Contact
email: andrea (dot) degasperi [at] ucd (dot) ie
office: Conway Institute, University College Dublin, Belfield, Dublin 4, Dublin, Ireland
previously at: School of Computing Science, University of Glasgow
office: Conway Institute, University College Dublin, Belfield, Dublin 4, Dublin, Ireland
previously at: School of Computing Science, University of Glasgow
Links
Interests
Modelling and analysis of biochemical interactions with formal languages, process algebras, rewriting rules and Petri-Nets. Multi-scale modelling of biological systems. Simulations with ordinary/partial differential equations and continuous time Markov chains. Sensitivity analysis of biochemical models. Probabilistic models and optimization algorithms.
Profile
I was born in Trento, Italy, and I obtained my BSc in Computer Science in 2005. After that I joined the double degree programme European Master in Informatics (EuMI), Life Science specialism, earning in Autumn 2007 both the Laurea Specialistica in Informatica from the University of Trento (with full marks and honour) and the Master in Informatics with Distinction from the University of Edinburgh. I earned my Ph.D. at the School of Computing Science of the University of Glasgow in September 2011. I'm currently a Post Doctoral researcher at the Systems Biology Ireland, Conway Institute, University College Dublin.
Attended/Planning to Attend Conferences and Workshops
- The 9th International Conference on Computational Methods in Systems Biology (CMSB 2011). September 21st - 23rd 2011, Paris, France.
- SICSA Workshop on Systems Medicine. May 11th 2011, Dundee, Scotland.
- SICSA Workshop on Probabilistic Modelling, Model-Checking and Planning. December 13th 2010, Glasgow, Scotland.
- The 11th International Conference on Systems Biology (ICSB2010). October 10th - 15th 2010, Edinburgh, Scotland.
- EPSRC Multi-scale modelling of Biological Systems. July 5th - 6th 2010, Stirling, Scotland.
- 43rd Annual Meeting for the Japanese Society of Developmental Biologists (JSDB 2010). June 21st - 23rd 2010, Kyoto, Japan.
- 1st International Workshop on Interactions between Computer Science and Biology (CS2Bio2010). June 10th 2010, Amsterdam, Netherlands.
- SICSA Workshop on Probabilistic Modelling, Model-Checking and Planning. March 17th 2010, Glasgow, Scotland.
- 8th Workshop on Process Algebra and Stochastically Timed Activities (PASTA 2009). August 26th - 27th 2009, Edinburgh, Scotland.
- Emerging Modelling Methodologies in Medicine and Biology Workshop. July 20th - 24th 2009, Edinburgh, Scotland.
- Bigraphs: a model for mobile agents. May 13th - 14th 2009, Edinburgh, Scotland.
- Formal Methods in Molecular Biology Dagstuhl Seminar. February 22nd - 27th 2009, Schloss Dagstuhl - Leibniz-Center for Informatics, Wadern, Germany.
- 8th International Workshop on Automated Verification of Critical Systems (AVoCS 2008). September 30th - October 1st 2008, Glasgow, Scotland.
- British Computer Society: Visions of Computer Science 2008 (BCS: VCS 2008). September 22nd - 24th 2008, Imperial College, London, United Kingdom.
- 7th Workshop on Process Algebra and Stochastically Timed Activities (PASTA 2008). July 30th - 31st 2008, Edinburgh, Scotland.
- From Biology to Concurrency and Back 2008 (FBTC 2008). A Satellite Workshop of ICALP 2008. July 12th 2008, Reykjavik, Iceland.
- SICSA Workshop on Systems Medicine. May 11th 2011, Dundee, Scotland.
- SICSA Workshop on Probabilistic Modelling, Model-Checking and Planning. December 13th 2010, Glasgow, Scotland.
- The 11th International Conference on Systems Biology (ICSB2010). October 10th - 15th 2010, Edinburgh, Scotland.
- EPSRC Multi-scale modelling of Biological Systems. July 5th - 6th 2010, Stirling, Scotland.
- 43rd Annual Meeting for the Japanese Society of Developmental Biologists (JSDB 2010). June 21st - 23rd 2010, Kyoto, Japan.
- 1st International Workshop on Interactions between Computer Science and Biology (CS2Bio2010). June 10th 2010, Amsterdam, Netherlands.
- SICSA Workshop on Probabilistic Modelling, Model-Checking and Planning. March 17th 2010, Glasgow, Scotland.
- 8th Workshop on Process Algebra and Stochastically Timed Activities (PASTA 2009). August 26th - 27th 2009, Edinburgh, Scotland.
- Emerging Modelling Methodologies in Medicine and Biology Workshop. July 20th - 24th 2009, Edinburgh, Scotland.
- Bigraphs: a model for mobile agents. May 13th - 14th 2009, Edinburgh, Scotland.
- Formal Methods in Molecular Biology Dagstuhl Seminar. February 22nd - 27th 2009, Schloss Dagstuhl - Leibniz-Center for Informatics, Wadern, Germany.
- 8th International Workshop on Automated Verification of Critical Systems (AVoCS 2008). September 30th - October 1st 2008, Glasgow, Scotland.
- British Computer Society: Visions of Computer Science 2008 (BCS: VCS 2008). September 22nd - 24th 2008, Imperial College, London, United Kingdom.
- 7th Workshop on Process Algebra and Stochastically Timed Activities (PASTA 2008). July 30th - 31st 2008, Edinburgh, Scotland.
- From Biology to Concurrency and Back 2008 (FBTC 2008). A Satellite Workshop of ICALP 2008. July 12th 2008, Reykjavik, Iceland.
Publications
Book Chapters:
- A. Degasperi and S. Gilmore. Sensitivity Analysis of Stochastic Models of Bistable Biochemical Reactions. In: M. Bernardo, P. Degano and G. Zavattaro eds, Formal Methods in Computational Systems Biology. SFM 2008, LNCS 5016, pages 1-20, Springer, 2008.
Journals:
- F. Ciocchetta, A. Degasperi, J. Heath, J. Hillston. Modelling and Analysis of the NF-kappaB pathway in Bio-PEPA. Transactions on Computational Systems Biology XII, LNBI 5945, pages 229-262, Springer, 2010.
Conferences/Workshops:
- A. Degasperi and M. Calder. Multi-Scale Modelling of Biological Systems in Process Algebra with Multi-Way Synchronisation. CMSB 2011, to appear in ACM Digital Library, 2011.
- A. Degasperi and M. Calder. Process Algebra with Hooks for Models of Pattern Formation. CS2Bio2010, ENTCS 268, pages 31-47, Elsevier, 2010.
- A. Degasperi and M. Calder. Relating PDEs in Cylindrical Coordinates and CTMCs with Levels of Concentration. CS2Bio2010, ENTCS 268, pages 49-59, Elsevier, 2010.
- A. Degasperi and M. Calder. On the Formalisation of Gradient Diffusion Models of Biological Systems. PASTA Workshop 2009, unreviewed, 2009. [pdf]
- O. Akman, F. Ciocchetta, A. Degasperi and M.L. Guerriero. Modelling Biological Clocks with Bio-PEPA: Stochasticity and Robustness for the Neurospora Crassa Circadian Network. CMSB2009, LNCS 5688, pages 52-67, Springer, 2009.
- F. Ciocchetta, A. Degasperi, J. Heath, J. Hillston. Modelling and Analysis of the NF-kappaB Pathway in Bio-PEPA. In R. Breitling, D.R. Gilbert, M. Heiner and C. Priami eds. Formal Methods in Molecular Biology. Number 09091 in Dagstuhl Seminar Proceedings, Dagstuhl, Germany, Schloss Dagstuhl ~ Leibniz-Zentrum fuer Informatik, Germany, unreviewed, 2009.
- F. Ciocchetta, A. Degasperi, J. Hillston, M. Calder. Some investigations concerning the CTMC and the ODE model derived from Bio-PEPA. FBTC 2008, ENTCS 229(1), pages 145-163, Elsevier, 2009.
Technical Reports:- A. Degasperi and M. Calder. Process Algebra with Hooks for Models of Pattern Formation. CS2Bio2010, ENTCS 268, pages 31-47, Elsevier, 2010.
- A. Degasperi and M. Calder. Relating PDEs in Cylindrical Coordinates and CTMCs with Levels of Concentration. CS2Bio2010, ENTCS 268, pages 49-59, Elsevier, 2010.
- A. Degasperi and M. Calder. On the Formalisation of Gradient Diffusion Models of Biological Systems. PASTA Workshop 2009, unreviewed, 2009. [pdf]
- O. Akman, F. Ciocchetta, A. Degasperi and M.L. Guerriero. Modelling Biological Clocks with Bio-PEPA: Stochasticity and Robustness for the Neurospora Crassa Circadian Network. CMSB2009, LNCS 5688, pages 52-67, Springer, 2009.
- F. Ciocchetta, A. Degasperi, J. Heath, J. Hillston. Modelling and Analysis of the NF-kappaB Pathway in Bio-PEPA. In R. Breitling, D.R. Gilbert, M. Heiner and C. Priami eds. Formal Methods in Molecular Biology. Number 09091 in Dagstuhl Seminar Proceedings, Dagstuhl, Germany, Schloss Dagstuhl ~ Leibniz-Zentrum fuer Informatik, Germany, unreviewed, 2009.
- F. Ciocchetta, A. Degasperi, J. Hillston, M. Calder. Some investigations concerning the CTMC and the ODE model derived from Bio-PEPA. FBTC 2008, ENTCS 229(1), pages 145-163, Elsevier, 2009.
- A. Degasperi and M. Calder. Process Algebra with Hooks for Models of Pattern Formation. University of Glasgow, Department of Computing Science Technical Report, 2010.
Posters:
- A. Degasperi and M. Calder. Multi-Scale Modelling of Biological Systems in Process Algebra. Presented at SICSA Workshop on Systems Medicine. May 11th 2011, Dundee, Scotland.
- A. Degasperi and M. Calder. Relating Reaction-Diffusion Models at Different Levels of Abstraction in Process Algebra. Presented at ICSB2010, Edinburgh, October 11th 2010.
- A. Degasperi, C. Delles, A. Dominiczak and M. Calder. Theoretical Computer Science for Improving Mathematical Modelling of Reactive Oxygen Species. Presented at BHF GCRC Site Visit, December 1st 2008.
- A. Degasperi and M. Calder. Relating Reaction-Diffusion Models at Different Levels of Abstraction in Process Algebra. Presented at ICSB2010, Edinburgh, October 11th 2010.
- A. Degasperi, C. Delles, A. Dominiczak and M. Calder. Theoretical Computer Science for Improving Mathematical Modelling of Reactive Oxygen Species. Presented at BHF GCRC Site Visit, December 1st 2008.
Reviewer
Visiting
- Jane Hillston and Federica Ciocchetta at the University of Edinburgh, Scotland. Every Friday, from January 16th to April 24th 2009.
Tutoring
- 2009/10, tutoring CS1P, first year Computing Science Course at the University of Glasgow.
- 2008/09, tutoring CS1P and CS1Q, first year Computing Science Courses at the University of Glasgow.
- 2008/09, tutoring CS1P and CS1Q, first year Computing Science Courses at the University of Glasgow.
Sponsors
- 2007-2011 Lord Kelvin / Adam Smith Scholarship Ph.D. Scholarship, University of Glasgow.
- 2006-2007 Scholarship for the European Master in Informatics (EuMI) awarded by the University of Trento (Italy).
- 2006-2007 Scholarship for the European Master in Informatics (EuMI) awarded by the University of Trento (Italy).
Curriculum Vitae