ReviewHeliyon2022
Review and assessment of Boolean approaches for inference of gene regulatory networks.
Review in Heliyon, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
What it found
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Who cites it
18 citing papers in PubMed.
- From prior knowledge to data-informed models: a review of Boolean network inference.Briefings in bioinformatics · 2026Review
- Research progress on the Sonic Hedgehog signaling pathway in the central nervous system: Novel insights.Neural regeneration research · 2026Article
- Sketchbook: logical model inference from Boolean network sketches.Bioinformatics advances · 2026Article
- HSTXGB: a hyperparameter self-tuning XGBoost method integrating pre- and post-processing for gene regulatory network inference.Frontiers in genetics · 2026Article
- Decoding yeast transcriptional regulation via a data-and mechanism-driven distributed large-scale network model.Synthetic and systems biotechnology · 2025Article
- Unlocking gene regulatory networks for crop resilience and sustainable agriculture.Nature biotechnology · 2025Review
- Critical assessment of the ability of Boolean threshold models to describe gene regulatory network dynamics.PNAS nexus · 2025Article
- Harnessing the analog computing power of regulatory networks with the Regulatory Network Machine.iScience · 2025Article
- LogicGep: Boolean networks inference using symbolic regression from time-series transcriptomic profiling data.Briefings in bioinformatics · 2024Article
- An optimal Bayesian intervention policy in response to unknown dynamic cell stimuli.Information sciences · 2024Article
- Concordant B and T Cell Heterogeneity Inferred from the Multiomic Landscape of Peripheral Blood Mononuclear Cells in a Crohn's Disease Cohort.Journal of Crohn's & colitis · 2024Article
- Preponderance of generalized chain functions in reconstructed Boolean models of biological networks.Scientific reports · 2024Article
- SAILoR: Structure-Aware Inference of Logic Rules.PloS one · 2024Article
- Kernel-Based Particle Filtering for Scalable Inference in Partially Observed Boolean Dynamical Systems.IFAC-PapersOnLine · 2024Article
- Modularity of biological systems: a link between structure and function.Journal of the Royal Society, Interface · 2023Article
- From time-series transcriptomics to gene regulatory networks: A review on inference methods.PLoS computational biology · 2023Review
- Network-based approaches for modeling disease regulation and progression.Computational and structural biotechnology journal · 2023Review
- Inference of regulatory networks through temporally sparse data.Frontiers in control engineering · 2022Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Boolean descriptions of gene regulatory networks can provide an insight into interactions between genes. Boolean networks hold predictive power, are easy to understand, and can be used to simulate the observed networks in different scenarios. We review fundamental and state-of-the-art methods for inference of Boolean networks. We introduce a methodology for a straightforward evaluation of Boolean inference approaches based on the generation of evaluation datasets, application of selected inference methods, and evaluation of performance measures to guide the selection of the best method for a given inference problem. We demonstrate this procedure on inference methods REVEAL (REVerse Engineering ALgorithm), Best-Fit Extension, MIBNI (Mutual Information-based Boolean Network Inference), GABNI (Genetic Algorithm-based Boolean Network Inference) and ATEN (AND/OR Tree ENsemble algorithm), which infers Boolean descriptions of gene regulatory networks from discretised time series data. Boolean inference approaches tend to perform better in terms of dynamic accuracy, and slightly worse in terms of structural correctness. We believe that the proposed methodology and provided guidelines will help researchers to develop Boolean inference approaches with a good predictive capability while maintaining structural correctness and biological relevance.
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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.