ArticleBMC systems biology2009
Reconstruction and logical modeling of glucose repression signaling pathways in Saccharomyces cerevisiae.
Article in BMC systems biology, 2009. 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.
- Construction of a globally modular recombinantSynthetic and systems biotechnology · 2026Article
- Engineering a universal and efficient platform for terpenoid synthesis in yeast.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Multi-scale model suggests the trade-off between protein and ATP demand as a driver of metabolic changes during yeast replicative ageing.PLoS computational biology · 2022Article
- Heuristic shortest hyperpaths in cell signaling hypergraphs.Algorithms for molecular biology : AMB · 2022Article
- Modelling of glucose repression signalling in yeast Saccharomyces cerevisiae.FEMS yeast research · 2022Review
- D-Xylose Sensing inInternational journal of molecular sciences · 2021Review
- A novel yeast hybrid modeling framework integrating Boolean and enzyme-constrained networks enables exploration of the interplay between signaling and metabolism.PLoS computational biology · 2021Article
- Hypergraph-based connectivity measures for signaling pathway topologies.PLoS computational biology · 2019Article
- p53 modeling as a route to mesothelioma patients stratification and novel therapeutic identification.Journal of translational medicine · 2018Article
- Robustness of Nutrient Signaling Is Maintained by Interconnectivity Between Signal Transduction Pathways.Frontiers in physiology · 2018Article
- An overview of bioinformatics methods for modeling biological pathways in yeast.Briefings in functional genomics · 2016Review
- Article
- Signaling hypergraphs.Trends in biotechnology · 2014Article
- Modeling approaches for qualitative and semi-quantitative analysis of cellular signaling networks.Cell communication and signaling : CCS · 2013Article
- Dynamics of DNA damage induced pathways to cancer.PloS one · 2013Article
- The Process-Interaction-Model: a common representation of rule-based and logical models allows studying signal transduction on different levels of detail.BMC bioinformatics · 2012Article
- An integrative model links multiple inputs and signaling pathways to the onset of DNA synthesis in hepatocytes.The FEBS journal · 2012Article
- Systems-biology approaches for predicting genomic evolution.Nature reviews. Genetics · 2011Review
- Towards genome-scale signalling network reconstructions.Nature reviews. Genetics · 2010Review
- Hypergraphs and cellular networks.PLoS computational biology · 2009Article
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3 authors.
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Abstract
backgroundIn the yeast Saccharomyces cerevisiae, the presence of high levels of glucose leads to an array of down-regulatory effects known as glucose repression. This process is complex due to the presence of feedback loops and crosstalk between different pathways, complicating the use of intuitive approaches to analyze the system.
resultsWe established a logical model of yeast glucose repression, formalized as a hypergraph. The model was constructed based on verified regulatory interactions and it includes 50 gene transcripts, 22 proteins, 5 metabolites and 118 hyperedges. We computed the logical steady states of all nodes in the network in order to simulate wildtype and deletion mutant responses to different sugar availabilities. Evaluation of the model predictive power was achieved by comparing changes in the logical state of gene nodes with transcriptome data. Overall, we observed 71% true predictions, and analyzed sources of errors and discrepancies for the remaining.
conclusionThough the binary nature of logical (Boolean) models entails inherent limitations, our model constitutes a primary tool for storing regulatory knowledge, searching for incoherencies in hypotheses and evaluating the effect of deleting regulatory elements involved in glucose repression.
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