ArticlePLoS computational biology2015
A Dynamic Gene Regulatory Network Model That Recovers the Cyclic Behavior of Arabidopsis thaliana Cell Cycle.
Article in PLoS computational biology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
20 citing papers in PubMed.
- Succession-diagram-based Markov chains reveal the attractor landscape of asynchronous Boolean networks.NPJ systems biology and applications · 2026Article
- A system-level model reveals that transcriptional stochasticity is required for hematopoietic stem cell differentiation.NPJ systems biology and applications · 2024Article
- A Model for the Gene Regulatory Network Along the Arabidopsis Fruit Medio-Lateral Axis: Rewiring the Pod Shatter Process.Plants (Basel, Switzerland) · 2024Article
- A Boolean model explains phenotypic plasticity changes underlying hepatic cancer stem cells emergence.NPJ systems biology and applications · 2024Article
- A neural network-based model framework for cell-fate decisions and development.Communications biology · 2024Article
- Models of Cell Processes are Far from the Edge of Chaos.PRX life · 2023Article
- Modelling how plant cell-cycle progression leads to cell size regulation.PLoS computational biology · 2023Article
- The flowering transition pathways converge into a complex gene regulatory network that underlies the phase changes of the shoot apical meristem inFrontiers in plant science · 2022Article
- Identification of dynamic driver sets controlling phenotypical landscapes.Computational and structural biotechnology journal · 2022Article
- Reverse engineering gene regulatory network based on complex-valued ordinary differential equation model.BMC bioinformatics · 2021Article
- TheProceedings of the National Academy of Sciences of the United States of America · 2021Article
- Hormonal Regulation of Stem Cell Proliferation at theFrontiers in plant science · 2021Review
- Qualitative Modeling, Analysis and Control of Synthetic Regulatory Circuits.Methods in molecular biology (Clifton, N.J.) · 2021Review
- Antifragility Predicts the Robustness and Evolvability of Biological Networks through Multi-Class Classification with a Convolutional Neural Network.Entropy (Basel, Switzerland) · 2020Article
- RMut: R package for a Boolean sensitivity analysis against various types of mutations.PloS one · 2019Article
- From Discrete to Continuous Modeling of Lymphocyte Development and Plasticity in Chronic Diseases.Frontiers in immunology · 2019Review
- Article
- Gene Regulatory Network Modeling of Macrophage Differentiation Corroborates the Continuum Hypothesis of Polarization States.Frontiers in physiology · 2018Article
- A dynamic genetic-hormonal regulatory network model explains multiple cellular behaviors of the root apical meristem of Arabidopsis thaliana.PLoS computational biology · 2017Article
- Qualitative Dynamical Modelling Can Formally Explain Mesoderm Specification and Predict Novel Developmental Phenotypes.PLoS computational biology · 2016Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Cell cycle control is fundamental in eukaryotic development. Several modeling efforts have been used to integrate the complex network of interacting molecular components involved in cell cycle dynamics. In this paper, we aimed at recovering the regulatory logic upstream of previously known components of cell cycle control, with the aim of understanding the mechanisms underlying the emergence of the cyclic behavior of such components. We focus on Arabidopsis thaliana, but given that many components of cell cycle regulation are conserved among eukaryotes, when experimental data for this system was not available, we considered experimental results from yeast and animal systems. We are proposing a Boolean gene regulatory network (GRN) that converges into only one robust limit cycle attractor that closely resembles the cyclic behavior of the key cell-cycle molecular components and other regulators considered here. We validate the model by comparing our in silico configurations with data from loss- and gain-of-function mutants, where the endocyclic behavior also was recovered. Additionally, we approximate a continuous model and recovered the temporal periodic expression profiles of the cell-cycle molecular components involved, thus suggesting that the single limit cycle attractor recovered with the Boolean model is not an artifact of its discrete and synchronous nature, but rather an emergent consequence of the inherent characteristics of the regulatory logic proposed here. This dynamical model, hence provides a novel theoretical framework to address cell cycle regulation in plants, and it can also be used to propose novel predictions regarding cell cycle regulation in other eukaryotes.
Indexed as
Identifiers
What OpenQuestion holds
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.