Davide Chiarugi
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- Davide �Chiarugi (11)
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- BCB '10: Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology (1)
- CMSB'04: Proceedings of the 20 international conference on Computational Methods in Systems Biology (1)
- CMSB'06: Proceedings of the 2006 international conference on Computational Methods in Systems Biology (1)
- Essays Dedicated to Pierpaolo Degano on Programming Languages with Applications to Biology and Security - Volume 9465 (1)
- SFM'08: Proceedings of the Formal methods for the design of computer, communication, and software systems 8th international conference on Formal methods for computational systems biology (1)
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- research-article
A proof theoretic view of spatial and temporal dependencies in biochemical systems
- C. Olarte
ECT, Universidade Federal do Rio Grande do Norte, Brazil
, - D. Chiarugi
Max Planck Institute of Colloids and Interfaces, Potsdam-Golm, Germany
, - M. Falaschi
Dept. of Information Engineering and Mathematics, Via Roma 56, Siena, Italy
, - D. Hermith
Dept. of Information Engineering and Mathematics, Via Roma 56, Siena, Italy
Theoretical Computer Science, Volume 641, Issue C•August 2016, pp 25-42 • https://doi.org/10.1016/j.tcs.2016.03.029The behavior of biochemical systems such as metabolic and signaling pathways may depend on either the location of the reactants or on the time needed for a reaction to occur. In this paper we propose a formalism for specifying and verifying properties ...
- 2Citation
MetricsTotal Citations2
- C. Olarte
- research-article
Verification of Spatial and Temporal Modalities in Biochemical Systems
- Davide Chiarugi
Max Planck Institute of Colloids and Interfaces, Potsdam-Golm, Germany
, - Moreno Falaschi
Dipartimento di Ingegneria dell'informazione e Scienze Matematiche, Università degli Studi di Siena, Italy
, - Diana Hermith
Dipartimento di Ingegneria dell'informazione e Scienze Matematiche, Università degli Studi di Siena, Italy
, - Carlos Olarte
ECT, Universidade Federal do Rio Grande do Norte, Brazil
Electronic Notes in Theoretical Computer Science (ENTCS), Volume 316, Issue C•September 2015, pp 29-44 • https://doi.org/10.1016/j.entcs.2015.06.009Biochemical systems such as metabolic and signaling pathways tend to be arranged in a physical space: the product of one reaction must be in the right place to become the reactant for the subsequent reaction in the pathway. Moreover, in some cases, the ...
- 2Citation
MetricsTotal Citations2
- Davide Chiarugi
- Article
A Declarative View of Signaling Pathways
- Davide Chiarugi
Department of Theory and Bio-Systems, Max Planck Institute for Colloids and Interfaces, Potsdam, Germany
, - Moreno Falaschi
Dipartimento di Ingegneria dell'Informazione e Scienze Matematiche, Universití di Siena, Siena, Italy
, - Carlos Olarte
ECT, Universidade do Rio Grande do Norte, Natal, Brazil
, - Catuscia Palamidessi
INRIA and LIX, École Polytechnique, Paris, France
Essays Dedicated to Pierpaolo Degano on Programming Languages with Applications to Biology and Security - Volume 9465•August 2015, pp 183-201Due to the inherent limitations of wet-lab techniques, the experimental data regarding cellular signaling pathways often consider single pathways or a small subset of them. We propose a methodology for composing signaling pathways data in a coherent ...
- 0Citation
MetricsTotal Citations0
- Davide Chiarugi
- research-article
On the impact of discreteness and abstractions on modelling noise in gene regulatory networks
- Chiara Bodei
Dip. di Informatica, Università di Pisa, Italy
, - Luca Bortolussi
Modelling and Simulation Group, University of Saarland, Campus E 1 3, Saarbruecken, Germany
, - Davide Chiarugi
Max Planck Institut of Colloids and Interfaces, Potsdam, Germany
, - Maria Luisa Guerriero
Systems Biology Ireland, University College Dublin, Ireland
, - Alberto Policriti
Dip. di Matematica e Informatica, Università di Udine, Udine, Italy
, - Alessandro Romanel
Centre for Integrative Biology (CIBIO), University of Trento, Italy
Computational Biology and Chemistry, Volume 56, Issue C•June 2015, pp 98-108 • https://doi.org/10.1016/j.compbiolchem.2015.04.004Graphical abstractDisplay Omitted HighlightsIn living cells gene expression is thoroughly regulated.Computational models help in understanding the mechanisms underlying gene regulation.Hybrid approaches balance model accuracy and computational ...
- 2Citation
MetricsTotal Citations2
- Chiara Bodei
- article
Simulating Signalling Pathways With BioWayS
- Davide Chiarugi
Dipartimento di Ingegneria dellInformazione e Scienze Matematiche, Universit� degli Studi di Siena, Italy
, - Moreno Falaschi
Dipartimento di Ingegneria dellInformazione e Scienze Matematiche, Universit� degli Studi di Siena, Italy
, - Diana Hermith
Dipartimento di Ingegneria dellInformazione e Scienze Matematiche, Universití degli Studi di Siena, Italy
, - Michell Guzman
Escuela de Ingeniería de Sistemas y Computación, Universidad del Valle Cali, Colombia
, - Carlos Olarte
Departamento de Electrónica y Ciencias de la Computación, Universidad Javeriana Cali, Colombia
Electronic Notes in Theoretical Computer Science (ENTCS), Volume 293•March, 2013, pp 17-34 • https://doi.org/10.1016/j.entcs.2013.02.016We report on a technique for modelling biological systems based on the ntcc calculus, a model of concurrency where systems are specified by means of constraints (i.e., formulae in logic). We show that the ability of ntcc to express partial information, ...
- 2Citation
MetricsTotal Citations2
- Davide Chiarugi
- research-article
Control Flow Analysis of Generalised Boolean Networks
- Chiara Bodei
Dipartimento di Informatica, Università di Pisa
, - Linda Brodo
Dipartimento di Scienze dei Linguaggi, Università di Sassari
, - Davide Chiarugi
Dipartimento di Scienze Matematiche e Informatiche, Università di Siena
Generalised Boolean Networks are a well known qualitative model used to analyse the evolution of genetic networks as well as generic biological pathways. Despite the qualitative abstraction due to the few threshold concentration values considered for ...
- 0Citation
MetricsTotal Citations0
- Chiara Bodei
- research-articlePublished By ACMPublished By ACM
Compositional modelling of signalling pathways in timed concurrent constraint programming
- Davide Chiarugi
Università di Siena, Italy
, - Moreno Falaschi
Università di Siena, Italy
, - Carlos Olarte
Universidad Javeriana, Cali, Colombia
, - Catuscia Palamidessi
INRIA and LIX, Ecole, Polytechnique, France
BCB '10: Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology•August 2010, pp 414-417• https://doi.org/10.1145/1854776.1854843The biological data regarding the signalling pathways often consider single pathways or a small number of them. We propose a methodology for composing this kind of data in a coherent framework, in order to be able to investigate a bigger number of ...
- 9Citation
- 131
- Downloads
MetricsTotal Citations9Total Downloads131
- Davide Chiarugi
- article
Control Flow Analysis for Brane Calculi
- Chiara Bodei
Dipartimento di Informatica, Università di Pisa, Via Pontecorvo, 3 - 56127 Pisa - Italia
, - Andrea Bracciali
Dipartimento di Informatica, Università di Pisa, Via Pontecorvo, 3 - 56127 Pisa - Italia
, - Davide Chiarugi
Dipartimento di Scienze Matematiche e Informatiche, Università di Siena, Pian dei Mantellini, 4 - 53100 Siena - Italia
Electronic Notes in Theoretical Computer Science (ENTCS), Volume 227•January, 2009, pp 59-75 • https://doi.org/10.1016/j.entcs.2008.12.104We introduce a Control Flow Analysis for Brane Calculi. This verification technique allows properties regarding the behaviour of biological systems to be checked. This is an approximate technique that focusses on the static specification of a system, ...
- 0Citation
MetricsTotal Citations0
- Chiara Bodei
- Article
Cells in silico: a holistic approach
- D. Chiarugi
Dipartimento di Scienze Matematiche e Informatiche, Università di Siena
, - P. Degano
Dipartimento di Informatica, Università di Pisa
, - J. B. Van Klinken
Dipartimento di Scienze Matematiche e Informatiche, Università di Siena
, - R. Marangoni
Dipartimento di Informatica, Università di Pisa and Istituto di Biofisica, CNR, Pisa
SFM'08: Proceedings of the Formal methods for the design of computer, communication, and software systems 8th international conference on Formal methods for computational systems biology•June 2008, pp 366-386This paper reports on our experience in modelling whole cells with process calculi. We followed a holistic approach, aiming at investigating the behaviour of biological objects at the system level, in particular of a hypothetical and a of real ...
- 1Citation
MetricsTotal Citations1
- D. Chiarugi
- Article
Feedbacks and oscillations in the virtual cell VICE
- D. Chiarugi
Dipartimento di Scienze Matematiche e Informatiche, Universit‘a di Siena
, - M. Chinellato
Dipartimento di Informatica, Universit‘a di Pisa
, - P. Degano
Dipartimento di Informatica, Universit‘a di Pisa
, - G. Lo Brutto
Dipartimento di Informatica, Universit‘a di Pisa
, - R. Marangoni
Dipartimento di Informatica, Universit‘a di Pisa
CMSB'06: Proceedings of the 2006 international conference on Computational Methods in Systems Biology•October 2006, pp 93-107We analyse an enhanced specification of VICE, a hypothetical prokaryote with a genome as basic as possible. Besides the most common metabolic pathways of prokaryotes in interphase, VICE also posseses a regulatory feedback circuit based on the enzyme ...
- 1Citation
MetricsTotal Citations1
- D. Chiarugi
- Article
VICE: a VIrtual CEll
- D. Chiarugi
Dipartimento di Informatica, Università di Pisa, Pisa, Italy
, - M. Curti
Dipartimento di Informatica, Università di Pisa, Pisa, Italy
, - P. Degano
Dipartimento di Informatica, Università di Pisa, Pisa, Italy
, - R. Marangoni
Dipartimento di Informatica, Università di Pisa, Pisa, Italy
CMSB'04: Proceedings of the 20 international conference on Computational Methods in Systems Biology•May 2004, pp 207-220• https://doi.org/10.1007/978-3-540-25974-9_16We report on the specification and analysis of VICE, a hypothetical cell with a genome as basic as possible. We used an enhanced version of the π-calculus and a prototype running it to study the behaviour of VICE. The results of our experimentation in ...
- 8Citation
MetricsTotal Citations8
- D. Chiarugi
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Please see the following 2007 Turing Award winners' profiles as examples: - History: Disambiguation of author names is of course required for precise identification of all the works, and only those works, by a unique individual. Of equal importance to ACM, author name normalization is also one critical prerequisite to building accurate citation and download statistics. For the past several years, ACM has worked to normalize author names, expand reference capture, and gather detailed usage statistics, all intended to provide the community with a robust set of publication metrics. The Author Profile Pages reveal the first result of these efforts.
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ACM Author-Izer is a unique service that enables ACM authors to generate and post links on both their homepage and institutional repository for visitors to download the definitive version of their articles from the ACM Digital Library at no charge.
Downloads from these sites are captured in official ACM statistics, improving the accuracy of usage and impact measurements. Consistently linking to definitive version of ACM articles should reduce user confusion over article versioning.
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How ACM Author-Izer Works
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The Service can be applied to all the articles you have ever published with ACM.
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ACM Author-Izer also provides code snippets for authors to display download and citation statistics for each “authorized” article on their personal pages. Downloads from these pages are captured in official ACM statistics, improving the accuracy of usage and impact measurements. Consistently linking to the definitive version of ACM articles should reduce user confusion over article versioning.
Note: You still retain the right to post your author-prepared preprint versions on your home pages and in your institutional repositories with DOI pointers to the definitive version permanently maintained in the ACM Digital Library. But any download of your preprint versions will not be counted in ACM usage statistics. If you use these AUTHOR-IZER links instead, usage by visitors to your page will be recorded in the ACM Digital Library and displayed on your page.
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- Q. What is ACM Author-Izer?
A. ACM Author-Izer is a unique, link-based, self-archiving service that enables ACM authors to generate and post links on either their home page or institutional repository for visitors to download the definitive version of their articles for free.
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- Q. What is an ACM Author Profile Page?
- A. The Author Profile Page initially collects all the professional information known about authors from the publications record as known by the ACM Digital Library. The Author Profile Page supplies a quick snapshot of an author's contribution to the field and some rudimentary measures of influence upon it. Over time, the contents of the Author Profile page may expand at the direction of the community. Please visit the ACM Author Profile documentation page for more background information on these pages.
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- Q. What happens if an author provides a URL that redirects to the author’s personal bibliography page?
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- Q. Does ACM Author-Izer provide benefits for authors?
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Authors who do not use ACM Author-Izer links will not have downloads from their local, personal bibliographies counted. They do, however, retain the existing right to post author-prepared preprint versions on their home pages or institutional repositories with DOI pointers to the definitive version permanently maintained in the ACM Digital Library.
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