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Yet, the topological and functional characterization of real GRNs is often still partial and an exhaustive picture of their functioning is missing.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Results<\/jats:title>\n                <jats:p>We here introduce <jats:sc>CABeRNET<\/jats:sc>, a Cytoscape app for the generation, simulation and analysis of Boolean models of GRNs, specifically focused on their augmentation when a only partial topological and functional characterization of the network is available. By generating large ensembles of networks in which user-defined entities and relations are added to the original core, <jats:sc>CABeRNET<\/jats:sc> allows to formulate hypotheses on the missing portions of real networks, as well to investigate their generic properties, in the spirit of complexity science.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Conclusions<\/jats:title>\n                <jats:p><jats:sc>CABeRNET<\/jats:sc> offers a series of innovative simulation and modeling functions and tools, including (but not being limited to) the dynamical characterization of the gene activation patterns ruling cell types and differentiation fates, and sophisticated robustness assessments, as in the case of gene knockouts. The integration within the widely used Cytoscape framework for the visualization and analysis of biological networks, makes <jats:sc>CABeRNET<\/jats:sc> a new essential instrument for both the bioinformatician and the computational biologist, as well as a computational support for the experimentalist. An example application concerning the analysis of an augmented T-helper cell GRN is provided.<\/jats:p>\n              <\/jats:sec>","DOI":"10.1186\/s12859-016-0914-z","type":"journal-article","created":{"date-parts":[[2016,2,4]],"date-time":"2016-02-04T13:06:29Z","timestamp":1454591189000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":13,"title":["CABeRNET: a Cytoscape app for augmented Boolean models of gene regulatory NETworks"],"prefix":"10.1186","volume":"17","author":[{"given":"Andrea","family":"Paroni","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alex","family":"Graudenzi","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Giulio","family":"Caravagna","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chiara","family":"Damiani","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Giancarlo","family":"Mauri","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Marco","family":"Antoniotti","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2016,2,4]]},"reference":[{"key":"914_CR1","doi-asserted-by":"crossref","DOI":"10.7551\/mitpress\/3087.001.0001","volume-title":"Foundations of Systems Biology","author":"H Kitano","year":"2001","unstructured":"Kitano H. 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