Microbial Metabolic Engineering and Bioproduction

Proteomics and constraint-based modelling reveal enzyme kinetic properties of Chlamydomonas reinhardtii on a genome scale

The paper integrates proteomics and constraint-based modeling to estimate in vivo enzyme turnover numbers for Chlamydomonas reinhardtii, improving metabolic model predictions.

Engineering the highly productive cyanobacterium Synechococcus sp. PCC 11901

The paper characterizes genetic tools for Synechococcus sp. PCC 11901, including an inducible promoter system, CRISPRi, and markerless genome editing with Cas12a.

A neural-mechanistic hybrid approach improving the predictive power of genome-scale metabolic models

This paper introduces a hybrid neural-mechanistic model that improves phenotype predictions for microorganisms by combining machine learning with constraint-based metabolic models.

De novo production of an antitumor precursor actinocin and other medicinal molecules from kynurenine pathway in Escherichia coli

Predictive Systems Biology Modeling: Unraveling Host Metabolic Disruptions and Potential Drug Targets in Acute Viral Infections

This paper introduces vhMM, a method to model host metabolic disruptions in viral infections and identify drug targets, finding effective compounds and linking cinnamon use to reduced SARS-CoV-2 infection rates.

Metabolic Interactive Nodular Network for Omics (MINNO): Refining and investigating metabolic networks based on empirical metabolomics data

The paper introduces MINNO, a tool that refines metabolic networks using empirical metabolomics data, demonstrating its application in studying non-model organisms like Borrelia species.

Functional Decomposition of Metabolism allows a system-level quantification of fluxes and protein allocation towards specific metabolic functions

The paper introduces a framework to quantify metabolic function contributions and protein allocation in E. coli, revealing energy balance and enzyme-flux relationships.

Optimal evaluation of energy yield and driving force in microbial metabolic pathway variants

This paper develops a method to evaluate energy yield and driving force in microbial metabolic pathways using thermodynamic principles and multi-objective optimization, applied to propionate oxidation and reverse TCA cycle.

EVMP: Enhancing machine learning models for synthetic promoter strength prediction by Extended Vision Mutant Priority framework

EVMP improves synthetic promoter strength prediction by effectively utilizing mutation information, achieving up to 61.30% enhancement in model performance.

Optimal protein production by a synthetic microbial consortium: Coexistence, distribution of labor, and syntrophy

This paper studies a synthetic microbial consortium of E. coli strains to optimize protein production by analyzing coexistence, labor distribution, and syntrophy in a chemostat model.

A strategy to detect metabolic changes induced by exposure to chemicals from large sets of condition-specific metabolic models computed with enumeration techniques

This paper introduces a strategy to detect metabolic changes from chemical exposure using transcriptomics data and metabolic models, identifying potential mechanisms of action in vitro.

Genome-scale metabolic model predicts mechanistic differences in metabolic gradient of spatially resolved small intestine villi

The paper uses spatial transcriptomics data to reconstruct location-specific genome-scale metabolic models in the small intestine, revealing metabolic differences between villus top and bottom enterocytes.

Literate programming for iterative design-build-test-learn cycles in bioengineering

The paper introduces teemi, an open-source platform for bioengineering that supports simulation, data integration, and machine learning for metabolic pathway design under FAIR principles.

Enhancing Escherichia coli Abiotic Stress Resistance through Ornithine Lipid Formation

This study engineers E. coli to produce ornithine lipids, improving stress resistance and biomass yield under phosphate limitation and low pH conditions.

Improved Production of Taxol(R) Precursors in S. cerevisiae using Combinatorial in silico Design and Metabolic Engineering

The paper uses in silico design and metabolic engineering to improve Taxol(R) precursor production in yeast, achieving a 50% increase in taxadiene yield.

Genetic circuits for feedback control of gamma-aminobutyric acid biosynthesis in probiotic Escherichia coli Nissle 1917

This paper designs genetic circuits in Escherichia coli to feedback control GABA production, improving biosynthesis through engineered NOT gates and biosensors.

Dynamic genome-based metabolic modeling of the predominant cellulolytic rumen bacterium Fibrobacter succinogenes S85

The paper develops dynamic metabolic models of F. succinogenes S85 using genome data and metabolic network reconstruction to simulate carbohydrate metabolism and metabolite production.

METABOLIC MODELLING AS A POWERFUL TOOL TO IDENTIFY CRITICAL COMPONENTS OF THE PNEUMOCYSTIS GROWTH MEDIUM

The paper develops a genome-scale metabolic model of Pneumocystis to identify critical components of its growth medium and improve in vitro culturing.

CHOmpact: a reduced metabolic model of Chinese hamster ovary cells with enhanced interpretability

The paper introduces CHOmpact, a reduced metabolic model of CHO cells that improves interpretability and physiological consistency compared to large-scale models.

Broaden the application of Yarrowia Lipolytica synthetic biology tools to explore the potential of Yarrowia clade biodiversity

This study demonstrates the application of Yarrowia lipolytica synthetic biology tools to six other Yarrowia clade members, showing their potential for biotechnological use.

Autotrophic growth of E. coli is achieved by a small number of genetic changes

This study identifies three genetic mutations enabling E. coli to grow autotrophically when combined with non-native enzymes for carbon fixation and energy production.

Mapping temperature-sensitive mutations at a genome-scale to engineer growth-switches in E. coli

The paper constructs a CRISPR library of E. coli mutants to identify temperature-sensitive mutants and demonstrates their use in engineering bacterial metabolite production.

AuCoMe: inferring and comparing metabolisms across heterogeneous sets of annotated genomes

AuCoMe reduces technical biases in metabolic network comparisons across diverse genomes and identifies shared and divergent metabolic traits.

Reconstructor: A COBRApy compatible tool for automated genome-scale metabolic network reconstruction with parsimonious flux-based gap-filling

Reconstructor is a user-friendly COBRApy tool for automated genome-scale metabolic network reconstruction with gap-filling, generating high-quality models for further biological analysis.

Resource allocation accounts for the large variabilityof rate-yield phenotypes across bacterial strains

The paper develops a model showing resource allocation strategies explain growth rate and yield variability in E. coli strains, supported by experimental data.

Transcriptomics data integration for context-specific modeling of Atlantic salmon metabolism: functional evaluation of methods based on metabolic tasks

The paper evaluates six methods for creating context-specific metabolic models of Atlantic salmon using transcriptomics data, finding that some methods better capture context-specific metabolism than others.

StressME: unified computing framework of Escherichia coli metabolism, gene expression, and stress responses

StressME integrates E. coli's metabolic and gene expression responses to thermal, oxidative, and acid stress, revealing cross-stress proteome allocation strategies and trade-offs.

POMBOX: a fission yeast toolkit for molecular and synthetic biology

The paper introduces POMBOX, a toolkit for constructing genetic circuits in fission yeast, enabling modular assembly of multi-gene pathways and testing synthetic elements in metabolic engineering.

Bringing large scale top-down metabolic modelling to eukaryotes with PhotoEukStein: a meta-model for unicellular phototrophs

The paper introduces PhotoEukStein, a meta-model for unicellular phototrophic eukaryotes, enabling automated derivation of genome-scale metabolic models from genomes to predict functional traits.

A landing pad system for multicopy gene integration in Issatchenkia orientalis

This paper develops a landing pad system for efficient multicopy gene integration in Issatchenkia orientalis using CRISPR-Cas9, enabling the construction of complex metabolic pathways with high integration efficiency.