17 (10), p.e10427-n/a

2021

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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