ArticleBio Systems
Relative stability of network states in Boolean network models of gene regulation in development.
Article in Bio Systems. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- Canalization as a stabilizing principle of gene regulatory networks: a discrete dynamical systems perspective.NPJ systems biology and applications · 2026Review
- Emergent dynamics of cellular decision making in multi-node mutually repressive regulatory networks.Journal of the Royal Society, Interface · 2025Article
- Biologically meaningful regulatory logic enhances the convergence rate in Boolean networks and bushiness of their state transition graph.Briefings in bioinformatics · 2024Article
- Preponderance of generalized chain functions in reconstructed Boolean models of biological networks.Scientific reports · 2024Article
- Statistical control of structural networks with limited interventions to minimize cellular phenotypic diversity represented by point attractors.Scientific reports · 2023Article
- Characterizing the Impact of Communication on Cellular and Collective Behavior Using a Three-Dimensional Multiscale Cellular Model.Entropy (Basel, Switzerland) · 2023Article
- Quantifying cancer cell plasticity with gene regulatory networks and single-cell dynamics.Frontiers in network physiology · 2023Review
- Article
- Inferring Gene Regulatory Networks Using the Improved Markov Blanket Discovery Algorithm.Interdisciplinary sciences, computational life sciences · 2022Article
- A preference for link operator functions can drive Boolean biological networks towards critical dynamics.Journal of biosciences · 2022Article
- The basis of easy controllability in Boolean networks.Nature communications · 2021Article
- Adaptive Landscape Shaped by Core Endogenous Network Coordinates Complex Early Progenitor Fate Commitments in Embryonic Pancreas.Scientific reports · 2020Article
- RWRNET: A Gene Regulatory Network Inference Algorithm Using Random Walk With Restart.Frontiers in genetics · 2020Article
- Developmentally-Inspired Biomimetic Culture Models to Produce Functional Islet-Like Cells From Pluripotent Precursors.Frontiers in bioengineering and biotechnology · 2020Review
- Analysis of Single-Cell Gene Pair Coexpression Landscapes by Stochastic Kinetic Modeling Reveals Gene-Pair Interactions in Development.Frontiers in genetics · 2019Article
- Determining Relative Dynamic Stability of Cell States Using Boolean Network Model.Scientific reports · 2018Article
- On the role of sparseness in the evolution of modularity in gene regulatory networks.PLoS computational biology · 2018Article
- The Human Cell Atlas.eLife · 2017Article
- Interrogating the topological robustness of gene regulatory circuits by randomization.PLoS computational biology · 2017Article
- Gene regulatory network underlying the immortalization of epithelial cells.BMC systems biology · 2017Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
Progress in cell type reprogramming has revived the interest in Waddington's concept of the epigenetic landscape. Recently researchers developed the quasi-potential theory to represent the Waddington's landscape. The Quasi-potential U(x), derived from interactions in the gene regulatory network (GRN) of a cell, quantifies the relative stability of network states, which determine the effort required for state transitions in a multi-stable dynamical system. However, quasi-potential landscapes, originally developed for continuous systems, are not suitable for discrete-valued networks which are important tools to study complex systems. In this paper, we provide a framework to quantify the landscape for discrete Boolean networks (BNs). We apply our framework to study pancreas cell differentiation where an ensemble of BN models is considered based on the structure of a minimal GRN for pancreas development. We impose biologically motivated structural constraints (corresponding to specific type of Boolean functions) and dynamical constraints (corresponding to stable attractor states) to limit the space of BN models for pancreas development. In addition, we enforce a novel functional constraint corresponding to the relative ordering of attractor states in BN models to restrict the space of BN models to the biological relevant class. We find that BNs with canalyzing/sign-compatible Boolean functions best capture the dynamics of pancreas cell differentiation. This framework can also determine the genes' influence on cell state transitions, and thus can facilitate the rational design of cell reprogramming protocols.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.