Computational Intelligence Methods for Bioinformatics and Biostatistics

1. Front Matter

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2. Invited Papers

   1. Coarse-Grained Modeling of the HIV–1 Protease Binding Mechanisms: I. Targeting Structural Flexibility of the Protease Flaps and Implications for Drug Design

      • Gennady M. Verkhivker

      Pages 1-12

   2. Coarse-Grained Modeling of the HIV–1 Protease Binding Mechanisms: II. Folding Inhibition

      • Gennady M. Verkhivker

      Pages 13-24

   3. Unsupervised Stability-Based Ensembles to Discover Reliable Structures in Complex Bio-molecular Data

      • Alberto Bertoni, Giorgio Valentini

      Pages 25-43

3. CIBB Regular Session

   1. Comparative In Silico Evaluation of MYB Transcription Factors in Eucalyptus, Sugarcane and Rice Transcriptomes

      • Nina M. Soares-Cavalcanti, Ana C. Wanderley-Nogueira, Luis C. Belarmino, Petra dos Santos Barros, Ana M. Benko-Iseppon

      Pages 44-55

   2. Building Maps of Drugs Mode-of-Action from Gene Expression Data

      • Francesco Iorio, Roberto Tagliaferri, Diego di Bernardo

      Pages 56-65

   3. In Silico Evaluation of Osmoprotectants in Eucalyptus Transcriptome

      • Petra dos Santos Barros, Nina M. Soares-Cavalcanti, Gabriela S. Vieira-Mello, Ana C. Wanderley-Nogueira, Tercílio Calsa-Junior, Ana M. Benko-Iseppon

      Pages 66-77

   4. Mining Association Rule Bases from Integrated Genomic Data and Annotations

      • Ricardo Martinez, Nicolas Pasquier, Claude Pasquier

      Pages 78-90

   5. Stability and Performances in Biclustering Algorithms

      • Maurizio Filippone, Francesco Masulli, Stefano Rovetta

      Pages 91-101

   6. Splice Site Prediction Using Artificial Neural Networks

      • ∅ystein Johansen, Tom Ryen, Trygve Eftes∅l, Thomas Kjosmoen, Peter Ruoff

      Pages 102-113

   7. Interval Length Analysis in Multi Layer Model

      • Vito Di Gesù, Giosuè Lo Bosco, Luca Pinello

      Pages 114-122

   8. A Multivariate Algorithm for Gene Selection Based on the Nearest Neighbor Probability

      • Enrico Ferrari, Marco Muselli

      Pages 123-131

   9. Control of Cellular Glycolysis by Perturbations in the Glucose Influx

      • Jaime Arturo de la Torre, Maria Carmen Lemos, Antonio Córdoba

      Pages 132-143

   10. Curating a Large-Scale Regulatory Network by Evaluating Its Consistency with Expression Datasets

       • Carito Guziolowski, Jeremy Gruel, Ovidiu Radulescu, Anne Siegel

       Pages 144-155

   11. Spatial Clustering of Molecular Dynamics Trajectories in Protein Unfolding Simulations

       • Pedro Gabriel Ferreira, Cândida G. Silva, Paulo J. Azevedo, Rui M. M. Brito

       Pages 156-166

   12. Clustering Bacteria Species Using Neural Gas: Preliminary Study

       • Claudio Mirabello, Riccardo Rizzo, Alfonso Urso, Salvatore Gaglio

       Pages 167-176

   13. A New Linear Initialization in SOM for Biomolecular Data

       • Antonino Fiannaca, Giuseppe Di Fatta, Alfonso Urso, Riccardo Rizzo, Salvatore Gaglio

       Pages 177-187

   14. 3D Volume Reconstruction and Biometric Analysis of Fetal Brain from MR Images

       • Paola Campadelli, Elena Casiraghi, Gabriele Lombardi, Graziano Serrao

       Pages 188-197

   15. Searching for Glycomics Role in Stem Cell Development

       • Anil Sorathiya, Tadas Jucikas, Stephanie Piecewicz, Shiladitya Sengupta, Pietro Liò

       Pages 198-209

   16. A New Protein Representation Based on Fragment Contacts: Towards an Improvement of Contact Maps Predictions

       • Pietro Di Lena, Luciano Margara, Marco Vassura, Piero Fariselli, Rita Casadio

       Pages 210-221

This book constitutes the thoroughly refereed post-conference proceedings of the Fifth International Meeting on Computational Intelligence Methods for Bioinformatics and Biostatistics, CIBB 2008, held in Vietri sul Mare, Italy, in October 2008. The 23 revised full papers presented together with 3 invited lectures were carefully reviewed and selected from 69 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 bioinformatics, systems biology and medical informatics with a particular focus on neural networks, machine learning, fuzzy logic, and evolutionary computation methods.

• bioinformatics
• biology
• computational intelligence
• evolution
• evolutionary computation
• fuzzy logic
• learning
• machine learning
• neural network

• DISI - Dipartimento di Informatica e Scienze dell’Informazione, Università di Genova, Genova, Italy

  Francesco Masulli

• DMI, Dipartimento di Matematica ed Informatica, Università di Salerno, Fisciano (Sa), Italy

  Roberto Tagliaferri

• Department of Pharmaceutical Chemistry, School of Pharmacy, The University of Kansas, Kansas, USA

  Gennady M. Verkhivker

Policies and ethics