Computational Intelligence Methods for Bioinformatics and Biostatistics

1. Front Matter

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2. Invited Lectures

   1. Modelling the Effect of Genes on the Dynamics of Probabilistic Spiking Neural Networks for Computational Neurogenetic Modelling

      • Nikola Kasabov, Stefan Schliebs, Ammar Mohemmed

      Pages 1-9

   2. Biostatistics Meets Bioinformatics in Integrating Information from Highdimensional Heterogeneous Genomic Data: Two Examples from Rare Genetic Diseases and Infectious Diseases

      • Clelia Di Serio, Danilo Pellin, Alessandro Ambrosi, Ingrid Glad, Arnoldo Frigessi

      Pages 10-20

3. Statistical Learning

   1. Bayesian Models for the Multi-sample Time-Course Microarray Experiments

      • Claudia Angelini, Daniela De Canditiis, Marianna Pensky, Naomi Brownstein

      Pages 21-35

   2. A Machine Learning Pipeline for Discriminant Pathways Identification

      • Annalisa Barla, Giuseppe Jurman, Roberto Visintainer, Margherita Squillario, Michele Filosi, Samantha Riccadonna et al.

      Pages 36-48

   3. Discovering Hidden Pathways in Bioinformatics

      • Paulo J. G. Lisboa, Ian H. Jarman, Terence A. Etchells, Simon J. Chambers, Davide Bacciu, Joe Whittaker et al.

      Pages 49-60

4. Genomics

   1. Reliability of miRNA Microarray Platforms: An Approach Based on Random Effects Linear Models

      • Niccolò Bassani, Federico Ambrogi, Cristina Battaglia, Elia Biganzoli

      Pages 61-72

   2. A Bioinformatics Procedure to Identify and Annotate Somatic Mutations in Whole-Exome Sequencing Data

      • Roberta Spinelli, Rocco Piazza, Alessandra Pirola, Simona Valletta, Roberta Rostagno, Angela Mogavero et al.

      Pages 73-82

5. Computational Intelligence for Health at the Edge

   1. Feature Selection for the Prediction and Visualization of Brain Tumor Types Using Proton Magnetic Resonance Spectroscopy Data

      • Félix Fernando González-Navarro, Lluís A. Belanche-Muñoz

      Pages 83-97

   2. On the Use of Graphical Models to Study ICU Outcome Prediction in Septic Patients Treated with Statins

      • Vicent J. Ribas, Jesús Caballero López, Anna Sáez de Tejada, Juan Carlos Ruiz-Rodríguez, Adolfo Ruiz-Sanmartín, Jordi Rello et al.

      Pages 98-111

   3. Integration of Biomolecular Interaction Data in a Genomic and Proteomic Data Warehouse to Support Biomedical Knowledge Discovery

      • Arif Canakoglu, Giorgio Ghisalberti, Marco Masseroli

      Pages 112-126

6. Proteomics

   1. Machine-Learning Methods to Predict Protein Interaction Sites in Folded Proteins

      • Castrense Savojardo, Piero Fariselli, Damiano Piovesan, Pier Luigi Martelli, Rita Casadio

      Pages 127-135

   2. Complementing Kernel-Based Visualization of Protein Sequences with Their Phylogenetic Tree

      • Martha Ivón Cárdenas, Alfredo Vellido, Iván Olier, Xavier Rovira, Jesús Giraldo

      Pages 136-149

   3. DEEN: A Simple and Fast Algorithm for Network Community Detection

      • Pavol Jancura, Dimitrios Mavroeidis, Elena Marchiori

      Pages 150-163

7. Intelligent Clinical Decision Support Systems (i-CDSS)

   1. Self-similarity in Physiological Time Series: New Perspectives from the Temporal Spectrum of Scale Exponents

      • Paolo Castiglioni

      Pages 164-175

   2. Support Vector Machines for Survival Regression

      • Antonio Eleuteri, Azzam F. G. Taktak

      Pages 176-189

   3. Boosted C5 Trees i-Biomarkers Panel for Invasive Bladder Cancer Progression Prediction

      • Alexandru George Floares, Irina Luludachi, Colin Dinney, Liana Adam

      Pages 190-200

8. Bioinformatics

   1. A Faster Algorithm for Motif Finding in Sequences from ChIP-Seq Data

      • Federico Zambelli, Giulio Pavesi

      Pages 201-212

   2. Case/Control Prediction from Illumina Methylation Microarray’s β and Two-Color Channels in the Presence of Batch Effects

      • Fabrice Colas, Jeanine J. Houwing-Duistermaat

      Pages 213-225

   3. Supporting the Design, Communication and Management of Bioinformatic Protocols through the Leaf Tool

      • Francesco Napolitano, Roberto Tagliaferri

      Pages 226-237

This book constitutes the thoroughly refereed post-proceedings of the 8th International Meeting on Computational Intelligence Methods for Bioinformatics and Biostatistics, CIBB 2011, held in Gargnano del Garda, Italy, in June/July 2011. The 19 papers, presented together with 2 keynote speeches, were carefully reviewed and selected from 24 submissions. The papers are organized in topical sections on statistical learning, genomics, computational intelligence for health at the edge, proteomics, intelligent clinical decision support systems (i-CDSS), bioinformatics, and data clustering.

• biomolecular databases
• combinatorial optimization
• gene expression analysis
• machine learning
• protein sequence
• algorithm analysis and problem complexity

• Department of Clinical Sciences and Community, University of Milan, Milan, Italy

  Elia Biganzoli, Federico Ambrogi

• Dpto. de Lenguajes y Sistemas Informáticos (LSI), Universidad Politecnica de la Catalunya, Barcelona, Spain

  Alfredo Vellido

• Department of Mathematics and Information Sciences, University of Salerno, Fisciano, Italy

  Roberto Tagliaferri

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