Mapping the attractor landscape of Boolean networks with biobalm

Result code in IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216224%3A14330%2F25%3A00142554" target="_blank" >RIV/00216224:14330/25:00142554 - isvavai.cz</a>

Result on the web

<a href="https://academic.oup.com/bioinformatics/article/41/5/btaf280/8125815" target="_blank" >https://academic.oup.com/bioinformatics/article/41/5/btaf280/8125815</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1093/bioinformatics/btaf280" target="_blank" >10.1093/bioinformatics/btaf280</a>

Result language

angličtina

Original language name

Mapping the attractor landscape of Boolean networks with biobalm

Original language description

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.

Czech name

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Czech description

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Type

J_imp - Article in a specialist periodical, which is included in the Web of Science database

CEP classification

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OECD FORD branch

10201 - Computer sciences, information science, bioinformathics (hardware development to be 2.2, social aspect to be 5.8)

Project

—

Continuities

R - Projekt Ramcoveho programu EK

Publication year

2025

Confidentiality

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Name of the periodical

BIOINFORMATICS

ISSN

1367-4803

e-ISSN

1367-4811

Volume of the periodical

41

Issue of the periodical within the volume

5

Country of publishing house

GB - UNITED KINGDOM

Number of pages

8

Pages from-to

1-8

UT code for WoS article

001493400600001

EID of the result in the Scopus database

2-s2.0-105006628370