From BIMIB

Alex Graudenzi

Contents 1 Position 2 Research Area 3 Focus Areas  4 Short Bio 5 Publications (last update: November 2011) 5.1 Papers on International Journals 5.2 Papers on Italian Journals 5.3 Lecture Notes in Computer Science 5.4 Conference Proceedings (English) 5.5 Technical reports (English) 6 Address

Position

Post-doc research associate

Research Area

Complex systems biology

Focus Areas 

Dynamical and generic properties of biological networks; models of gene regulatory networks; models of catalytic reaction networks.

Short Bio

Post-doc research associate at the Bioinformatics, Natural Calculus and Systems Biology of the Department of Informatics, Systems and Communications of the University of Milan - Bicocca (BIMIB), from May, 1st, 2011.

Post-doc research associate at the European Centre for Living Technology of the University Ca' Foscari of Venice from March, 4th, 2010 to March, 3rd, 2011. 

Ph. D. in "Multiscale Modelling, Computational Simulation and Characterization in Material and Life Sciences" at the University of Modena and Reggio Emilia in March 2010, with the thesis “Criticality and Perturbations in Boolean Models of Gene Regulatory Networks”.

Master of Science (Italian Laurea Magistrale) in April 2006 in "Economy and Management of Networks and Innovations" at the University of Modena and Reggio Emilia, with first class honors (cum laude).

Author of several publications on important international journals and international conference proceedings.

Responsible lecturer for a module of the course of “Modeling and Simulation” belonging to the Master of Science in Economics and Management of Networks and Innovation at the University of Modena and Reggio Emilia.

Editor of: M. Villani, A. Graudenzi, A. Barbieri (2009): Workshop Proceedings of the XI Conference of the Italian Association for Artificial Intelligence, Reggio Emilia, 9-12/12/2009. ISBN: 978-88-903581-1-1.

At the Department of Social, Cognitive and Quantitative Sciences of the University of Modena and Reggio Emilia his research interests were mainly focused on the study of models of complex biological systems, with particular regard to models of gene regulatory networks, through the application of the concepts and the methods provided by the science of complex systems.

At the European Centre for Living Technology of the University Ca’ Foscari of Venice his efforts were devoted toward the analysis and the characterization of models of catalytic reaction networks, within the broader theme of the origin of life.

At BIMIB his attention will be directed to the modeling and the simulation of the human intestinal crypts in conjunction with the development of colon-rectal cancer (CRC), under the RETRONET project funded by the Lombardy Region (Regione Lombardia) grant ASTIL (regional decree 1669 of June 18 2010) and by the Università degli Studi di Milano - Bicocca.

Publications (last update: November 2011)

Papers on International Journals

• De Matteis, G., Graudenzi, A., Antoniotti, M., (2011): A review of spatial computational models for multi-cellular systems, with regard to intestinal crypts and colorectal cancer development. Submitted to the Journal of Mathematical Biology.
• Filisetti, A., Graudenzi, A., Serra, R., Villani, M., Fuchslin, R. M., Packard, N., Kauffman, S. A., Poli, I., (2011): A stochastic model of autocatalytic reaction networks. Accepted for the publication on Theory in Biosciences.
• Filisetti, A., Graudenzi, A., Serra, R., Villani, M., De Lucrezia, D., Fuchslin, R. M., Kauffman, S. A., Packard, N., Poli, I., (2011): A stochastic model of the emergence of autocatalytic cycles. Journal of Systems Chemistry, 2:2 doi:10.1186/1759-2208-2-2.
• Graudenzi, A., Serra, R., Villani, M., Colacci, A., Kauffman, S.A., (2011): Robustness analysis of a Boolean model of gene regulatory network with memory. Journal of Computational Biology, Volume 18, Number 4, Pp. 559–577.
• Graudenzi, A., Serra, R., Villani, M., Damiani, C., Colacci, A., Kauffman, S.A., (2011): Dynamical properties of a Boolean model of gene regulatory network with memory. Journal of Computational Biology. Ahead of print.
• Serra, R., Villani, M., Graudenzi, A., Colacci A., Kauffman S.A., (2008): The simulation of gene knock-out in scale-free random Boolean models of genetic networks. Networks and Heterogeneous Media, Vol. 3, n. 2: 333-343.
• Serra, R., Villani. M., Graudenzi, A., Kauffman, S.A., (2007): Why a simple model of genetic regulatory networks describes the distribution of avalanches in gene expression data. J. Theor. Biol. 249 : 449-460.

Papers on Italian Journals

• Serra, R., Villani, M., Damiani, C., Graudenzi, A., Colacci, A., (2008): Comunicazione cellulare, livelli e strutture ordinate. Sistemi Intelligenti, Anno XX, n. 2 / agosto 2008: 209-220.

Lecture Notes in Computer Science

• Serra, R., Villani, M., Damiani, C., Graudenzi A., Colacci A. (2008): The diffusion of perturbations in a model of coupled random Boolean networks, Lecture Notes in Computer Science, Springer Berlin/Heidelberg, Vol. 5191: 315-322, doi: 10.1007/978-3-540-79992-4_40.

Conference Proceedings (English)

• Graudenzi, A., Caravagna, G., De Matteis, G., Antoniotti, M. (2012): A multiscale model of intestinal crypts dynamics. Submitted to Wivace 2012, Workshop Italiano di Vita Artificiale e Computazione Evolutiva, Parma, 20-21 Febbraio 2012.
• Filisetti, A., Graudenzi, A. (2012): The influence of different kinetic rates on the dynamics of a simple model of catalytic reaction network. Submitted to Wivace 2012, Workshop Italiano di Vita Artificiale e Computazione Evolutiva, Parma, 20-21 Febbraio 2012.
• Graudenzi, A., De Matteis, G., Alhazov, A., Caravagna, G., Mauri, G., Antoniotti, M. (2011): Multiscale multicellular modeling for the description of intestinal crypt dynamics and the colorectal cancer development (long abstract and poster). Accepted for the publication on the proceedings of NETTAB 2011 Workshop focused on Clinical Bioinformatics. October 12-14, 2011, Pavia, Italy.
• Filisetti, A., Graudenzi, A., Serra, R., Villani, M., De Lucrezia, D., Poli, I. (2011): The role of energy in a stochastic model of the emergence of autocatalytic sets. Accepted for the publication on the proceedings of ECAL 2011, European Conference on Artificial Life.
• Filisetti, A., Graudenzi, A., Serra, R., Villani, M., De Lucrezia, D., Poli, I. (2011): The influence of the energetic constraints in a stochastic model of catalytic reaction networks (abstract). Accepted for the presentation at ECCS 2011, European Conference on Complex Systems.
• Filisetti, A., Serra, R., Villani, M., Graudenzi, A., Fuchslin, R. M., Poli, I., (2010): The influence of the residence time on the dynamics of catalytic reaction networks of molecules. In Apolloni, B., Bassis, S., Esposito, A., Morabito, C. F., (eds.) Neural Nets WIRN10 - Proceedings of the 20th Italian Workshop on Neural Nets. Frontiers in Artificial Intelligence and Applications, Volume 226, 2011: 243 – 251; ISBN: 978-1-60750-691-1.
• Damiani, C., Graudenzi, A., Serra, R., Villani, M., Colacci, A., (2009): On the fate of perturbations in critical random Boolean networks. Proceedings of the European Conference on Complex Systems, ECCS 09; ISBN:0-9554123-1-5.
• Damiani, C., Graudenzi, A., Villani, M. (2009): How critical random Boolean networks may be affected by the interaction with others. In Serra, R., Villani, M., Poli, I., (eds.): Artificial Life and Evolutionary Computation - Proceedings of Wivace 08, World Scientific: 259-270; ISBN:978-981-4287-44-9.
• Graudenzi, A., Serra. R. (2009): A new model of genetic network: the Gene Protein Boolean Network. In Serra, R., Villani, M., Poli, I., (eds.): Artificial Life and Evolutionary Computation - Proceedings of Wivace 08, World Scientific: 283 – 291 ; ISBN:978-981-4287-44-9.
• Graudenzi, A., Serra, R., Villani, M., Damiani, C., Colacci, A, Kauffman, S.A., (2009): Timing of molecular processes in a synchronous Boolean model of genetic regulatory network. Proceedings of the European Conference on Complex Systems, ECCS 09: 87-97; ISBN:0-9554123-1-5.
• Serra, R., Graudenzi, A., Villani, M. (2009): Genetic regulatory networks and neural networks. In Apolloni, B., Bassis, S., Marinaro, M. (eds.): New Directions in Neural Networks - 18th Italian Workshop on Neural Networks: WIRN 2008. Frontiers in Artificial Intelligence and Applications, Vol. 193. KBIES book series, IOS Press, Amsterdam: 109-117; ISBN:978-1-58603-984-4.
• Serra, R., Villani, M., Damiani, C., Graudenzi, A., Ingrami, P. & Colacci, A. (2009): Investigating cell criticality. In Minati, G., Abram, M., Pessa, E., (eds.): Processes of emergence of systems and systemic properties. Towards a general theory of emergence. World Scientific: 649-657; ISBN:978-981-279-346-1.
• Serra, R., Villani, M., Damiani, C., Graudenzi, A., Colacci, A. & Kauffamn, S.A. (2007): Interacting random Boolean networks. In Jost, J., Helbing D., (eds.): Proceedings of ECCS07: European Conference on Complex Systems. CD-Rom, paper #35.
• Serra, R., Villani, M., Graudenzi, A., Colacci, A. & Kauffman, S.A. (2007): The influence of the topology of regulatory networks on the distribution of avalanches in gene expression data. In Jost, J., Helbing D., (eds.): Proceedings of ECCS07: European Conference on Complex Systems. CD-Rom, paper #115.
• Villani, M., Serra, R., Graudenzi, A. & Kauffman, S.A. (2006): On the distribution of small avalanches in random Boolean networks. In Ruusovori, P., Manninen, T., Huttunen, H., Linne, M-L., Yli-Harja, O., (eds.): Proceedings of the 4th Workshop on computational and systems biology. Tampere (Finland): TICSP: 93-96; ISBN:952-15-1619-4.

Technical reports (English)

• De Matteis, G., Graudenzi, A., Antoniotti, M., (2011): Reviewing the existing computational models of intestinal crypts and colorectal cancer. Submitted to Quaderni del Dipartimento, Dipartimento di Informatica, Sistemistica e Comunicazione, Università degli Studi di Milano Bicocca.
  

Address

Department of Informatics, Systems and Communication

University of Milan Bicocca

Building U14 - Room 1002

Viale Sarca 336 I-20126 Milan (MI) Italy