ArticlePloS one2012
Ergodic sets as cell phenotype of budding yeast cell cycle.
Article in PloS one, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- A comprehensive mechanistic multicellular model of the human immune system spanning 11 diseases.Frontiers in immunology · 2026Article
- Reconstruction of gene regulatory networks for Caenorhabditis elegans using tree-shaped gene expression data.Briefings in bioinformatics · 2024Article
- LncRNAs of Saccharomyces cerevisiae bypass the cell cycle arrest imposed by ethanol stress.PLoS computational biology · 2022Article
- The constrained disorder principle defines living organisms and provides a method for correcting disturbed biological systems.Computational and structural biotechnology journal · 2022Article
- Identification of dynamic driver sets controlling phenotypical landscapes.Computational and structural biotechnology journal · 2022Article
- Antifragility Predicts the Robustness and Evolvability of Biological Networks through Multi-Class Classification with a Convolutional Neural Network.Entropy (Basel, Switzerland) · 2020Article
- The CoLoMoTo Interactive Notebook: Accessible and Reproducible Computational Analyses for Qualitative Biological Networks.Frontiers in physiology · 2018Article
- A Mechanistic Computational Model Reveals That Plasticity of CD4Frontiers in physiology · 2018Article
- Identification of Biologically Essential Nodes via Determinative Power in Logical Models of Cellular Processes.Frontiers in physiology · 2018Article
- Advances and challenges in logical modeling of cell cycle regulation: perspective for multi-scale, integrative yeast cell models.FEMS yeast research · 2017Review
- Systems Perturbation Analysis of a Large-Scale Signal Transduction Model Reveals Potentially Influential Candidates for Cancer Therapeutics.Frontiers in bioengineering and biotechnology · 2016Article
- Logical Modeling and Dynamical Analysis of Cellular Networks.Frontiers in genetics · 2016Review
- Design, Assessment, and in vivo Evaluation of a Computational Model Illustrating the Role of CAV1 in CD4(+) T-lymphocytes.Frontiers in immunology · 2014Article
- Learning restricted Boolean network model by time-series data.EURASIP journal on bioinformatics & systems biology · 2014Article
- SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools.BMC systems biology · 2013Article
- Recent development and biomedical applications of probabilistic Boolean networks.Cell communication and signaling : CCS · 2013Review
- A comprehensive, multi-scale dynamical model of ErbB receptor signal transduction in human mammary epithelial cells.PloS one · 2013Article
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2 authors.
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Abstract
It has been suggested that irreducible sets of states in Probabilistic Boolean Networks correspond to cellular phenotype. In this study, we identify such sets of states for each phase of the budding yeast cell cycle. We find that these "ergodic sets" underly the cyclin activity levels during each phase of the cell cycle. Our results compare to the observations made in several laboratory experiments as well as the results of differential equation models. Dynamical studies of this model: (i) indicate that under stochastic external signals the continuous oscillating waves of cyclin activity and the opposing waves of CKIs emerge from the logic of a Boolean-based regulatory network without the need for specific biochemical/kinetic parameters; (ii) suggest that the yeast cell cycle network is robust to the varying behavior of cell size (e.g., cell division under nitrogen deprived conditions); (iii) suggest the irreversibility of the Start signal is a function of logic of the G1 regulon, and changing the structure of the regulatory network can render start reversible.
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