ArticlePLoS computational biology2018
COBRAme: A computational framework for genome-scale models of metabolism and gene expression.
Article in PLoS computational biology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 73 papers.
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Who cites it
73 citing papers in PubMed.
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- Constraint-Based Metabolic Modeling Approach for Microbial Communities.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Predicting Strain-Specific Metabolic Capabilities in the GenusComputational and structural biotechnology journal · 2026Article
- The Dawn of High-Throughput and Genome-Scale Kinetic Modeling: Recent Advances and Future Directions.ACS synthetic biology · 2025Review
- Minimization of proteome reallocation explains metabolic transition in hierarchical utilization of carbon sources.mSystems · 2025Article
- Model of metabolism and gene expression predicts proteome allocation in Pseudomonas putida.NPJ systems biology and applications · 2025Article
- New insights in metabolism modelling to decipher plant-microbe interactions.The New phytologist · 2025Review
- RBC-GEM: A genome-scale metabolic model for systems biology of the human red blood cell.PLoS computational biology · 2025Article
- Deciphering metabolic differentiation during Bacillus subtilis sporulation.Nature communications · 2025Article
- Enhancing genome-scale metabolic models with kinetic data: resolving growth and citramalate production trade-offs inBioinformatics advances · 2025Article
- A Multi-Omics, Machine Learning-Aware, Genome-Wide Metabolic Model of Bacillus Subtilis Refines the Gene Expression and Cell Growth Prediction.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Article
- Integration of proteomic data with genome-scale metabolic models: A methodological overview.Protein science : a publication of the Protein Society · 2024Review
- Current State, Challenges, and Opportunities in Genome-Scale Resource Allocation Models: A Mathematical Perspective.Metabolites · 2024Review
- Proteome allocation is linked to transcriptional regulation through a modularized transcriptome.Nature communications · 2024Article
- Construction of an enzyme-constrained metabolic network model for Myceliophthora thermophila using machine learning-based kMicrobial cell factories · 2024Article
13 more citing papers are in PubMed but not listed here.
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8 authors.
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Abstract
Genome-scale models of metabolism and macromolecular expression (ME-models) explicitly compute the optimal proteome composition of a growing cell. ME-models expand upon the well-established genome-scale models of metabolism (M-models), and they enable a new fundamental understanding of cellular growth. ME-models have increased predictive capabilities and accuracy due to their inclusion of the biosynthetic costs for the machinery of life, but they come with a significant increase in model size and complexity. This challenge results in models which are both difficult to compute and challenging to understand conceptually. As a result, ME-models exist for only two organisms (Escherichia coli and Thermotoga maritima) and are still used by relatively few researchers. To address these challenges, we have developed a new software framework called COBRAme for building and simulating ME-models. It is coded in Python and built on COBRApy, a popular platform for using M-models. COBRAme streamlines computation and analysis of ME-models. It provides tools to simplify constructing and editing ME-models to enable ME-model reconstructions for new organisms. We used COBRAme to reconstruct a condensed E. coli ME-model called iJL1678b-ME. This reformulated model gives functionally identical solutions to previous E. coli ME-models while using 1/6 the number of free variables and solving in less than 10 minutes, a marked improvement over the 6 hour solve time of previous ME-model formulations. Errors in previous ME-models were also corrected leading to 52 additional genes that must be expressed in iJL1678b-ME to grow aerobically in glucose minimal in silico media. This manuscript outlines the architecture of COBRAme and demonstrates how ME-models can be created, modified, and shared most efficiently using the new software framework.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.