title: GESTODIFFERENT: a Cytoscape plugin for the generation and the identification of gene regulatory networks describing a stochastic cell differentiation process.
abstract: CONCLUSIONS
  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.
  
  
  BACKGROUND
  Freely available at http://bimib.disco.unimib.it/index.php/Retronet#GESTODifferent or at the Cytoscape App Store http://apps.cytoscape.org/.
authors.affiliation: Department of Informatics, Systems and Communication, University of Milan Bicocca, Viale Sarca 336, 20126, Milano, Italy. marco.antoniotti@unimib.it
authors.forename: Marco
authors.initials: M
authors.lastname: Antoniotti
authors.forename: Gary D
authors.initials: GD
authors.lastname: Bader
authors.forename: Giulio
authors.initials: G
authors.lastname: Caravagna
authors.forename: Silvia
authors.initials: S
authors.lastname: Crippa
authors.forename: Alex
authors.initials: A
authors.lastname: Graudenzi
authors.forename: Giancarlo
authors.initials: G
authors.lastname: Mauri
mesh_terms: D002454:Cell Differentiation / Q000235:genetics*; D019070:Cell Lineage; D053263:Gene Regulatory Networks; D008957:Models, Genetic; D012984:Software; D013269:Stochastic Processes