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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.