{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,17]],"date-time":"2026-08-17T23:14:34Z","timestamp":1787008474934,"version":"build-2736575974"},"reference-count":6,"publisher":"Oxford University Press (OUP)","issue":"4","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2013,2,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Summary: The characterization of the complex phenomenon of cell differentiation is a key goal of both systems and computational biology. GeStoDifferent is a Cytoscape plugin aimed at the generation and the identification of gene regulatory networks (GRNs) describing an arbitrary stochastic cell differentiation process. The (dynamical) model adopted to describe general GRNs is that of noisy random Boolean networks (NRBNs), with a specific focus on their emergent dynamical behavior. GeStoDifferent explores the space of GRNs by filtering the NRBN instances inconsistent with a stochastic lineage differentiation tree representing the cell lineages that can be obtained by following the fate of a stem cell descendant. Matched networks can then be analyzed by Cytoscape network analysis algorithms or, for instance, used to define (multiscale) models of cellular dynamics.<\/jats:p>\n                  <jats:p>Availability: Freely available at http:\/\/bimib.disco.unimib.it\/index.php\/Retronet#GESTODifferent or at the Cytoscape App Store http:\/\/apps.cytoscape.org\/.<\/jats:p>\n                  <jats:p>Contact: \u00a0marco.antoniotti@unimib.it<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts726","type":"journal-article","created":{"date-parts":[[2013,1,4]],"date-time":"2013-01-04T20:14:19Z","timestamp":1357330459000},"page":"513-514","source":"Crossref","is-referenced-by-count":7,"title":["G\n                    <scp>e<\/scp>\n                    S\n                    <scp>to<\/scp>\n                    D\n                    <scp>ifferent<\/scp>\n                    : a Cytoscape plugin for the generation and the identification of gene regulatory networks describing a stochastic cell differentiation process"],"prefix":"10.1093","volume":"29","author":[{"given":"Marco","family":"Antoniotti","sequence":"first","affiliation":[{"name":"1 Department of Informatics, Systems and Communication, University of Milan Bicocca, Viale Sarca 336, 20126, Milano, Italy and 2Bader Lab, The Donnelly Centre, University of Toronto, 160 College Street, M5S 3E1, Toronto, Ontario, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gary D.","family":"Bader","sequence":"additional","affiliation":[{"name":"1 Department of Informatics, Systems and Communication, University of Milan Bicocca, Viale Sarca 336, 20126, Milano, Italy and 2Bader Lab, The Donnelly Centre, University of Toronto, 160 College Street, M5S 3E1, Toronto, Ontario, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Giulio","family":"Caravagna","sequence":"additional","affiliation":[{"name":"1 Department of Informatics, Systems and Communication, University of Milan Bicocca, Viale Sarca 336, 20126, Milano, Italy and 2Bader Lab, The Donnelly Centre, University of Toronto, 160 College Street, M5S 3E1, Toronto, Ontario, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Silvia","family":"Crippa","sequence":"additional","affiliation":[{"name":"1 Department of Informatics, Systems and Communication, University of Milan Bicocca, Viale Sarca 336, 20126, Milano, Italy and 2Bader Lab, The Donnelly Centre, University of Toronto, 160 College Street, M5S 3E1, Toronto, Ontario, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alex","family":"Graudenzi","sequence":"additional","affiliation":[{"name":"1 Department of Informatics, Systems and Communication, University of Milan Bicocca, Viale Sarca 336, 20126, Milano, Italy and 2Bader Lab, The Donnelly Centre, University of Toronto, 160 College Street, M5S 3E1, Toronto, Ontario, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Giancarlo","family":"Mauri","sequence":"additional","affiliation":[{"name":"1 Department of Informatics, Systems and Communication, University of Milan Bicocca, Viale Sarca 336, 20126, Milano, Italy and 2Bader Lab, The Donnelly Centre, University of Toronto, 160 College Street, M5S 3E1, Toronto, Ontario, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2013,1,3]]},"reference":[{"key":"2023012810245232400_bts726-B1","article-title":"A multiscale model of intestinal crypts dynamics","volume-title":"Proceedings of the Italian Workshop on Artificial Life and Evolutionary Computation, WIVACE 2012","author":"Graudenzi","year":"2012"},{"key":"2023012810245232400_bts726-B2","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0002922","article-title":"Noise driven stem cell and progenitor population dynamics","volume":"3","author":"Hoffman","year":"2008","journal-title":"PLoS ONE"},{"key":"2023012810245232400_bts726-B3","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. 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