Programme Outline


Sunday September 5th

Registration (Sala Della Muta, Piazza Cavour)


Prof. Fulvio Esposito
(Dean of the Faculty of Science and Technology)


Bioinformatics at Unicam
Prof. Gloria Cristalli
(Coordinator of the Course in Bioinformatics)

Opening Lecture

Chair: Flavio Corradini
14:15 - 15:00
Modelling Biological Network [Presentation, 36Kb]
Anna Ingolfsdottir
(University of Iceland, Reykjavik, Iceland, BRICS, Dept. of Computer Science, Aalborg University)

15:00 - 16:30 Session 1: Computational Biology I

Chair: Roberto Marangoni
Maximum Likelihood and Statistical Model Selection Methods Applied to Protein Interaction Network Data
    Michael P.H. Stumpf, Piers J. Ingram
(Imperial College London, UK)

A MultiAgent System for Protein Secondary Structure Prediction [Presentation, 424Kb]
    Giuliano Armano, Gianmaria Mancosu, Alessandro Orro, (UniversitÓ di Cagliari, Italy)
Using Secondary Structure Information to Perform Multiple Alignment [Presentation, 244Kb]
    Giuliano Armano, Alessandro Orro (UniversitÓ di Cagliari), Luciano Milanesi (ITB-CNR, Milano Italy)
16:00 - 16:30

Coffee break



17:00 - 18:15

Session 2: Computational Biology II

Pablo Gonzalez

Computer-Aided DNA Base Calling from Forward and Reverse Electropherograms [Presentation, 528Kb]
Valerio Freschi, Alessandro Bogliolo (UniversitÓ di Urbino, Italy)
Random Subspace Ensembles for the Bio-molecular Diagnosis of Tumors [Presentation, 124Kb]
Alberto Bertoni, Raffaella Folgieri and Giorgio Valentini (UniversitÓ degli Studi di Milano, Italy)
Short communication:
A Quest for EDC-related Genes in the Context of Bio-medical Literature [Presentation, 176Kb]
Massimo Ubaldi, Laura Soverchia, Roberto Ciccocioppo, Gilberto Mosconi and Alberta Maria Polzonetti (UniversitÓ di Camerino, Italy)
20:00           Welcome wine party

Monday September 6th

9:00 - 10:00 Invited Lecture
chair: Roberto Ciccocioppo

Microarrays Methods and Applications [Presentation, 5,292Kb]

Gary Hardiman, (Unversity of California, USA)

10:00 - 11:00   Session 3: Computational Biology III
chair: Michael P.H. Stumpf
Satellite Event:
Workshop on theory and practice on Gene-Array technology

BDD-Based Algorithms in Genetic Linkage Analysis

Anna Ingolfsdottir,(University of Iceland,  BRICS, Dept. of Computer Science, Aalborg University)
Daniel Gudbjartsson, Gunnar Gunnarsson, Thorvaldur Thorvaldsson, (DeCode Genetics, Reykjavik, Iceland)

Experimental design for microarray studies.

Wolfgang Sommer, (Neurotec, Karolinska Institute, Huddinge University Hospital, M 57, S-14186 Stockholm, Sweden)

Towards Motif Detection in Networks: Frequency Concepts and Flexible Search [Presentation, 888Kb]

Falk Schreiber, Henning Schw÷bbermeyer (Bioinformatics Center Gatersleben-Halle, Germany)

Sample preparation, amplification and labeling for array analysis

Franco Martinez, (Celbio S.p.A,  Milan, Italy)

11:00 - 11:30

Coffee break

11:30 - 13:30

Poster Session: For the complete click here
                            or see below

Satellite Event:
Workshop on theory and practice on Gene-Array technology

Forget limitations of the past: a complete solution for RNA amplification

Annamaria Guiducci,  (MWG Biotech, Srl Florence , Italy)

Ready...Set...Scan! What's inside a microarray scanner?

Nicola Bortoletto,  (Bio-Rad Laboratories srl Segrate MI, Italy)

Basic principles in data analysis and visualization

Pasquale De Luca, (SZN-BioGeM, Naples, Italy)

THE MWG oligo-array concept: Progression is a matter of trust

Lucilla Biagini (MWG Biotech Srl, Florence, Italy)

13:30 - 15:00


15:00 - 16:00 Discussion Panel:

Models and Metaphors from Biology to Computer Science and Bioinformatics

Expected participants:
as biologists,

Alfredo Colosimo
 (UniversitÓ di Roma "La Sapienza" Italy)
Giorgio Valle "Bioinformatics applied to the analysis of genomes ",  (UniversitÓ di Padova, Italy)
Cristina Miceli and Maurizio Massi [Presentation, 48Kb]
 (UniversitÓ di Camerino, Italy)

as computer scientists
Luca Cardelli
 (Microsoft Reseach, UK)
Pierpaolo Degano
 (UniversitÓ di Pisa, Italy)
Anna Inglfsdottir

 (University of Iceland, Reykjavik Iceland,
 BRICS, Dept. of Computer Science,
 Aalborg University)
Paola Quaglia
 (UniversitÓ di Trento, Italy)

moderated by

Andrea Omicini and Emanuela Merelli

Satellite Event:
Workshop on theory and practice on Gene-Array technology

Guided discussion on the  major topics emerged in the morning session

Coffee break

16:00 - 16:30
16:30 - 19:30 Social Event:

Grotte di Frasassi or
Guided Tour of Camerino and visit to the "Vitalini Castle"

Satellite Event:
Workshop on theory and practice on Gene-Array technology

Guided discussion on the  major topics emerged in the morning session


Social Dinner (at Vitalini Castle)  

Tuesday September 7th

9:00 - 10:00 Invited Lecture

Chair: Andrea Omicini
Languages and Notations for Systems Biology [Presentation, 2,868Kb]
 Luca Cardelli (Microsoft Research Cambridge, UK)
10:00- 11:00 Session 4: Systems Biology

Chair: Piepaolo Degano
Modelling, Simulation and Visualisation of Stem Cell Behaviour [Presentation, 320Kb]
Mark d'Inverno and Jane Prophet (University of Westmister, UK)
Modeling Kohn Interaction Maps with Beta Binders: an Example
Federica Ciocchetta, Corrado Priami, Paola Quaglia (UniversitÓ di Trento, Italy)

11:00 - 11:30

Coffee break

11:30 - 12:00

Modeling Gene Expression [Presentation, 304Kb]
 Jasmin Őarić, Isabel Rojas, Esther Ratsch, Renate Kania, Ulrike Wittig (EML Research gGmbH, Germany)
Aldo Gangemi (CNR, Italy)

12:00 - 13:00   Session 5: Bioinformatics Engineering

Chair: Anna Ingolfsdottir
    Specifying In Silico Experiments as Coordinations of Coarse-Grained Processes [Presentation, 76Kb]
Ane Tr÷ger and Alvaro A. A. Fernandes (University of Manchester, UK)
    Short Communications:
    Bioinformatics Engineering: A Process Methodology                                                             Paola Inverardi, Daniele Pavone, Pietro Recchilongo, Alessandra Tessitore (UniversitÓ di L'Aquila, Italy)
    An Agent-oriented Conceptual Framework for Biological Systems [Presentation, 144Kb]
Nicola Cannata (UniversitÓ di Padova), Flavio Corradini, Emanuela Merelli (UniversitÓ di Camerino), Andrea Omicini, Alessandro Ricci (UniversitÓ di Bologna, Italy)
13:00 - 13:15 Closing Remarks and Announcement of NETTAB 2005 [Presentation, 88Kb]


    P1  Dave Angulo (DePaul University) Alex Schilling, Kevin Drew, Tim Freeman (University of Chicago)

 Mass Spectra Analysis on the Illinois BioGrid


 Saverio Alberti, Marco Trerotola (UniversitÓ di Chieti, Italy) and Andrew Emerson (CINECA, Italy)

 On the detection of spliced chimeric mRNAs in sequence databanks  

 Anna Marabotti and Angelo M. Facchiano (ISA-CNR, Italy)

 Comparative modelling of human galactose-1-phosphate  

 uridylyltransferase and of its galactosemia-related mutant Q188R: A molecular explanation of the structural effects of the mutation


 Susan Costantini,   

 Giovanni Colonna and

 Angelo M. Facchiano (Seconda UniveritÓ di Napoli, Italy)

 Prediction of the secondary structure of proteins: The amino acid propensities in proteins belonging to different secondary structural classes


 Jason S. Iacovoni (INSERM, F), Allouche (INRIA, France), and Herve Prats (INSERM, France)


 GeneHuggers Divide and Conquer modules: parallelized sequence database mining of complex genomes

    P6  Acquadro F., Mello Grand M, Segir R, Vizzini L, Scatolini M and Chiorino G. (Bioinformatics Pharmacogenomics Laboratory, Italy)

 Gene Expression Profiling on a cohort of 50 early stage prostate cancer patients


 Arlinde Christina, Karolinska

 Ploner, A. and Sommer W. (Institutet, Stockholm, Sweden)

 Effect of a priori filtering on microarray derived candidate gene lists with p-values adjusted for false discovery rate.


 Fusetti L., Maran V., Parma P. I (LEA, Istituto, Italy ), Damin F., Chiari M. (CNR Milano), Greppi G.F. (UniversitÓ di Milano, Italy)

 Bovine Gene Expression Profiling In Lipid Metabolism By Microarray Analysis  

 Antonietta La Terza (UniversitÓ di Camerino), Roberto Marangoni,

Nadia Pisanti (UniversitÓ di Pisa, Italy), Sabrina Barchetta, Cristina Miceli (UniversitÓ di Camerino, Italy)

 Bioinformatic tools to identify structured motifs in the upstream regions of stress-response-involved genes in Tetrahymena thermophila


 Mario Compiani (UniversitÓ di Camerino, Italy), Emidio Capriotti, Rita Casadio (UniversitÓ di Bologna, Italy)

 Computation of the Folding Rates of wild type and mutant Proteins

 Ezio Bartocci, Flavio Corradini,

 Emanuela Merelli (UniversitÓ di Camerino, I)

 An overview of  Service Discovery for biological distributed applications  

 Flavio Corradini, Chiara Ercoli,

 Emanuela Merelli, Barbara Re (UniversitÓ di Camerino, Italy)

 A Matchmaker for BioMoby  

 Mauro Angeletti, Ezio Bartocci,

 Arianna Baldoncini, Rosario Culmone (UniversitÓ di Camerino, Italy)

 The interactome jigsaw puzzle: putting together the complete picture of protein-protein interactions using the Bioagent platform


 Domenico Marra, Paolo Romano (IST, Italy)

 Mutation data interoperability: SRS implementation of the TP53 IARC mutation database providing XML output


 Shahlaa Kasim (IT Department, Al-Zahra College for Women, Oman)

 On Searching Data in Peer-to-Peer Network


 Bill Andreopoulos (York University, Toronto, Canada)

 Knowledge-based clustering of numerical data sets incorporating confidence values: applications to yeast genomic data sets


 Chen-Tsun Chuang,

 Cheng-Chia Yang and

 Mei-Fen Huang (China Medical University, Taiwan)

 Repetitive sequence analysis of human chromosome X


 Francesco Gianfelici (UniversitÓ Politecnica delle Marche, Italy)

 A Self-Organizing P2P Network Based on Multi-Layer Structure


 Roberto Garello (Politecnico di Torino, Italy), Francesco Mininni (SAISME, Torino), Franco Chiaraluce, and Ennio Gambi (UniversitÓ Politecnica delle Marche, Italy)

 Sequence analysis based on genomic signal processing


 Wolfgang Sommer, Christina Arlinde (Institutet, Stockholm, Sweden), Massimo Ubaldi (UniversitÓ di Camerino, Italy)

 Experimental design for microarray studies