Microbial Metabolic Engineering and Bioproduction

Elementary growth modes/vectors and minimal autocatalytic sets for kinetic/constraint-based models of cellular growth

The paper introduces and analyzes elementary growth modes and vectors for kinetic models of cellular growth, showing their relationships to other concepts and deriving bounds on growth rates.

Automatic reconstruction of metabolic pathways from identified biosynthetic gene clusters

The paper develops a pipeline to automatically reconstruct metabolic pathways from biosynthetic gene clusters, demonstrating its utility in genome-scale metabolic modeling for heterologous compound production.

Automated Rational Strain Construction Based on High-Throughput Conjugation

This paper presents an automated workflow for rational strain construction in Corynebacterium glutamicum, including plasmid creation and conjugative transfer, along with a custom software tool.

A genome-scale metabolic network model and machine learning predict amino acid concentrations in Chinese Hamster Ovary cell cultures

The paper integrates machine learning with genome-scale metabolic models to accurately predict amino acid concentrations in Chinese Hamster Ovary cell cultures over time.

Optimized gene expression from bacterial chromosome by high-throughput integration and screening

The paper optimizes gene expression in bacterial chromosomes through random integration and high-throughput screening, achieving high isobutanol production in Escherichia coli.

Diversity-based enumeration of optimal context-specific metabolic networks

This paper introduces DEXOM, a method to enumerate diverse optimal metabolic networks from multi-omics data to improve in-silico gene essentiality predictions in yeast.

A multi-phase multi-objective genome-scale model shows diverse redox balance strategies in yeasts

This paper develops a dynamic genome-scale model to analyze redox balance strategies in yeasts during batch cultures, showing how cryotolerant strains achieve metabolic stability.

Multiomics data collection, visualization, and utilization for guiding metabolic engineering

The paper presents tools for storing, visualizing, and leveraging multiomics data to predict outcomes of bioengineering efforts.

CASTLE: A database of synthetic lethal sets predicted from genome-scale metabolic networks

CASTLE is a database of synthetic lethal sets predicted from metabolic networks of over 130 organisms using the Fast-SL algorithm.

GEM-based metabolic profiling for Human Bone Osteosarcoma under different glucose and glutamine availability

The paper develops a framework to integrate metabolic gene expression and nutrient availability into genome-scale metabolic models to study osteosarcoma metabolism under different glucose and glutamine conditions.

Automated design of synthetic microbial communities

This paper designs synthetic microbial communities using quorum sensing and Bayesian methods to identify stable interactions in chemostat environments.

MASSpy: Building, simulating, and visualizing dynamic biological models in Python using mass action kinetics

MASSpy provides a framework for dynamic metabolic modeling using mass action kinetics, integrating with existing tools and supporting simulation and uncertainty quantification.

Physicochemical and metabolic constraints for thermodynamics-based stoichiometric modelling under mesophilic growth conditions

This study compares thermodynamics-based flux analysis and metabolic flux analysis in Escherichia coli using experimental data to evaluate their predictive capabilities and identify limitations.

A Lysate Proteome Engineering Strategy for Enhancing Cell-Free Metabolite Production

This paper describes a method to enhance cell-free metabolite production by engineering crude lysates using MAGE to selectively remove proteins, resulting in increased pyruvate production.

Integrative computational approach identifies new targets in CD4+ T cell-mediated immune disorders

The paper identifies 68 potential drug targets for three autoimmune diseases by integrating genome-scale metabolic models with gene expression data and in vitro validation.

Pseudomonas aeruginosa reverse diauxie is an optimized, resource utilization strategy

This study quantifies Pseudomonas aeruginosa's reverse diauxie metabolic strategy, showing its preference for nonfermentable carbon sources over glucose, which enhances its ecological success and virulence.

Bayesian genome scale modelling identifies thermal determinants of yeast metabolism

This paper uses Bayesian modeling to identify temperature-dependent enzymes in yeast metabolism, revealing squalene epoxidase as a key rate-limiting enzyme and demonstrating its role in thermotolerance.

An engineered lactate responding promoter system operating in glucose-rich and anaerobic environments.

The paper engineers a lactate biosensor system that functions in glucose-rich and anaerobic environments by modifying a natural promoter.

Temperature regulation as a tool to program synthetic microbial community composition

The paper demonstrates that temperature regulation can program synthetic microbial community composition by leveraging thermal niches of Escherichia coli and Pseudomonas putida.

Joint Universal Modular Plasmids (JUMP): A flexible and comprehensive platform for synthetic biology

The paper introduces JUMP, a universal plasmid platform for synthetic biology that enables flexible and compatible modular cloning across different vectors and toolkits.

Efficient reaction deletion algorithms for redesignof constraint-based metabolic networks for metabolite production with weak coupling

The paper develops an algorithm to achieve growth coupling for metabolite production in yeast under anaerobic conditions, achieving success for 91.3% of metabolites.

Two-species community design of Lactic Acid Bacteria for optimal production of Lactate

The paper introduces a computational framework to design two-species microbial communities for optimal lactate production using genome-scale metabolic models.

In-depth computational analysis of natural and artificial carbon fixation pathways

The paper compares natural and artificial carbon fixation pathways using computational methods to evaluate their ATP-efficiency and specific activity.

Genome-scale reconstructions to assess metabolic phylogeny and organism clustering

The paper constructs genome-scale metabolic reconstructions for 975 organisms using AutoKEGGRec and uses them to generate phylogenetic trees that closely resemble the Tree of Life.

Metage2Metabo: metabolic complementarity applied to genomes of large-scale microbiotas for the identification of keystone species

Metage2Metabo identifies keystone species in large microbiotas by analyzing metabolic networks and complementarity.

Unlocking Elementary Conversion Modes: ecmtool unveils all capabilities of metabolic networks

This paper introduces ecmtool, a tool that enumerates elementary conversion modes to fully characterize metabolic capabilities from genome-scale networks.

Simultaneous integration of gene expression and nutrient availability for studying metabolism of hepatocellular carcinoma

This study integrates gene expression and nutrient availability data to model metabolism in hepatocellular carcinoma, showing glucose affects proliferation and lactate production more than glutamine.

Engineering precursor pools for increasing production of odd-chain fatty acids in Yarrowia lipolytica

This study enhances odd-chain fatty acid production in Yarrowia lipolytica by engineering precursor pools and optimizing culture conditions, achieving 1.87 g/L OCFA titer.

Error propagation in constraint-based modeling of Chinese hamster ovary cells

This study examines how measurement errors and sampling frequency affect exchange rate accuracy and subsequent FBA predictions in CHO cells.

Does co-expression of Yarrowia lipolytica genes encoding Yas1p, Yas2p and Yas3p make a potential alkane-responsive biosensor in Saccharomyces cerevisiae?

The paper evaluates the potential of Yarrowia lipolytica's alkane-sensing TFs as a biosensor in Saccharomyces cerevisiae but finds they do not function as expected in the new host.