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Recent
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COPYRIGHT:
Most of the papers available from this page are draft version of papers
appeared in print, whose copyright is held by the publisher. While the
papers can be used for personal use, redistribution or reprinting for
commercial purposes is prohibited. As regards papers published by Springer
and Elsevier, the original publications are available at
www.springerlink.com and www.sciencedirect.com, respectively.
R.
Barbuti, A. Maggiolo-Schettini, P. Milazzo and S. Tini
"An Overview
on Operational Semantics in Membrane Computing" [pdf]
[@WorldScientific]
International Journal of
Foundations of Computer Science, World Scientific Publishing, in press.
R. Barbuti, M. Dezani-Ciancaglini, A. Maggiolo-Schettini, P.
Milazzo and A. Troina
"A Formalism for the Description of Protein
Interaction" [pdf]
Fundamenta
Informaticae, in press.
R. Barbuti, A. Maggiolo-Schettini, P.
Milazzo and S. Tini
"Membrane Systems Working in Generating and
Accepting Modes: Expressiveness and Encodings" [pdf]
[@springer]
11th Conference on Membrane
Computing (CMC11), Jena, Germany, August 2010, LNCS, in press. (appeared in the pre-proceedings with the title "On the
Expressive Power of Membrane Systems Working in Accepting Mode").
R.
Barbuti, A. Maggiolo-Schettini, P. Milazzo and S.
Tini
"Compositional Semantics of Spiking Neural P Systems"
[pdf]
[@elsevier]
Journal
of Logic and Algebraic Programming, Volume 79, Issue 6, pages 304-316,
2010.
T.A.
Basuki, A. Cerone, R. Barbuti, A. Maggiolo-Schettini, P. Milazzo and E.
Rossi
"Modelling the Dynamics of an Aedes albopictus Population"
[@eptcs]
1st
Int. Workshop on Applications of Membrane computing, Concurrency and
Agent-based modelling in POPulation biology (AMCA-POP 2010), Jena,
Germany, August 2010, EPTCS 33, pages 18-36, 2010.
R. Barbuti, G.
Caravagna, P. Milazzo, A. Maggiolo-Schettini and S. Tini
"Aspects of
Multiscale Modelling in a Process Algebra for Biological Systems"
[pdf]
Int. Meeting on Membrane Computing and Biologically Inspired
Process Calculi (MeCBIC'10), EPTCS, Jena, Germany, August 2010, in press.
G. Caravagna, A. d'Onofrio, P. Milazzo and R.
Barbuti
"Tumour Suppression by Immune System Through Stochastic
Oscillations" [@elsevier]
Journal of Theoretical Biology,
Volume 265, Issue 3, pages 336-345, 2010.
R.
Barbuti, A. Maggiolo-Schettini, P. Milazzo, G. Pardini and L.
Tesei
"Spatial P Systems" [pdf] [@springer]
Natural Computing, in press.
R.
Barbuti, A. Maggiolo-Schettini, P. Milazzo and S.
Tini
"Compositional Semantics of Spiking Neural P Systems"
[pdf]
[@elsevier]
Journal of Logic and Algebraic
Programming, Volume 79, Issue 6, pages 304-316.
R.Barbuti,
D.P.Gruska, A.Maggiolo-Schettini and P.Milazzo
"A Notion of
Biological Diagnosability Inspired by the Notion of Opacity in Systems
Security" [pdf]
Fundamenta Informaticae, Volume
102, Issue 1, pages 19-34, 2010. A preliminary version appeared in Int.
Workshop on Concurrency, Specification and Programming (CS&P'09).
R.Barbuti, G.Caravagna, A.Maggiolo-Schettini and
P.Milazzo
"On the Interpretation of Delays in Delay Stochastic
Simulation of Biological Systems" [@eptcs]
2nd
Int. Workshop on Computational Models for Cell Processes (CompMod'09),
Eindhoven, the Netherlands, November, 2009, EPTCS 6, pages 17-29, 2009.
R.Barbuti, A.Maggiolo-Schettini, P.Milazzo, G.Pardini and
A.Rama
"A Process Calculus for Molecular Interaction Maps"
[@eptcs]
3rd
Int. Meeting on Membrane Computing and Biologically Inspired Process
Calculi (MeCBIC'09), Bologna, Italy, September, 2009, EPTCS 11, pages
35-50, 2009.
R.Barbuti, F.Levi, P.Milazzo and
G.Scatena
"Probabilistic Model Checking of Biological Systems with
Uncertain Kinetic Rates" [pdf]
[@springer]
3rd
Int. Conference on Reachability Problems (RP'06), Ecole Polytechnique,
France, September 2009, Springer LNCS 5797, pages 64-78, 2009.
R.Barbuti, D.Lepri, A.Maggiolo-Schettini, P.Milazzo, G.Pardini and
A.Rama
"Simulation of Kohn's Molecular Interaction Maps Through
Traslation into Stochastic CLS+" [pdf]
[@springer]
7th
Int. Conference Perspectives of System Informatics, Novosibirsk, Russia,
June 2009, Springer LNCS 5947, pages 58-69, 2009.
R.Barbuti,
A.Maggiolo-Schettini, P.Milazzo and L.Tesei
"Timed P Automata"
[pdf]
Fundamenta Informaticae, Volume
94, Number 1, pages 1-19, 2009. A
preliminary version appeared in Int. Meeting on Membrane Computing and
Biologically Inspired Process Calculi (MeCBIC'08), Elsevier ENTCS, Volume
227, pages 21-36, Iasi, Romania, September, 2008. (available here:
[pdf]
[@elsevier])
R.Barbuti, G. Caravagna, A.Maggiolo-Schettini and
P.Milazzo
"P Systems with endosomes" [pdf]
[@IJCCC]
International Journal of Computers,
Communications & Control, Volume IV, Number 3, pages 214-223,
2009. A preliminary version appeared in 7th Brainstorming Week on Membrane
Computing, Seville, Spain, February, 2009.
R.Barbuti, A.Maggiolo-Schettini, P.Milazzo and A.Troina
"A
Methodology for the Stochastic Modelling and Simulation of Sympatric
Speciation by Sexual Selection" [pdf] [@WorldScientific]
Journal of Biological Systems,
World Scientific Publishing, Volume 17, Issue 3, pages 349-376, 2009.
R.Barbuti, A.Maggiolo-Schettini, P.Milazzo and S.Tini
"P
Systems with Transport and Diffusion Membrane Channels" [pdf]
Fundamenta Informaticae, Volume
93, Number 1-3, pages 17-31, 2009. A preliminary version appeared in Int.
Workshop on Concurrency, Specification and Programming (CS&P'08),
Gross Vaeter, Germany, September, 2008.
R.Barbuti, G.Caravagna,
A.Maggiolo-Schettini and P.Milazzo
"An Intermediate Language for
Stochastic Simulation of Biological Systems" [pdf]
[@elsevier]
Theoretical Computer Science,
Volume 410, Issue 33-34, pages 3085-3109, 2009.
R.Barbuti,
A.Maggiolo-Schettini, P.Milazzo and G.Pardini
"Spatial Calculus of
Looping Sequences" [pdf]
[@elsevier]
Int.
Workshop From Biology to Concurrency and Back (FBTC'08), Elsevier ENTCS,
Volume 229, Number 1, pages 21-39, Reykjavik, Iceland, July, 2008.
R.Barbuti, A.Maggiolo-Schettini, P.Milazzo and S.Tini
"A P
Systems Flat Form Preserving Step-by-step Behaviour" [pdf]
Fundamenta Informaticae, Volume
87, Number 1, pages 1-34, 2008.
R.Barbuti, A.Maggiolo-Schettini,
P.Milazzo, P. Tiberi and A.Troina
"Stochastic CLS for the Modeling
and Simulation of Biological Systems" [pdf]
[@springer]
Transactions on Computational Systems
Biology IX, Springer LNCS journal, Volume 5121, pages 86-113, 2008.
R.Barbuti, A.Maggiolo-Schettini, P.Milazzo and
S.Tini
"Towards a P Systems Normal Form Preserving Step-by-step
Behaviour" [pdf]
6th
Brainstorming Week on Membrane Computing, Seville, Spain, February, 2008.
R.Barbuti, G.Caravagna, A.Maggiolo-Schettini, P.Milazzo and
G.Pardini
"The Calculus of Looping Sequences" [pdf]
[@springer]
Chapter
in: M.Bernardo, P.Degano and G.Zavattaro (Eds.): Formal Methods for
Computational Systems Biology (SFM 2008), Springer LNCS 5016, pages
387-423, 2008.
R.Barbuti, A.Maggiolo-Schettini, P.Milazzo and
S.Tini
"Compositional Semantics and Behavioral Equivalences for P
Systems" [pdf]
[@elsevier]
Theoretical Computer Science,
Volume 395, Issue 1, pages 77-100, 2008.
R.Barbuti,
A.Maggiolo-Schettini, P.Milazzo and A.Troina
"Bisimulations in
Calculi Modelling Membranes" [pdf]
[@springer]
Formal Aspects of Computing,
Volume 20, Issue 4-5, pages 351-377, 2008. (©British Computer Society)
R.Barbuti, G.Caravagna, A.Maggiolo-Schettini and
P.Milazzo
"An Intermediate Language for Simulation of Biological
Systems" [pdf]
[@elsevier]
Int.
Workshop From Biology to Concurrency and Back (FBTC'07), Elsevier ENTCS
194 (3), pages 19-34, Lisbon, Portugal, September, 2007.
R.Barbuti, A.Maggiolo-Schettini, P.Milazzo and A.Troina
"The
Calculus of Looping Sequences for Modeling Biological Membranes"
[pdf]
[@springer]
Invited
paper at the 8th Workshop on Membrane Computing (WMC8), Springer LNCS
4860, pages 54-76, Thessaloniki, Greece, June, 2007.
R.Barbuti,
A.Maggiolo-Schettini and P.Milazzo
"Extending the Calculus of
Looping Sequences to Model Protein Interaction at the Domain Level"
[pdf]
[@springer]
International
Symposium on Bioinformatics Research and Applications (ISBRA'07), Springer
LNBI 4463, pages 638-649, Atlanta, GA, May, 2007.
R.Barbuti,
A.Maggiolo-Schettini, P.Milazzo and A.Troina
"Bisimulation
Congruences in the Calculus of Looping Sequences" [pdf]
[@springer]
International
Colloquium on Theoretical Aspects of Computing (ICTAC'06), Springer LNCS
4281, pages 93-107, Tunis, Tunisia, November, 2006.
R.Barbuti,
A.Maggiolo-Schettini, P.Milazzo and A.Troina
"A Calculus of Looping
Sequences for Modelling Microbiological Systems" [pdf]
Fundamenta Informaticae, Volume
72, Number 1-3, pages 21-35, 2006. A preliminary version appeared in
Concurrency Specification and Programming (CS&P'05), Ruciane-Nida,
Poland, September 2005.
R.Barbuti, A.Maggiolo-Schettini, P.Milazzo
and A.Troina
"An Alternative to Gillespie's Algorithm for Simulating
Chemical Reactions" [pdf]
Computational
Methods in Systems Biology (CMSB'05), Edinburgh, Scotland, April 2005.
R.Barbuti, S.Cataudella, A.Maggiolo-Schettini, P.Milazzo and
A.Troina
"A Probabilistic Model for Molecular Systems"
[pdf]
Fundamenta Informaticae, Volume
67, Number 1-3, pages 13-27, June-July 2005. A preliminary version
appeared in Concurrency Specification and Programming (CS&P'04),
Caputh, Germany, September 2004. |
