|
|
F. Masulli, L. Peterson, R.
Tagliaferri (Ed.s)
Proceedings of CIBB 2009
Sixth International Meeting on Computational Intelligence Methods for Bioinformatics and Biostatistics
Oratorio San Filippo Neri, Genova
(Italy) October 15-17, 2009
ISBN
978-88-903537-2-7 (memory
drive)
DMI Proceedings Series, volume 3, DMI Univ. Salerno, Italy, 2009
 |
INNS International Neural Network Society SIG on Bioinformatics |
 |
GNCS Gruppo Nazionale Calcolo Scientifico |
 |
HHF Human Health
Foundation Onlus |
 |
DISI Dept. Computer and Information Sciences - Univ. Genova (Italy) |
 |
DMI Dipartimento di Matematica e Informatica - Univ. Salerno (Italy) |
 |
IEEE CIS Computational Intelligence Society |
 |
SIREN Italian Neural Networks Society |
 |
RNBIO The Italian Network for Oncology
Bioinformatics |
| Regione
Liguria (Italy) | |
| Universita' di Genova
(Italy) |
Welcome to CIBB 2009
The 6th International Meeting on Computational Intelligence Methods for Bioinformatics and Biostatistics (CIBB 2009) held at Oratorio San Filippo Neri in Genova (Italy) – October 15-17 2009, is aimed to provide a forum open to researchers from different disciplines to present and discuss problems concerning computational techniques in Bioinformatics, Systems Biology and Medical Informatics with a particular focus on Neural Networks, Machine Learning, Fuzzy Logic, and Evolutionary Computation methods.
The CIBB meetings series is organized by the Special Interest Group on Bioinformatics of the International Neural Network Society (INNS). From 2004 to 2007, CIBB meetings have been held with an increasing number of participants with the format of a special session of bigger conferences, namely WIRN 2004 in Perugia, WILF 2005 in Crema, FLINS 2006 in Genova and WILF 2007 in Camogli. Given the great success of the special session at WILF 2007 that included 26 papers after a strong selection, starting from the 2008 edition held in Vietri, has become an autonomous conference. Selections of papers presented at the CIBB meetings have been published in extended revised form in international scientific journals, and starting from 2008, contributions are also collected in proceedings on CD/pen-drive support and in post-conference volumes of selected extended papers in the LNBI/LNCS Series of Springer-Verlag.
The 6th CIBB meeting is a joint operation of the Special Interest Groups on Bioinformatics and Biopattern of INNS and of the Task Force on Neural Networks of the IEEE CIS Technical Committee on Bioinformatics and Bioengineering with the collaboration of the Gruppo Nazionale Calcolo Scientifico (GNCS), the Italian Neural Networks Society (SIREN), the Dept. of Computer and Information Sciences - Univ. Genova, Italy (DISI), and the Dept. of Mathematics and Computer Science - Univ. Salerno, Italy (DMI), and with the technical sponsorship of the University of Genova, Italy, of IEEE CIS and of Regione Liguria. The meeting includes 31 presentations selected after a peer reviewing process and four special sessions, namely, Using Game-Theoretical Tools in Bioinformatics, DCB 2009-Data Clustering and Bioinformatics, Combining Bayesian and Machine Learning Approaches in Bioinformatics: State of Art and Future Perspectives, ISMDS 2009-Intelligent Systems for Medical Decisions Support that extend and deepen the main topics of CIBB.
We would like to thank the organizers of the special sessions, C. Angelini, A. Baughman, A. Floares, P. Lio', F. Manolache, L. Milanesi, F. Patrone, V.P. Plagianakos, and D.K. Tasoulis, for their effort in attracting so many good papers. Moreover, special thanks are due to the Program Committee members and reviewers for their commitment to the task of providing high-quality reviews. Last, but not least, we would like to thank the invited speakers G. Bernot and T. Nomura, and the tutorial presenters S. Motta, F. Pappalardo, and F. Patrone.
The Chairs of CIBB 2009
Francesco Masulli, Leif Peterson, and Roberto Tagliaferri
Committees
Chairs:
Francesco Masulli, University of Genova, Italy
and Temple University, PA, USA
Leif E. Peterson,
Methodist Hospital Research Institute, Houston, TX,
USA
Roberto Tagliaferri, University of Salerno, Italy
Scientific Program
Committee:
Klaus-Peter Adlassnig, Medical University of Vienna, Austria
Gilles Bernot, University of Nice Sophia
Antipolis, France
Domenico Bordo, National Cancer Research Institute, Genova, Italy
Mario Cannataro, University of Magna Graecia,
Catanzaro, Italy
Giovanni Cuda, University of Magna Graecia, Catanzaro, Italy
Joaquin Dopazo, Centro de Investigación Príncipe
Felipe, Valencia, Spain
Enrico Formenti, University of Nice Sophia Antipolis, France
Antonio Giordano, University of Siena, Italy
& Temple Univ, Philadelphia, PA, USA
Emmanuel
Ifeachor, University of Plymouth, UK
Nicolas Le Novere, Wellcome-Trust Genome Campus,
Hinxton, UK
Pietro Lio', University of Cambridge, UK
Giancarlo
Mauri, University of Milano Bicocca,
Italy
Oleg Okun, Precise
Biometrics AB, Sweden
Giulio Pavesi, University of Milan, Italy
David Alejandro
Pelta, University of Granada, Spain
Jagath Rajapakse, Nanyang Technological
University, Singapore
Volker Roth, University of Basel, Switzerland
Giuseppe
Russo, Temple Univ, Philadelphia, PA, USA
Anna Tramontano, Sapienza University, Rome,
Italy
Giorgio Valentini, University of Milan, Italy
Gennady M.
Verkhivker, University of Kansas, KS & UC San Diego,
CA, USA
L. Gwenn Volkert, Kent
State University, Kent, OH, USA
CIBB Steering Committee:
Pierre Baldi, University
of California, Irvine, CA, USA
Alexandru Floares,
Oncological Institute Cluj-Napoca,
Romania
Jon Garibaldi, University of Nottingham, UK
Francesco
Masulli, University of Genova, Italy and Temple
University, PA, USA
Roberto Tagliaferri, University of Salerno, Italy
Local Organizing
Committee:
Paolo Romano, National Cancer Research Institute, Genova, Italy
Stefano Rovetta, University of Genova,
Italy
Congress Management:
Laura Montanari,
University of Genova, Italy
Daniela Peghini, University of Genova,
Italy
Technical Program
Thursday, October 15, 2009
9:00 AM - Registration desk opening
9:30 AM - 12:30 PM - Tutorials
2:00 PM - Welcome Address
2:15 – 3:10 PM - Keynote Talk #1: Open Platform for Physiome and Systems Biology (invited). Speaker: Taishin Nomura, Department of Mechanical Science and Bioengineering, Graduate School of Engineering Science, Osaka University, Japan
3:10 - 4:10 PM - Session GEA1: Gene Expression Analysis - 1
3:10 PM - Non-Parametric MANOVA Methods for Detecting Differentially Expressed Genes in Real-Time RT-PCR experiments, N. Bassani, F. Ambrogi, R. Bosotti, M. Bertolotti, A. Isacchi, E. Biganzoli
3:30 PM - In Silico Screening and Comparative Modeling of Sugarcane Defensins, L. C. Belarmino, P.V.S.Z. Capriles, D. Guerra Albuquerque Cabral, L.E. Dardene, A. Barbosa-Silva, S. Crovella, A.M. Benko-Iseppon
3:50 PM - Regularized k-Means Clustering for Dimension Reduction Applied to Supervised Classification, V. Nikulin, G.J. McLachlan
4:10 - 4:40 PM Coffee Break
4:40 PM - 5:50 PM - Special Session - GTTB: Using Game-Theoretical Tools in Bioinformatics. Chair: F. Patrone
4:40 PM - Introduction to the Special Session, F. Patrone
4:50 PM - Coalitional Games to Measure the Centrality of Genes on Interaction Networks, S. Moretti, V. Fragnelli, F. Patrone, S. Bonassi
5:10 PM - Microarray Data Analysis Via Weighted Indices and Weighted Majority Games, R, Lucchetti, P. Radrizzani
5:30 PM - An Application of Microarray Games to Gene Expression Analysis: The Microarray Genes Signature, V. Mirisola, S. Moretti, S. Bonassi, A. Gennari, M.P. Sormani, U. Pfeffer
9:00 AM - Registration desk opening
9:30 AM - 10:25 AM
- Keynote Talk #2: On the Use of Temporal Formal Logic to
Deduce the Parameters of a Gene Regulatory Network Model (invited)
Speaker: Gilles Bernot, University of Nice Sophia
Antipolis, Polytech'Nice-Sophia, School of Engineering, Nice,
France
10:25 AM – 11:10 AM - Panel: INNS and IEEE-CIS Perspectives in Bioinformatics and Biostatistics. Participants: E. Biganzoli, F. Masulli, L. Peterson, R. Tagliaferri
11:10 AM – 11:40 AM Coffee Break
11:40 AM – 1:30 PM - Special Session CBML: Combining Bayesian and Machine Learning Approaches in Bioinformatics: State of Art and Future Perspectives. Chairs: C. Angelini, P. Lio', L. Milanesi
11.40 AM - Introduction to the Special Session, C. Angelini, P. Lio', L. Milanesi
11.50 AM - Combining Replicates and Nearby Species Data: Methodologies, Examples and Results Interpretation, C. Angelini, I. De Feis, R. van der Wath, V.-A. Nguyen, P. Lio'
12:10 PM - Multiple Sequence Alignment with Genetic Algorithms, M. Botta, G. Negro
12:30 PM - A Statistical Base-Calling Methodology for the Illumina High-Throughput DNA Sequencing Platform, W. Gilks
12:50 PM - Principal Components Analysis in the Space of Phylogenetic Trees, T.M.W. Nye
1:10 PM - Can We Infer Historical Population Movements from Principal Component Analysis of Genetic Data? A 30-Year Old Argument Rages on, S. Rosset, N. El Karoui
1:30 PM - 3:00 PM - Break
3:00 PM – 4:20 PM - Session GEA2: Gene Expression Analysis - 2
3:00 PM -TimeDelay-ARACNE: Reverse Engineering of Gene Networks from Time-Course Data by an Information Theoretic Approach, P. Zoppoli, S. Morganella, M. Ceccarelli
3:20 PM - In Silico Screening for Pathogenesis Related-2 Gene Candidates in Vigna Unguiculata, A.C. Wanderley-Nogueira, N. da Mota Soares-Cavalcanti, L.C. Belarmino, A. Barbosa-Silva, E. Akio Kido, S.J. Hadad do Monte, V. Pandolfi, T. Calsa-Junior, A.M. Benko-Iseppon
3:40 PM - Predicting Gene Expression from Heterogeneous Data, M. Re, G. Valentini
4:00 PM - Statistical Analysis of Differential Gene Expression Levels in Small Microarray Experiments, P.F. Stifanelli, G. Zaza, F. Sallustio, T.M. Creanza, F.P. Schena, N. Ancona
4:20 PM – 4:50 PM Coffee Break
4:50 PM – 6:10 PM - Session TB: Tools for Bioinformatics
4:50 PM - PS-COILS: A New Method for Coiled-Coil Prediction that Exploits both Single-Sequence and Evolutionary Information, L. Bartoli, P. Fariselli, R. Casadio
5:10 PM - Grid Based Application For SNPs Genome Wide Studies, A. Calabria, D. Di Pasquale, M. Gnocchi, P. Cozzi, A. Orro, G. Trombetti, L. Milanesi
5:30 PM - Intelligent Text Processing Techniques for Textual-Profile Gene Characterization, F. Esposito, M. Biba, S. Ferilli
5:50 PM - SILACAnalyzer - A Tool for Differential Quantitation of Stable Isotope Derived Data, L. Nilse, M. Sturm, D. Trudgian, M. Salek, P.F.G. Sims, K.M. Carroll, S.J. Hubbard
8.30 PM - Conference Dinner
Saturday, October 17, 2009
9:00 AM - Registration desk opening
9:30 AM - 10:25 AM - Keynote Talk #3: Covariance-Matrix Self-Adaptation
Evolution Strategies and other Metaheuristic Techniques for Neural Adaptive
Learning. Speaker: Leif E.
Peterson, Methodist Hospital Research Institute Houston, TX, USA
10:25 AM - 12:25 PM - Special Session DCB 2009: Data Clustering and Bioinformatics, Chairs: V.P. Plagianakos and D.K. Tasoulis
10:25 AM - Introduction to the Special Session, V.P. Plagianakos and D.K. Tasoulis
10:35 AM - Multiple Clustering Solutions Analysis Through Lest-Square Consensus Algorithms, L. Murino, C. Angelini, I. Bifulco, I. De Feis, G. Raiconi, R. Tagliaferri
10:55 AM - Projection Based Clustering at Gene Expression Data, S.K. Tasoulis, V.P. Plagianakos, D.K. Tasoulis
10:15 AM – 11:45 AM Coffee Break
11:45 PM - Biclustering of Microarray Data based on Modular Singular Value Decomposition, V.N.M. Aradhya, F. Masulli, S. Rovetta
12:05 PM - Searching a Multivariate Partition Space Using MAX-SAT, S. Liverani, J. Cussens, J.Q. Smith
12:25 PM – 1:25 PM - Session NP: New Perspectives
12:25 PM - Predicting Protein-Protein Interactions with k-Nearest Neighbors Classification Algorithm, M.R. Guarracino, A. Nebbia
12:45 PM - Simulations of the EGFR - KRAS - MAPK Signalling Network in Colon Cancer. Virtual Mutations and Virtual Treatments with Inhibitors Have More Important Effects than a 10 Times Range of Normal Parameters and Rates Fluctuation, N. Castagnino, L. Tortolina, R. Montagna, R. Pesenti, B. Anahi, S. Parodi
1:05 PM - Gene Data Fusion: A Prototype for Conflict Reporting Facility Transcriptome, A. Calabria, A. Maurino, F. Macciardi, L. Milanesi
1:25 PM – 3:00 PM Break
3:00 PM – 4:50 PM - Special Session: ISMDS 2009 - Intelligent Systems for Medical Decisions Support, Chairs: A. Floares, F. Manolache, A. Baughman
3:00 PM - Introduction to the Special Session, A. Floares, F. Manolache, A. Baughman
3:10 PM - Using Computational Intelligence to Develop Intelligent Clinical Decision Support Systems, A. Floares
3:30 PM - Different Methodologies for Patient Stratification Using Survival Data, A.S. Fernandes, D. Bacciu, I.H. Jarman, T.A. Etchells, J.M. Fonseca, P., P.J.G. Lisboa
3:50 PM - 3D Reconstruction of Mouse Brain from a Sequence of 2D Brain Slices in Application to Allen Brain Atlas, A. Osokin, D. Vetrov, D. Kropotov
4:10 PM - A Proposed Knowledge Based Approach for Solving Proteomics Issues, A. Fiannaca, S. Gaglio, M. La Rosa, D. Peri, R. Rizzo. A. Urso
4:30 PM - Prediction of Novel Biomarkers in Prostate
Cancer, F. Masulli, M.E. Monville, S. Rovetta, G.
Russo
9:30 AM – 11.00 PM - Tutorial #1: ImmunoGrid Simulator. Speakers: Santo Motta and Francesco Pappalardo, Department of Mathematics and Computer Science, University of Catania, Italy
11.00 AM – 12.30 PM -
Tutorial #2: Basics of Game Theory for
Bioinformatics. Speaker:
Fioravante Patrone, Dipartimento di Ingegneria della Produzione,
Termoenergetica e Ingegneria della Produzione, University of Genova,
Italy