title: Cascade: a R package to study, predict and simulate the diffusion of a signal through a temporal gene network.
abstract: CONCLUSIONS
  Temporal gene interactions, in response to environmental stress, form a complex system that can be efficiently described using gene regulatory networks. They allow highlighting the more influential genes and spotting some targets for biological intervention experiments. Despite that many reverse engineering tools have been designed, the Cascade package is an integrated solution adding several new and original key features such as the ability to predict changes in gene expressions after a biological perturbation in the network and graphical outputs that allow monitoring the spread of a signal through the network.
  
  
  METHODS
  The R package Cascade is available online at http://www-math.u-strasbg.fr/genpred/spip.php?rubrique4.
authors.affiliation: INSERM UMR S_1109, Labex Transplantex, FMTS, Hôpitaux and Faculté de Médecine, Université de Strasbourg, 67085 Strasbourg Cedex and IRMA, CNRS UMR 7501, Labex IRMIA, Université de Strasbourg, 67084 Strasbourg Cedex, France.
authors.forename: Nicolas
authors.initials: N
authors.lastname: Jung
authors.forename: Frédéric
authors.initials: F
authors.lastname: Bertrand
authors.forename: Seiamak
authors.initials: S
authors.lastname: Bahram
authors.forename: Laurent
authors.initials: L
authors.lastname: Vallat
authors.forename: Myriam
authors.initials: M
authors.lastname: Maumy-Bertrand
mesh_terms: D000818:Animals; D002478:Cells, Cultured; D019295:Computational Biology; D003196:Computer Graphics; D003198:Computer Simulation; D020869:Gene Expression Profiling; D053263:Gene Regulatory Networks; D008214:Lymphocytes / Q000276:immunology* / Q000378:metabolism; D051379:Mice; D015398:Signal Transduction / Q000235:genetics*; D012984:Software