ArticleGenome biology2016
Mapping the landscape of metabolic goals of a cell.
Article in Genome biology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- CellTarget: a convex optimisation approach to discover cellular objectives.NPJ systems biology and applications · 2026Article
- Accurate prediction of gene deletion phenotypes with Flux Cone Learning.Nature communications · 2025Article
- Metabolic Objectives and Trade-Offs: Inference and Applications.Metabolites · 2025Review
- Inferring metabolic objectives and trade-offs in single cells during embryogenesis.Cell systems · 2025Article
- In silico encounters: harnessing metabolic modelling to understand plant-microbe interactions.FEMS microbiology reviews · 2025Review
- BioModTool: from biomass composition data to structured biomass objective functions for genome-scale metabolic models.Bioinformatics advances · 2025Article
- Quantitative principles of microbial metabolism shared across scales.Nature microbiology · 2024Review
- Genome-scale modeling predicts metabolic differences between macrophage subtypes in colorectal cancer.iScience · 2023Article
- Ensemble-based genome-scale modeling predicts metabolic differences between macrophage subtypes in colorectal cancer.bioRxiv : the preprint server for biology · 2023Article
- Relationship between fitness and heterogeneity in exponentially growing microbial populations.Biophysical journal · 2022Article
- Predicting Metabolic Adaptation Under Dynamic Substrate Conditions Using a Resource-Dependent Kinetic Model: A Case Study UsingFrontiers in molecular biosciences · 2022Article
- Addressing uncertainty in genome-scale metabolic model reconstruction and analysis.Genome biology · 2021Review
- Metabolic Modelling as a Framework for Metabolomics Data Integration and Analysis.Metabolites · 2020Review
- A model for the interplay between plastic tradeoffs and evolution in changing environments.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Identification of Cancer-associated metabolic vulnerabilities by modeling multi-objective optimality in metabolism.Cell communication and signaling : CCS · 2019Article
- BOFdat: Generating biomass objective functions for genome-scale metabolic models from experimental data.PLoS computational biology · 2019Article
- FLYCOP: metabolic modeling-based analysis and engineering microbial communities.Bioinformatics (Oxford, England) · 2018Article
- An introduction to the maximum entropy approach and its application to inference problems in biology.Heliyon · 2018Review
- Article
- Influence of Glucose Availability and CRP Acetylation on the Genome-Wide Transcriptional Response ofFrontiers in microbiology · 2018Article
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5 authors.
Funding
Abstract
Genome-scale flux balance models of metabolism provide testable predictions of all metabolic rates in an organism, by assuming that the cell is optimizing a metabolic goal known as the objective function. We introduce an efficient inverse flux balance analysis (invFBA) approach, based on linear programming duality, to characterize the space of possible objective functions compatible with measured fluxes. After testing our algorithm on simulated E. coli data and time-dependent S. oneidensis fluxes inferred from gene expression, we apply our inverse approach to flux measurements in long-term evolved E. coli strains, revealing objective functions that provide insight into metabolic adaptation trajectories.
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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.