Nicola Cannata, PhD, MBM
Born in Venezia-Mestre (Italy), the 15th May 1966
e-mail: [email protected]
Skype: nicola.cannata
Twitter: @Nico_Cann
Lecturer (Research Assistant Professor) in Computer Science and Bioinformatics at University of
Camerino
Co-Founder, President of the board and CEO, Next Generation Bioinformatics SRL (“NGB”),
Camerino (Italy)
Co-Founder and President of the Board of Directors, BMR Genomics SRL, Padova (Italy)
Shareholder and partner, B-Sm@rk LTD, Dublin (Ireland)
Shareholder, e-Lios (e-Linking online systems) SRL, Camerino (Italy)
Member of the BITS (Bioinformatics ITalian Society)
Member of the GRIN (GRuppo di INformatica, group of Italian Computer Science University
Professors)
Since November 2005 I’m at the Computer Science division of the School of Science and
Technology, University of Camerino, in the research group of Prof. Flavio Corradini and Emanuela
Merelli. My research interests include computer science (databases, development of software
systems, including web sites and mobile applications, ontologies, workflows, multi agent systems)
bioinformatics and in general Information Technology for health and life sciences.
I'm strongly involved in the transfer of knowledge, business development and in academic
entrepreneurship.
From november 1996 to october 2005 I was (reaching a Senior position) in the Genomics and
Bioinformatics Laboratory of CRIBI Biotechnology Centre at the University of Padova. I was in the
research group of Prof. Giorgio Valle and Gerolamo Lanfranchi, mainly in the design of databases,
strategies, algorithms and programs for the management and the analysis of the genomics and
transcriptomics sequences and gene expression experiments produced in the lab.
At the University of Camerino I’m involved in the teaching of database systems for the BSc in
Computer Science, in the teaching of computer science and bioinformatics for the BSc in
Biosciences and Biotechnology, and in the teaching of Bioinformatics Programming (module of
Genomics and Proteomics) for the MSc in Biological Sciences. At the University of Padova I was
involved in the establishment and teaching of the three courses in Bioinformatics for the BSc in
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Molecular Biology and collaborated to the e-learning development project of the Faculty of
Science.
My studies include a PhD in Biotechnology at University of Padova and a degree in Computer
Science at the University of Pisa, separated by some (non-academic) work for IT firms. I obtained
also a Master in Business and Management from the University of Padova.
PRIZES AND AWARDS
“Research Ideas For Business” University of Camerino competition 2010
First prize (3.000€) for the proposal “Portable biomedical ontologies for health”
Business Plan competition "Start Cup Umbria-Marche 2009"
Second prize (15.000€) for the business plan “Next Generation Bioinformatics”
FUNDING
“Progetto IMPRESA – Start Up Phase” 2011
10.000€ in consulting services for the startup phase of “Next Generation Bioinformatics”
“Progetto IMPRESA – Birth Phase” 2010
3.000€ in consulting services for the business plan “Next Generation Bioinformatics”
STUDIES
Master in Business and Management, 04/12/2009
Università di Padova
Thesis: “An academic-corporate spin-off for delivering bioinformatics services: the business plan
Tutors: Prof. Giacomo Boesso , faculty of Economy, Università di Padova; prof. Giorgio Valle,
dept. of Biology, Università di Padova
Courses: Accounting and Finance, Management in Organisations, Marketing Management and
Customer Behaviour, Operations Management, Corporate Social Responsibility, Management of
Knowledge, Strategic Management, Business Planning
In my MBM thesis I designed the business plan of an academic-corporate spin-off for delivering
bioinformatics services, aiming at satisfying a strong need for difficultly obtainable scientific and
technical competences.
PhD in Biotechnology, 07/02/2003
CRIBI biotechnology centre, Università di Padova
Thesis: “Analisi bioinformatica dell’espressione genica in muscolo scheletrico umano” (in italian;
“Bioinformatics analysis of gene expression in human skeletal muscle”)
Tutor: prof. Giorgio Valle, dept. of Biology, Università di Padova
Courses: Molecular Biology 1, Genetic 1, Genetic Engineering, Molecular Biology 2
The aspect that I better investigated in my PhD thesis is that of the construction of relational models
representing the biological entities involved in the regulation of gene expression, both at the
transcriptional and post-transcriptional level. The work is based on two different resources
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produced at the CRIBI Center of the University of Padua, which I actively participated to develop:
the TRAIT database of human skeletal muscle transcripts and the database of their expression
profiles in various tissues and cellular lines at different developmental stages and ages, analyzed by
hybridization on cDNA microarrays.
Degree in Computer Science, 23/04/1993
Università di Pisa
Votation: 110/110 cum laude
Thesis: “Un modello formale di reti data-flow per sistemi di controllo” (in italian; “A formal model
of data-flow networks for control systems”)
Courses: Geometry, Algebra, Theory and Application of Calculating Machines, Mathematic
Analysis 1, Physics 1, Numerical Calculus, Statistics and Probability Calculus, Systems for
Elaboration of Information 1, Mathematic Analysis 2, Operating Research, Physics 2, Systems for
Elaboration of Information 2, Methods for treatment of Information, Systems Theory, Bioelectronics, Elaboration of Non-Numerical Information, Formal Languages and Compilers, Project
of Numerical Systems.
My studies included operating systems, concurrent languages (CSP), computation theory, formal
languages and compilers, AI, mathematical logic, knowledge representation, vision, neural
networks, bioelectronics, PROLOG and COMMON LISP languages, Object Oriented programming
(CLOS), project of parallel architectures, firmware and microprogramming. In the thesis, developed
at CNUCE Institute of CNR, Pisa with prof. Luca Simoncini, dr. Andrea Bondavalli and dr. Cinzia
Bernardeschi, I studied formalism for data-flow networks and proposed an extension of an existing
model to formalize a data-flow language particularly suited for implementation of distributed
control systems with high requisite on parallelism, modularity and reliability.
High School Diploma in Computer Science, 12/07/1985
Technical Institute “ITIS C. Zuccante”, Venezia-Mestre
Votation: 58/60 (highest given from the final exam commission)
Courses: Computer Science, Analogic and Digital Electronics, Systems and Automation, Italian
Literature, Hystory, Mathematic Analysys, Statistics and Probability Calculus, English Language,
Physics, Chemistry, Natural Sciences.
I learnt programming in BASIC, FORTRAN, PASCAL and ASSEMBLERS (UNIVAC, DATA
GENERAL, 6502) and microprocessor control systems. For the final exam I programmed an
electronic-sheet (some kind of precursor of MS-EXCEL!) and projected and implemented a little
prototype of a microprocessor controlled system for the automatic regulation of the luminosity
inside an environment. In this period I developed also ad-hoc programs for some clients.
COURSES AND SCHOOLS
E-Learning course. “Progetto E-learning Università di Padova”
Padova, Italia. January-June 2004
28 hours lectures, practical activities, demonstrations, development of a Faculty level e-learning
project.
XV International School for Computer Science Researcher
“Algorithmics for Data Mining and Pattern Discovery”
Lipari (ME), Italia. 13-26/07/2003
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Lectures: Economic and Game-Theoretic Aspects of Information Systems, Pattern Discovery in the
Post Genomic Era, Search and Data Mining in the Internet Age, Authoritative Sources in a
Hyperlinked Environment, A New Science of Discovery and the Algorithmics of Surprise, Activist
Data Mining, Data Cleaning, Spectral Methods in Data Mining, Indexing Compressing and
Searching Texts, Large Scale Text Indexing: Data Structures Algorithmic Design and Engineering,
Post Genomic Data Mining: Discovering Patterns in Genomes Transcriptomes and Haplotypes,
Network Expression Inference.
XI International School for Computer Science Researcher
“Computational Biology”
Lipari (ME), Italia. 20/06/1999-03/07/1999
Lectures: String Algorithmics, Dynamic Programming in Computational Biology, Pairwise and
Multiple Sequence Alignment, Algorithm for Protein Structure Prediction, Protein-Ligand Docking,
Organization of Large Biological Databases, Genomics via Optical Mapping, Algorithms for
Genomic Sequences, Molecular Philogeny, Motifs in Sequences, Genomic Distance, Philogeny and
Algorithm, Molecular Biology and its Mathematics, Protein Structure.
TEACHING
Academic Year 2011-2012
Basi di Dati e Laboratorio di Basi di Dati (“Didactic duty”),
BSc in Computer Science, Università di Camerino
42+48 hours lectures and practicals. Relational database: model and languages. Methodologies and
models for database design. DBMS architecture. Supporting the students in the different phases of
SQL database projects.
Bioinformatics Programming (module of Genomics and Proteomics) (“Didactic duty”),
MSc in Biological Sciences, Università di Camerino
24 hours lectures: Bioinformatics Web Services, Bioinformatics Visual Programming with
workflows and Taverna, Bioinformatics Programming with Perl.
Academic Year 2010-2011
Basi di Dati e Laboratorio di Basi di Dati (“Didactic duty”),
BSc in Computer Science, Università di Camerino
42+48 hours lectures and practicals. Relational database: model and languages. Methodologies and
models for database design. DBMS architecture. Supporting the students in the different phases of
SQL database projects.
Computer Science (“Didactic duty”),
BSc in Biosciences and Biotechnologies, Università di Camerino
40 hours lectures and practicals: Boolean algebra, introduction to data structures and algorithms,
representation of information, introduction to databases and SQL, introduction to bioinformatics
and “-omics” disciplines, reference web resources for bioinformatics and “-omics” disciplines.
Bioinformatics Programming (module of Genomics and Proteomics) (“Didactic duty”),
MSc in Biological Sciences, Università di Camerino
24 hours lectures: Bioinformatics Web Services, Bioinformatics Visual Programming with
workflows and Taverna, Bioinformatics Programming with Perl.
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Academic Year 2009-2010
Basi di Dati e Laboratorio di Basi di Dati (“Didactic duty”),
BSc in Computer Science, Università di Camerino
42+48 hours lectures and practicals. Relational database: model and languages. Methodologies and
models for database design. DBMS architecture. Supporting the students in the different phases of
SQL database projects.
Computer Science (“Didactic duty”),
BSc in Biosciences and Biotechnologies, Università di Camerino
40 hours lectures and practicals: Boolean algebra, introduction to data structures and algorithms,
representation of information, introduction to databases and SQL, introduction to bioinformatics
and “-omics” disciplines, reference web resources for bioinformatics and “-omics” disciplines.
Bioinformatics Programming (module of Genomics and Proteomics) (“Didactic duty”),
MSc in Biological Sciences, Università di Camerino
24 hours lectures: Bioinformatics Web Services, Bioinformatics Visual Programming with
workflows and Taverna, Bioinformatics Programming with Perl.
Academic Year 2008-2009
Laboratorio di Basi di Dati (“Didactic duty”),
BSc in Computer Science, Università di Camerino
54 hours lectures and practicals. DBMS architecture. Supporting the students in the different phases
of SQL DB projects.
Introduction to Computer Science (“Didactic duty”),
BSc in Biotechnologies, Università di Camerino
38 hours lectures and practicals: Boolean algebra, introduction to data structures and algorithms,
representation of information, introduction to databases and SQL, introduction to bioinformatics
and “-omics” disciplines, reference web resources for bioinformatics and “-omics” disciplines.
Academic Year 2007-2008
Laboratorio di Basi di Dati (“Didactic duty”),
BSc in Computer Science, Università di Camerino
36 hours lectures and practicals. DBMS architecture. Supporting the students in the different phases
of SQL DB projects.
Introduction to Computer Science (“Didactic duty”),
BSc in Biotechnologies, Università di Camerino
35 hours lectures and practicals: Boolean algebra, introduction to data structures and algorithms,
representation of information, introduction to databases and SQL, introduction to bioinformatics
and “-omics” disciplines, reference web resources for bioinformatics and “-omics” disciplines.
Academic Year 2006-2007
Laboratorio di Basi di Dati (“On-contract professor”),
BSc in Computer Science, Università di Camerino
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42 hours lectures and practicals. DBMS architecture. Supporting the students in the different phases
of SQL DB projects.
Introduction to Computer Science (“On-contract professor”),
BSc in Biotechnologies, Università di Camerino
35 hours lectures and practicals: Boolean algebra, introduction to data structures and algorithms,
representation of information, introduction to databases and SQL, introduction to bioinformatics
and “-omics” disciplines, reference web resources for bioinformatics and “-omics” disciplines.
Academic Year 2005-2006
Bioinformatica e laboratorio (“On-contract professor”),
BSc in Agro-Industrial Biotechnologies, Università di Pisa
16-hours lectures and 12 hours practicals: introduction to the use of Bioinformatics resources on the
web.
Academic Year 2004-2005
Bioinformatica 3 (“On-contract professor”),
BSc in Molecular Biology, Università di Padova
40 hours lectures and 16 hours practicals: biological databanks, project implementation and
management of relational databases, development of WEB interfaces to biological databanks, Perl
programming language and its application to the management and analysis of biological databanks
and sequence data. Adoption of Moodle as an e-learning platform for the course.
Academic Year 2003-2004
Bioinformatica e laboratorio (“On-contract professor”),
BSc in Agro-Industrial Biotechnologies, Università di Pisa
16 hours lectures and 12 hours practicals: introduction to the use of Bioinformatics resources on the
web.
Bioinformatica 3 (“On-contract professor”),
BSc in Molecular Biology, Università di Padova
40 hours lectures and 16 hours practicals: biological databanks, project implementation and
management of relational databases, development of WEB interfaces to biological databanks, Perl
programming language and its application to the management and analysis of biological databanks
and sequence data.
Biologia Molecolare 2,
BSc in Molecular Biology, Università di Padova
1 hour lecture: Bioinformatics of eukaryotic promoters.
Academic Year 2002-2003
Bioinformatica 3,
BSc in Molecular Biology, Università di Padova
30 hours lectures and 18 hours practicals: biological databanks, project, implementation and
management of relational databases, development of WEB interfaces to biological databanks, Perl
programming language and its application to the management and analisys of biological databanks
and sequence data.
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Bioinformatica 2,
BSc in Molecular Biology, Università di Padova
1 hour lecture: algorithms for alignment of biological sequences.
Academic Year 2001-2002
Bioinformatica 1, BSc in Molecular Biology, Università di Padova
9 hours practicals on biological databanks web accession, textual and similarity search, protein
domains and sorting prediction.
Academic Year 2000-2001
Biologia Molecolare 2,
MSc in Biological Science, Università di Padova
5 hours lectures: introduction to Computer Science and to Bioinformatics.
Informatica,
BSc in Molecular Biology, Università di Padova
9 hours practicals: principles of computer usage, operating systems, common use WINDOWS
programs, Java programming
Java programming course,
40 hours lectures on Java programming for my research group
Academic Year 1999-2000
Introduction to computer science
32 hours lectures on Principles of Computer Science, Perl language, HTML, CGI-BIN
programming, Relational Databases and MySQL for my research group
PhD STUDENTS
Kumar Singh Saurabh.
PhD Student in Life Sciences and Public Health.
School of Advanced Studies. Università di Camerino (2011-2014)
Tutor
TUTOR OF THESES
Cristiano Virgulti. " Bioinformatica: Rassegna di database di variazioni genetiche" (in italian;
Bioinformatics: a review of databases of genetic variation)
BSc thesis in Computer Science. Università di Camerino (2012)
Tutor
Francesco Fortunati. " Sviluppo di app Android per laboratori di ricerca biomolecolare" (in italian;
Development of Android apps for biomolecular research laboratories)
BSc thesis in Computer Science. Università di Camerino (2012)
Tutor
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Stefano Ciocchetti. "Restyling del portale delle biblioteche Unicam" (in italian; Restyling of the
portal of Unicam’s libraries)
BSc thesis in Computer Science. Università di Camerino (2011)
Tutor
Andrea Marcelli. "MySmark EDU: reportistica per docenti" (in italian; MySmark EDU: reporting
for teachers)
BSc thesis in Computer Science. Università di Camerino (2011)
Tutor
Mario De Filippis. "Geografia della Giustizia: una Base di Dati " (in italian; Geography of Justice:
a Database)
BSc thesis in Computer Science. Università di Camerino (2011)
Tutor
Matteo Benedetti. "Progettazione e sviluppo di nuovi servizi per il catalogo bibliografico web di
ateneo" (in italian; Design and development of new services for the web bibliographic catalogue of
the university)
BSc thesis in Computer Science. Università di Camerino (2009)
Tutor
Francesco Mosconi. "Catalogo bibliografico web di ateneo: estensione delle funzionalità" (in
italian; Bibliographic catalogue of the university: extension of functionality)
BSc thesis in Computer Science. Università di Camerino (2009)
Tutor
Claudio Forcato. "Orion: a Spatial Multiagent System Framework for Cellular Simulation.
Implementation of Molecular Movement at the Mesoscale"
MSc thesis in Bionformatics. Università di Camerino (2006)
Co-tutor
Michele Mattioni. "Orion: a Multiagent System Framework for Cellular Simulation.
Implementation of Metabolic Reaction at the Mesoscale"
MSc thesis in Bionformatics. Università di Camerino (2006)
Co-tutor
Luana Leoni. "Un’ontologia delle risorse per il Resourceome Bioinformatico" (in italian; A
resource ontology for the Bioinformatics Resourceome)
MSc thesis in Computer Science. Università di Camerino (2006)
Co-tutor
Arianna Baldoncini. "Orion: a spatial Multi Agent System framework for Computational Cellular
Dynamics of metabolic pathways"
MSc thesis in Bionformatics. Università di Camerino (2006)
Co-tutor
Francesca Piersigilli. "The Bioinformatics Resourceome Architecture"
MSc thesis in Computer Science. Università di Camerino (2006)
Co-tutor
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Giorgio Fabbro. "Analisi comparativa dei pattern di sequenza caratterizzanti i genomi batterici
sequenziati (in italian; Comparative analysis of the sequence pattern characterizing the sequenced
bacterial genomes)"
MSc thesis in Molecular Biology. Università di Padova (2005)
Co-tutor
Briano Casotto. "Sviluppo di un sistema per l'analisi di biosequenze (in italian; Development of a
system for biosequences analysis)"
BSc thesis in Computer Science. Università di Venezia (2005)
Co-tutor
Massimiliano Molin. "Interfaccia per un sistema per l'individuazione di motivi biologici
interessanti (in italian; Interface for a system for the individuation of interesting biological motifs)"
BSc thesis in Computer Science. Università di Venezia (2005)
Co-tutor
Davide Rossi. "GGR - Gestione Gruppi Ricerca (in italian; management of research groups)"
BSc thesis in Computer Science. Università di Venezia (2005)
Co-tutor
Massimiliano Brancalion. "GGR - Gestione Gruppi Ricerca (in italian; management of research
groups)"
BSc thesis in Computer Science. Università di Venezia (2005)
Co-tutor
Claudio Fusco. "GGR - Gestione Gruppi Ricerca (in italian; management of research groups)"
BSc thesis in Computer Science. Università di Venezia (2005)
Co-tutor
Marco Paoli. "Analisi bioinformatica di pattern nucleotidici degenerati per la discriminazione di
introni ed esoni (in italian; Bioinformatics analysis of degenerated nucleotidic patterns for
intron/exon discrimination)"
BSc thesis in Molecular Biology. Università di Padova (2004)
Co-tutor
Alice Vanzo. "Ricerca bioinformatica di pattern discriminanti strutture secondarie in sequenze
proteiche (in italian; Bioinformatics research of pattern discriminating secondary structures in
proten sequences)"
BSc thesis in Molecular Biology. Università di Padova (2004)
Co-tutor
Andrea Telatin. "Ricerche di sequenze regolatorie della trascrizione tramite analisi bioinformatica
delle interazioni tra fattori di trascrizione (in italian; Research of transcription regulatory sequence
by bioinformatics analysis of transcription factors interactions)"
BSc thesis in Moecular Biology. Università di Padova (2004)
Co-tutor
Mirco Menesello. "Analisi bioinformatica del complesso SRP in Photobacterium profundum (in
italian; Bioinformatics analysis of the SRP complex in Photobacterium proundum)"
BSc thesis in Molecular Biology. Università di Padova (2004)
Co-tutor
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Giulio Marcon. "Dna sequencing: the computational point of view"
MSc thesis in Computer Science. Università di Venezia (2004)
Co-tutor
Stefano Zennaro. "Progettazione di un'interfaccia grafica per la suite di programmi Molphy (In
italian; project of a graphic interface for the Molphy programs suite)"
BSc thesis in Computer Science. Università di Venezia (2004)
Co-tutor
Claudio Forcato. "Ricerca bioinformatica di pattern degenerati discriminanti tra due popolazioni di
sequenze (in italian; Bioinformatics search for degenerated discriminating patterns between two
sequence populations"
BSc thesis in Molecular Biology. Università di Padova (2004)
Co-tutor
Giorgio Fabbro. "Sviluppo e impiego di un sistema bioinformatico per la ricerca di pattern
inaspettati in sequenze genomiche (in italian; Development and use of a bioinformatic system for
research of unexpected patterns in genomic sequences)"
BSc thesis in Molecular Biology. Università di Padova (2003)
Co-tutor
Pasin Anna. “Ricerca di pattern nucleotidici discriminanti tramite analisi comparata di introni ed
esoni” (in italian: “Search of discriminant nucleotidic patterns by the comparative analysis of
introns and exons”).
BSc Thesis in Molecular Biology, Università di Padova. (2003)
Co-tutor
Dal Monego Simeone. “Sviluppo di un microarray di cDNA muscolari di topo: sequenziamento di
EST, gestione bioinformatica del progetto e selezione dei campioni rappresentativi dei trascritti” (in
italian; “Development of a microarray of mouse muscle cDNA: EST sequencing, bioinformatics
management of the project and selection of the samples representing the transcripts”).
MSc Thesis in Biological Sciences, Università di Padova. (2002)
Co-tutor
PRESENTATIONS AND INVITED TALKS
“Agents based modelling and simulation of cellular processes”
Mini workshop on "Computational approaches to biology”, Galileo PhD School. Pisa, Italy, 25/10/
2007
“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, 13/06/ 2007
“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), Italy, 10/07/ 2006
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“Semantic Network for E-Resources - An experience from E-science”
First Workshop on E-Government Ontologies, Sirolo(AN), Italy, 08/10/2005
“An introduction to Systems Biology”
Department of Informatics and Mathematics. University of Camerino, Camerino(MC), Italy,
16/06/2005
“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, 07/09/ 2004
“How can we use Agents for simulation and modelling of cellular processes?”.
AgentLink III Technical Forum I – BioAgents. Roma, Italia. 02/07/2004
“Agents for BIOLIMS and for Distributed Databases Querying?”.
AgentLink III Technical Forum I – BioAgents. Roma, Italia. 02/07/2004
“ECCB2003: an overview”
Department of Computer Science, University of Venezia. Mestre (VE), Italia. 23/10/2003
“Simplifying aminoacid alphabets by means of a branch and bound algorithm and
substitution matrices”. Gruppo di Cooperazione Bioinformatica. Certosa di Pontignano (SI), Italy.
16/03/2002
“A data flow language for control systems and its application in managing processes for
Genomic Projects”. I Italian Workshop on Genome Research and Sequencing Technology. San
Miniato (PI), Italy. 04/06/1997
MEMBER OF COMMITTEE
Member of the Scientific Committee for the business plan competition “Start Cup Perugia
Camerino 2008”
CO-CHAIR OF WORKSHOPS
FBTC 2008. Second International Workshop “From Biology To Concurrency and back”. Satellite
workshop of ICALP 2008.
Reykjavik, Iceland, July 12, 2008
FBTC 2007. First International Workshop “From Biology To Concurrency and back”. Satellite
workshop of CONCUR 2007.
Lisbon, Portugal, September 8, 2007
NETTAB2007. VII International Workshop on Network Tools and Applications in Biology: “A
Semantic Web for Bioinformatics: Goals, Tools, Systems, Applications”
Pisa, Italia. June 12-15, 2007
MEMBER OF PROGRAM COMMITEE FOR WORKSHOPS
WOA2011. XII Italian Workshop from Objects to Agents
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Rende (CS), Italia, July 4-6, 2011
WOA2010. XI Italian Workshop from Objects to Agents
Rimini, Italia. September 6-7, 2010
WOA2008. IX Italian Workshop from Objects to Agents “Evolution of agent development:
methodologies, tools, platforms and languages”
Palermo, Italia. November 17-18, 2008
MAS&BIO 2008. International Workshop on Multi Agents Systems and Bioinformatics.
Cagliari, Italia, September 11, 2008
NETTAB2008. VIII International Workshop on Network Tools and Applications in Biology:
“Bioinformatics Methods for Biomedical Complex System Applications”
Varenna, Como lake, Italia. May 19-21, 2008
MAGS*BIOMED2007. International Workshop on Multi-Agent and Grid Systems for Medicine,
Computational Biology, and Bioinformatics
Leipzig, Germany. September 24-26, 2007
WOA2007. VIII Italian Workshop from Objects to Agents “Agents and industry: technological
applications of software agents”
Genova, Italia. September 24-25, 2007
WOA2006. VII Italian Workshop from Objects to Agents “Grid, P2P and Self-* systems”
Catania, Italia. September 26-27, 2006
WOA2005. VI Italian Workshop from Objects to Agents “Simulation and Formal Analysis of
Complex Systems”
Camerino (MC), Italia. November 14-16, 2005
MAS*BIOMED2005. First International Workshop on Multi-Agent Systems for Medicine,
Computational Biology, and Bioinformatics
Utrecht, The Netherlands. July 25, 2005
REVIEWER
Reviewer of articles for many Bioinformatics and Computer Science journals including
Bioinformatics, BMC Bioinformatics, Journal of Biomedical Informatics, IEEE Transactions on
Information Technology in Biomedicine, Theoretical Computer Science, Knowledge and
Information Systems, Government Information Quarterly. Reviewer of articles for Bioinformatics
and Computer Science workshops and conferences including FCT, MATES, BITS, NETTAB, BSB.
PARTECIPATION AT MEETINGS, WORKSHOPS, CONFERENCES
BIO-IT WORLD EUROPE 2011. Third International Conference and Expo (at BIOTECHNICA)
Hannover, Germany, October 11-13, 2009
BITS2011. VIII Bioinformatics ITalian Society meeting
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Pisa, Italia. June 20-22, 2011
KICK- OFF MEETING EU-FP7 Project microAqua (Universal Microarrays for the evaluation of
fresh-water Quality based on detection of pathogens and their toxins)
Berlin, Germany. March 31-April 1, 2011
BIO-IT WORLD EUROPE 2009. First International Conference and Expo (at BIOTECHNICA)
Hannover, Germany, October 5-8, 2009
FBTC 2008. Second International Workshop “From Biology To Concurrency and back”.
Reykjavik, Iceland, July 12, 2008
NGFN SMP Bioinformatics workshop. From Bioinformatics to Medical Systems Biology
Heidelberg, Germany. November 12-13, 2007
SYSBIOHEALTH2007. First International Symposium in Systems Biology for Health.
Milano, Italy. October 16-19, 2007
CMSB2007. V International Conference on Computational Methods in Systems Biology
Edinburgh, UK. September 20-21, 2007
FBTC2007. I International Workshop “From Biology To Concurrency and back
Lisbon, Portugal. September 8, 2007
CONCUR2007. XVIII International Conference on Concurrency Theory
Lisbon, Portugal. September 4-7, 2007
EXPRESS2007.
Lisbon, Portugal. September 3, 2007
NETTAB2007. VII International Workshop on Network Tools and Applications in Biology: “A
Semantic Web for Bioinformatics: Goals, Tools, Systems, Applications”, Pisa, Italy, June 12-15,
2007
BITS2007. IV Bioinformatics ITalian Society meeting
Napoli, Italia. April 26-28, 2007
CMSB2006. IV International Conference on Computational Methods in Systems Biology
Trento, Italia. October 18-19, 2006
CONVERGING SCIENCES 2006. II International conference
Trento, Italia. October 16-17, 2006
NETTAB2006. VI International Workshop on Network Tools and Applications in Biology:
“Distributed Applications, Web Services, Tools and GRID Infrastructures for Bioinformatics”
S. Margherita di Pula (CA), Italia. July 10-13, 2006
BITS2006. III Bioinformatics ITalian Society meeting
Bologna, Italia. April 28-29, 2006
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WOA2005. Italian Workshop on Simulation and Formal Analysis of Complex Systems: “Ffom
Objects to Agents”
Camerino (MC), Italia. November14-16, 2005
ICSB2005. VI International Conference on Systems Biology
Boston, Ma., USA. October 19-24, 2005
NETTAB2005. V International Workshop on Network Tools and Applications in Biology:
“Workflows management: new abilities for the biological information overflow”
Napoli, Italia. October 05-07, 2005
BITS2005. II Bioinformatics ITalian Society meeting
Milano, Italia. March 18-19, 2005
ICSB2004. V International Conference on Systems Biology
Heidelberg, Germany. October 09-13, 2004
NETTAB2004. IV International Workshop on Network Tools and Applications in Biology:
“Models and Metaphors from Biology to Bioinformatics Tools”
Camerino (MC), Italia. September 05-07, 2004
ISMB/ECCB2004. XII International Conference on Intelligent Systems for Molecular Biology /
III European Conference on Computational Biology
Glasgow, UK. August 01-04, 2004
WEB04. Workshop on Education in Bioinformatics
Glasgow, UK. July 30, 2004
ALIII-TFI. AgentLink III Technical Forum I on BioAgents
Roma, Italia. July 02, 2004
BITS2004. I Bioinformatics ITalian Society meeting
Padova, Italia. March 26-27 , 2004
ECCB2003. II European Conference on Computational Biology
Paris, France. September 27-30, 2003
Sequence Databases and Ontologies workshop (organized by IMPG and PBIL)
Paris, France. September 26, 2003
BIONOVA2003. Forum and Exhibition on Biotechnology and Bioengineering
Padova, Italy. June 04-06, 2003
BIOCOMP2002. Gruppo di Cooperazione Bioinformatica
Certosa di Pontignano (SI), Italy. March 15-16, 2002
BIONOVA2001. II conference and Exhibition on Biotechnology and Bioengineering
Padova, Italy. 28/11-01/12/2001
Telethon X Scientific Convention
14
Riva del Garda (TN), Italy. November 18-20, 2001
BIOCOMP2001. Gruppo di Cooperazione Bioinformatica
Certosa di Pontignano (SI), Italy. February 17-18, 2001
Telethon IX Scientific Convention
Rimini, Italy. November12-14, 2000
PRIN99. Project Meeting
Giovinazzo (BA), Italy. July10-11, 2000
BIOCOMP2000. Gruppo di Cooperazione Bioinformatica
Certosa di Pontignano (SI), Italy. March 03-04, 2000
BIONOVA1999. I Mostra convegno Biotecnologie e Bioingegneria
Padova, Italy. November 24-27, 1999
Telethon VI Scientific Convention
Bologna, Italy. November 12-14, 1997
I Italian Workshop on Genome Research and Sequencing Technology
San Miniato (PI), Italy. June 02-04, 1997
WORK POSITIONS
10/2007-now
University of Camerino, dept. of Mathematics and Computer Science
Lecturer (research assistant professor) in Computer Science
11/2005-09/2007
University of Camerino, dept. of Mathematics and Computer Science
PostDoc Collaboration Contract in Project FIRB RBLA0332RH_003, University of Camerino
11/2004-10/2005
Telethon Foundation
PostDoc Collaboration Contract in Project GSP04289, CRIBI bioinformatics lab
05/2002-10/2004
Università di Padova, dept. of Biology
Research collaborator (University Researcher), CRIBI bioinformatics lab
01/2002-04/2002
Telethon Foundation
Collaboration Contract in Project B57-3, CRIBI bioinformatics lab
03/2000-12/2001
Università di Padova, dept. of Biology
Collaboration Contract in Project PRIN99, CRIBI bioinformatics lab
03/1998-02/2000
Telethon Foundation
15
Collaboration Contract in Project B41, CRIBI bioinformatics lab
11/1996-02/1998
Telethon Foundation
Fellowship in Project B39, CRIBI bioinformatics lab
09/1994-05/1996
ELDA Ingegneria spa, Treviso
C and UNIFACE analyst/programmer, project-head and testing responsible.
07/1994-08/1994
AIVE spa, Venezia
COBOL/DB2 Programmer
03/1993-03/1994
Library System City of Venezia. Quarter library number 16
Conscience Objector alternative to military service in quarter library number 16, helping the staff
and the users of the library
GRANTS
FIRB RBLA0332RH_003
Ministero Istruzione, Università e Ricerca, 2005
“Interdisciplinary laboratory of Bioinformatics Technology”
GSP04289
Telethon Foundation, 2004
“Functional genomics of skeletal and cardiac muscles”
GP0101/01
Telethon Foundation, 2001
“Multi centre bioinformatic project for a systematic investigation of genes expressed in human
skeletal muscle” in collaboration with prof. Graziano Pesole, Università di Milano
B57-3
Telethon Foundation, 2001
“Functional Genomics of Skeletal Muscle”
PRIN99
Ministero Istruzione, Università e Ricerca, 1999
“Bioinformatics and Genomic Research: Development of a database of transcripts expressed in
human skeletal muscle as a prototype of a general database of transcripts”
B41
Telethon Foundation, 1998
“Integrated molecular analysis of gene expression in human skeletal muscle”
B39
Telethon Foundation, 1996
16
DIRECTED PROJECTS
EU-FP7 Project microAqua (NGB SRL 2011)
Official Web site, database and internal web site for data management and analysis
OTHER WORKS
President of board of directors. BMR Genomics SRL (2005-2007; 2011-)
E-Learning Science Faculty Project (2004)
Analysis of the e-learning existing situation in the Science Faculty at University of Padova.
Planning of the e-learning development with the installation and configuration of a LMS
(MOODLE) server for all the courses of the Faculty. Spreading of the e-learning culture with
presentations, on-line forum, direct help and demonstrations to the professors.
In collaboration with Prof. Piero Benedetti, Prof. Roberto Bisson, Dott. Ornella Pantano and
Giuseppe Cortese, Faculty of Science, University of Padova.
BITS meeting organization (2004)
Logistic organization of the I meeting of the Bioinformatics ITalian Society held in Padova in
March 2004. Responsible of the web site for the registrations and the pubblications of the congress.
In collaboration with Prof. Giorgio Valle and Giorgio Fabbro, CRIBI.
Distributed similarity searches (1999)
Project and development (JAVA, Perl) of a system for the distribution of similarity searches on a
network of LINUX servers, with the automatic mirroring of the sequence databases on the servers.
In collaboration with Rosario Dioguardi and Paolo Scannapieco.
The “NEW” BIOLIMS (1998)
Project and development (JAVA) of a visual environment for the definition (Editor) and the
execution (RTS) of automatic data-flow control systems for the management of the sequencing lab
at CRIBI (BIOLIMS). Its application in the DNA sequencing projects of Arabidopsis thaliana,
Homo sapiens EST, Psycobacterium profundum and others.
MOGM (1997)
Project and development (Perl, mSQL, HTML) of the database and the web interface for the
handling of information related to the Genetic Modified Organism at the Department of Biology. In
collaboration with Prof. Gerolamo Lanfranchi, Dept. of Biology.
System Definition Language (1996-1997)
Project and development (C) of a language (and its compiler!) for the definition and the execution
of automatic control systems, based on the data-flow paradigm. Its application in the DNA
sequencing projects of Human Skeletal Muscle EST, Saccharomices cerevisiae, Ciona intestinalis
and others.
.BMR DNA SEQUENCING SERVICE (2000-2005)
Project and development (MySQL, Perl, JAVA, HTML) of the database, web interface and the
procedure for the operativity and the management of the DNA sequencing service at CRIBI. In
collaboration with Barbara Simionati, CRIBI.
Management of my research group (1996-2005)
17
Project and development (MySQL, Perl, JAVA, HTML) of the database and the web interface for
the management of my research group: staff, seminars, meeting, publications, theses, messaging. In
collaboration with Emanuela Bertocco
18
PUBLICATIONS
Book Chapters
Cannata N., Corradini F., Merelli E., Piersigilli F., and Vito L.
2. Towards Bioinformatics Resourceomes
In “Biomedical Data and Applications”, Edited by Sidhu, A. S.; Dillon, T. Series: Studies in
Computational Intelligence , Vol. 224. Springer, Heidelberg, Germany (2009) pp. 13-36
ISBN 978-3-642-02192-3
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, Cambridge, UK (2004) pp. 309-343
ISBN 0-9545232-0-2
Special issues of journals edited
Theoretical Computer Science
Volume 411, Issue 20, Pages 1995-2077 (28 April 2010)
Hybrid Automata and Oscillatory Behavior in Biological Systems
Edited by N. Cannata, E. Merelli, I. Ulidowski
Theoretical Computer Science
Volume 410, Issues 33-34, Pages 3035-3186 (21 August 2009)
Concurrent Systems Biology: To Nadia Busi (1968–2007)
Edited by N. Cannata and E. Merelli
Electronic Notes in Theoretical Computer Science
Volume 229, Issue 1, Pages 1-182 (28 February 2009)
Proceedings of the Second Workshop From Biology to Concurrency and Back (FBTC 2008),
Reykjavik, Iceland,12 July 2008
Edited by N. Cannata, E. Merelli and I. Ulidowski
BMC Bioinformatics
Volume 9 Suppl 4 (25 April 2008)
A Semantic Web for Bioinformatics: Goals, Tools, Systems, Applications
from Seventh International Workshop on Network Tools and Applications in Biology (NETTAB
2007), Pisa, Italy. 12-15 June 2007
Edited by Paolo Romano, Michael Schroeder, Nicola Cannata and Roberto Marangoni
Electronic Notes in Theoretical Computer Science
Volume 194, Issue 3, Pages 1-180 (20 January 2008)
Proceedings of the First Workshop "From Biology To Concurrency and back (FBTC 2007)",
Lisbon, Portugal, 08 September 2007
Edited by N. Cannata and E. Merelli
Journal Articles
Maccagnan A., Riva M., Feltrin E., Simionati B., Vardanega T., Valle G., Cannata N.
19
Combining ontologies and workflows to design formal protocols for biological laboratories
Automated Experimentation 2010, 2:3 (23 April 2010)
Cannata N., Merelli E., Ulidowski I.
Preface (Hybrid automata and oscillatory behaviour in biological systems)
Theoretical Computer Science, 411(20): 1997-1998, (2010)
Cannata N., Merelli E., Ulidowski I.
Preface (From Biology To Concurrency and back 2008)
Electronic Notes in Theoretical Computer Science, 229: 1-2 (2009)
Cannata N., Merelli E.
Preface (Concurrent Systems Biology: To Nadia Busi (1968–2007))
Theoretical Computer Science, 410(33-34): 3037-3038, (2009)
Cannata N., Schröder M., Marangoni R, RomanoP.
A Semantic Web for bioinformatics: goals, tools, systems, applications
BMC Bioinformatics, 9(Suppl 4):S1 (2008)
Cannata N., Merelli E.
Preface (From Biology To Concurrency and back 2007)
Electronic Notes in Theoretical Computer Science, 194: 1-3 (2008)
Cannata N., Corradini F., Merelli E.
Multiagent modelling and simulation of carbohydrate oxidation in cell.
Int. J. Modelling, Identification and Control, 3(1): 17-28 (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: 531-533 (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): 582-588 (2005)
20
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 317 (5714) (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)
Articles at conferences (with ISBN and peer review)
Maccagnan A, Cannata N, Valle G, Vardanega T. Mapping OBI and XPDL to a MDE Framework
for Laboratory Information Processing.
The Fourth International Conference on Information, Process, and Knowledge Management
(eKNOW 2012), Valencia, Spain, January 30 - February 4, 2012.
In “Conference Proceedings”, Edited by Jaime Lloret Mauri, Pascal Lorenz. Valencia, Spain (2012)
pp. 150-154
ISBN: 978-1-61208-181-6
Articles and communications to congresses, proceedings, technical reports
Maccagnan A, Vardanega T, Feltrin E, Valle G, Riva M, Cannata N. A Multi-Agent System for the
Automated Handling of Experimental Protocols in Biological Laboratories.
XI Italian Workshop from Objects to Agents (WOA 2010), Rimini, Italy, September 6-7, 2010.
Cannata N, Corradini F, Merelli E, Tesei L. A Spatial Simulator for Metabolic Pathways
International Workshop on Multi Agents Systems and Bioinformatics (MAS&BIO 2008), Cagliari,
Italia, September 11 2008
21
Alfieri R, Cannata N, Merelli E, Milanesi L, Tesei L. Using SKOS to formalize parameter
estimation in systems biology
VIII International Workshop on Network Tools and Applications in Biology: “Bioinformatics
Methods for Biomedical Complex System Applications” (NETTAB 2008), Varenna, Como lake,
Italy, May 19-21 2008, p.13-15.
Cannata N, Corradini F, Merelli E, Tesei L. A spatial model and simulator for metabolic pathways
VIII International Workshop on Network Tools and Applications in Biology: “Bioinformatics
Methods for Biomedical Complex System Applications” (NETTAB 2008), Varenna, Como lake,
Italy, May 19-21 2008, p.40-42.
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 machineunderstandable 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. 45-49
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
22
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 Dipartimento Informatica, Università di Venezia 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.
23
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 2730 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
24
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
25
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
26
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
27
