{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,23]],"date-time":"2026-10-23T10:42:33Z","timestamp":1792752153009,"version":"4.5.0"},"reference-count":44,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2025,5,6]],"date-time":"2025-05-06T00:00:00Z","timestamp":1746489600000},"content-version":"vor","delay-in-days":5,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000001","name":"NSF","doi-asserted-by":"publisher","award":["MCB1715826"],"award-info":[{"award-number":["MCB1715826"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,5,6]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>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\u2019s 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.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We present a new approach to SD construction for asynchronously updated Boolean networks, implemented in the biologist\u2019s 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.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>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.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaf280","type":"journal-article","created":{"date-parts":[[2025,5,6]],"date-time":"2025-05-06T16:45:00Z","timestamp":1746549900000},"source":"Crossref","is-referenced-by-count":8,"title":["Mapping the attractor landscape of Boolean networks with biobalm"],"prefix":"10.1093","volume":"41","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6581-998X","authenticated-orcid":false,"given":"Van-Giang","family":"Trinh","sequence":"first","affiliation":[{"name":"LIRICA Team, Aix-Marseille University , Marseille 13397,","place":["France"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0007-0884-5541","authenticated-orcid":false,"given":"Kyu Hyong","family":"Park","sequence":"additional","affiliation":[{"name":"Department of Physics, Pennsylvania State University , University Park, PA 16802,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1993-0331","authenticated-orcid":false,"given":"Samuel","family":"Pastva","sequence":"additional","affiliation":[{"name":"Faculty of Informatics, Masaryk University , Brno 60200, Czech Republic"},{"name":"Institute of Science and Technology Austria , Klosterneuburg 3400,","place":["Austria"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4356-9809","authenticated-orcid":false,"given":"Jordan C","family":"Rozum","sequence":"additional","affiliation":[{"name":"Department of Systems Science and Industrial Engineering, Binghamton University (State University of New York) , Binghamton, NY 13850,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2025,5,6]]},"reference":[{"key":"2025052401120831700_btaf280-B1","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/S0022-5193(03)00035-3","article-title":"The topology of the regulatory interactions predicts the expression pattern of the segment polarity genes in Drosophila melanogaster","volume":"223","author":"Albert","year":"2003","journal-title":"J Theor Biol"},{"key":"2025052401120831700_btaf280-B2","doi-asserted-by":"crossref","first-page":"e2456","DOI":"10.1371\/journal.pone.0002456","article-title":"Critical dynamics in genetic regulatory networks: examples from four kingdoms","volume":"3","author":"Balleza","year":"2008","journal-title":"PLOS One"},{"key":"2025052401120831700_btaf280-B3","first-page":"505","volume-title":"Proceedings of CAV","author":"Benes","year":"2021"},{"key":"2025052401120831700_btaf280-B4","doi-asserted-by":"crossref","first-page":"4978","DOI":"10.1093\/bioinformatics\/btac624","article-title":"AEON.py: Python library for attractor analysis in asynchronous Boolean networks","volume":"38","author":"Bene\u0161","year":"2022","journal-title":"Bioinform"},{"key":"2025052401120831700_btaf280-B5","doi-asserted-by":"crossref","first-page":"1046","DOI":"10.3389\/fphys.2018.01046","article-title":"CANA: a Python package for quantifying control and canalization in Boolean networks","volume":"9","author":"Correia","year":"2018","journal-title":"Front Physiol"},{"key":"2025052401120831700_btaf280-B6","doi-asserted-by":"crossref","first-page":"739","DOI":"10.1209\/0295-5075\/2\/10\/001","article-title":"Phase transitions in two-dimensional Kauffman cellular automata","volume":"2","author":"Derrida","year":"1986","journal-title":"Europhys Lett"},{"key":"2025052401120831700_btaf280-B7","doi-asserted-by":"crossref","first-page":"563","DOI":"10.1007\/s10884-013-9312-7","article-title":"Dynamics and control at feedback vertex sets. 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