Microbial Metabolic Engineering and Bioproduction

Specific growth rates and growth stoichiometries of Saccharomycotina yeasts on ethanol as sole carbon and energy substrate

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

Inferring Metabolic States from Single Cell Transcriptomic Data via Geometric Deep Learning

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

Optimizing Fed-Batch Processes with Dynamic Control Flux Balance Analysis

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.

Optimal Protein Allocation Controls the Inhibition of GltA and AcnB in Neisseria gonorrhoeae

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

The Serine Shunt enables formate conversion to formaldehyde in vivo

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.

In vitro transcription-based biosensing of glycolate for prototyping of a complex enzyme cascade

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.

Sustainable production of 2,3,5,6-Tetramethylpyrazine at high titer in engineered Corynebacterium glutamicum using statistical design of experiments

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.

Evaluating the feasibility of medium chain oleochemical synthesis using microbial chain elongation

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.

Bayesian 13C-metabolic flux analysis of parallel tracer experiments in granulocytes: A directional shift within the non-oxidative pentose phosphate pathway supports phagocytosis

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

Physiological constraints limiting the growth of Drosophila larvae

This study uses in vitro and in silico experiments to model Drosophila larval development and metabolism, predicting growth and critical developmental processes.

Efficiency Estimates for Electromicrobial Production of Branched-chain Hydrocarbons

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.

Characterization and diversification of AraC/XylS family regulators guided by transposon sequencing

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.

md_harmonize: a Python package for atom-level harmonization of public metabolic data-bases

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

Engineering a Synthetic Escherichia coli Coculture for Compartmentalized de novo Biosynthesis of Isobutyl Butyrate from Mixed Sugars

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.

Sysrecon: A systematic data-driven tool for genome-scale metabolic reconstructions

Sysrecon is a tool that systematically breaks down genome-scale metabolic reconstructions into quantifiable steps to improve reproducibility and standardization.

Enzyme fluctuations data improve inference of metabolic interaction networks with an inverse differential Jacobian approach

This paper improves metabolic interaction network inference by incorporating enzyme fluctuation data into an inverse differential Jacobian algorithm, showing better performance in breast cancer datasets.

Yeast9: A Consensus Yeast Metabolic Model Enables Quantitative Analysis of Cellular Metabolism By Incorporating Big Data

Yeast9 improves yeast metabolic modeling by integrating multi-omics data, showing better prediction of growth rates and gene function than transcriptomics.

Microbial pathway thermodynamics: structural models unveil anabolic and catabolic processes

The paper presents strategies to split microbial metabolic equations into anabolic and catabolic components and evaluates their thermodynamic efficiency.

Upper Limit Efficiency Estimates for Electromicrobial Production of Drop-In Jet Fuels

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

Understanding and exploitation of host stress responses to protein production using novel transcriptomic analytics

This study identifies novel transcriptional responses to protein production stress in E. coli using transcriptomic analytics and applies findings to optimize protein production.

Genome-scale metabolic models reveal determinants of phenotypic differences in non-Saccharomyces yeasts

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: a target point guided method for growth-coupled production using knockouts

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.

An enzyme activation network provides evidence for extensive regulatory crosstalk between metabolic pathways

The paper maps enzyme activation networks in yeast, revealing widespread regulatory crosstalk between metabolic pathways and highlighting the role of essential metabolites in metabolic plasticity.

Rewiring Saccharomyces cerevisiae metabolism for optimised Taxol(R) precursors production

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 limitations of phenotype prediction in metabolism

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

Accurate and rapid determination of metabolic flux by deep learning of isotope patterns

This paper introduces ML-Flux, a deep learning framework for accurately and rapidly determining metabolic flux from isotope patterns, outperforming existing methods in speed and accuracy.

Development of Corynebacterium glutamicum as a monoterpene production platform

This paper develops and optimizes a mevalonate-based monoterpene production platform in Corynebacterium glutamicum, achieving high titers of several monoterpenes.

Proteomes Reveal Metabolic Capabilities of Yarrowia lipolytica for Biological Upcycling of Polyethylene into High-Value Chemicals

This study identifies how Yarrowia lipolytica metabolizes hydrocarbons and DP oil, revealing proteome reallocation for growth and chemical production, but also growth inhibition due to reduced protein biosynthesis.

Development of a genome scale metabolic model for the lager hybrid yeast S. pastorianus to understand evolution of metabolic pathways in industrial settings.

The paper develops a genome-scale metabolic model for S. pastorianus to predict metabolic pathway evolution and aid industrial strain optimization.

Genome-scale metabolic models consistently predict in vitro characteristics of Corynebacterium striatum

This paper creates and validates five strain-specific genome-scale metabolic models for Corynebacterium striatum using in silico and in vitro methods, and introduces software for model curation.