Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics

1. Front Matter

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2. Effect of Using Varying Negative Examples in Transcription Factor Binding Site Predictions

   1. Effect of Using Varying Negative Examples in Transcription Factor Binding Site Predictions

      • Faisal Rezwan, Yi Sun, Neil Davey, Rod Adams, Alistair G. Rust, Mark Robinson

      Pages 1-12

   2. A New Evolutionary Gene Regulatory Network Reverse Engineering Tool

      • Antonella Farinaccio, Leonardo Vanneschi, Paolo Provero, Giancarlo Mauri, Mario Giacobini

      Pages 13-24

   3. ML-Consensus: A General Consensus Model for Variable-Length Transcription Factor Binding Sites

      • Saad Quader, Nathan Snyder, Kevin Su, Ericka Mochan, Chun-Hsi Huang

      Pages 25-36

   4. Applying Linear Models to Learn Regulation Programs in a Transcription Regulatory Module Network

      • Jianlong Qi, Tom Michoel, Gregory Butler

      Pages 37-47

   5. ATHENA Optimization: The Effect of Initial Parameter Settings across Different Genetic Models

      • Emily R. Holzinger, Scott M. Dudek, Eric C. Torstenson, Marylyn D. Ritchie

      Pages 48-58

   6. Validating a Threshold-Based Boolean Model of Regulatory Networks on a Biological Organism

      • Christian Darabos, Ferdinando Di Cunto, Marco Tomassini, Jason H. Moore, Paolo Provero, Mario Giacobini

      Pages 59-68

   7. A Nearest Neighbour-Based Approach for Viral Protein Structure Prediction

      • Gualberto Asencio Cortés, Jesús S. Aguilar-Ruiz, Alfonso E. Márquez Chamorro

      Pages 69-76

   8. Annotated Stochastic Context Free Grammars for Analysis and Synthesis of Proteins

      • Eva Sciacca, Salvatore Spinella, Dino Ienco, Paola Giannini

      Pages 77-88

   9. Finding Motifs in DNA Sequences Applying a Multiobjective Artificial Bee Colony (MOABC) Algorithm

      • David L. González-Álvarez, Miguel A. Vega-Rodríguez, Juan A. Gómez-Pulido, Juan M. Sánchez-Pérez

      Pages 89-100

   10. An Evolutionary Approach for Protein Contact Map Prediction

       • Alfonso E. Márquez Chamorro, Federico Divina, Jesús S. Aguilar-Ruiz, Gualberto Asencio Cortés

       Pages 101-110

   11. Multi-Neighborhood Search for Discrimination of Signal Peptides and Transmembrane Segments

       • Sami Laroum, Béatrice Duval, Dominique Tessier, Jin-Kao Hao

       Pages 111-122

   12. Approximation of Graph Kernel Similarities for Chemical Graphs by Kernel Principal Component Analysis

       • Georg Hinselmann, Andreas Jahn, Nikolas Fechner, Lars Rosenbaum, Andreas Zell

       Pages 123-134

3. Posters

   1. Experimental Approach for Bacterial Strains Characterization

      • Fabien Chhel, Adrien Goëffon, Frédéric Lardeux, Frédéric Saubion, Gilles Hunault, Tristan Boureau

      Pages 135-140

   2. Do Diseases Spreading on Bipartite Networks Have Some Evolutionary Advantage?

      • Luca Ferreri, Ezio Venturino, Mario Giacobini

      Pages 141-146

   3. Genetic Algorithm Optimization of Force Field Parameters: Application to a Coarse-Grained Model of RNA

      • Filip Leonarski, Fabio Trovato, Valentina Tozzini, Joanna Trylska

      Pages 147-152

   4. A Decision Tree-Based Method for Protein Contact Map Prediction

      • Cosme Ernesto Santiesteban Toca, Alfonso E. Márquez Chamorro, Gualberto Asencio Cortés, Jesus S. Aguilar-Ruiz

      Pages 153-158

   5. A Comparison of Machine Learning Methods for the Prediction of Breast Cancer

      • Sara Silva, Orlando Anunciação, Marco Lotz

      Pages 159-170

   6. An Automatic Identification and Resolution System for Protein-Related Abbreviations in Scientific Papers

      • Paolo Atzeni, Fabio Polticelli, Daniele Toti

      Pages 171-176

   7. Protein Complex Discovery from Protein Interaction Network with High False-Positive Rate

      • Yunku Yeu, Jaegyoon Ahn, Youngmi Yoon, Sanghyun Park

      Pages 177-182

This book constitutes the refereed proceedings of the 9th European Conference on Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics, EvoBIO 2011, held in Torino, Italy, in April 2011 co-located with the Evo* 2011 events. The 12 revised full papers presented together with 7 poster papers were carefully reviewed and selected from numerous submissions. All papers included topics of interest such as biomarker discovery, cell simulation and modeling, ecological modeling, fluxomics, gene networks, biotechnology, metabolomics, microarray analysis, phylogenetics, protein interactions, proteomics, sequence analysis and alignment, and systems biology.

• biological networks analysis
• biological organisms
• multiobjective optimization
• protein analysis
• swarm intelligence
• algorithm analysis and problem complexity
• data structures

• Institute for High-Performance Computing and Networking (ICAR), Italian National Research Council (CNR), Italy

  Clara Pizzuti

• Center for Human Genetics Research, Vanderbilt University, Nashville, USA

  Marylyn D. Ritchie

• Department of Animal Production Epidemiology and Ecology, University of Torino, Grugliasco, Italy

  Mario Giacobini

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