Department of Mathematics and Computer Science

università’ DEGLI STUDI DI CAMERINO

Nicola Cannata, PhD

Publications for Nicola Cannata (updated 2006/10/01)

 

Book Chapters

 

Valle, G., Vezzi, A., Cannata, N.

11. Genomics and Bioinformatics.

In "The internet for cell and molecular biologist - 2nd edition. Edited by Cabibbo A., Grant R.P., Helmer-Citterich M." Horizon Bioscience (2004) pp. 309-343

 

Journal Articles

 

Cannata N., Corradini F., Merelli E.

Multiagent modelling and simulation of carbohydrate oxidation in cell.

Int. J. Modelling, Identification and Control, In press (2008)

 

Bartocci E., Cacciagrano D., Cannata N., Corradini F., Merelli E, Milanesi L., Romano P.

An Agent-based Multilayer Architecture for Bioinformatics Grids.

IEEE Transactions on Nanobioscience, 6(2): 142-148 (2007)

 

Cannata N., Corradini F., Merelli E.

A Resourceomic Grid for bioinformatics.

Future Generation Computer Systems 23(3): 510-516 (2007)

 

Merelli E, Armano G, Cannata N, Corradini F, d'Inverno M, Doms A, Lord P, Martin A, Milanesi L, Moller S, Schroeder M, Luck M.

Agents in bioinformatics, computational and systems biology.

Briefings in Bioinformatics. 8(1):45-59. Epub 2006 May 26. (2007)

 

Cannata, N., Merelli E., Altman R.B.

Time to organize the bioinformatics resourceome

PloS Computational Biology 1(7): e76 (2005)

 

Cannata, N., Corradini, F., Merelli, E., Omicini, A., Ricci, A.

An Agent-oriented Conceptual Framework for Systems Biology

LNCS 3737 - Transactions on Computational Systems Biology III: 105-122 (2005)

 

Campagna, D., Romualdi, C., Vitulo, N., Del Favero, M., Lexa, M., Cannata, N., and Valle, G.,

RAP: a new computer program for de novo identification of repeated sequences in whole genomes

Bioinformatics 21 (5): 582-8 (2005)

 

Vezzi A, Campanaro S, D'Angelo M, Simonato F, Vitulo N, Lauro FM, Cestaro A, Malacrida G, Simionati B, Cannata N, Romualdi C, Bartlett DH, Valle G.

Life at depth: Photobacterium profundum genome sequence and expression analysis

Science (Mar. 4): 1459-1461 (2005)

 

Romualdi C, Campanaro S, Campagna D, Celegato B, Cannata N, Toppo S, Valle G, and Lanfranchi G

Pattern recognition in gene expression profiling using DNA array: a comparative study of different statistical methods applied to cancer classification

Hum. Mol. Genet. 12 (8): 823-836 (2003)

 

Toppo, S., Cannata, N., Fontana P., Romualdi, C., Laveder, P., Bertocco, E., Lanfranchi, G. and Valle, G.

TRAIT (TRAnscript Integrated Table): a knowledgebase of human skeletal muscle transcripts

Bioinformatics 19 (5): 661-662 (2003)

 

Cannata, N., Toppo, S., Romualdi, C. and Valle, G.

Simplifying amino acid alphabets by means of a branch and bound algorithm and substitution matrices.

Bioinformatics 18 (8): 1102-1108 (2002)

 

Stanchi, F., Bertocco, E., Toppo, S., Dioguardi, R., Simionati, B., Cannata, N., Zimbello, R., Lanfranchi, G. and Valle, G.

Characterization of 16 novel human genes showing high similarity to yeast sequences.

Yeast 18 (1): 69-80 (2001)

 

Bortoluzzi, S., Rampoldi, L., Simionati, B., Zimbello, R., Barbon, A., d'Alessi F, Tiso, N., Pallavicini, A., Toppo, S., Cannata, N., Valle, G., Lanfranchi,G. and Danieli, G.A.

A comprehensive, high-resolution genomic transcript map of human skeletal muscle.

Genome. Res. 8 (8): 817-825 (1998)

 

Conferences’ abstracts and proceedings, technical reports, ...

 

Cannata N, Corradini F, Piersigilli F, Merelli E and Vito L. Semantic Resource Management in MAS.

VIII Italian Workshop from Objects to Agents: “Agents and industry: technological applications of software agents” (WOA 2007), Genova, Italy, September 24-25, 2007, p. 42-47.

 

Cannata N, Corradini F, Gabrielli S, Leoni L, Merelli E, Piersigilli F, Vito L. Intuitive and machine-understandable organization of the bioinformatics domain and related resources with Resourceomes

VII International Workshop on Network Tools and Applications in Biology: “A Semantic Web for Bioinformatics: Goals, Tools, Systems, Applications” (NETTAB 2007), Pisa, Italy, June 12-15 2007, p. 35-46.

 

Angeletti M, Baldoncini A, Cannata N, Corradini F, Culmone R, Forcato C, Mattioni M and Merelli E. Spatial behavioral modeling and simulation of metabolic pathways with Orion

IV Bioinformatics ITalian Society meeting (BITS 2007), Napoli, Italy, April 26-28 2006,  p. 70.

 

Bartocci E, Cacciagrano D., Cannata N, Corradini F, Merelli E, Milanesi L, Romano P

A GRID-based multilayer architecture for bioinformatics

VI International Workshop on Network Tools and Applications in Biology: “Distributed Applications, Web Services, Tools and GRID Infrastructures for Bioinformatics” (NETTAB 2006), S. Margherita di Pula (CA), Italia. July 10-13, 2006,  pp.

 

Angeletti M, Baldoncini A, Cannata N, Corradini F, Culmone R, Forcato C, Mattioni M, Merelli E, Piergallini R

Orion: a spatial Multi Agent System framework for Computational Cellular Dynamics of metabolic pathways

III Bioinformatics ITalian Society meeting (BITS 2006), Bologna, Italy, April 28-29 2006,  p. Abstract 3

 

Bartocci E, Cannata N, Corradini F, Merelli E, Milanesi L, Romano P

A multilayer architecture to support bioinformaticians of today and tomorrow

III Bioinformatics ITalian Society meeting (BITS 2006), Bologna, Italy, April 28-29 2006,  p. Abstract 12

 

Cannata N, Corradini F, Di Berardini MR, Mariani F, Merelli E, Trivelli M, Ubaldi M

Modelling and simulation of the E.coli-Lambda interactions

III Bioinformatics ITalian Society meeting (BITS 2006), Bologna, Italy, April 28-29 2006,  p. Abstract 23

 

Cannata N, Corradini F, La Terza A, Merelli E, Miceli C

Modelling of the eukariotic heat-shock response with probabilistic timed automata

III Bioinformatics ITalian Society meeting (BITS 2006), Bologna, Italy, April 28-29 2006,  p. Abstract 24

 

Cannata N, Corradini F, Leoni L, Merelli E, Piersigilli F

A resource ontology for bioinformatics Resourceomes

III Bioinformatics ITalian Society meeting (BITS 2006), Bologna, Italy, April 28-29 2006,  p. Abstract 25

 

Cannata, N., Cocco, N., Simeoni M.

Abstraction and trees for biosequences analysis (Revised version of CS-2005-7)

Rapporto di ricerca Dipartimento Informatica, Università di Venezia CS-2005-11, October 2005.

 

Cannata, N., Cocco, N., Simeoni M.

k-tries and abstraction for biosequences analysis

Rapporto di Ricerca Dipartimento Informatica, Università di Venezia CS-2005-7, May 2005.

 

Bilardi A., Campagna D., Campanaro S., Cestaro A., Levorin F., Vitulo N., Vezzi A., Valle G., Cannata N.

Quest for rho dependent terminators in prokaryotic genomes

II Bioinformatics ITalian Society meeting (BITS 2005), Milano, Italy, March 17-19 2005,  p. Abstract 13

 

Campagna D., Romualdi C.,Vitulo N., Del Favero M., Lexa M., Cannata N., Valle G.

RapH and RapD: two indexes designed for de novo identification of repeats in whole genomes

II Bioinformatics ITalian Society meeting (BITS 2005), Milano, Italy, March 17-19 2005,  p. Abstract 18

 

Marcon, G., Cannata, N., Llabrés, M., Simeoni, M., Valle, G.

Ordering BAC Clones from Fingerprint Data obtained through Four Enzymes Digestion and Fluorescent Labeling.

V Spanish Bioinformatics Conference 2004 (JBI 2004), Barcelona, Spain, November 29-30, 2004, pp. 182-190

 

Marcon, G., Cannata, N., Llabrés, M., Simeoni, M., Valle, G.

Ordering BAC clones from fingerprint data obtained through four enzymes digestion and fluorescent labeling

Workshop on Genomes: Information, Structure, and Complexity (GISC 2004). Dobbiaco (BZ), Italy, September 25, 2004,  pp. 1-13

 

G. Marcon, N. Cannata, M. Llabrés, M. Simeoni, G. Valle

Ordering BAC clones from fingerprint data

Rapporto di Ricerca CS-2004-6, September 2004.

 

Cannata, N., Corradini, F., Merelli, E., Omicini, A., Ricci, A.

An Agent-oriented Conceptual Framework for Biological Systems Simulation

IV International Workshop on Network Tools and Applications in Biology: “Models and Metaphors from Biology to Bioinformatics Tools” (NETTAB 2004), Camerino(MC), Italy, September 5-7, 2004,  pp. 167-180

 

Cannata, N., Forcato, C., Fabbro, G., Pasin, A., Balen, J., Valle, G.

Searching for discriminating degenerated patterns between two populations of sequences

I Bioinformatics ITalian Society meeting (BITS 2004), Padova, March 26-27 2004,  p. Abstract 67

 

Vitulo, N., Cestaro, A., Vezzi, A., Campanaro, S., Simonato, F., Lauro, F., Malacrida, G., Simionati, B.,Cannata, N., Bartlett, D., Valle, G.

Development of tools based on UCSC and KEGG for the annotation of the Photobacterium profundum genome

I Bioinformatics ITalian Society meeting (BITS 2004), Padova, March 26-27 2004,  p. Abstract 68

 

Toppo, S., Cannata, N., Romualdi, C., Tosatto, S., Lexa M., Campanaro S., Laveder, P., Cestaro, A., Vitulo, N., Campagna, D., Bertocco, E., Scannapieco, P., Dal Favero, M., Lanfranchi, G. and Valle, G.

Telethon project B.57 - Bioinformatics and muscle TRAIT database

XII Scientific Convention Telethon, Riva del Garda(Italy), November 23-25 2003,  p. 69

 

Toppo, S., Cannata, N., Romualdi, C., Laveder, P., Lanfranchi, G. and Valle, G.

TRAIT: a knowledgebase to retrieve annotated and differentially expressed transcripts found in human skeletal muscle

II European Conference on Computational Biology (ECCB2003), Paris (FRANCE), September 27-30 2003,  pp. 141-142

 

Toppo, S., Cannata, N., Romualdi, C., Laveder, P., Lanfranchi, G. and Valle, G.

TRAIT: a knowledgebase to retrieve annotated and differentially expressed transcripts found in human skeletal muscle

The Seventh Annual International Conference on Research in Computational Molecular Biology (RECOMB2003), Berlino (Germania), 10-13 Aprile 2003 

 

Toppo, S., Cannata, N., Romualdi, C., Fontana, P., Laveder, P., Lanfranchi, G., Valle, G.

Muscle-TRAIT: an integrated platform for storage, annotation and retrieval of data related to muscle transcripts.

Gruppo di cooperazione BIOINFORMATICA, Certosa di Pontignano (SI), 15-16 Marzo 2002 

 

Cannata, N., Toppo, S., Romualdi, C., Valle, G.

Simplifying amino acid alphabets by means of a branch and bound algorithm and substitution matrices.

Gruppo di cooperazione BIOINFORMATICA, Certosa di Pontignano (SI), 15-16 Marzo 2002 

 

Romualdi, C., Celegato, B., Campanaro, S., Cannata, N., Toppo, S., Valle, G., Lanfranchi G.

Management and Statistical Analysis of Microarrays Data.

Gruppo di cooperazione BIOINFORMATICA, Certosa di Pontignano (SI), 15-16 Marzo 2002 

 

Romualdi, C., Celegato, B., Campanaro, S., Cannata, N., Toppo, S., Valle, G. and Lanfranchi, G.

Statistical pattern recognition in gene expression profiling: a comparative approach of different methods applied to cancer classification

IV Convegno Federazione Italiana Scienze della Vita (FISV), Riva del Garda - TN (Italy), 20-23 Settembre 2002,  p. 7

 

Toppo, S., Cannata, N., Romualdi, C., Laveder, P., Fontana, P., Lanfranchi, G. and Valle, G.

MUSCLE-TRAIT: an integrated platform for storage, annotation and retrieval of data related to muscle transcripts

IV Convegno Federazione Italiana Scienze della Vita (FISV), Riva del Garda - TN (Italy), 20-23 Settembre 2002,  p. 8

 

Romualdi, C., Campanaro, S., Campagna, D., Celegato, B., Cannata, N., Toppo. S., Valle, G. and Lanfranchi, G.

Functional genomics of skeletal muscle - 3) Pattern recognition in gene expression profiling using dna array. A comparative study of different statistical

methods applied to the classification of muscolar dystrophies

XI Scientific Convention Telethon, Riva del Garda(Italy), November 24-26 2002,  p. 66

 

Toppo, S., Cannata, N., Romualdi, C., Bertocco, E., Laveder, P., Lanfranchi, G. and Valle, G.

Functional genomics of skeletal muscle - 5) TRAIT: a knowledgebase to retrieve annotated and differentially expressed transcripts expressed in human

skeletal muscle

XI Scientific Convention Telethon, Riva del Garda(Italy), November 24-26 2002,  p. 68

 

Cannata, N., Grillo, G., Licciulli, F., Iacono, M., Liuni, S., Toppo, S., Helmer-Citterich, M., Valle, G. and Pesole, G.

UTRait: a specialized database of mRNA untranslated regions from genes expressed in the skeletal muscle

XI Scientific Convention Telethon, Riva del Garda(Italy), November 24-26 2002,  p. 133

 

Vezzi, A., D'Angelo, M., Vitulo, N., Cestaro, A., Campanaro, S., Cannata, N., Simionati, B., Zimbello, R., Lauro, F.M., Bartlett, D.H., Valle., G.

Genome sequencing and analysis of the psychrotolerant and piezophilic bacterium Photobacterium Profundum

The 4th International Congress on Extremophiles, Naples (Italy), September 22-26, 2002,  p. 248

 

Vezzi, A., D'Angelo, M., Vitulo, N., Cestaro, A., Campanaro, S., Cannata, N., Simonato, F., Simionati, B., Zimbello, R. and Valle., G.

Analisi del genoma del batterio piezofilo/psicrofilo Photobacterium Profundum

IV Convegno Federazione Italiana Scienze della Vita (FISV), Riva del Garda - TN (Italy), 20-23 Settembre 2002,  p. 111

 

Bertocco, E., Cannata, N., Toppo, S., Fontana, P., Scannapieco, P., Valle, G.

From sequence to function using links to ortholog genes.

Gruppo di cooperazione BIOINFORMATICA, Certosa di Pontignano (SI), 17-18 Febbraio 2001 

 

Toppo, S., Fontana, P., Cannata, N., Scannapieco, P., Bertocco, E. and Valle, G.

TRAIT: a database of transcripts expressed in human skeletal muscle.

Gruppo di cooperazione BIOINFORMATICA, Certosa di Pontignano (SI), 17-18 Febbraio 2001 

 

Valle G., Toppo S., Cannata N., Romualdi C., Fontana P., Laveder P. Lanfranchi G.

MUSCLE-TRAIT: an integrated platform for storage, annotations and retrieval of data related to muscle transcripts

X Convention Scientifica Telethon, Riva del Garda (Italy), November 18-20, 2001,  pp. 60-62

 

Lanfranchi, G., Bean, C., Campanaro, S., Cannata, N., Celegato, B., De Pittà, C., Ievolella, C., Laveder, P., Millino, C., Pacchioni, B., Romualdi, C., Salamon, M.,

Toppo, S., Trevisan, S., Valle G.

Functional genomics of skeletal muscle

X Convention Scientifica Telethon, Riva del Garda (Italy), November 18-20 2001,  p. 117

 

Toppo, S., Cannata, N., Scannapieco, P., Fontana, P., Dioguardi, R., Bertocco, E., Lanfranchi, G. and Valle, G.

Trait: an integrated database of transcripts expressed in human skeletal muscle.

IX Convention Scientifica Telethon, Rimini (Italy), November 12-14, 2000,  p. 93

 

Pacchioni, B., Trevisan, S., Ievolella, C., Laveder, P., Pallavicini, A., Cannata, N., Toppo, S., Dioguardi, R., Piétu, G., Imbeaud, S., Bortoli, S., Auffray, C., Mouly,

V., Butler-Browne, G., Valle, G. and Lanfranchi, G.

Gene expression profiling of human skeletal muscle using cDNA macroarrays.

IX Convention Scientifica Telethon, Rimini (Italy), November 12-14, 2000,  p. 96

 

Lanfranchi, G., Pacchioni, B., Trevisan, S., Ievolella, C., Laveder, P., Pallavicini, A., Cannata, N., Toppo, S., Dioguardi, R., Valle, G., Piétu, G., Imbeaud, S., Bortoli,

S., Auffray, C., Butler-Browne, G. and Mouly,V.

Studio dei profili di espressione genica del muscolo scheletrico umano durante il differenziamento e l'invecchiamento mediante cDNA macroarrays.

II Convegno FISV, Riva del Garda, Trento (Italy), September 30-October 4, 2000,  p. 233

 

Valle, G., Toppo, S., Cannata, N., Pallavicini, A., Laveder, P., Ievolella, C., Stanchi, F., Pacchioni, B., Trevisan, S., Salamon, M., Bortoletto, G., Dioguardi, R.,

Scannapieco, P., Frigimelica, E., Zimbello, R., Simionati, B. and Lanfranchi, G.

A database of transcripts expressed in human skeletal muscle.

International Meeting BAM 2000 - Basics and applications of muscle plasticity, Abano Terme, Padova (Italy), June 11-13, 2000,  p. 86

 

Lanfranchi, G., Pacchioni, B., Trevisan, S., Toppo, S., Cannata, N., Ievolella, C., Pallavicini, A., Laveder, P., Valle, G., Imbeaud, S., Eveno, E., Mariane-Samson, R.,

Soury-Segurens, B., Renault, V., Fayein, N.A., Decraene, C., Matingou, C., Devignes, M

Gene expression profiling of human skeletal muscle during ageing and differentiation using an arrayed collection of 3'-end muscle cDNAs.

International Meeting BAM 2000 - Basics and applications of muscle plasticity, Abano Terme, Padova (Italy),  p. 74

 

Imbeaud, S., Eveno, E., Mariage-Samson, R., Soury-Segurens, B., Fayein, N.A., Decraene, C., Matingou, C., Butler-Browne, G., Devignes, M.D., Piétu, G., Auffray,

C., Pacchioni, B., Trevisan, S., Dioguardi, R., Toppo, S., Cannata, N., Ievolella, C., Pallavi

Towards a knowledge base of the human skeletal muscle transcriptome integrating sequence, map and expression data.

International Congress 

 

Cannata, N., Dioguardi, R., Fontana, P., Scannapieco, P., Toppo, S., Lanfranchi, G. and Valle, G.

An integrated knowledge-base of gene expression in human skeletal muscle.

Gruppo di cooperazione BIOINFORMATICA, Certosa di Pontignano (SI), 3-4 Marzo 2000 

 

Pallavicini, A., Laveder, P., Toppo, S., Cannata, N., Pacchioni, B., Trevisan, S., Ievolella, C., Simionati, B., Zimbello, R., Frigimelica, E., Stanchi, F., Scannapieco, P.,

De Pittà, C., Salamon, M., Bortoletto, G., Lanfranchi, G. and Valle, G.

Integrated molecular analysis of gene expression in human skeletal muscle.

VIII Telethon scientific convention (1999). Rimini, November 14-16 

 

Lanfranchi, G., Pallavicini, A., Toppo, S., Cannata, N., Dioguardi, R., Laveder, P., Pacchioni, B., Trevisan, S., Simionati, B., Zimbello, R., Ievolella, C., Formentin,

E., Faulkner, G., Valle, G.

Gene expression in human skeletal muscle.

Cold Spring Harbor Symposium on Genome Sequencing and Biology. Cold Spring Harbor, New York, May 1999,  pp. 19-23

 

Ievolella, C., Dioguardi, D., Cannata, N., Toppo, S., Branno, M. and Valle, G.

Analisi di 1037 EST di larve di Ciona intestinalis

3rd Italian Workshop on Genome Research and Sequencing Technology, Baia delle Zagare (Fg), 14-16 Giugno 1999 

 

Pallavicini, A., Toppo, S., Pacchioni, B., Trevisan, S., Zimbello, R., Simionati, B., Ievolella, C., Stanchi, F., Formentin, E., Cannata, N., Dioguardi, R., Scannapieco,

P., Lanfranchi, G. and Valle, G.

Integrated molecular analysis of gene expression in human skeletal muscle.

VII Telethon scientific convention (1998). Roma, November 15-17 

 

Cannata N., Toppo S. and Valle G.

A data-flow language for control systems and its application in managing processes for Genomic Projects.

1st Italian Workshop on Genome Research and Sequencing Technology. San Miniato (PI) 2-4 june 1997

Articles in PubMed

Articles in DBLP