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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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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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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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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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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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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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Editorial: Multi-Omics Technologies for Optimizing Synthetic Biomanufacturing

Frontiers in bioengineering and biotechnology, 2021-12, Vol.9, p.818010-818010

2021

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Single-cell omics analysis with genome-scale metabolic modeling

Current opinion in biotechnology, 2024-04, Vol.86, p.103078-103078, Article 103078

2024

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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

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

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

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

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

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

Editorial: Multi-Omics Technologies for Optimizing Synthetic Biomanufacturing

Single-cell omics analysis with genome-scale metabolic modeling

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