title: A Graph Based Framework to Model Virus Integration Sites.
abstract: With next generation sequencing thousands of virus and viral vector integration genome targets are now under investigation to uncover specific integration preferences and to define clusters of integration, termed common integration sites (CIS), that may allow to assess gene therapy safety or to detect disease related genomic features such as oncogenes. Here, we addressed the challenge to: 1) define the notion of CIS on graph models, 2) demonstrate that the structure of CIS enters in the category of scale-free networks and 3) show that our network approach analyzes CIS dynamically in an integrated systems biology framework using the Retroviral Transposon Tagged Cancer Gene Database (RTCGD) as a testing dataset.
authors.affiliation: Department of Translational Oncology, National Center for Tumor Diseases and German Cancer Research Center, Im Neuenheimer Feld 581, 69120 Heidelberg, Germany.
authors.forename: Raffaele
authors.initials: R
authors.lastname: Fronza
authors.affiliation: Department of Translational Oncology, National Center for Tumor Diseases and German Cancer Research Center, Im Neuenheimer Feld 581, 69120 Heidelberg, Germany; Department of Control and Computer Engineering, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Torino, Italy.
authors.forename: Alessandro
authors.initials: A
authors.lastname: Vasciaveo
authors.affiliation: Department of Control and Computer Engineering, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Torino, Italy.
authors.forename: Alfredo
authors.initials: A
authors.lastname: Benso
authors.affiliation: Department of Translational Oncology, National Center for Tumor Diseases and German Cancer Research Center, Im Neuenheimer Feld 581, 69120 Heidelberg, Germany.
authors.forename: Manfred
authors.initials: M
authors.lastname: Schmidt
keywords: Gene therapy; Genomics; Insertional mutagenesis; Systems biology