ArticlePLoS computational biology2018
On the role of sparseness in the evolution of modularity in gene regulatory networks.
Article in PLoS computational biology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- Bayesian inference of gene regulatory networks at stochastic steady state.Journal of the Royal Society, Interface · 2026Article
- Network resilience of the human interactome to pan-cancer mutations reveals conserved pathway vulnerabilities.iScience · 2026Article
- Network stress: a wiring diagram of whole stress genes.Horticulture research · 2026Article
- Canalization as a stabilizing principle of gene regulatory networks: a discrete dynamical systems perspective.NPJ systems biology and applications · 2026Review
- Bayesian Inference of Gene Regulatory Networks at Stochastic Steady State.bioRxiv : the preprint server for biology · 2026Article
- The switch-liker's guide to plant synthetic gene circuits.The Plant journal : for cell and molecular biology · 2025Review
- CastNet: a systems-level sequence evolution simulator.BMC bioinformatics · 2023Article
- Cellular and Natural Viral Engineering in Cognition-Based Evolution.Communicative & integrative biology · 2023Review
- Early effects of gene duplication on the robustness and phenotypic variability of gene regulatory networks.BMC bioinformatics · 2022Article
- Benchmarking imputation methods for network inference using a novel method of synthetic scRNA-seq data generation.BMC bioinformatics · 2022Article
- An eco-evo-devo genetic network model of stress response.Horticulture research · 2022Article
- System Principles Governing the Organization, Architecture, Dynamics, and Evolution of Gene Regulatory Networks.Frontiers in bioengineering and biotechnology · 2022Article
- Review
- Multiple responses contribute to the enhanced drought tolerance of the autotetraploid Ziziphus jujuba Mill. var. spinosa.Cell & bioscience · 2021Article
- Detection of Genes inGenes · 2021Article
- Polyploidy: an evolutionary and ecological force in stressful times.The Plant cell · 2021Review
- The evolutionary conundrum of whole-genome duplication.American journal of botany · 2020Article
- Network architectures supporting learnability.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2020Article
- Modeling somatic computation with non-neural bioelectric networks.Scientific reports · 2019Article
- Using digital organisms to study the evolutionary consequences of whole genome duplication and polyploidy.PloS one · 2019Article
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1 author.
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Abstract
Modularity is a widespread property in biological systems. It implies that interactions occur mainly within groups of system elements. A modular arrangement facilitates adjustment of one module without perturbing the rest of the system. Therefore, modularity of developmental mechanisms is a major factor for evolvability, the potential to produce beneficial variation from random genetic change. Understanding how modularity evolves in gene regulatory networks, that create the distinct gene activity patterns that characterize different parts of an organism, is key to developmental and evolutionary biology. One hypothesis for the evolution of modules suggests that interactions between some sets of genes become maladaptive when selection favours additional gene activity patterns. The removal of such interactions by selection would result in the formation of modules. A second hypothesis suggests that modularity evolves in response to sparseness, the scarcity of interactions within a system. Here I simulate the evolution of gene regulatory networks and analyse diverse experimentally sustained networks to study the relationship between sparseness and modularity. My results suggest that sparseness alone is neither sufficient nor necessary to explain modularity in gene regulatory networks. However, sparseness amplifies the effects of forms of selection that, like selection for additional gene activity patterns, already produce an increase in modularity. That evolution of new gene activity patterns is frequent across evolution also supports that it is a major factor in the evolution of modularity. That sparseness is widespread across gene regulatory networks indicates that it may have facilitated the evolution of modules in a wide variety of cases.
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