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The paper systematically compares novel fluorescent proteins in budding yeast to evaluate their characteristics for research applications.

The paper develops a glucose biosensor, TINGL, for measuring intracellular glucose dynamics in yeast and human cells, showing it detects glucose concentrations up to 1 mM and responds to glucose addition in starved cells.

Gempipe improves multi-strain genome-scale metabolic model reconstruction by combining reference and reference-free methods, enhancing accuracy and enabling strain-specific metabolic analysis.

The paper develops an E. coli strain for enhanced threonine production using metabolic modeling and experiments, and explores its application for producing high-value chemicals like 2,5-dimethylpyrazine.

The paper develops a theoretical framework to analyze microbial community dynamics by linking metabolic stoichiometry, growth rates, and biomass carrying capacity.

The paper develops a multiscale computational model integrating metabolism, growth, and cell cycle in yeast to predict that fermentation modulates cell size under different growth conditions.

This study shows that uni-obligate endosymbionts have lost metabolic genes present in free-living bacteria and bi-obligate endosymbionts, suggesting a stochastic ratchet model for endosymbiotic fate.

This study introduces MINN, a metabolic-informed neural network that integrates multi-omics data to predict metabolic fluxes in E. coli, outperforming pure ML and pFBA methods.

This study identifies mitochondrial efficiency as the key factor determining the Crabtree effect in yeasts by comparing Pichia kluyveri and Saccharomyces cerevisiae.

This study investigates how budding yeast adapts to sucrose transitions by analyzing cAMP signaling dynamics and their impact on growth and metabolism.

The paper introduces a method to distinguish between fermentative and respiratory metabolisms in single yeast cells using a fluorescent biosensor and a respiratory inhibitor.

Standard-GEM provides a template for reproducible genome-scale metabolic model development following FAIR principles and software best practices.

This study uses a resource allocation model to compare metabolic strategies in Saccharomyces cerevisiae under different conditions, finding increased energy costs in respiratory-deficient strains.

The paper develops a computational model of fission yeast metabolism to explore resource allocation and metabolic strategies under different glucose conditions.

The paper shows that Saccharomyces cerevisiae maintains excess glycolytic enzyme capacity under glucose-limited conditions as an adaptation to environmental nutrient fluctuations.

The paper develops a physiologically informed kinetic model of yeast glycolysis connected to central metabolism, showing it captures experimental dynamics and explains pathway contributions under glucose perturbations.

The paper develops a whole-cell metabolic model for yeast to predict compartment-specific proteome constraints that explain metabolic strategies under different growth conditions.

The paper identifies nutrient uptake constraints in Lactococcus lactis using a proteome-constrained model and experimental data, showing how these constraints influence metabolic fluxes and fitness in nutrient-rich environments.

The paper develops a dynamic genome-scale model to compare redox balancing strategies in yeast species during fermentation, revealing novel metabolic pathways in cryotolerant strains.

This paper develops a dynamic genome-scale model to analyze redox balance strategies in yeasts during batch cultures, showing how cryotolerant strains achieve metabolic stability.

This paper introduces ecmtool, a tool that enumerates elementary conversion modes to fully characterize metabolic capabilities from genome-scale networks.

Memote, open-source Python software, runs a community-maintained, partly scored test suite (consistency, biomass, annotations, optional experimental data) on SBML-encoded genome-scale metabolic models, once or through continuous integration.

The paper develops a pH-insensitive ATP biosensor for yeast and shows single-cell heterogeneity in ATP dynamics during nutrient transitions.

The paper develops a theory to describe all possible molecular states of cellular self-fabrication, identifying Elementary Growth Modes as the fundamental building blocks of cellular phenotype.

The paper shows that overflow metabolism arises from two growth-limiting constraints across different metabolic models.

This paper systematically evaluates genome-scale metabolic reconstruction tools to determine their quality and suitability for different applications.

The paper shows that maximizing microbial growth rate limits the number of active metabolic pathways to the number of enzyme expression constraints, explaining simple metabolic behaviors through evolutionary optimization.

This study shows how kefir, a natural microbial community, achieves stable coexistence through spatio-temporal niche partitioning and metabolic cooperation during milk fermentation.

The paper characterizes 27 fluorescent proteins in vivo in yeast, finding differences from in vitro data and showing how codon optimization affects their properties.