Microbial Metabolic Engineering and Bioproduction

Genome-scale metabolic modelling when changes in environmental conditions affect biomass composition

This paper introduces two computational methods, BTW and HIP, to improve genome-scale metabolic models by accounting for environmental effects on biomass composition, showing differences in model performance and phenotypic predictions.

MOFA: Multi-Objective Flux Analysis for the COBRA Toolbox

The paper introduces MOFA, an add-on tool for the COBRA Toolbox that enables multi-objective flux analysis of metabolic trade-offs using genome-scale models.

Finding metabolic pathways in large networks through atom-conserving substrate-product pairs

The paper introduces a method to find metabolic pathways in large networks by using atom-conserving substrate-product pairs and graph search algorithms.

Predictive evolution of metabolic phenotypes using model-designed selection niches

This paper predicts the evolution of fitness-costly traits by designing selection niches using metabolic models and validates it in yeast for increased aroma compound secretion.

High Throughput Fitness Profiling Reveals Loss Of GacS-GacA Regulation Improves Indigoidine Production In Pseudomonas putida

The paper identifies gene deletions that enhance indigoidine production in Pseudomonas putida using fitness profiling and bioreactor experiments.

The Bioprocess TEA Calculator: An online techno-economic analysis tool to evaluate the commercial competitiveness of potential bioprocesses

The paper introduces an online tool for techno-economic analysis of bioprocesses, enabling researchers to evaluate commercial competitiveness based on process parameters and strain engineering outcomes.

TranSyT, an innovative framework for identifying transport systems

TranSyT automates the integration of transport reactions into genome-scale metabolic models by compiling curated transporter data and providing rapid genome annotation.

Constraint-based metabolic control analysis for rational strain engineering

This paper introduces a constraint-based framework, Network Response Analysis (NRA), to improve metabolic engineering by incorporating physiological constraints and genome editing limitations.

Genome Scale-Differential Flux Analysis reveals deregulation of lung cell metabolism on SARS Cov2 infection

The paper develops a genome-scale differential flux analysis method to identify metabolic changes in human lung cells infected with SARS-CoV-2, revealing deregulation in lipid metabolism.

Optogenetic Amplification Circuits for Light-Induced Metabolic Control

The paper introduces OptoAMP circuits that amplify light-induced transcriptional responses in microbial metabolism, improving control over metabolic pathways in fermentations.

A novel yeast hybrid modeling framework integrating Boolean and enzyme-constrained networks enables exploration of the interplay between signaling and metabolism

The paper develops a hybrid modeling framework integrating Boolean and enzyme-constrained networks to study the interplay between nutrient signaling and metabolism in yeast, revealing new insights into their regulatory effects.

In silico analysis of the fast-growing thermophile Geobacillus sp. LC300 using a novel genome-scale metabolic model

The paper constructs a genome-scale metabolic model for Geobacillus sp. LC300 and uses it to predict metabolic engineering strategies for industrial compound production.

The interplay between growth rate and nutrient quality defines gene expression capacity

This study investigates how growth rate and nutrient quality affect gene expression capacity in bacteria, showing that metabolism governs resource usage and that low growth in high-quality medium maximizes synthetic gene expression.

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

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.

Genome-scale metabolic model of the diatom Thalassiosira pseudonana highlights the importance of nitrogen and sulfur metabolism in redox balance

The paper constructs a genome-scale metabolic model of Thalassiosira pseudonana to show how nitrogen and sulfur metabolism help balance redox states and influence organic matter secretion.

Systematic evaluation of parameters for genome-scale metabolic models of cultured mammalian cells

The paper evaluates parameters for genome-scale metabolic models of cultured mammalian cells, finding that homeostasis, dynamic morphology, and biomass composition are critical for accurate predictions.

Synthetic promoter based azide biosensor toolkit to advance chemical-biology

The paper introduces a synthetic promoter-based azide biosensor toolkit for in vivo detection of azide anions in E. coli, offering tunable GFP expression and low-cost protein expression.

Probabilistic Thermodynamic Analysis of Metabolic Networks

The paper introduces a probabilistic framework for analyzing metabolic networks by integrating thermodynamics and flux constraints, revealing new insights into E. coli metabolism.

The effects of model complexity and size on metabolic flux distribution and control. Case study in E. coli.

The paper systematically reduces a genome-scale metabolic model of E. coli to study how model complexity affects metabolic sensitivity coefficients and shows consistent metabolic engineering conclusions across different model sizes.

Cofactor specificity of glucose-6-phosphate dehydrogenase isozymes in Pseudomonas putida reveals a general principle underlying glycolytic strategies in bacteria

The paper analyzes G6PDH isozymes in Pseudomonas putida to show how cofactor specificity and gene duplication contribute to redox balance and metabolic strategies in bacteria.

Control and regulation of acetate overflow in Escherichia coli

This study develops a kinetic model of E. coli metabolism to explain acetate overflow, showing acetate regulates glucose metabolism and is not a wasteful by-product.

gapseq: Informed prediction of bacterial metabolic pathways and reconstruction of accurate metabolic models

gapseq predicts bacterial metabolic pathways and reconstructs metabolic models with high accuracy using sequence homology and pathway topology, outperforming existing tools.

The first multi-tissue diel genome-scale metabolic model of a woody plant highlights the suberin biosynthesis pathways in Quercus suber

This paper develops the first multi-tissue diel genome-scale metabolic model for Quercus suber, highlighting suberin biosynthesis pathways and enabling analysis of tissue interactions.

A multi-phase multi-objective dynamic genome-scale model shows different redox balancing among yeast species in fermentation

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.

Protein allocation and enzymatic constraints explain Escherichia coli wildtype and mutant phenotypes

This study develops a protein allocation model to predict Escherichia coli wildtype and mutant phenotypes by integrating protein distribution with metabolic fluxes.

Analysis of Metabolic Network Disruption in Engineered Microbial Hosts due to Enzyme Promiscuity

The paper develops a computational method to identify enzyme promiscuity-induced metabolic network disruptions in engineered microbial hosts and evaluates its application in two case studies.

multiTFA: a Python package for multi-variate Thermodynamics-based Flux Analysis

The paper introduces multiTFA, a Python package that improves thermodynamic-based flux analysis by incorporating multivariate treatment of thermodynamic variables, reducing uncertainty in reaction Gibbs free energy ranges.

Construction of a third NAD+ de novo biosynthesis pathway

This paper describes a new NAD+ de novo biosynthesis pathway in E. coli that starts from chorismate and demonstrates its utility in cofactor engineering for chemical production.

Integrating continuous hypermutation with high-throughput screening for optimization of cis,cis-muconic acid production in yeast

The paper develops a directed evolution workflow combining OrthoRep and a transcription factor-based biosensor to optimize cis,cis-muconic acid production in yeast, achieving >13-fold higher titers.

High-quality genome-scale metabolic model of Aurantiochytrium sp. T66

This paper reconstructs a high-quality genome-scale metabolic model for Aurantiochytrium sp. T66, improving upon previous models and validating its accuracy with experimental data.