Giovanni Scardoni, PhD

                                research fellow at CBMC

 

giovanni.scardoni(at)gmail.com                       

Center for BioMedical Computing                       

University of Verona                       

Istituti biologici, blocco A                       

Strada le Grazie 8, 37134, Verona                       

Italy EU                       

 

Designed and developed software for biological network analysis

Interference 1.0  Cytoscape plug-in for virtual knock-out experiments on Biological networks, based on the centralities interference notion.

CentiScaPe 2.1  and CentiScaPe 2.0 for Cytoscape 3.0!. CentiScaPe 1.0, 1.1, 1.2 and 1.21 (for Cytoscape 2.8.x).  Cytoscape plug-in for network centralities.

PeSca 3.0 (Path Extraction by Smallest Cost Algorithm). Cytoscape plug-in for shortest paths extraction

Metabolica 1.0 Cytoscape plug-in for extracting network motifs.

     

    Publications

 

    Oral presentations

  • Protein network analysis with CentiScaPe and Interference plug-ins. Cytoscape retreat 2012, December 14, 2012, San Francisco (California).

  • Network analysis Cytoscape plugins.July 18, 2012. Ideker Lab, UCSD, La Jolla (California).

  • Protein network analysis with CentiScaPe and Interference plug-ins: the case of leukocyte integrin activation network. 20th Annual International Conference onIntelligent Systems for Molecular Biology (ISMB), Technlogy Track Session, July 17, Long Beach (California).

  • Identifying critical road network areas with node centralities interference and robustness. 3rd Workshop on Complex Networks, Comple-Net 2012. March 7, 2012, Melbourne (Florida).

  • Network centralities interference and robustness. Net-Works 2011, October 26-28, El Escorial, Madrid (Spain).

  • Biological networks analysis course of Algorithm and programming languages for Bioinformatics, Degree in Bioinformatics, University of Verona. June 6, 2011, Verona (Italy).

  • Computational analysis of biological networks”. Parc de Recerca Biomedica Barcelona (PRBB).February 18, 2011, Barcelona (Spain).

  • Computational analysis of biological networks”. COSBI, February 8, 2011, Trento (Italy).

  • Analyzing biological networks with CentiScaPe, Cytoscape retreat 2010, July 18, 2010, Ann Arbour (Michigan).

  • Biological networks analysis, course of Discrete biological models, (prof. Giuditta Franco, Degree in Bioinformatics, University of Verona. June 23, 2009, Verona (Italy).

  • Biological networks analysis, course of Infobiotics (prof. Giuditta Franco), Degree in biotechnologies, University of Verona. April 15, 2009, Verona (Italy).

  • Analyzing biological Pathways by Abstract Interpretation, workshop AIDA – Abstractinterpretation. February 17, 2006, Pisa (Italy).

     

    Posters

  • NetBio-SIG, Network Biology SIG: On the Analysis and Visualization of Networks in Biology.“Network centralities interference”. July 2011, Vienna.

  • Netsci2011, the international school and conference on network science   (http://www.netsci2011.net/). “Network centralities interference”. June 2011, Budapest.

  • Netsci2011, the international school and conference on network science  (http://www.netsci2011.net/). “A measure for network complexity”. June 2011, Budapest.

  • Netsci2010, the international school and conference on network science  (http://www.netsci2010.net/). “Biological network analysis with CentiScaPe”. May 2010, Boston.

     

    Schools and courses

  • Course in Biology, University of Padova, Italy, Faculty of agriculture. October 2011 – January 2012

  • 2nd International School of Advanced BioMedicine and BioInformatics on MolecularBioMedicine, Medical Genomics and BioInformatics. June 18-25, 2005, Pantelleria (Italy).

  • 1st Permanent European School in Bioinformatics (Biosapiens). July 7-13, 2004, Verona (Italy)

  • 2nd ESF Training Course on Molecular Interaction. July 13-16, 2004, Verona (Italy).

  • Course of computational methods for diagnostic: neural networks, genetics algorithms and fuzzylogics. March 10, 2006, Verona (Italy).

     

    Attended conferences

  • Netsci, the international school and conference on network science. Netsci2008, June 23-27, 2008,Norwich Research Park (UK). Netsci2009, June 29 – July 3, 2009, Venezia (Italy). Netsci2010, may 10-14, 2010 , Boston (Massachusetts). Netsci2011, June 8-10, 2011, Budapest (Hungary).

  • Cytoscape retreat 2007, November 6-9, 2007, Amsterdam (Netherlands). Cytoscape retreat 2010,Ann Arbour (Michigan).

  • Meeting on Abstract Interpretation Development and Applications (AIDA). February 17, 2006, Pisa (Italy).

  • 1st Meeting on Abstract Interpretation Development and Applications (AIDA). Final Meeting on Constraint-based Verification of Reactive Systems (CoVer). February 7, 2005. Verona.

  • 11th Static Analysis Symposium (SAS'04), August 26-28, Verona (Italy)..

  • 3rd Meeting on Constraint-based Verification of Reactive Systems (CoVer). June 18, Parma (Italy).

  • The 31st Annual ACM SIGPLAN _ SIGACT Symposium on Principles of Programming Languages (POPL'04). January 14-16, 2004. Venezia

  • Meeting on Constraint-based Verification of Reactive Systems (CoVer). September 25-26, 2003. Firenze (Italy).