BOOK CHAPTERS
[2010]
1 - M. Cavaliere, Tommaso Mazza
A (Natural) Computing Perspective on Cellular Processes,
In Elements of Computational Systems Biology, Wiley Book series on Bioinformatics, edited by Huma M. Lodhi and Stephen H. Muggleton, 115-140, 2010
JOURNALS
[2012]
14 – A. Piepoli, F. Tavano, M. Copetti, Tommaso Mazza, O. Palumbo, A. Panza, F. F. di Mola, V. Pazienza, G. Biscaglia, G. Mazzoccoli, N. Mastrodonato, M. Carella, F. Pellegrini, P. di Sebastiano, A. Andriulli.
miRNA expression profiles identify drivers in colon and pancreatic cancers.
PLoS One, 2012 (To appear).
13 – Tommaso Mazza, P. Ballarini, R. Guido, D. Prandi.
The relevance of topology in parallel simulation of biological networks.
IEEE/ACM Transaction on Computational Biology and Bioinformatics (TCBB), 9(3):911-923, 2012.
12 – E. Dassi, A. Malossini, A. Re, Tommaso Mazza, T. Tebaldi, L. Caputi, A. Quattrone.
AURA: Atlas of UTR Regulatory Actiity.
Bioinformatics, 28(1):142-144, 2012.
[2011]
11 - Eusebio Chiefari, Sinan Tanyolaç, Francesco Paonessa, Clive R. Pullinger, Carmelo Capula, Stefania Iiritano, Tommaso Mazza, Michele Forlin, Alfredo Fusco, Vincent Durlach, Anne Durlach, Mary J. Malloy, John P. Kane, Steven W. Heiner, Mirella Filocamo, Daniela P. Foti, Ira D. Goldfine, Antonio Brunetti.
HMGA1 functional variants are frequent and expose a great risk to type 2 diabetes [abstract]
Diabetes & Metabolism, 37:A22-A22, 2011.
10 - Eusebio Chiefari, Sinan Tanyolaç, Francesco Paonessa, Clive R. Pullinger, Carmelo Capula, Stefania Iiritano, Tommaso Mazza, Michele Forlin, Alfredo Fusco, Vincent Durlach, Anne Durlach, Mary J. Malloy, John P. Kane, Steven W. Heiner, Mirella Filocamo, Daniela P. Foti, Ira D. Goldfine, Antonio Brunetti.
Functional Variants of the HMGA1 Gene and Type 2 Diabetes Mellitus.
JAMA, 305 (9):903-912, 2011.
[2010]
9 - Tommaso Mazza
Editorial: Accelerating systems biology,
Briefings in Bioinformatics, 11(3):267-269, 2010
8 - Tommaso Mazza, A. Romanel, F. Jordán
Estimating the divisibility of complex biological networks by sparseness indices,
Briefings in Bioinformatics, 11(3):364-374, 2010.
7 - Tommaso Mazza, G. Iaccarino, C. Priami
Snazer: the simulations and networks analyzer,
BMC Systems Biology, 4(1), January 2010.
[2009]
6 - E. Chiefari, F. Paonessa, S. Tanyolac, C. Capula, Tommaso Mazza, M. Forlin, S. Iritano, A. Fusco, D. Foti, I. D. Goldfine, A. Brunetti
Functional Variants of the Gene for the Architectural Transcription Factor HMGA1 are Frequent and Confer a High Risk for Type 2 Diabetes Mellitus. [abstract]
Diabetes, 58:A49-A49, 2009
5 - E. Chiefari, F. Paonessa, S. Tanyolac, C. Capula, Tommaso Mazza, M. Forlin, S. Iritano, A. Fusco, D. Foti, I. D. Goldfine, A. Brunetti
Functional Variants of the Gene for the Architectural Transcription Factor HMGA1 are Frequent and Confer a High Risk for Type 2 Diabetes Mellitus. [abstract]
Diabetes and Vascular Disease Research, 7(1):95-96, November, 2009
4 - P. Ballarini, R.Guido, Tommaso Mazza, D. Prandi
Taming the complexity of biological pathways through parallel computing,
Briefings in Bioinformatics, 10(3):278-288, February 2009.
[2007]
3 - S. Sedwards, Tommaso Mazza
Cyto-Sim: A Formal Language Model and Stochastic Simulator of Membrane-Enclosed Biochemical Processes,
Bioinformatics, 23(20): 2800-2802, 2007.
2 - M. Cannataro, P. H. Guzzi, Tommaso Mazza, G. Tradigo, P. Veltri
Using Ontologies for Preprocessing and Mining Spectra Data on the Grid.
Future Generation Computer System, 23(1):55-60, 2007.
[2006]
1 - M. Cannataro, P. H. Guzzi, Tommaso Mazza, G. Tradigo, P. Veltri
Managing Ontologies for Grid Computing,
Multiagent and Grid Systems, 2(1):29-44, 2006, IOS Press.
CONFERENCE PROCEEDINGS
[2010]
27 – Tommaso Mazza, D. Prandi
Stability Analysis of Biological Network Topologies during Stochastic Simulation.
Proceedings of SIMUTools 2011. Barcelona, Spain, 2011. pp. 51-56.
26 – M. Forlin, Tommaso Mazza, D. Prandi
Predicting the effects of parameters changes in stochastic models through parallel synthetic experiments and multivariate analysis.
Proceedings of HiBi2010. Twente, The Nederlands, pp. 105-115, 2010.
[2009]
25 - E. Chiefari, F. Paonessa, S. Tanyolac, C. Capula, Tommaso Mazza, M. Forlin, S. Iritano, B. Arcidiacono, K. Possidente, A. Nocera, D. Foti, I. D. Goldfine, A. Brunetti [poster]
Genetic syndromes of extreme insulin resistance and diabetes mellitus due to defect in insulin receptor gene transcription.
XY Scientific Telethon Convention, p. 282, Riva del Garda, March 2009.
24 - P. Ballarini, M. Forlin, Tommaso Mazza, D. Prandi
Efficient Parallel Statistical Model Checking of Biochemical Networks.
In Proceedings of Parallel and Distributed Methods in verifiCation (PDMC 09), Electronic Proceedings in Theoretical Computer Sci, Eindhoven, The Netherlands, 14:47-61, November, 2009
23 - P. Ballarini, Tommaso Mazza, A. Palmisano, A. Csikasz-Nagy
Studying irreversible transitions in a model of cell cycle regulation.
In Proceedings of the third International Workshop on Practical Applications of Stochastic Modelling (PASM 2008), ENTCS 232, pp. 39-53, 2009.
22 - G. Iaccarino, Tommaso Mazza
Fastest parallel molecular algorithms for the Elliptic Curve Discrete Logarithm Problem over GF(2n).
BADS 2009, ACM press, pp. 95-104, Barcelona, June 2009.
[2008]
21 - Tommaso Mazza, M. Cavaliere
Cell Cycle and Tumor Growth in Membrane Systems with Peripheral Proteins.
In Proceedings of MeCBIC 2008, ENTCS 227, pp. 127-141, 2008
20 - L. Dematte', Tommaso Mazza
On Parallel Stochastic Simulation of Diffusive Systems.
In Proceedings of the sixth International Conference on Computational Methods in Systems Biology (CMSB2008), LNBI 5307, pp. 191–210 , 2008.
19 - Tommaso Mazza, Rosita Guido
Guidelines for parallel simulation of biological reactive systems.
In Proceedings of "Bioinformatics Methods for Biomedical Complex System Applications" (Nettab 2008), (2):83-85, 2008
18 - Tommaso Mazza, Aurora Nocera
A formal lightweight view of the p53-dependent G1/S checkpoint control.
In Proceedings of "Prague International Workshop on Membrane Computing", 35-46, 2008
[2007]
17 - Tommaso Mazza
Towards a Complete Covering of SBML Functionalities.
In Proceedings of the Eight Workshop on Membrane Computing (WMC8), LNCS 4860, 425 - 444, 2007
16 - Tommaso Mazza
Stochastic Simulation as an Effective Cell Analysis Tool.
In Proceedings of the 2nd International Joint Conferences on Computer, Information, and Systems Sciences, and Engineering (CISSE 2006), to appear in Advances and Innovations in Systems, Computing Sciences and Software Engineering – Springer Press
[2006]
15 - P.H. Guzzi, M. Cannataro, M. Gaspari, Tommaso Mazza, B. Quaresima, P. Veltri, F.S. Costanzo
Analysis and Classification of Proteomics Data, a Case Study.
The 19th IEEE International Symposium on Computer-Based Medical Systems (CBMS’05), June 22- 23, 2006, Salt Lake City, Utah, USA, pp., IEEE Press.
14 - M. Cannataro, P.H. Guzzi, Tommaso Mazza, A. Oliverio, G. Tradigo, P. Veltri
An Architecture for Managing Mass Spectrometry Proteomics Data
Int. Workshop Heterogeneous and Distributed Information Retrieval (HDIR-05), in conjunction with ACM SIGIR 2005, August 19th, 2005 - Salvador, Brazil, ACM Press 2005
13 - G. Franco, P.H. Guzzi, Tommaso Mazza, V. Manca
Mitotic Oscillators as MP Graphs
In Proceesings of the 7th International Workshop in Membrane Computing, WMC 2006, Leiden, Nederland, published in Lecture Notes in Computer Science, Springer, 344 – 356, July 2006.
12 - Tommaso Mazza, M. Gaspari, M. Cannataro, G. Cuda, P. H. Guzzi, G. Tradigo, P. Veltri
A novel approach to integrate MS/MS sequence information from multiple proteomic experiments performed by ICAT labelling and LC-MS/MS analysis
USHUPO-2006 Conference, 11-13 March, 2006, Boston, USA.
[2005]
11 - M. Cannataro, P.H. Guzzi, Tommaso Mazza, G. Tradigo and P. Veltri
Algorithms and Databases in Bioinformatics: Towards a Proteomic Ontology
6th IEEE International Conference on Information Technology: Coding and Computing, ITCC- 2005, Volume 1, 4-6 April 2005, Las Vegas, Nevada, USA, pp 322-328, IEEE Computer Society Press, 2005.
10 - M. Cannataro, P.H. Guzzi, Tommaso Mazza and P. Veltri
Using Ontologies in PROTEUS for Modeling Proteomics Data Mining Applications
Third International Conference on Healthgrids, (HealthGRID 2005), 7th - 9th April 2005, Oxford, United Kingdom, Kluwer Academic Publishers, 2005.
9 - M. Cannataro, P. Guzzi, Tommaso Mazza, P. Veltri
MS-Analyzer: Intelligent Preprocessing, Management, and Data Mining Analysis of Mass Spectrometry Data on the Grid
Proceedings of The First International Conference on Semantics, Knowledge and Grid (SKG-05), Nov. 27-29, 2005, Beijing, China. IEEE Press.
8 - M. Cannataro, P. H. Guzzi, Tommaso Mazza, G. Tradigo, P. Veltri
Preprocessing, Management, and Analysis of Mass Spectrometry Proteomics Data
In workshop Workflows management: new abilities for the biological information overflow-NETTAB 2005, 5-7 October 2005, Napoli.
7 - M. Cannataro, P.H. Guzzi, Tommaso Mazza, G. Tradigo and P. Veltri
Preprocessing of Mass Spectrometry Proteomics Data on the Grid
The 18th IEEE International Symposium on Computer-Based Medical Systems (CBMS’05), Trinity College Dublin, 23-24 June 2005, Dublin, Ireland.
6 - M. Cannataro, P.H. Guzzi, Tommaso Mazza, G. Tradigo, P. Veltri
On the Preprocessing of Mass Spectrometry Protemics Data
XV Italian Workshop on Neural Networks (WIRN 2005), IASS "Eduardo R. Caianiello", Vietri sul Mare (SA) Italy, June 8-11, 2005, LNCS, Springer-Verlag
5 - M. Cannataro, P.H. Guzzi, Tommaso Mazza, P. Veltri
Distributed Management of Ontologies on the Grid
14th IEEE Int. Workshops on Enabling Technologies: Infrastructures for Collaborative Enterprises (WETICE-2005) - Emerging Technologies for Next generation GRID (ETNGRID-2005), IEEE Computer Society Press.
4 - M. Cannataro, P.H. Guzzi, Tommaso Mazza and P. Veltri
Using PROTEUS for modeling and Ontology based Designing of Proteomics Experiments
In Proceedings of the Workshop on Grid Computing and Its Application to Data Analysis (GADA). Lecture Notes in Computer Science 3292 Springer 2004.
3 - M. Cannataro, P.H. Guzzi, Tommaso Mazza, and P. Veltri
Using Ontologies in Proteus for Modeling Data Mining Analysis of Proteomics Experiments
in Knowledge Discovery and Ontologies (KDO-2004) Workshop at ECML/PKDD 2004 15th, European Conference on Machine Learning (ECML). Pisa, October 2004
2 - Baudi, Cannataro, Casadonte, Costanzo, Cuda, Faniello, Gaspari, Guzzi, Mazza, Tagliaferri, Tradigo, Venuta and Veltri
Mass Spectrometry Data Analysis for Early Detection of Inherited Breast Cancer
accepted paper in CIBB 2004 – International Meeting on Computational Intelligence Methods for Bioinformatics and Biostatistics. Notes in Computer Science, Wirn 2004, June 2004
1 - M. Cannataro, P.H. Guzzi Tommaso Mazza and P. Veltri
Ontology-Based Data Mining Analysis of Proteomics Data on the Grid
in Workshop on Data Mining and the Grid (DM-Grid 2004). In conjunction with The Fourth IEEE International Conference on Data Mining (ICDM 2004). Brighton, November 2004 pag. 232-243.
TECHNICAL REPORTS
6 - Tommaso Mazza, M. Cavaliere
Cell Cycle and Tumor Growth in Membrane Systems with Peripheral Proteins
The Microsoft Research – University of Trento Centre for Computational and Systems Biology. TR-15-2008
5 - L. Dematte’, Tommaso Mazza
An Optimistic Reaction-Diffusion Simulator
The Microsoft Research – University of Trento Centre for Computational and Systems Biology. TR-08-2008
4 - S. Sedwards, Tommaso Mazza
Cyto-Sim: A Formal Language Model and Stochastic Simulator of Membrane-Enclosed Biochemical Processes
The Microsoft Research – University of Trento Centre for Computational and Systems Biology. TR- 06-2008
3 - Tommaso Mazza
A Walk through Chemical-Like Reactions Kinetics
Technical Report, Dipartimento Medicina Sperimentale e Clinica, Università Magna Græcia di Catanzaro, Italy, N.1/2007 (Feb. 2007).
2 - Tommaso Mazza, P.H. Guzzi, M.Cannataro, and P. Veltri
Problems, Algorithms, Software Tools and Databases in Proteomics: a Tutorial
Technical Report, Dipartimento Medicina Sperimentale e Clinica, Università Magna Græcia di Catanzaro, Italy, N.2/2004 (April 2004).
1 - P.H. Guzzi, Tommaso Mazza, M.Cannataro, and P. Veltri
Towards a Proteomic Ontology: a Survey of Proteomic Algorithms and Biological Databases
Technical Report, Dipartimento Medicina Sperimentale e Clinica, Università Magna Græcia di Catanzaro, Italy, N.1/2004 (Aprile 2004).
OTHER PUBLICATIONS
Tommaso Mazza, P.H. Guzzi
Java: all’Orizzonte della Bioinformatica
Java Software Distribution 2006 (JSD2006)
Java evangelism joint project with: Ministero dell'Istruzione, dell'Università e della Ricerca (MIUR), la Direzione Generale per i Sistemi Informativi (DGSI) le società Onyx Systems e K-Tech. (cd-rom)
P.H. Guzzi, Tommaso Mazza
Jena Project: Managing di Ontologie con Java
Java Software Distribution 2006 (JSD2006)
Java evangelism joint project with: Ministero dell'Istruzione, dell'Università e della Ricerca (MIUR), la Direzione Generale per i Sistemi Informativi (DGSI) le società Onyx Systems e K-Tech. (cd-rom)
Tommaso Mazza, P.H. Guzzi
Java e la Riflessione computazionale. Java Software Distribution 2006 (JSD2006)
Java evangelism joint project with: Ministero dell'Istruzione, dell'Università e della Ricerca (MIUR), la Direzione Generale per i Sistemi Informativi (DGSI) le società Onyx Systems e K-Tech. (cd-rom)
TALKS
01 October 2010
Predicting the effects of parameters changes in stochastic models through parallel synthetic experiments and multivariate analysis (HiBi2010, Enschede, The Nederland)
01 April 2009
A parallel perspective of the dynamics of biological reactive systems (Microsoft Research Cambridge) - invited
27 March 2009
Standard languages for systems biology (CoSBi internal courses) -invited
03 September 2008
Cell Cycle and Tumor Growth in Membrane Systems with Peripheral Proteins (MeCBIC2008 workshop, Iasi, Romania)
02 June 2008
A formal lightweight view of the p53-dependent G1/S checkpoint control (Prague International Workshop on Membrane Computing, Prague, Czech Republic)
9 May 2008
Guidelines for parallel simulation of biological reactive systems (Nettab2008 conference, Varenna, Como Lake, Italy)
26 June 2007
Towards a complete covering of SBML functionalities (WMC8 Conference, Thessaloniki, Greece)
25 May 2006
High throughput Proteomics (ITC-irst, Trento (Italy) - invited
9 April 2005
Using ontologies in PROTEUS for modeling proteomics data mining applications (Healthgrid 2005 Conference, Oxford, United Kingdom)
7 March 2005
Mass Spectrometry: some algorithmic approaches (ICAR-CNR, Cosenza (Italy) - invited