Computational Intelligence Methods for Bioinformatics and Biostatistics: 6th International Meeting, CIBB 2009, Genoa, Italy, October 15-17, 2009, Revised Selected Papers / Edition 1

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This book constitutes the thoroughly refereed post-conference proceedings of the Sixth International Meeting on Computational Intelligence Methods for Bioinformatics and Biostatistics, CIBB 2009, held in Genova, Italy, in October 2009. The revised 23 full papers presented were carefully reviewed and selected from 57 submissions. The main goal of the CIBB meetings is to provide a forum open to researchers from different disciplines to present and discuss problems concerning computational techniques in tools for bioinformatics, gene expression analysis and new perspectives in bioinformatics together with 4 special sessions on using game-theoretical tools in bioinformatics, combining Bayesian and machine learning approaches in bioinformatics: state of the art and future perspectives, data clustering and bioinformatics (DCB 2009) and on intelligent systems for medical decisions support (ISMDS 2009).

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Table of Contents

Tools for Bioinformatics

The ImmunoGrid Simulator: How to Use It Francesco Pappalardo Mark Halling-Brown Marzio Pennisi Ferdinando Chiacchio Clare E. Sansom Adrian J. Shepherd David S. Moss Santo Motta Vladimir Brusic 1

Improving Coiled-Coil Prediction with Evolutionary Information Piero Fariselli Lisa Bartoli Rita Casadio 20

Intelligent Text Processing Techniques for Textual-Profile Gene Characterization Floriana Esposito Marenglen Biba Stefano Ferilli 33

SILACAnalyzer - A Tool for Differential Quantitation of Stable Isotope Derived Data Lars Nilse Marc Sturm David Trudgian Mogjiborahman Salek Paul F.G. Sims Kathleen M. Carroll Simon J. Hubbard 45

Gene Expression Analysis

Non-parametric MANOVA Methods for Detecting Differentially Expressed Genes in Real-Time RT-PCR Experiments Niccoló Bassani Federico Ambrogi Roberta Bosotti Matteo Bertolotti Antonella Isacchi Elia Biganzoli 56

In Silico Screening for Pathogenesis Related-2 Gene Candidates in Vigna Unguiculata Transcriptome Ana Carolina Wanderley-Nogueira Nina da Mota Soares-Cavalcanti Luis Carlos Belarmino Adriano Barbosa-Silva Ederson Akio Kido Semiramis Jamil Hadad do Monte Valesca Pandolfi Tercilio Calsa-Junior Ana Maria Benko-Iseppon 70

Penalized Principal Component Analysis of Microarray Data Vladimir Nikulin Geoffrey J. McLachlan 82

An Information Theoretic Approach to Reverse Engineering of Regulatory Gene Networks from Time-Course Data Pietro Zoppoli Sandro Morganella Michele Ceccarelli 97

New Perspectives in Bioinformatics

On the Use of Temporal Formal Logic to Model Gene Regulatory Networks Gilles Bernot Jean-Paul Comet 112

Predicting Protein-Protein Interactions with K-Nearest Neighbors Classification Algorithm Mario R. Guarracino Adriano Nebbia 139

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 Fluctuations Nicoletta Castagnino Lorenzo Tortolina Roberto Montagna Raffaele Pesenti Anahi Balbi Silvio Parodi 151

Special Session on "Using Game-Theoretical Tools in Bioinformatics"

Basics of Game Theory for Bioinformatics Fioravante Patrone 165

Microarray Data Analysis via Weighted Indices and Weighted Majority Games Roberto Lucchetti Paola Radrizzani 179

Special Session on "Combining Bayesian and Machine Learning Approaches in Bioinformatics: State of Art and Future Perspectives"

Combining Replicates and Nearby Species Data: A Bayesian Approach Claudia Angelini Italia De Feis Viet Anh Nguyen Richard van der Wath Pietro Liò 191

Multiple Sequence Alignment with Genetic Algorithms Marco Botta Guido Negro 206

Special Session on "Data Clustering and Bioinformatics" (DCB 2009)

Multiple Clustering Solutions Analysis through Least-Squares Consensus Algorithms Loredana Murino Claudia Angelini Ida Bifulco Italia De Feis Giancarlo Raiconi Roberto Tagliaferri 215

Projection Based Clustering of Gene Expression Data Sotiris K. Tasoulis Vassilis P. Plagianakos Dimitris K. Tasoulis 228

Searching a Multivariate Partition Space Using MAX-SAT Silvia Liverani James Cussens Jim Q. Smith 240

A Novel Approach for Biclustering Gene Expression Data Using Modular Singular Value Decomposition V.N. Manjunath Aradhya Francesco Masulli Stefano Rovetta 254

Special Session on "Intelligent Systems for Medical Decisions Support" (ISMDS 2009)

Using Computational Intelligence to Develop Intelligent Clinical Decision Support Systems Alexandru G. Floares 266

Different Methodologies for Patient Stratification Using Survival Data Ana S. Fernandes Davide Bacciu Ian H. Jarman Terence A. Etchells José M. Fonseca Paulo J.G. Lisboa 276

3-D Mouse Brain Model Reconstruction from a Sequence of 2-D Slices in Application to Allen Brain Atlas Anton Osokin Dmitry Vetrov Dmitry Kropotov 291

A Proposed Knowledge Based Approach for Solving Proteomics Issues Antonino Fiannaca Salavatore Gaglio Massimo La Rosa Daniele Peri Riccardo Rizzo Alfonso Urso 304

Author Index 319

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