{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,13]],"date-time":"2026-01-13T21:37:57Z","timestamp":1768340277483,"version":"3.49.0"},"reference-count":22,"publisher":"Oxford University Press (OUP)","issue":"21","license":[{"start":{"date-parts":[[2017,6,29]],"date-time":"2017-06-29T00:00:00Z","timestamp":1498694400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/100007869","name":"FNR","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100007869","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,11,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Mathematical modelling of regulatory networks allows for the discovery of knowledge at the system level. However, existing modelling tools are often computation-heavy and do not offer intuitive ways to explore the model, to test hypotheses or to interpret the results biologically.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We have developed a computational approach to contextualize logical models of regulatory networks with biological measurements based on a probabilistic description of rule-based interactions between the different molecules. Here, we propose a Matlab toolbox, FALCON, to automatically and efficiently build and contextualize networks, which includes a pipeline for conducting parameter analysis, knockouts and easy and fast model investigation. The contextualized models could then provide qualitative and quantitative information about the network and suggest hypotheses about biological processes.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>FALCON is freely available for non-commercial users on GitHub under the GPLv3 licence. The toolbox, installation instructions, full documentation and test datasets are available at https:\/\/github.com\/sysbiolux\/FALCON. FALCON runs under Matlab (MathWorks) and requires the Optimization Toolbox.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btx380","type":"journal-article","created":{"date-parts":[[2017,6,26]],"date-time":"2017-06-26T11:08:47Z","timestamp":1498475327000},"page":"3431-3436","source":"Crossref","is-referenced-by-count":10,"title":["FALCON: a toolbox for the fast contextualization of logical networks"],"prefix":"10.1093","volume":"33","author":[{"given":"S\u00e9bastien","family":"De Landtsheer","sequence":"first","affiliation":[{"name":"Systems Biology Group, Life Sciences Research Unit, University of Luxembourg, Belvaux, Luxembourg"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Panuwat","family":"Trairatphisan","sequence":"additional","affiliation":[{"name":"Systems Biology Group, Life Sciences Research Unit, University of Luxembourg, Belvaux, Luxembourg"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Philippe","family":"Lucarelli","sequence":"additional","affiliation":[{"name":"Systems Biology Group, Life Sciences Research Unit, University of Luxembourg, Belvaux, Luxembourg"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Thomas","family":"Sauter","sequence":"additional","affiliation":[{"name":"Systems Biology Group, Life Sciences Research Unit, University of Luxembourg, Belvaux, Luxembourg"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2017,6,29]]},"reference":[{"key":"2023051506355209100_btx380-B1","doi-asserted-by":"crossref","first-page":"110","DOI":"10.1038\/msb4100158","article-title":"How to infer gene networks from expression profiles","volume":"3","author":"Bansal","year":"2007","journal-title":"Mol. Syst. Biol"},{"key":"2023051506355209100_btx380-B2","doi-asserted-by":"crossref","first-page":"261","DOI":"10.1177\/0049124104268644","article-title":"Multimodel inference: understanding AIC and BIC in model selection","volume":"33","author":"Burnham","year":"2004","journal-title":"Sociol. Methods Res"},{"key":"2023051506355209100_btx380-B3","first-page":"249","author":"Glorot","year":"2010"},{"key":"2023051506355209100_btx380-B4","doi-asserted-by":"crossref","first-page":"437","DOI":"10.1016\/0022-5193(69)90015-0","article-title":"Metabolic stability and epigenesis in randomly constructed genetic nets","volume":"22","author":"Kauffman","year":"1969","journal-title":"J. Theor. Biol"},{"key":"2023051506355209100_btx380-B5","doi-asserted-by":"crossref","first-page":"2.","DOI":"10.1186\/1752-0509-1-2","article-title":"Structural and functional analysis of cellular networks with CellNetAnalyzer","volume":"1","author":"Klamt","year":"2007","journal-title":"BMC Syst. Biol"},{"key":"2023051506355209100_btx380-B6","doi-asserted-by":"crossref","first-page":"814","DOI":"10.1016\/j.sigpro.2005.06.008","article-title":"Relationships between probabilistic Boolean networks and dynamic Bayesian networks as models of gene regulatory networks","volume":"86","author":"L\u00e4hdesm\u00e4ki","year":"2006","journal-title":"Signal Process"},{"key":"2023051506355209100_btx380-B7","doi-asserted-by":"crossref","first-page":"146","DOI":"10.1038\/nrg3885","article-title":"Quantitative and logic modelling of molecular and gene networks","volume":"16","author":"Le Nov\u00e8re","year":"2015","journal-title":"Nat. Rev. Genet"},{"key":"2023051506355209100_btx380-B8","first-page":"4791","article-title":"The yeast cell-cycle network is robustly designed","volume":"101","author":"Li","year":"2004","journal-title":"PNAS"},{"key":"2023051506355209100_btx380-B150","first-page":"45003","volume-title":"Phys. Biol","author":"MacNamara","year":"2012"},{"key":"2023051506355209100_btx380-B151","first-page":"593","volume-title":"Bioinformatics","author":"Mendoza","year":"1999"},{"key":"2023051506355209100_btx380-B9","doi-asserted-by":"crossref","first-page":"309","DOI":"10.1007\/978-3-319-45177-0_19","volume-title":"Computational Methods in Systems Biology","author":"Mizera","year":"2016"},{"key":"2023051506355209100_btx380-B10","doi-asserted-by":"crossref","first-page":"3216","DOI":"10.1021\/bi902202q","article-title":"Logic-based models for the analysis of cell signaling networks","volume":"49","author":"Morris","year":"2010","journal-title":"Biochemistry"},{"key":"2023051506355209100_btx380-B11","first-page":"mr7.","article-title":"Crowdsourcing network inference: the DREAM predictive signaling network challenge","volume":"4","author":"Prill","year":"2011","journal-title":"Sci. Signal"},{"key":"2023051506355209100_btx380-B12","doi-asserted-by":"crossref","first-page":"1923","DOI":"10.1093\/bioinformatics\/btp358","article-title":"Structural and practical identifiability analysis of partially observed dynamical models by exploiting the profile likelihood","volume":"25","author":"Raue","year":"2009","journal-title":"Bioinformatics"},{"key":"2023051506355209100_btx380-B13","doi-asserted-by":"crossref","first-page":"e163.","DOI":"10.1371\/journal.pcbi.0030163","article-title":"A logical model provides insights into T cell receptor signaling","volume":"3","author":"Saez-Rodriguez","year":"2007","journal-title":"PLoS Comput. Biol"},{"key":"2023051506355209100_btx380-B14","doi-asserted-by":"crossref","first-page":"e1000595.","DOI":"10.1371\/journal.pcbi.1000595","article-title":"ON\/OFF and beyond - a Boolean model of apoptosis","volume":"5","author":"Schlatter","year":"2009","journal-title":"PLoS Comput. Biol"},{"key":"2023051506355209100_btx380-B15","doi-asserted-by":"crossref","first-page":"133.","DOI":"10.1186\/1752-0509-6-133","article-title":"Cell- NOptR: a flexible toolkit to train protein signaling networks to data using multiple logic formalisms","volume":"6","author":"Terfve","year":"2012","journal-title":"BMC Syst. Biol"},{"key":"2023051506355209100_btx380-B16","doi-asserted-by":"crossref","first-page":"46.","DOI":"10.1186\/1478-811X-11-46","article-title":"Recent development and biomedical applications of probabilistic Boolean networks","volume":"11","author":"Trairatphisan","year":"2013","journal-title":"Cell Commun. Signal. CCS"},{"key":"2023051506355209100_btx380-B17","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0098001","article-title":"optPBN: an optimisation toolbox for probabilistic Boolean networks","volume":"9","author":"Trairatphisan","year":"2014","journal-title":"PLoS ONE"},{"key":"2023051506355209100_btx380-B18","doi-asserted-by":"crossref","first-page":"e0156223.","DOI":"10.1371\/journal.pone.0156223","article-title":"A probabilistic Boolean network approach for the analysis of cancer-specific signalling: PDGF signalling in GIST","volume":"11","author":"Trairatphisan","year":"2016","journal-title":"PLoS One"},{"key":"2023051506355209100_btx380-B19","doi-asserted-by":"crossref","first-page":"20130505","DOI":"10.1098\/rsif.2013.0505","article-title":"Reverse engineering and identification in systems biology: strategies, perspectives and challenges","volume":"11","author":"Villaverde","year":"2014","journal-title":"J. R. Soc. Interface"},{"key":"2023051506355209100_btx380-B20","first-page":"1","article-title":"An Interior algorithm for nonlinear optimization that combines line search and trust region steps","volume":"107","author":"Waltz","year":"2004","journal-title":"Math. Program"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/33\/21\/3431\/50315499\/bioinformatics_33_21_3431.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/33\/21\/3431\/50315499\/bioinformatics_33_21_3431.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,5,15]],"date-time":"2023-05-15T06:36:27Z","timestamp":1684132587000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/33\/21\/3431\/3897376"}},"subtitle":[],"editor":[{"given":"Bonnie","family":"Berger","sequence":"additional","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2017,6,29]]},"references-count":22,"journal-issue":{"issue":"21","published-print":{"date-parts":[[2017,11,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btx380","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2017,11,1]]},"published":{"date-parts":[[2017,6,29]]}}}