ArticleBMC systems biology2013
Mapping condition-dependent regulation of metabolism in yeast through genome-scale modeling.
Article in BMC systems biology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 50 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
50 citing papers in PubMed.
- Strategies and applications for alleviating carbon catabolite repression.Synthetic and systems biotechnology · 2027Review
- Grow AI virtual cells: three data pillars and closed-loop learning.Cell research · 2025Article
- Comprehensive evaluation of the capacities of microbial cell factories.Nature communications · 2025Article
- Article
- Investigating the Role of β-Disodium Glycerophosphate and Urea in Promoting Growth ofFoods (Basel, Switzerland) · 2024Article
- Applications of genome-scale metabolic models to investigate microbial metabolic adaptations in response to genetic or environmental perturbations.Briefings in bioinformatics · 2023Review
- FLUXestimator: a webserver for predicting metabolic flux and variations using transcriptomics data.Nucleic acids research · 2023Article
- A High-Quality Genome-Scale Model forACS synthetic biology · 2023Article
- Flux estimation analysis systematically characterizes the metabolic shifts of the central metabolism pathway in human cancer.Frontiers in oncology · 2023Article
- Multi-scale models of whole cells: progress and challenges.Frontiers in cell and developmental biology · 2023Review
- Quantitative modeling of human liver reveals dysregulation of glycosphingolipid pathways in nonalcoholic fatty liver disease.iScience · 2022Article
- Genome-scale modeling of yeast metabolism: retrospectives and perspectives.FEMS yeast research · 2022Review
- Exploring the associations between transcript levels and fluxes in constraint-based models of metabolism.BMC bioinformatics · 2021Article
- Evaluating accessibility, usability and interoperability of genome-scale metabolic models for diverse yeasts species.FEMS yeast research · 2021Article
- Genome-scale metabolic reconstruction of the non-model yeastMetabolic engineering communications · 2020Article
- Bidirectional titration of yeast gene expression using a pooled CRISPR guide RNA approach.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- A consensus S. cerevisiae metabolic model Yeast8 and its ecosystem for comprehensively probing cellular metabolism.Nature communications · 2019Article
- Metabolic flux analysis for metabolome data validation of naturally xylose-fermenting yeasts.BMC biotechnology · 2019Article
- Current status and applications of genome-scale metabolic models.Genome biology · 2019Review
- Genomic sequencing, genome-scale metabolic network reconstruction, and in silico flux analysis of the grape endophytic fungus Alternaria sp. MG1.Microbial cell factories · 2019Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
Abstract
backgroundThe genome-scale metabolic model of Saccharomyces cerevisiae, first presented in 2003, was the first genome-scale network reconstruction for a eukaryotic organism. Since then continuous efforts have been made in order to improve and expand the yeast metabolic network.
resultsHere we present iTO977, a comprehensive genome-scale metabolic model that contains more reactions, metabolites and genes than previous models. The model was constructed based on two earlier reconstructions, namely iIN800 and the consensus network, and then improved and expanded using gap-filling methods and by introducing new reactions and pathways based on studies of the literature and databases. The model was shown to perform well both for growth simulations in different media and gene essentiality analysis for single and double knock-outs. Further, the model was used as a scaffold for integrating transcriptomics, and flux data from four different conditions in order to identify transcriptionally controlled reactions, i.e. reactions that change both in flux and transcription between the compared conditions.
conclusionWe present a new yeast model that represents a comprehensive up-to-date collection of knowledge on yeast metabolism. The model was used for simulating the yeast metabolism under four different growth conditions and experimental data from these four conditions was integrated to the model. The model together with experimental data is a useful tool to identify condition-dependent changes of metabolism between different environmental conditions.
Indexed as
Identifiers
What OpenQuestion holds
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.