Recent and ongoing activities

• The Spider Calculus: Computing in Active Graphs. [bib] [pdf]
  Benjamin C. Pierce, Alessandro Romanel, Daniel Wagner.
• Estimating the divisibility of complex biological networks by sparseness indices.
  Tommaso Mazza, Alessandro Romanel, Ferenc Jordán.
  Briefings in Bioinformatics. To appear.
• Programming Biology in BlenX.
  Lorenzo Dematté, Roberto Larcher, Alida Palmisano, Corrado Priami, Alessandro Romanel.
  In Systems Biology for Signaling Networks, © Springer. To appear.

Book Chapters

• The BlenX Language: A Tutorial. [doi] [bib] [pdf]
  Lorenzo Dematté, Corrado Priami, Alessandro Romanel.
  In SFM 2008, LNCS 5016:313-365, © Springer, 2008.
• Simple Methods for Peak and Valley Detection in Time Series Microarray Data. [doi] [bib] [pdf]
  Andrea Sboner, Alessandro Romanel, Andrea Malossini, Federica Ciocchetta, Francesca Demichelis, Ivano Azzini, Enrico Blanzieri, Rossana Dell'Anna.
  In Methods of Microarray Data Analysis V, © Springer, 2006.

International Journals

• Modelling self-assembly in BlenX. [doi] [pdf]
  Roberto Larcher, Corrado Priami, Alessandro Romanel.
  Transactions on Computational Systems Biology XII, LNCS 5945:163-198, © Springer, 2010.
• On the Computational Power of BlenX. [doi] [bib] [pdf]
  Alessandro Romanel, Corrado Priami.
  Theoretical Computer Science 411(2):542-565, Elsevier, 2010.
• Evolving BlenX programs to simulate the evolution of biological networks. [doi] [bib] [pdf]
  Lorenzo Dematté, Corrado Priami, Alessandro Romanel, Orkun Soyer.
  Theoretical Computer Science 408(1):83-96, Elsevier, 2008.
• The Beta Workbench: a computational tool to study the dynamics of biological systems. [doi] [bib]
  Lorenzo Dematté, Corrado Priami, Alessandro Romanel.
  Briefings in Bioinformatics 9(5):437-449, Oxford Journals, 2008.
• On the Decidability and Complexity of the Structural Congruence for Beta-binders. [doi] [bib] [pdf]
  Alessandro Romanel, Corrado Priami.
  Theoretical Computer Science 404(1-2):156-169, Elsevier, 2008.
• Modelling and simulation of biological processes in BlenX. [doi] [bib]
  Lorenzo Dematté, Corrado Priami, Alessandro Romanel.
  SIGMETRICS Performance Evaluation Review 35:32-39, ACM, 2008.

International Conferences and Workshops

• Towards a process calculi approach to study the evolution of biological networks. [url] [bib] [pdf]
  Alessandro Romanel.
  In Proceedings of 8th Workshop on Process Algebra and Stochastically Timed Activities (PASTA), 2009
• BlenX Static and Dynamic Semantics.[doi] [bib] [pdf]
  Corrado Priami, Paola Quaglia, Alessandro Romanel.
  In Proceedings of 20th International Conference on Concurrency Theory (CONCUR), LNCS 5710:37-52, © Springer, 2009.
• Exploiting non-Markovian Bio-Processes.[doi] [bib] [pdf]
  Ivan Mura, Davide Prandi, Corrado Priami, Alessandro Romanel.
  In Proceedings of 7th Workshop on Quantitative Aspects of Programming Languages (QAPL), ENTCS 253(3):83-98, Elsevier, 2009.
• A Formal and Integrated Framework to Simulate Evolution of Biological Pathways.[doi] [bib]
  Lorenzo Dematté, Corrado Priami, Alessandro Romanel, Orkun Soyer.
  In Proceedings of International Conference on Computational Methods in Systems Biology (CMSB), LNBI 4695:106-120, © Springer, 2007.
• BetaWB: modelling and simulating biological processes. [bib] [pdf]
  Lorenzo Dematté, Corrado Priami, Alessandro Romanel.
  In Proceedings of Summer Computer Simulation Conference (SCSC) 2007.
• Effective Index: A formal measure of drug effects. [bib] [pdf]
  Lorenzo Dematté, Davide Prandi, Corrado Priami, Alessandro Romanel.
  In Proceedings of 2nd Conference Foundations of Systems Biology in Engineering (FOSBE) 2007.
• Modeling Static Biological Compartments with Beta-binders.[doi] [bib] [pdf]
  Maria Luisa Guerriero, Corrado Priami, Alessandro Romanel.
  In Proceedings of Algebraic Biology, Second International Conference (AB) 2007, LNCS 4545:247-261, © Springer-Verlag, 2007.
• The Decidability of the Structural Congruence for Beta-binders. [doi] [bib]
  Corrado Priami, Alessandro Romanel.
  In Proceedings of Workshop on Membrane Computing and Biologically Inspired Process Calculi (MeCBIC) 2006, ENTCS 171(2):155-170, Elsevier, 2007.

Posters, Abstracts and Extended Abstracts

• Analyzing various models of Circadian Clock and Cell Cycle coupling. [url] [bib]
  Paolo Ballarini, Attila Csikász-Nagy, Adrien Faure, Roberto Larcher, Paola Lecca, Tommaso Mazza, Ivan Mura, Ferenc Jordán, Alida Palmisano, Alessandro Romanel, Sean Sedwards, Heike Siebert, Sylvain Soliman, Denis Thieffry and Judit Zámborszky.
  Formal Methods in Molecular Biology, Dagsthul seminar proceedings 09091, 2009.
• Varying the level of abstraction in stochastic molecular dynamics models.
  Ivan Mura, Alida Palmisano, Sean Sedwards, Lorenzo Dematté, Alessandro Romanel.
  International Conference on Systems Biology (ICSB) 2008.
• A Novel Quality Control Procedure for Gene Expression Time Series.
  Andrea Sboner, Alessandro Romanel, Andrea Malossini, Francesca Demichelis, Federica Ciocchetta, Marco Stenico, Enrico Blanzieri, Rossana Dell'Anna.
  BITS Annual Meeting 2005.

Selected Technical Reports

• Simulation of non-Markovian Processes in BlenX.[bib] [pdf]
  Davide Prandi, Corrado Priami, Alessandro Romanel.
  TR-11-2008 The Microsoft Research - University of Trento Centre for Computational and Systems Biology.
• The Beta Workbench. [bib] [pdf]
  Lorenzo Dematté, Corrado Priami, Alessandro Romanel.
  TR-03-2007 The Microsoft Research - University of Trento Centre for Computational and Systems Biology.
• Simple methods for peak and valley detection in time series microarray data. [pdf]
  Andrea Sboner, Alessandro Romanel, Andrea Malossini, Federica Ciocchetta, Francesca Demichelis, Ivano Azzini, Enrico Blanzieri, Rossana Dell'Anna. Technical Report DIT-05-015, Informatica e Telecomunicazioni, University of Trento, 2005.

Thesis

• Una Macchina Astratta Stocastica per Beta-Binders. [pdf]
  Alessandro Romanel.
  Master Thesis. Dipartimento di Informatica e Telecomunicazioni, Università di Trento, March 2006.
• Estensione Stocastica di un Calcolo per Modellare i Sistemi Biologici. [pdf]
  Alessandro Romanel.
  Bachelor Thesis. Dipartimento di Informatica e Telecomunicazioni, Università di Trento, January 2004.