{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,6]],"date-time":"2026-03-06T00:05:56Z","timestamp":1772755556015,"version":"3.50.1"},"reference-count":12,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2021,12,7]],"date-time":"2021-12-07T00:00:00Z","timestamp":1638835200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/100000001","name":"NSF","doi-asserted-by":"publisher","award":["PHY 1545832"],"award-info":[{"award-number":["PHY 1545832"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"NSF","doi-asserted-by":"publisher","award":["MCB 1715826"],"award-info":[{"award-number":["MCB 1715826"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"NSF","doi-asserted-by":"publisher","award":["IIS 1814405 to R.A."],"award-info":[{"award-number":["IIS 1814405 to R.A."]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Stand Up to Cancer Foundation\/The V Foundation Convergence Scholar Award","award":["D2015-039 to J.G.T.Z."],"award-info":[{"award-number":["D2015-039 to J.G.T.Z."]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,2,7]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Summary<\/jats:title><jats:p>pystablemotifs is a Python 3 library for analyzing Boolean networks. Its non-heuristic and exhaustive attractor identification algorithm was previously presented in Rozum et al. (2021). Here, we illustrate its performance improvements over similar methods and discuss how it uses outputs of the attractor identification process to drive a system to one of its attractors from any initial state. We implement six attractor control algorithms, five of which are new in this work. By design, these algorithms can return different control strategies, allowing for synergistic use. We also give a brief overview of the other tools implemented in pystablemotifs.<\/jats:p><\/jats:sec><jats:sec><jats:title>Availability and implementation<\/jats:title><jats:p>The source code is on GitHub at https:\/\/github.com\/jcrozum\/pystablemotifs\/.<\/jats:p><\/jats:sec><jats:sec><jats:title>Supplementary information<\/jats:title><jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p><\/jats:sec>","DOI":"10.1093\/bioinformatics\/btab825","type":"journal-article","created":{"date-parts":[[2021,12,2]],"date-time":"2021-12-02T20:14:26Z","timestamp":1638476066000},"page":"1465-1466","source":"Crossref","is-referenced-by-count":34,"title":["pystablemotifs: Python library for attractor identification and control in Boolean networks"],"prefix":"10.1093","volume":"38","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4356-9809","authenticated-orcid":false,"given":"Jordan C","family":"Rozum","sequence":"first","affiliation":[{"name":"Department of Physics, The Pennsylvania State University , University Park, PA 16802, USA"}]},{"given":"D\u00e1vid","family":"Deritei","sequence":"additional","affiliation":[{"name":"Department of Molecular Biology, Semmelweis University , Budapest 1085, Hungary"},{"name":"Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School , Boston, MA 02115, USA"}]},{"given":"Kyu Hyong","family":"Park","sequence":"additional","affiliation":[{"name":"Department of Physics, The Pennsylvania State University , University Park, PA 16802, USA"}]},{"given":"Jorge","family":"G\u00f3mez Tejeda Za\u00f1udo","sequence":"additional","affiliation":[{"name":"Eli and Edythe L. Broad Institute of MIT and Harvard , Cambridge, MA 02142, USA"},{"name":"Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School , Boston, MA 02115, USA"}]},{"given":"R\u00e9ka","family":"Albert","sequence":"additional","affiliation":[{"name":"Department of Physics, The Pennsylvania State University , University Park, PA 16802, USA"},{"name":"Department of Biology, The Pennsylvania State University , University Park, PA 16802, USA"}]}],"member":"286","published-online":{"date-parts":[[2021,12,7]]},"reference":[{"key":"2023020108550432000_btab825-B1","doi-asserted-by":"crossref","first-page":"770","DOI":"10.1093\/bioinformatics\/btw682","article-title":"PyBoolNet: a Python package for the generation, analysis and visualization of Boolean networks","volume":"33","author":"Klarner","year":"2016","journal-title":"Bioinformatics"},{"key":"2023020108550432000_btab825-B2","doi-asserted-by":"crossref","first-page":"927","DOI":"10.3389\/fphys.2020.00927","article-title":"A guard cell abscisic acid (ABA) network model that captures the stomatal resting state","volume":"11","author":"Maheshwari","year":"2020","journal-title":"Front. 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