Microbial Metabolic Engineering and Bioproduction

Analysis of the genome-scale metabolic model of Bacillus subtilis to design novel in-silico strategies for native and recombinant L-asparaginase overproduction

Harnessing photosynthetic bacterium for light-powered biocatalysis

This study demonstrates the use of photosynthetic bacteria to power biocatalytic reactions using light, achieving high conversion rates of various substrates into valuable chemicals.

A microbial community growth model for dynamic phenotype predictions

This paper introduces CommPhitting, a dynamic model that predicts microbial community phenotype abundances and growth kinetics using experimental data and optimization.

Accuracy and data efficiency in deep learning models of protein expression

This study compares model accuracy and data efficiency across machine learning models for predicting protein expression from DNA sequences using experimental data from E. coli and S. cerevisiae.

The necessity of considering enzymes as compartments in constraint-based genomescale metabolic models

This paper identifies prediction anomalies in a constraint-based metabolic model by incorporating enzyme compartmentalization, improving pathway structure accuracy and resolving constraint conflicts.

Engineering Pseudomonas putida KT2440 for chain length tailored free fatty acid and oleochemical production

This paper engineers Pseudomonas putida KT2440 to produce medium- and long-chain free fatty acids and oleochemicals, achieving titers up to 670 mg/L.

Directed evolution of generalist biosensors for single ring aromatics

The paper describes the directed evolution of biosensors to improve detection of phloroglucinol and related single-ring aromatics.

ChiMera: An easy to use pipeline for Bacterial Genome Based Metabolic Network Reconstruction, Evaluation and Visualization

ChiMera is a pipeline that reconstructs, evaluates, and visualizes bacterial genome-scale metabolic models using efficient tools and a user-friendly interface.

An updated genome-scale model for Xylella fastidiosa subsp. pauca De Donno

The paper updates a genome-scale metabolic model for Xylella fastidiosa subsp. pauca, validating it against experimental data for aerobic metabolism and gum production.

Synthetic in vivo compartmentalisation improves metabolic flux and modulates the product profile of promiscuous enzymes

This paper demonstrates that synthetic in vivo compartmentalisation of enzymes in yeast significantly increases product titre and modulates product ratios.

Exploration of the autonomous replication region and its utilization for expression vectors in cyanobacteria.

This study identifies an autonomous replication region in cyanobacteria and develops an expression vector system using it, demonstrating broad host compatibility and inducible gene expression.

Linking enzyme expression to metabolic flux

The paper demonstrates how enzyme levels influence metabolic flux through three paradigms and introduces an algorithm to predict flux changes from enzyme expression in yeast and humans.

Inferring a cell's capabilities from omics data with ImmCellFie

ImmCellFie infers cell metabolic capabilities from transcriptomic or proteomic data using genome-scale models and provides interactive analysis tools.

Evolution shapes metabolic function and niche-specific antimicrobial targets in pathobionts

The paper identifies niche-specific metabolic targets in pathobionts by analyzing genome-scale metabolic networks and demonstrates their potential for targeted antimicrobial therapies.

NICEgame: A workflow for annotating the knowledge gaps in metabolic reconstructions, using known and hypothetical reactions

NICEgame identifies and resolves metabolic gaps in genome-scale models by suggesting alternative reactions and genes, improving gene essentiality predictions in E. coli.

gMCStool: automated network-based tool to search for metabolic vulnerabilities in cancer

gMCStool identifies metabolic vulnerabilities in cancer by predicting synthetic lethal interactions using genome-scale metabolic networks and RNA-seq data.

Tailoring and optimizing fatty acid production by oleaginous yeasts through the systematic exploration of their physiological fitness

This study optimizes fatty acid production in oleaginous yeasts by identifying optimal C/N ratios and temperatures using RSM and analyzing fatty acid composition changes.

Integrated rational and evolutionary engineering of genome-reduced Pseudomonas putida strains empowers synthetic formate assimilation

The paper engineers genome-reduced Pseudomonas putida strains to assimilate formate as a carbon source using a modular approach and adaptive evolution, achieving faster growth and two distinct catabolic pathways.

Controlling microbial co-culture based on substrate pulsing can lead to stability through differential fitness advantages

The paper demonstrates that substrate pulsing in microbial co-cultures can stabilize interactions by creating periodic fitness advantages, validated through computational modeling and experimental testing.

Quantitative Relationship between Intracellular Metabolic Responses against Nutrient Conditions and Metabolic Inhibitions

The paper establishes a universal quantitative relationship between metabolic responses to nutrient conditions and metabolic inhibition, validated across models and applicable without prior knowledge of system details.

Metabolic robustness to growth temperature of cold adapted bacterium

The paper investigates metabolic robustness and transcriptomic reprogramming in a cold-adapted bacterium at different temperatures, revealing key intermediates and pathway cross-talk involved in adaptation.

Engineered synthetic one-carbon fixation exceeds yield of the Calvin Cycle

The paper engineers a synthetic one-carbon fixation pathway in Cupriavidus necator that achieves higher biomass yield than the native Calvin Cycle.

NEMETEX: a Python software for the visualisation of the network of metabolic exchanges

NEMETEX visualizes metabolic exchange networks from metagenomics and flux balance analysis data, integrating abundance, taxonomy, and exchange rates for easier interpretation.

The choice of the objective function in flux balance analysis is crucial for predicting replicative lifespans in yeast

This study shows that choosing the right objective function in flux balance analysis improves predictions of replicative lifespan in yeast.

MAMBA: a model-driven, constraint-based multiomic integration method

MAMBA integrates semi-quantitative metabolomic data with gene-centric omics to improve metabolic network characterization and metabolite prediction in yeast under heat stress.

Novel Context-Specific Genome-Scale Modelling Explores the Potential of Chlamydomonas reinhardtii for Synthetic Biology Applications

The paper develops a pipeline to predict cellular metabolism from gene expression data using genome-scale models, applied to study TAG overproduction in Chlamydomonas reinhardtii.

Optimal metabolic states in cells

The paper presents a unified theory of optimal metabolic states by formulating metabolic behavior as an economic problem with fitness objectives, linking existing models through shared optimality conditions.

The value structure of metabolic states

This paper introduces a framework to unify metabolic modeling by defining value structures that represent metabolic trade-offs as economic variables.

Synthetic carbon fixation via the autocatalytic serine threonine cycle

The paper engineers a synthetic C1-assimilation cycle in E. coli to enable growth on formate, demonstrating the feasibility of synthetic carbon fixation from CO2.

Resurrecting essential amino acid biosynthesis in a mammalian cell

This paper demonstrates the successful restoration of valine biosynthesis in mammalian cells by integrating synthetic pathways from E. coli, showing that ancient metabolic pathways can be reactivated in metazoans.