{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,11,6]],"date-time":"2026-11-06T18:25:03Z","timestamp":1793989503504,"version":"4.8.0"},"reference-count":10,"publisher":"Wiley","issue":"4","license":[{"start":{"date-parts":[[2026,9,23]],"date-time":"2026-09-23T00:00:00Z","timestamp":1790121600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2026,9,23]],"date-time":"2026-09-23T00:00:00Z","timestamp":1790121600000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/doi.wiley.com\/10.1002\/tdm_license_1.1"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["92374107"],"award-info":[{"award-number":["92374107"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["62373216"],"award-info":[{"award-number":["62373216"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Quant. Biol."],"published-print":{"date-parts":[[2026,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Steady\u2010state attractor detection differs fundamentally between discrete Boolean network (BN) and continuous diffusion\u2010based models because they operate on different state spaces and exhibit distinct dynamic behaviors. Here, we propose cell dynamics on energy landscape (CellLand) to systematically compare BN and diffusion\u2010based approaches for quantifying cellular dynamics on the energy landscape, with a particular focus on attractor identification under in silico gene perturbations. Although the energy landscape provides a unifying conceptual framework, BN\u2010based models face specific challenges, including state space explosion and pronounced sensitivity to network architecture, when assessing attractor stability and transition accessibility. Nevertheless, BN\u2010based analyses can remain reliable and interpretable when the underlying network topology is suitable, while being comparatively less sensitive to parameter estimation uncertainty and technical noise. Importantly, we show that attractor identification depends critically on network structure, and that no general theory currently exists for optimizing BN topology for dynamic cell\u2010state modeling. Our findings deepen the comparative understanding of BN and diffusion\u2010based frameworks and provide practical guidelines for selecting and designing models for robust simulation of complex gene\u2010regulatory systems under perturbations.<\/jats:p>","DOI":"10.1002\/qub2.70056","type":"journal-article","created":{"date-parts":[[2026,9,24]],"date-time":"2026-09-24T04:20:58Z","timestamp":1790223658000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Cell dynamics on energy landscape: Comparing attractor detection in Boolean network and diffusion\u2010based models under in silico gene perturbations"],"prefix":"10.1002","volume":"14","author":[{"given":"Lingyu","family":"Li","sequence":"first","affiliation":[{"name":"School of Biomedical Sciences The University of Hong Kong  Hong Kong China"},{"name":"Department of Mathematics The University of Hong Kong  Hong Kong China"},{"name":"Department of Biomedical Engineering School of Control Science and Engineering Shandong University  Jinan China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Liangjie","family":"Sun","sequence":"additional","affiliation":[{"name":"Department of Mathematics The University of Hong Kong  Hong Kong China"},{"name":"Institute for Life and Medical Sciences Kyoto University  Kyoto Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shumin","family":"Li","sequence":"additional","affiliation":[{"name":"School of Artificial Intelligence Shenzhen University  Shenzhen China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wai\u2010Ki","family":"Ching","sequence":"additional","affiliation":[{"name":"Department of Mathematics The University of Hong Kong  Hong Kong China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhi\u2010Ping","family":"Liu","sequence":"additional","affiliation":[{"name":"Department of Biomedical Engineering School of Control Science and Engineering Shandong University  Jinan China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2026,9,23]]},"reference":[{"key":"e_1_2_6_2_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2026.04.028"},{"key":"e_1_2_6_3_1","doi-asserted-by":"publisher","DOI":"10.1016\/0022-5193(69)90015-0"},{"key":"e_1_2_6_4_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btad256"},{"key":"e_1_2_6_5_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-026-70528-7"},{"key":"e_1_2_6_6_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1722609115"},{"key":"e_1_2_6_7_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.isci.2022.105499"},{"key":"e_1_2_6_8_1","doi-asserted-by":"publisher","DOI":"10.1002\/advs.202003133"},{"key":"e_1_2_6_9_1","doi-asserted-by":"publisher","DOI":"10.1093\/nsr\/nwae052"},{"key":"e_1_2_6_10_1","doi-asserted-by":"publisher","DOI":"10.1038\/s42003-026-09758-w"},{"key":"e_1_2_6_11_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-022-31066-0"}],"container-title":["Quantitative Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1002\/qub2.70056","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/full-xml\/10.1002\/qub2.70056","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1002\/qub2.70056","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,11,6]],"date-time":"2026-11-06T17:39:57Z","timestamp":1793986797000},"score":1,"resource":{"primary":{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/10.1002\/qub2.70056"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9,23]]},"references-count":10,"journal-issue":{"issue":"4","published-print":{"date-parts":[[2026,12]]}},"alternative-id":["10.1002\/qub2.70056"],"URL":"https:\/\/doi.org\/10.1002\/qub2.70056","archive":["Portico"],"relation":{},"ISSN":["2095-4689","2095-4697"],"issn-type":[{"value":"2095-4689","type":"print"},{"value":"2095-4697","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,9,23]]},"assertion":[{"value":"2025-12-29","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2026-06-05","order":2,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2026-09-23","order":3,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}],"article-number":"e70056"}}