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A systematic assessment of current genome-scale metabolic reconstruction tools

Genome Biology, 2019-08, Vol.20 (1), p.158-20, Article 158

2019

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Metabolic cooperation and spatiotemporal niche partitioning in a kefir microbial community

Nature microbiology, 2021-02, Vol.6 (2), p.196-208

2021

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Whole-cell modeling in yeast predicts compartment-specific proteome constraints that drive metabolic strategies

Nature communications, 2022-02, Vol.13 (1), p.801-801, Article 801

2022

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In vivo characterisation of fluorescent proteins in budding yeast

Scientific reports, 2019-02, Vol.9 (1), p.2234-2234, Article 2234

2019

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Shifts in growth strategies reflect tradeoffs in cellular economics

Molecular systems biology, 2009, Vol.5 (1), p.323-n/a

2009

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Bet-hedging during bacterial diauxic shift

Proceedings of the National Academy of Sciences - PNAS, 2014-05, Vol.111 (20), p.7427-7432

2014

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The common message of constraint-based optimization approaches: overflow metabolism is caused by two growth-limiting constraints

Cellular and molecular life sciences : CMLS, 2020-02, Vol.77 (3), p.441-453

2020

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Availability of public goods shapes the evolution of competing metabolic strategies

Proceedings of the National Academy of Sciences - PNAS, 2013-08, Vol.110 (35), p.14302-14307

2013

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Lost in Transition: Start-Up of Glycolysis Yields Subpopulations of Nongrowing Cells

Science (American Association for the Advancement of Science), 2014-02, Vol.343 (6174), p.987-987

2014

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Proteome constraints reveal targets for improving microbial fitness in nutrient‐rich environments

Molecular systems biology, 2021-04, Vol.17 (4), p.e10093-n/a

2021

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Community flux balance analysis for microbial consortia at balanced growth

PloS one, 2013-05, Vol.8 (5), p.e64567-e64567

2013

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RedCom: A strategy for reduced metabolic modeling of complex microbial communities and its application for analyzing experimental datasets from anaerobic digestion

PLoS computational biology, 2019-02, Vol.15 (2), p.e1006759-e1006759

2019

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Population dynamics of microbial cross-feeding are determined by co-localization probabilities and cooperation-independent cheater growth

The ISME Journal, 2021-10, Vol.15 (10), p.3050-3061

2021

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Microbial competition reduces metabolic interaction distances to the low µm-range

The ISME Journal, 2021-03, Vol.15 (3), p.688-701

2021

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Elementary Growth Modes provide a molecular description of cellular self-fabrication

PLoS computational biology, 2020-01, Vol.16 (1), p.e1007559-e1007559

2020

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Exploring metabolic pathway reconstruction and genome-wide expression profiling in Lactobacillus reuteri to define functional probiotic features

PloS one, 2011-04, Vol.6 (4), p.e18783-e18783

2011

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A yeast FRET biosensor enlightens cAMP signalling

Molecular biology of the cell, 2021-06, Vol.32 (13), p.mbcE20050319-1240

2021

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Genome-Scale Metabolic Reconstruction of Acetobacter pasteurianus 386B, a Candidate Functional Starter Culture for Cocoa Bean Fermentation

Frontiers in microbiology, 2019-12, Vol.10, p.2801

2019

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The number of active metabolic pathways is bounded by the number of cellular constraints at maximal metabolic rates

PLoS computational biology, 2019-03, Vol.15 (3), p.e1006858-e1006858

2019

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Model-based quantification of metabolic interactions from dynamic microbial-community data

PloS one, 2017-03, Vol.12 (3), p.e0173183-e0173183

2017

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Analysis of Growth of Lactobacillus plantarum WCFS1 on a Complex Medium Using a Genome-scale Metabolic Model

The Journal of biological chemistry, 2006-12, Vol.281 (52), p.40041-40048

2006

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Reconstructing the metabolic network of a bacterium from its genome

Trends in microbiology (Regular ed.), 2005-11, Vol.13 (11), p.550-558

2005

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An excess of glycolytic enzymes under glucose‐limited conditions may enable Saccharomyces cerevisiae to adapt to nutrient availability

FEBS letters, 2022-12, Vol.596 (24), p.3203-3210

2022

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Maintaining maximal metabolic flux by gene expression control

PLoS computational biology, 2018-09, Vol.14 (9), p.e1006412-e1006412

2018

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Genome-Scale Model of Streptococcus thermophilus LMG18311 for Metabolic Comparison of Lactic Acid Bacteria

Applied and Environmental Microbiology, 2009-06, Vol.75 (11), p.3627-3633

2009

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A systematic assessment of current genome-scale metabolic reconstruction tools

Metabolic cooperation and spatiotemporal niche partitioning in a kefir microbial community

Whole-cell modeling in yeast predicts compartment-specific proteome constraints that drive metabolic strategies

In vivo characterisation of fluorescent proteins in budding yeast

Shifts in growth strategies reflect tradeoffs in cellular economics

Bet-hedging during bacterial diauxic shift

The common message of constraint-based optimization approaches: overflow metabolism is caused by two growth-limiting constraints

Availability of public goods shapes the evolution of competing metabolic strategies

Lost in Transition: Start-Up of Glycolysis Yields Subpopulations of Nongrowing Cells

Proteome constraints reveal targets for improving microbial fitness in nutrient‐rich environments

Community flux balance analysis for microbial consortia at balanced growth

RedCom: A strategy for reduced metabolic modeling of complex microbial communities and its application for analyzing experimental datasets from anaerobic digestion

Population dynamics of microbial cross-feeding are determined by co-localization probabilities and cooperation-independent cheater growth

Microbial competition reduces metabolic interaction distances to the low µm-range

Elementary Growth Modes provide a molecular description of cellular self-fabrication

Exploring metabolic pathway reconstruction and genome-wide expression profiling in Lactobacillus reuteri to define functional probiotic features

A yeast FRET biosensor enlightens cAMP signalling

Genome-Scale Metabolic Reconstruction of Acetobacter pasteurianus 386B, a Candidate Functional Starter Culture for Cocoa Bean Fermentation

The number of active metabolic pathways is bounded by the number of cellular constraints at maximal metabolic rates

Model-based quantification of metabolic interactions from dynamic microbial-community data

Analysis of Growth of Lactobacillus plantarum WCFS1 on a Complex Medium Using a Genome-scale Metabolic Model

Reconstructing the metabolic network of a bacterium from its genome

An excess of glycolytic enzymes under glucose‐limited conditions may enable Saccharomyces cerevisiae to adapt to nutrient availability

Maintaining maximal metabolic flux by gene expression control

Genome-Scale Model of Streptococcus thermophilus LMG18311 for Metabolic Comparison of Lactic Acid Bacteria

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