{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,6]],"date-time":"2026-03-06T00:05:55Z","timestamp":1772755555949,"version":"3.50.1"},"reference-count":15,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2020,8,26]],"date-time":"2020-08-26T00:00:00Z","timestamp":1598400000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"SEC-PBN"},{"name":"AlgoReCell","award":["INTER\/ANR\/15\/11191283"],"award-info":[{"award-number":["INTER\/ANR\/15\/11191283"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,5,5]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Direct cell reprogramming, also called transdifferentiation, has great potential for tissue engineering and regenerative medicine. Boolean networks, a popular modelling framework for gene regulatory networks, make it possible to identify intervention targets for direct cell reprogramming with computational methods. In this work, we present our software, CABEAN, for the control of asynchronous Boolean networks. CABEAN identifies efficacious nodes, whose perturbations can drive the dynamics of a network from a source attractor (the initial cell type) to a target attractor (the desired cell type). CABEAN provides several control methods integrating practical constraints. Thus, it has the ability to provide a rich set of control sets, such that biologists can select suitable ones for validation based on specific experimental settings.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The executable binary and the user guide of the software are publicly available at https:\/\/satoss.uni.lu\/software\/CABEAN\/.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaa752","type":"journal-article","created":{"date-parts":[[2020,8,19]],"date-time":"2020-08-19T19:26:54Z","timestamp":1597865214000},"page":"879-881","source":"Crossref","is-referenced-by-count":31,"title":["CABEAN: a software for the control of asynchronous Boolean networks"],"prefix":"10.1093","volume":"37","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6519-4588","authenticated-orcid":false,"given":"Cui","family":"Su","sequence":"first","affiliation":[{"name":"Interdisciplinary Centre for Security, Reliability and Trust, University of Luxembourg , 4365 Esch-sur-Alzette, Luxembourg"}]},{"given":"Jun","family":"Pang","sequence":"additional","affiliation":[{"name":"Interdisciplinary Centre for Security, Reliability and Trust, University of Luxembourg , 4365 Esch-sur-Alzette, Luxembourg"},{"name":"Faculty of Science, Technology and Medicine, University of Luxembourg , 4365 Esch-sur-Alzette, Luxembourg"}]}],"member":"286","published-online":{"date-parts":[[2020,8,26]]},"reference":[{"key":"2023051704121467000_btaa752-B1","doi-asserted-by":"crossref","first-page":"1574","DOI":"10.1109\/TCBB.2018.2889102","article-title":"Causal reasoning on Boolean control networks based on abduction: theory and application to cancer drug discovery","volume":"16","author":"Biane","year":"2019","journal-title":"IEEE\/ACM Trans. Comput. Biol. Bioinf"},{"key":"2023051704121467000_btaa752-B2","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":"2023051704121467000_btaa752-B3","doi-asserted-by":"crossref","first-page":"14","DOI":"10.1186\/s13036-019-0144-9","article-title":"Direct cell reprogramming for tissue engineering and regenerative medicine","volume":"13","author":"Grath","year":"2019","journal-title":"J. Biol. Eng"},{"key":"2023051704121467000_btaa752-B4","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":"2017","journal-title":"Bioinformatics"},{"key":"2023051704121467000_btaa752-B5","doi-asserted-by":"crossref","first-page":"S5","DOI":"10.1186\/1471-2164-13-S6-S5","article-title":"Application of Max-SAT-based ATPG to optimal cancer therapy design","volume":"13","author":"Lin","year":"2012","journal-title":"BMC Genomics"},{"key":"2023051704121467000_btaa752-B6","doi-asserted-by":"crossref","first-page":"9","DOI":"10.1007\/s10009-015-0378-x","article-title":"MCMAS: an open-source model checker for the verification of multi-agent systems","volume":"19","author":"Lomuscio","year":"2017","journal-title":"J. Softw. Tools Technol. Transf"},{"key":"2023051704121467000_btaa752-B7","first-page":"3","author":"Mandon","year":"2019"},{"key":"2023051704121467000_btaa752-B8","doi-asserted-by":"crossref","first-page":"94","DOI":"10.1186\/s12918-016-0332-x","article-title":"Identification of control targets in Boolean molecular network models via computational algebra","volume":"10","author":"Murrugarra","year":"2016","journal-title":"BMC Syst. Biol"},{"key":"2023051704121467000_btaa752-B9","doi-asserted-by":"crossref","first-page":"1378","DOI":"10.1093\/bioinformatics\/btq124","article-title":"BoolNet-an R package for generation, reconstruction and analysis of Boolean networks","volume":"26","author":"M\u00fcssel","year":"2010","journal-title":"Bioinformatics"},{"key":"2023051704121467000_btaa752-B10","first-page":"11","author":"Paul","year":"2018"},{"key":"2023051704121467000_btaa752-B11","author":"Paul","year":"2019"},{"key":"2023051704121467000_btaa752-B12","doi-asserted-by":"crossref","first-page":"171852","DOI":"10.1098\/rsos.171852","article-title":"Therapeutic target discovery using Boolean network attractors: improvements of kali","volume":"5","author":"Poret","year":"2018","journal-title":"R. Soc. Open Sci"},{"key":"2023051704121467000_btaa752-B13","first-page":"234","author":"Su","year":"2020"},{"key":"2023051704121467000_btaa752-B14","first-page":"707","author":"Su","year":"2019"},{"key":"2023051704121467000_btaa752-B15","doi-asserted-by":"crossref","first-page":"e1004193","DOI":"10.1371\/journal.pcbi.1004193","article-title":"Cell fate reprogramming by control of intracellular network dynamics","volume":"11","author":"Za\u00f1udo","year":"2015","journal-title":"PLOS Comput. Biol"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btaa752\/34774661\/btaa752.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/37\/6\/879\/50356523\/btaa752.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/37\/6\/879\/50356523\/btaa752.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,5,17]],"date-time":"2023-05-17T04:12:46Z","timestamp":1684296766000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/37\/6\/879\/5897411"}},"subtitle":[],"editor":[{"given":"Pier","family":"Luigi Martelli","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2020,8,26]]},"references-count":15,"journal-issue":{"issue":"6","published-print":{"date-parts":[[2021,5,5]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btaa752","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2021,3,15]]},"published":{"date-parts":[[2020,8,26]]}}}