Mapping the attractor landscape of Boolean networks with biobalm

Trinh VG, Park KH, Pastva S, Rozum JC. 2025. Mapping the attractor landscape of Boolean networks with biobalm. Bioinformatics. 41(5), btaf280.

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Journal Article | Published | English

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Author
Trinh, Van Giang; Park, Kyu Hyong; Pastva, SamuelISTA ; Rozum, Jordan C.

Corresponding author has ISTA affiliation

Abstract
Motivation: Boolean networks are popular dynamical models of cellular processes in systems biology. Their attractors model phenotypes that arise from the interplay of key regulatory subcircuits. A succession diagram (SD) describes this interplay in a discrete analog of Waddington’s epigenetic attractor landscape that allows for fast identification of attractors and attractor control strategies. Efficient computational tools for studying SDs are essential for the understanding of Boolean attractor landscapes and connecting them to their biological functions. Results: We present a new approach to SD construction for asynchronously updated Boolean networks, implemented in the biologist’s Boolean attractor landscape mapper, biobalm. We compare biobalm to similar tools and find a substantial performance increase in SD construction, attractor identification, and attractor control. We perform the most comprehensive comparative analysis to date of the SD structure in experimentally-validated Boolean models of cell processes and random ensembles. We find that random models (including critical Kauffman networks) have relatively small SDs, indicating simple decision structures. In contrast, nonrandom models from the literature are enriched in extremely large SDs, indicating an abundance of decision points and suggesting the presence of complex Waddington landscapes in nature. Availability and implementation: The tool biobalm is available online at https://github.com/jcrozum/biobalm. Further data, scripts for testing, analysis, and figure generation are available online at https://github.com/jcrozum/biobalm-analysis and in the reproducibility artefact at https://doi.org/10.5281/zenodo.13854760.
Publishing Year
Date Published
2025-05-01
Journal Title
Bioinformatics
Publisher
Oxford University Press
Acknowledgement
V.-G.T. was supported by Institut Carnot STAR, Marseille, France. K.H.P. was supported by NSF grant MCB1715826 to Réka Albert. S.P. has received funding from the European Union’s Horizon 2020 Research and Innovation Programme under the Marie Sklodowska-Curie Grant Agreement No. 101034413. J.C.R. was supported by internal departmental funds provided by Luis M. Rocha. No funding bodies had any role in study design, analysis, decision to publish, or preparation of the article.
Volume
41
Issue
5
Article Number
btaf280
eISSN
IST-REx-ID

Cite this

Trinh VG, Park KH, Pastva S, Rozum JC. Mapping the attractor landscape of Boolean networks with biobalm. Bioinformatics. 2025;41(5). doi:10.1093/bioinformatics/btaf280
Trinh, V. G., Park, K. H., Pastva, S., & Rozum, J. C. (2025). Mapping the attractor landscape of Boolean networks with biobalm. Bioinformatics. Oxford University Press. https://doi.org/10.1093/bioinformatics/btaf280
Trinh, Van Giang, Kyu Hyong Park, Samuel Pastva, and Jordan C. Rozum. “Mapping the Attractor Landscape of Boolean Networks with Biobalm.” Bioinformatics. Oxford University Press, 2025. https://doi.org/10.1093/bioinformatics/btaf280.
V. G. Trinh, K. H. Park, S. Pastva, and J. C. Rozum, “Mapping the attractor landscape of Boolean networks with biobalm,” Bioinformatics, vol. 41, no. 5. Oxford University Press, 2025.
Trinh VG, Park KH, Pastva S, Rozum JC. 2025. Mapping the attractor landscape of Boolean networks with biobalm. Bioinformatics. 41(5), btaf280.
Trinh, Van Giang, et al. “Mapping the Attractor Landscape of Boolean Networks with Biobalm.” Bioinformatics, vol. 41, no. 5, btaf280, Oxford University Press, 2025, doi:10.1093/bioinformatics/btaf280.
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2025-06-10
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