ReviewCurrent opinion in biotechnology2015
Computing the functional proteome: recent progress and future prospects for genome-scale models.
Review in Current opinion in biotechnology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
28 citing papers in PubMed.
- Coarse-grained resource allocation modeling for decoding and rewiring microbial metabolism.Trends in microbiology · 2026Review
- High-quality genome-scale metabolic network reconstruction of probiotic bacterium Escherichia coli Nissle 1917.BMC bioinformatics · 2022Article
- Reconstruction of a catalogue of genome-scale metabolic models with enzymatic constraints using GECKO 2.0.Nature communications · 2022Article
- Article
- Genome-Scale Reconstruction of Microbial Dynamic Phenotype: Successes and Challenges.Microorganisms · 2021Review
- Metabolic modelling reveals broad changes in gut microbial metabolism in inflammatory bowel disease patients with dysbiosis.NPJ systems biology and applications · 2021Article
- A Standardized Brain Molecular Atlas: A Resource for Systems Modeling and Simulation.Frontiers in molecular neuroscience · 2021Article
- Integrative characterization of the near-minimal bacterium Mesoplasma florum.Molecular systems biology · 2020Article
- Searching for principles of microbial physiology.FEMS microbiology reviews · 2020Review
- Combining mechanistic and machine learning models for predictive engineering and optimization of tryptophan metabolism.Nature communications · 2020Article
- Phenotypic analysis combined with tandem mass tags (TMT) labeling reveal the heterogeneity of strawberry stolon buds.BMC plant biology · 2019Article
- DynamicME: dynamic simulation and refinement of integrated models of metabolism and protein expression.BMC systems biology · 2019Article
- Metabolic modeling and response surface analysis of an Escherichia coli strain engineered for shikimic acid production.BMC systems biology · 2018Article
- COBRAme: A computational framework for genome-scale models of metabolism and gene expression.PLoS computational biology · 2018Article
- Constraint-based modeling in microbial food biotechnology.Biochemical Society transactions · 2018Review
- Population FBA predicts metabolic phenotypes in yeast.PLoS computational biology · 2017Article
- Improving the phenotype predictions of a yeast genome-scale metabolic model by incorporating enzymatic constraints.Molecular systems biology · 2017Article
- Discovering missing reactions of metabolic networks by using gene co-expression data.Scientific reports · 2017Article
- Principles of proteome allocation are revealed using proteomic data and genome-scale models.Scientific reports · 2016Article
- solveME: fast and reliable solution of nonlinear ME models.BMC bioinformatics · 2016Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
Constraint-based models enable the computation of feasible, optimal, and realized biological phenotypes from reaction network reconstructions and constraints on their operation. To date, stoichiometric reconstructions have largely focused on metabolism, resulting in genome-scale metabolic models (M-Models). Recent expansions in network content to encompass proteome synthesis have resulted in models of metabolism and protein expression (ME-Models). ME-Models advance the predictions possible with constraint-based models from network flux states to the spatially resolved molecular composition of a cell. Specifically, ME-Models enable the prediction of transcriptome and proteome allocation and limitations, and basal expression states and regulatory needs. Continued expansion in reconstruction content and constraints will result in an increasingly refined representation of cellular composition and behavior.
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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.