Computer science is no more about computers than astronomy is about telescopes.

Edsger W. Dijkstra

Contact Informations
  • Email: bonzanni No more spam for me, Thanks.few.vu.nl
  • Tel: +31 20 598 3714
  • Room: P1.20
  • Vrije Universiteit Amsterdam
  • De Boelelaan 1081a,
  • 1081 HV Amsterdam
  • The Netherlands
Short Biography

I was born on December 15th 1980 in Ponte San Pietro (Italy). I obtained a M.Sc. degree in Computer Science from the University of Milano-Bicocca in March 2007. Currently I'm a PhD student at Vrije Universiteit Amsterdam under the supervision of Wan Fokkink, Jaap Heringa, and Anton Feenstra.

Research Interests
Executable Biology

The last decade has seen a rapid and successful development in the collaboration between biologists and computer scientists in the area of systems biology and bioinformatics.

Executable biology focuses on the design of executable computer algorithms that mimic biological phenomena and suggests the integration of formal models and algorithmic approaches into biological research.

Current Projects
Cell Behaviour Analysis with Formal, High-Performance Verification Techniques

The goal of the project is to describe biological cells, compartments (organelles) and molecules (e.g., DNA and proteins) by formal interaction patterns/models. Using the formal models, the aim will be to derive fundamentally new insights in cellular behaviour that go beyond the current formalisations in terms of ordinary differential equations. I share this project with another PhD student, Elżbieta Krępska. You can find detailed informations about the project here.

ENFIN: Workpackage 6, Systems-level modeling

ENFIN stands for Experimental Network for Functional INtegration. The ENFIN project is funded by the European Commission within its FP6 Programme, under the thematic area "Life sciences, genomics and biotechnology for health", contract number LSHG-CT-2005-518254. The workpackage 6 focuses on the integration of diverse experimental data into models of complex cellular processes that allow some level of testable predictions of the cell behavior under variable conditions, or in response to a stimulus. You can find detailed informations about the project here.

Publications

  • N. Bonzanni, N. Zhang, S. G. Oliver, and J. Fisher. The role of proteosome-mediated proteolysis in modulating potentially harmful transcription factor activity in Saccharomyces cerevisiae. Bioinformatics 27(13): 283-287, ISMB/ECCB (2011)

  • N. Bonzanni, K. A. Feenstra, W. Fokkink, and E. Krępska. What Can Formal Methods Bring to Systems Biology? FM 2009: Formal Methods, Second World Congress, Eindhoven, The Netherlands, November 2-6, 2009. Proceedings., Lecture Notes in Computer Science 5850

  • N. Bonzanni, E. Krępska, K. A. Feenstra, W. Fokkink, T. Kielmann, H. Bal, and J. Heringa. Executing Multicellular Differentiation: Quantitative Predictive Modelling of C. elegans Vulval Development. Bioinformatics 25(16): 2049-2056 (2009)

  • E. Krępska, N. Bonzanni, K. A. Feenstra, W. Fokkink, T. Kielmann, H. E. Bal, and J. Heringa. Design Issues for Qualitative Modelling of Biological Cells with Petri Nets. First International Workshop on Formal Methods in Systems Biology (FMSB 2008), Cambridge, UK, June 4-5, 2008. Proceedings, Lecture Notes in Computer Science 5054, pp. 48-62

  • L. Bernardinello, N. Bonzanni, M. Mascheroni, and L. Pomello. Modeling symport/antiport P systems with a class of hierarchical Petri nets. 8th International Workshop on Membrane Computing (WMC 2007), Thessaloniki, Greece, June 25-28, 2007. Revised Selected and Invited Papers, Lecture Notes in Computer Science 4860, pp. 124-137

Personal Stuff and Amenities
Feedback