ArticleNature communications2019
A comprehensive, mechanistically detailed, and executable model of the cell division cycle in Saccharomyces cerevisiae.
Article in Nature communications, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed.
- Stochastic phenotypic switching arises in response to directional selection in experimentally evolved multicellular yeast.Communications biology · 2025Article
- A modular model integrating metabolism, growth, and cell cycle predicts that fermentation is required to modulate cell size in yeast populations.PLoS computational biology · 2025Article
- Extending the G1 phase improves the production of lipophilic compounds in yeast by boosting enzyme expression and increasing cell size.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Modeling the START transition in the budding yeast cell cycle.PLoS computational biology · 2024Article
- Signal execution modes emerge in biochemical reaction networks calibrated to experimental data.iScience · 2024Article
- Data integration strategies for whole-cell modeling.FEMS yeast research · 2024Review
- Reusable rule-based cell cycle model explains compartment-resolved dynamics of 16 observables in RPE-1 cells.PLoS computational biology · 2024Article
- Microbiome modeling: a beginner's guide.Frontiers in microbiology · 2024Review
- Technologies for whole-cell modeling: Genome-wide reconstruction of a cell in silico.Development, growth & differentiation · 2023Review
- kboolnet: a toolkit for the verification, validation, and visualization of reaction-contingency (rxncon) models.BMC bioinformatics · 2023Article
- A detailed molecular network map and model of the NLRP3 inflammasome.Frontiers in immunology · 2023Review
- MEMMAL: A tool for expanding large-scale mechanistic models with machine learned associations and big datasets.Frontiers in systems biology · 2023Article
- Computational speed-up of large-scale, single-cell model simulations via a fully integrated SBML-based format.Bioinformatics advances · 2023Article
- A continuous-time stochastic Boolean model provides a quantitative description of the budding yeast cell cycle.Scientific reports · 2022Article
- A yeast cell cycle model integrating stress, signaling, and physiology.FEMS yeast research · 2022Article
- A scalable, open-source implementation of a large-scale mechanistic model for single cell proliferation and death signaling.Nature communications · 2022Article
- LncRNAs of Saccharomyces cerevisiae bypass the cell cycle arrest imposed by ethanol stress.PLoS computational biology · 2022Article
- Mini-batch optimization enables training of ODE models on large-scale datasets.Nature communications · 2022Article
- Identification of periodic attractors in Boolean networks using a priori information.PLoS computational biology · 2022Article
- Bacterial genome reductions: Tools, applications, and challenges.Frontiers in genome editing · 2022Review
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Understanding how cellular functions emerge from the underlying molecular mechanisms is a key challenge in biology. This will require computational models, whose predictive power is expected to increase with coverage and precision of formulation. Genome-scale models revolutionised the metabolic field and made the first whole-cell model possible. However, the lack of genome-scale models of signalling networks blocks the development of eukaryotic whole-cell models. Here, we present a comprehensive mechanistic model of the molecular network that controls the cell division cycle in Saccharomyces cerevisiae. We use rxncon, the reaction-contingency language, to neutralise the scalability issues preventing formulation, visualisation and simulation of signalling networks at the genome-scale. We use parameter-free modelling to validate the network and to predict genotype-to-phenotype relationships down to residue resolution. This mechanistic genome-scale model offers a new perspective on eukaryotic cell cycle control, and opens up for similar models-and eventually whole-cell models-of human cells.
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