Microbial Metabolic Engineering and Bioproduction

The paper integrates ChIP-exo and RNA-seq data to identify Cra's binding sites and regulon genes in E. coli, revealing its role in optimizing growth on poor carbon sources through metabolic regulation.

The paper identifies the stringency of promoter sequences in Clostridium and shows that adjusting mutation rates in promoter library synthesis improves functionality in this organism.

This study investigates the relationship between Jacobian and modal matrices in metabolic kinetic models, showing how network structure and reaction kinetics determine modal sparsity and complexity.

ProbAnnoWeb and ProbAnnoPy fill gaps in metabolic reconstructions by using probabilistic annotations specific to the target organism.

RetroPath2.0 is an open-source retrosynthesis workflow that streamlines pathway design for metabolic engineering by using generalized reaction rules and KNIME.

MitoCore is a manually curated constraint-based model of human central metabolism that accurately simulates normal and abnormal conditions, including mitochondrial diseases and hypoxia.

This paper reports the metabolic engineering of Escherichia coli to produce valerenadiene, achieving 62.0 mg/L with optimized promoters and pathways.

This paper introduces MODCELL, a modular cell engineering framework validated experimentally to enhance strain design for biochemical production by coupling modular chassis cells with exchangeable production modules.

This paper introduces a subgraph mining method to predict biochemical transformations between molecules using only their structures, without requiring thermodynamic or curated data.

This study quantifies the regulatory cost of cellular growth control using a Maximum Entropy approach in E. coli and human cells, showing different regulatory strategies and linking inverse temperature to growth dynamics.

The paper uses constraint-based modeling and gene expression data to identify new potential drug targets against colistin-resistant A. baumannii.

The paper introduces MuGENT, a method for high-efficiency multiplex genome editing in Vibrio natriegens using natural transformation.

The paper introduces IDREAM, a method that combines gene regulatory and metabolic networks to improve phenotype prediction in yeast, showing better accuracy than existing methods.

This study shows that programming mRNA decay with MazF can redirect cellular resources to synthetic circuits, enhancing target functions like fluorescent reporter expression and gluconate metabolism.

The paper shows that autocatalytic cycles in E. coli central carbon metabolism require specific enzyme expression and substrate affinity constraints to maintain stable fluxes.

This paper constructs synthetic microbial consortia of cyanobacteria and heterotrophs to study robustness and photoproduction capabilities.