ArticleScientific reports2017
Reliable and efficient solution of genome-scale models of Metabolism and macromolecular Expression.
Article in Scientific reports, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed.
- Article
- Predicting Strain-Specific Metabolic Capabilities in the GenusComputational and structural biotechnology journal · 2026Article
- The FBA solution space kernel: introduction and illustrative examples.BMC bioinformatics · 2025Article
- Model of metabolism and gene expression predicts proteome allocation in Pseudomonas putida.NPJ systems biology and applications · 2025Article
- Deciphering metabolic differentiation during Bacillus subtilis sporulation.Nature communications · 2025Article
- 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
- Cardinality optimization in constraint-based modelling: application to human metabolism.Bioinformatics (Oxford, England) · 2023Article
- Multi-scale models of whole cells: progress and challenges.Frontiers in cell and developmental biology · 2023Review
- Predicting stress response and improved protein overproduction in Bacillus subtilis.NPJ systems biology and applications · 2022Article
- Computation of condition-dependent proteome allocation reveals variability in the macro and micro nutrient requirements for growth.PLoS computational biology · 2021Article
- Kinetic profiling of metabolic specialists demonstrates stability and consistency of in vivo enzyme turnover numbers.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- The ETFL formulation allows multi-omics integration in thermodynamics-compliant metabolism and expression models.Nature communications · 2020Article
- Cellular responses to reactive oxygen species are predicted from molecular mechanisms.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- Systems Biology and Multi-Omics Integration: Viewpoints from the Metabolomics Research Community.Metabolites · 2019Article
- The genetic basis for adaptation of model-designed syntrophic co-cultures.PLoS computational biology · 2019Article
- Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0.Nature protocols · 2019Article
- DynamicME: dynamic simulation and refinement of integrated models of metabolism and protein expression.BMC systems biology · 2019Article
- Machine learning applied to enzyme turnover numbers reveals protein structural correlates and improves metabolic models.Nature communications · 2018Article
- Modeling the multi-scale mechanisms of macromolecular resource allocation.Current opinion in microbiology · 2018Review
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
Constraint-Based Reconstruction and Analysis (COBRA) is currently the only methodology that permits integrated modeling of Metabolism and macromolecular Expression (ME) at genome-scale. Linear optimization computes steady-state flux solutions to ME models, but flux values are spread over many orders of magnitude. Data values also have greatly varying magnitudes. Standard double-precision solvers may return inaccurate solutions or report that no solution exists. Exact simplex solvers based on rational arithmetic require a near-optimal warm start to be practical on large problems (current ME models have 70,000 constraints and variables and will grow larger). We have developed a quadruple-precision version of our linear and nonlinear optimizer MINOS, and a solution procedure (DQQ) involving Double and Quad MINOS that achieves reliability and efficiency for ME models and other challenging problems tested here. DQQ will enable extensive use of large linear and nonlinear models in systems biology and other applications involving multiscale data.
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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.