Important ME Modeling Literature

ME Models

• In silico modeling of metabolism and gene product expression at genome scale
  First ME-model built for Thermotoga maritima, integrating gene expression and metabolism.
• Genome-scale models of metabolism and gene expression
  Introduced the first integrated ME-model for Escherichia coli, linking transcription, translation, and metabolism.
• COBRAme: A computational framework for genome-scale models of metabolism and gene expression
  Reformulated Escherichia coli ME-model using symbolic Python framework and standardized constraints.
• Genome-scale modeling of Bacillus subtilis metabolism and gene expression
  Built iJT964-ME for Bacillus subtilis, capturing stress response and proteome allocation.
• Reconstruction and modeling of a genome-scale metabolic network for Clostridium ljungdahlii
  Developed an ME-model for Clostridium ljungdahlii to study acetogenic carbon fixation and protein burden.
• ME-model of Pseudomonas putida improves multi-omics prediction of proteome allocation
  First ME-model of Pseudomonas putida demonstrating improved prediction of proteome constraints.
• AcidifyME: A genome-scale model of acid stress in Escherichia coli
  Simulated acid stress adaptation by integrating transcriptomic constraints into an E. coli ME-model.
• FoldME: Protein folding in genome-scale models
  Added chaperone folding machinery into E. coli ME-models to predict folding costs and temperature sensitivity.
• OxidizeME: Modeling oxidative stress in Escherichia coli
  Included ROS damage and iron-sulfur cluster maintenance into E. coli genome-scale ME simulations.
• StressME: Genome-scale modeling of stress iModulons
  A genome-scale model of metabolism and expression for E. coli that contains thermal, acid, and oxidative stress mechanisms (AcidifyME, FoldME, OxidizeME)

Tools and Packages

• COBRAme: A computational framework for genome-scale models of metabolism and gene expression
  Python framework for symbolic construction and simulation of ME-models.
  GitHub
• solveME: Fast and reliable solution of nonlinear ME models
  Extended benchmarking and implementation
  High-precision solver (quad MINOS) for ME-model optimization.
  GitHub
• coralME: A modular pipeline for automated ME-model reconstruction
  Pipeline for automated reconstruction of ME-models from annotated genomes.
  GitHub
• DynamicME: dynamic simulation and refinement of integrated models of metabolism and protein expression
  Framework for dynamic time-course simulation and ensemble refinement of ME-model predictions.
  GitHub
• BiGG Models: A platform for integrating, standardizing and sharing genome-scale models
  Updated database infrastructure and tools
  Central resource for curated genome-scale metabolic models.
  Website

Other Papers

• Principles of proteome allocation are revealed using proteomic data and genome-scale models
  Introduced proteome sector constraints into ME-models using quantitative proteomics, enabling accurate prediction of wild-type E. coli growth and fluxes across diverse environments while capturing stress-related proteome hedging.
• Quantification and classification of E. coli proteome utilization and unused protein costs across environments
  Used ME-models and absolute proteomics to quantify unused protein expression in E. coli, showing it imposes significant fitness costs while enabling adaptive hedging against environmental uncertainty.
• Machine learning applied to enzyme turnover numbers reveals protein structural correlates and improves metabolic models
  Developed machine learning models to predict enzyme turnover numbers in E. coli, improving ME-model parameterization and enabling more accurate genome-scale proteome predictions.
• Kinetic profiling of metabolic specialists demonstrates stability and consistency of in vivo enzyme turnover numbers
  Estimated in vivo enzyme kcats using evolved E. coli knockout strains, showing they are robust to genetic perturbations and improve genome-scale proteome predictions compared to traditional in vitro values.
• Reconstructing organisms in silico: genome-scale models and their emerging applications
  Reviewed the development and applications of genome-scale models (GEMs), highlighting advances in E. coli modeling, strain-specific reconstructions, ME-models, and stress response simulations.