ArticleScientific reports2014
toyLIFE: a computational framework to study the multi-level organisation of the genotype-phenotype map.
Article in Scientific reports, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- A shark-inspired general model of tooth morphogenesis unveils developmental asymmetries in phenotype transitions.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Phenotypic-dependent variability and the emergence of tolerance in bacterial populations.PLoS computational biology · 2021Article
- Gene duplication and subsequent diversification strongly affect phenotypic evolvability and robustness.Royal Society open science · 2021Article
- Populations of genetic circuits are unable to find the fittest solution in a multilevel genotype-phenotype map.Journal of the Royal Society, Interface · 2020Article
- Model genotype-phenotype mappings and the algorithmic structure of evolution.Journal of the Royal Society, Interface · 2019Article
- Human Systems Biology and Metabolic Modelling: A Review-From Disease Metabolism to Precision Medicine.BioMed research international · 2019Review
- On the networked architecture of genotype spaces and its critical effects on molecular evolution.Open biology · 2018Review
- Adding levels of complexity enhances robustness and evolvability in a multilevel genotype-phenotype map.Journal of the Royal Society, Interface · 2018Article
- The space of genotypes is a network of networks: implications for evolutionary and extinction dynamics.Scientific reports · 2017Article
- Structural properties of genotype-phenotype maps.Journal of the Royal Society, Interface · 2017Review
- Distribution of genotype network sizes in sequence-to-structure genotype-phenotype maps.Journal of the Royal Society, Interface · 2017Article
- Adaptive multiscapes: an up-to-date metaphor to visualize molecular adaptation.Biology direct · 2017Article
- The genotype-phenotype map of an evolving digital organism.PLoS computational biology · 2017Article
- Multiplex methods provide effective integration of multi-omic data in genome-scale models.BMC bioinformatics · 2016Article
- Predictive analytics of environmental adaptability in multi-omic network models.Scientific reports · 2015Article
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Authors and funding
4 authors.
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Abstract
The genotype-phenotype map is an essential object to understand organismal complexity and adaptability. However, its experimental characterisation is a daunting task. Thus, simple models have been proposed and investigated. They have revealed that genotypes differ in their robustness to mutations; phenotypes are represented by a broadly varying number of genotypes, and simple point mutations suffice to navigate the space of genotypes while maintaining a phenotype. Nonetheless, most current models focus only on one level of the map (folded molecules, gene regulatory networks, or networks of metabolic reactions), so that many relevant questions cannot be addressed. Here we introduce toyLIFE, a multi-level model for the genotype-phenotype map based on simple genomes and interaction rules from which a complex behaviour at upper levels emerges -remarkably plastic gene regulatory networks and metabolism. toyLIFE is a tool that permits the investigation of how different levels are coupled, in particular how and where mutations affect phenotype or how the presence of certain metabolites determines the dynamics of toyLIFE gene regulatory networks. The model can easily incorporate evolution through more complex mutations, recombination, or gene duplication and deletion, thus opening an avenue to explore extended genotype-phenotype maps.
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