Microbial Metabolic Engineering and Bioproduction

An integrated identifiability and metabolic flux analysis workflow for reducing and repairing dynamic CHO metabolic models

The paper develops a workflow to reduce and repair dynamic metabolic models of CHO cells using identifiability analysis and metabolic flux analysis, improving prediction accuracy for specific growth rate and productivity.

Automated anaerobic cultivation and phenotyping of diverse chain-elongating bacteria

This study develops an automated system for anaerobic cultivation and phenotyping of chain-elongating bacteria, revealing metabolic diversity and chain-length specificity principles.

Genomic and environmental determinants of circular single-stranded DNA production in engineered E. coli

This study identifies genomic and environmental factors affecting circular single-stranded DNA (cssDNA) yield in engineered E. coli and improves production efficiency.

Emergent metabolic cooperation in communities of microbes that maximise growth rate by optimal protein expression

This paper develops a mathematical framework to model microbial communities optimizing growth rates through metabolic cooperation and resource allocation.

The biosynthesis of FAD nucleotide analogues in Escherichia coli alters its sensitivity to aminoglycoside antibiotics

This study shows that engineering FAD biosynthesis in E. coli to produce nucleotide analogues increases tolerance to aminoglycoside antibiotics by altering metabolic pathways.

Improved Biosynthesis of Ethylene Glycol from Xylose in Engineered E. coli Utilizing Two-Stage Dynamic Control

This study improves ethylene glycol production from xylose in E. coli using two-stage dynamic control, achieving 140 g/L in 70 hours with 92% theoretical yield.

Nutrient control enables metabolic reconstruction of L. rhamnosus GG and analysis of secretions

The paper presents the first curated genome-scale metabolic model for L. rhamnosus GG, validated using multiple approaches and provides insights into its nutrient requirements and secretions.

Stochasticity in Metabolism: Oxidative Stress Response Phenotypes As Emergent Consequences of Network Topology

The paper models oxidative stress response in E. coli using a genome-scale metabolic model to show that bimodal killing under H2O2 stress emerges from network topology and stochastic sampling.

Topological Complementarity Predicts Synergistic Drug Pairs in Branched Metabolic Networks.

The paper identifies synergistic drug pairs in branched metabolic networks by analyzing topological complementarity in the E. coli folate pathway.

Integrating Metabolic Networks into Hybrid Bioprocess Models

This paper introduces FBA-Hyb, a hybrid model integrating metabolic networks into bioprocess modeling, achieving higher predictive accuracy and stoichiometric consistency.

In silico prediction of metabolic trait robustness in microbial cells

This paper introduces TRAEV, a computational framework to predict the evolutionary robustness of metabolic traits in microbial cells, validated using yeast strains in controlled environments.

Glycogen removal enhances ethylene production in Synechocystis sp. PCC 6803 but exposes a 2-oxoglutarate-GS-GOGAT-phosphate constraint

This study shows that removing glycogen in Synechocystis sp. PCC 6803 increases ethylene production but creates a metabolic constraint involving 2-oxoglutarate, GS-GOGAT, and phosphate.

FluxSprout: Single-cell metabolic modeling of vascular sprouting in zebrafish

FluxSprout identifies metabolic dependencies in zebrafish sprouting angiogenesis by integrating single-cell RNA sequencing with genome-scale metabolic modeling, revealing biosynthetic capacity as a key feature of sprouting vessels.

Additive and dominance gene effects described by a logistic function in concentration-limited metabolic pathways at steady state out of equilibrium

The paper models additive and dominance gene effects in metabolic pathways using logistic functions and applies it to experimental data on amylose accumulation in plants.

Metabolic engineering of Yarrowia lipolytica for higher fatty alcohol production

This study engineers Yarrowia lipolytica to produce fatty alcohols by disrupting lipid metabolism pathways and optimizing culture conditions, achieving titers up to 19.4 g/L.

The Sensitivity of 13C-Metabolic Flux Analysis to Biomass Composition Underscores the Need for Accurate Biomass Formulation in Escherichia coli

This study shows that 13C-MFA in E. coli is sensitive to biomass composition, emphasizing the need for accurate biomass formulations in flux analysis.

The ModelSEED Biochemistry Database, 2026 update: grading multi-source thermodynamics

The paper updates the ModelSEED Biochemistry Database with expanded compounds and reactions, integrating multi-source thermodynamic data and grading reaction reliability.

kinGEMs: A Robust and Scalable Framework for Resource-Constraint Models through Stochastic Tuning of Deep Learning-Predicted Kinetic Parameters

This paper introduces kinGEMs, a framework that integrates deep learning-predicted kinetic parameters into genome-scale models to improve metabolic modeling accuracy and scalability.

Genome-scale metabolic models for a synthetic soil microbial community as a path for understanding community functioning

The paper develops genome-scale metabolic models for a synthetic soil microbial community to understand metabolic interactions and community function.

Dynamic flux balance analysis of cancer metabolism using expression-based human cell line models

This study uses dynamic flux balance analysis to model cancer cell metabolism, revealing dependencies on growth media and cell-line specificities, and identifying potential therapeutic targets.

Experimental trophic flexibility guides a compartmentalized genome-scale model of red microalgae Galdieria sulphuraria

The paper develops an organelle-resolved genome-scale metabolic model for Galdieria sulphuraria that links trophic state and substrate identity with carbon use and product capacity.

Does specific membrane surface area constrain Escherichia coli energy spillage and therefore aerobic and anaerobic growth rates?

This study quantifies how specific membrane surface area (sMSA) constrains Escherichia coli growth rates and energy metabolism across aerobic and anaerobic conditions.

13C-Metabolic Flux Analysis of Substrate Co-Metabolism in the Methylotrophic Acetogen Eubacterium limosum.

This study uses 13C-MFA to analyze co-metabolism in Eubacterium limosum, finding that glucose cofeeding reduces flux through the Wood-Ljungdahl pathway and that cysteine provides gluconeogenic carbon.

Comprehensive calculation of product and ATP yields for glucose fermentation

The paper calculates product and ATP yields for glucose fermentation by analyzing a pan-catabolic network of anaerobic digestion, revealing many novel conversions and varying ATP yields.

MetworkPy: A Python Package for Graph- and Information-theoretic Investigation of Metabolic Networks

MetworkPy provides a Python package for objective-free graph- and information-theoretic analysis of genome-scale metabolic models to identify metabolic features perturbed by transcription factors.

Exchange of metabolic pathway intermediates as the origin for metabolite cross-feeding interactions in E. coli auxotrophic co-cultures

This study shows that histidinol exchange enables metabolite cross-feeding in E. coli auxotrophs under methionine limitation, supporting mutualistic interactions through pathway intermediate accumulation.

StereoMapper: Clarifying Metabolite Identity Through Stereochemically Aware Relationship Assignment

StereoMapper clarifies metabolite identity by assigning stereochemically aware relationships, achieving high performance in benchmark datasets and improving GEM accuracy.

Evolutionary stabilisation of stressful metabolism via integrated biocomputing and essential-gene metabolic locking circuits

The paper develops synthetic genetic circuits in yeast to stabilize metabolic stress from terpene production, showing that coupling essential genes to synthetic pathways improves strain stability.

SynBioCrow: provenance-preserving integration of complementary retrosynthesis engines for biosynthetic pathway design

SynBioCrow integrates retrosynthesis engines to improve pathway design but does not claim validated complete-pathway recovery.

Organizing principles of the cellular electron economy

The paper introduces the concept of the cellular electron economy to quantify and organize electron flow across metabolism in microorganisms, revealing how carbon sources and electron disposal capacity shape metabolic organization.