Microbial Metabolic Engineering and Bioproduction

This paper introduces a framework for rational strain design in E. coli that minimizes phenotype perturbation using mixed-integer linear programming and kinetic models to improve anthranilate production.

BioISO is a tool that aids in the manual curation of genome-scale metabolic models by reducing search spaces and improving debugging through recursive algorithms and flux balance analysis.

dingo samples metabolic flux spaces efficiently using advanced random walks and rounding methods, outperforming existing tools for large models.

This paper introduces a reinforcement learning algorithm to model microbial metabolism and evolution, showing improved prediction of stable metabolic strategies in heterogeneous communities.

This paper demonstrates that waste streams from mammalian and fungal cell cultures can be used as feed for bacterial fermentations to increase productivity and resource efficiency in bioprocessing.

This study characterizes metabolic rewiring in Komagataella phaffii under glucose-limited near-zero growth conditions using a genome-scale metabolic model and cultivation data.

This study measures growth rates and biomass yields of Saccharomycotina yeasts on ethanol, finding that species with Complex-I genes achieve higher biomass yields.

This paper introduces GEFMAP, a geometric deep learning method to predict metabolic flux from scRNA-seq data, estimating reaction rates in metabolic networks.

This study uses genome-scale models to optimize chondroitin production in E. coli, achieving up to 535 mg/L in fed-batch fermentation.

This paper improves dynamic flux balance analysis for fed-batch processes by reducing KKT constraints and adapting the algorithm to predict optimal process length and feeding profiles.

The paper shows that optimal protein allocation in Neisseria gonorrhoeae enhances GltA and AcnB activity, delaying acetate overflow for ATP production.

The paper introduces the Serine Shunt as a novel formate reduction pathway in E. coli, demonstrating its in vivo activity and efficiency for converting formate to formaldehyde.

This paper develops an in vitro transcription-based biosensing workflow to quantify glycolate production in the CETCH cycle, showing high correlation with LC-MS at lower cost and faster speed.

This paper engineers Corynebacterium glutamicum to produce 2,3,5,6-tetramethylpyrazine (TMP) at high titer using statistical design of experiments to optimize media composition.

This study evaluates the feasibility of expanding the product range of chain elongating bacteria to produce C9-C12 fatty acids and other derivatives using metabolic engineering and constraint-based modelling.

The paper uses Bayesian 13C-metabolic flux analysis to show phagocytosis reverses non-oxidative PPP flux direction in granulocytes.

This study calculates the efficiency of electromicrobial production of jet fuel blends containing branched-chain hydrocarbons and finds that increasing branched-chain content slightly reduces energy conversion efficiency.

The paper uses transposon sequencing data to characterize AraC/XylS family regulators in Pseudomonas putida, identifying inducer responses and improving inducible systems in E. coli.

The paper predicts bacterial carbon utilization traits from genomes using statistical models, outperforming constraint-based models and generalizing to phylogenetically distant taxa.

md_harmonize harmonizes compounds and metabolic reactions across databases by generating unique identifiers based on atom structures for improved metabolic network analysis.

This paper engineers a synthetic E. coli coculture to compartmentalize sugar utilization and ester biosynthesis pathways, achieving 31-fold higher isobutyl butyrate production than monocultures.

The paper identifies a native phosphoglycolate salvage pathway in Komagataella phaffii that recycles 2-phosphoglycolate, similar to plant pathways, and suggests it can enhance autotrophic growth.

The paper calculates the upper limit electrical-to-energy conversion efficiency for producing jet fuels using electromicrobial pathways.

This study engineers the complete reductive glycine pathway in yeast to enable formate and CO2 assimilation, achieving 8-fold improved growth through adaptive evolution and reverse-engineering.

The paper uses genome-scale metabolic models to identify metabolic differences between non-Saccharomyces yeasts, finding that Complex I in the electron transport chain distinguishes Metschnikowia pulcherrima from other species.

OptEnvelope identifies optimal knockout strategies for coupling growth and metabolite production using mixed-integer linear programming, benchmarked on E. coli and S. cerevisiae for acetate, glycerol, succinate, and ethanol.

This paper evolves a Saccharomyces cerevisiae strain tolerant to oxidative stress, leading to higher taxadiene production, and identifies metabolic changes contributing to this improvement.

The paper presents a framework using genome-scale metabolic reconstructions to interpret genotype-to-phenotype associations and identifies limitations in phenotype prediction in metabolism.

This study constructs a multi-organ maize metabolic model to analyze temperature stress responses, identifying a thermodynamics-reducing power-energy generation axis that differentiates heat and cold stress.

This study investigates how heterologous protein production affects metabolic fluxes in Pseudomonas putida, finding that it reshuffles periplasmic metabolism and decouples catabolism from anabolism.