ArticleScientific reports2021
Using linkage logic theory to control dynamics of a gene regulatory network of a chordate embryo.
Article in Scientific reports, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed.
- Network topology creates independent control of multiple checkpoints in the cell cycle system.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- RENGE infers gene regulatory networks using time-series single-cell RNA-seq data with CRISPR perturbations.Communications biology · 2023Article
- Mathematical modeling for developmental processes.Development, growth & differentiation · 2023Review
- Controlling complex dynamical systems based on the structure of the networks.Biophysics and physicobiology · 2023Article
- Leveraging network structure in nonlinear control.NPJ systems biology and applications · 2022Review
- NETISCE: a network-based tool for cell fate reprogramming.NPJ systems biology and applications · 2022Article
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Authors and funding
5 authors.
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Abstract
Linkage logic theory provides a mathematical criterion to control network dynamics by manipulating activities of a subset of network nodes, which are collectively called a feedback vertex set (FVS). Because many biological functions emerge from dynamics of biological networks, this theory provides a promising tool for controlling biological functions. By manipulating the activity of FVS molecules identified in a gene regulatory network (GRN) for fate specification of seven tissues in ascidian embryos, we previously succeeded in reproducing six of the seven cell types. Simultaneously, we discovered that the experimentally reconstituted GRN lacked information sufficient to reproduce muscle cells. Here, we utilized linkage logic theory as a tool to find missing edges in the GRN. Then, we identified a FVS from an updated version of the GRN and confirmed that manipulating the activity of this FVS was sufficient to induce all seven cell types, even in a multi-cellular environment. Thus, linkage logic theory provides tools to find missing edges in experimentally reconstituted networks, to determine whether reconstituted networks contain sufficient information to fulfil expected functions, and to reprogram cell fate.
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