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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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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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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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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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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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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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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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Handling uncertainty in dynamic models: the pentose phosphate pathway in Trypanosoma brucei

PLoS computational biology, 2013-12, Vol.9 (12), p.e1003371-e1003371

2013

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

Applied microbiology and biotechnology, 2018-11, Vol.102 (22), p.9541-9548

2018

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Advances in genome-scale metabolic models of industrially important fungi

Current opinion in biotechnology, 2023-12, Vol.84, p.103005-103005, Article 103005

2023

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Dynamic modelling under uncertainty: the case of Trypanosoma brucei energy metabolism

PLoS computational biology, 2012-01, Vol.8 (1), p.e1002352-e1002352

2012

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

Nature protocols, 2024-03, Vol.19 (3), p.629-667

2024

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

Proceedings of the National Academy of Sciences - PNAS, 2023-02, Vol.120 (6), p.e2217868120-e2217868120

2023

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

Biotechnology and bioengineering, 2021-12, Vol.118 (12), p.4800-4814

2021

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A domino effect in drug action: from metabolic assault towards parasite differentiation

Molecular microbiology, 2011-01, Vol.79 (1), p.94-108

2011

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

Briefings in bioinformatics, 2023-03, Vol.24 (2)

2023

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

Biotechnology and bioengineering, 2016-05, Vol.113 (5), p.961-969

2016

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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

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

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

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

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

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

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

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

Handling uncertainty in dynamic models: the pentose phosphate pathway in Trypanosoma brucei

Single-cell omics analysis with genome-scale metabolic modeling

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

Advances in genome-scale metabolic models of industrially important fungi

Dynamic modelling under uncertainty: the case of Trypanosoma brucei energy metabolism

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

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

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

A domino effect in drug action: from metabolic assault towards parasite differentiation

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

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

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