Pattern Recognition in Bioinformatics

1. Front Matter

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2. Bio-molecular Networks and Pathway Analysis

   1. A Fast Agglomerative Community Detection Method for Protein Complex Discovery in Protein Interaction Networks

      • Mohammad S. Rahman, Alioune Ngom

      Pages 1-12

   2. Inferring Gene Regulatory Networks from Time-Series Expressions Using Random Forests Ensemble

      • D. A. K. Maduranga, Jie Zheng, Piyushkumar A. Mundra, Jagath C. Rajapakse

      Pages 13-22

   3. Local Topological Signatures for Network-Based Prediction of Biological Function

      • Wynand Winterbach, Piet Van Mieghem, Marcel J. T. Reinders, Huijuan Wang, Dick de Ridder

      Pages 23-34

   4. Mutational Genomics for Cancer Pathway Discovery

      • Jeroen de Ridder, Jaap Kool, Anthony G. Uren, Jan Bot, Johann de Jong, Alistair G. Rust et al.

      Pages 35-46

   5. Outlier Gene Set Analysis Combined with Top Scoring Pair Provides Robust Biomarkers of Pathway Activity

      • Michael F. Ochs, Jason E. Farrar, Michael Considine, Yingying Wei, Soheil Meschinchi, Robert J. Arceci

      Pages 47-58

   6. Restricted Neighborhood Search Clustering Revisited: An Evolutionary Computation Perspective

      • Clara Pizzuti, Simona E. Rombo

      Pages 59-68

3. Learning, Classification, and Clustering

   1. Class Dependent Feature Weighting and K-Nearest Neighbor Classification

      • Elena Marchiori

      Pages 69-78

   2. Simultaneous Sample and Gene Selection Using T-score and Approximate Support Vectors

      • Piyushkumar A. Mundra, Jagath C. Rajapakse, D. A. K. Maduranga

      Pages 79-90

   3. Versatile Sparse Matrix Factorization and Its Applications in High-Dimensional Biological Data Analysis

      • Yifeng Li, Alioune Ngom

      Pages 91-101

4. Data Mining and Knowledge Discovery

   1. A Local Structural Prediction Algorithm for RNA Triple Helix Structure

      • Bay-Yuan Hsu, Thomas K. F. Wong, Wing-Kai Hon, Xinyi Liu, Tak-Wah Lam, Siu-Ming Yiu

      Pages 102-113

   2. Combining Protein Fragment Feature-Based Resampling and Local Optimisation

      • Trent Higgs, Lukas Folkman, Bela Stantic

      Pages 114-125

   3. Experimental Determination of Intrinsic Drosophila Embryo Coordinates by Evolutionary Computation

      • Alexander V. Spirov, Carlos E. Vanario-Alonso, Ekaterina N. Spirova, David M. Holloway

      Pages 126-137

   4. Identifying Informative Genes for Prediction of Breast Cancer Subtypes

      • Iman Rezaeian, Yifeng Li, Martin Crozier, Eran Andrechek, Alioune Ngom, Luis Rueda et al.

      Pages 138-148

   5. Predicting Therapeutic Targets with Integration of Heterogeneous Data Sources

      • Yan-Fen Dai, Yin-Ying Wang, Xing-Ming Zhao

      Pages 149-158

   6. Using Predictive Models to Engineer Biology: A Case Study in Codon Optimization

      • Alexey A. Gritsenko, Marcel J. T. Reinders, Dick de Ridder

      Pages 159-171

5. Protein: Structure, Function, and Interaction

   1. Active Learning for Protein Function Prediction in Protein-Protein Interaction Networks

      • Wei Xiong, Luyu Xie, Jihong Guan, Shuigeng Zhou

      Pages 172-183

   2. Conditional Random Fields for Protein Function Prediction

      • Thies Gehrmann, Marco Loog, Marcel J. T. Reinders, Dick de Ridder

      Pages 184-195

   3. Enhancing Protein Fold Prediction Accuracy Using Evolutionary and Structural Features

      • Abdollah Dehzangi, Kuldip Paliwal, James Lyons, Alok Sharma, Abdul Sattar

      Pages 196-207

   4. Exploring Potential Discriminatory Information Embedded in PSSM to Enhance Protein Structural Class Prediction Accuracy

      • Abdollah Dehzangi, Kuldip Paliwal, James Lyons, Alok Sharma, Abdul Sattar

      Pages 208-219

This book constitutes the refereed proceedings of the 8th IAPR International Conference on Pattern Recognition in Bioinformatics, PRIB 2013, held in Nice, France, in June 2013. The 25 revised full papers presented were carefully reviewed and selected from 43 submissions. The papers are organized in topical sections on bio-molecular networks and pathway analysis; learning, classification, and clustering; data mining and knowledge discovery; protein: structure, function, and interaction; motifs, sites, and sequence analysis.

• computational biology
• gene regulatory networks
• information theory
• protein structure prediction
• support vector regression
• algorithm analysis and problem complexity

• School of Computer Science, University of Windsor, Windsor, Canada

  Alioune Ngom

• I3S Research Lab., Nice Sophia Antipolis University, Sophia Antipolis Cedex, France

  Enrico Formenti

• LERIA - Faculté des Sciences, Université d’Angers, Angers Cedex 01, France

  Jin-Kao Hao

• School of Electronics and Information Engineering, Tongji University, Shanghai, China

  Xing-Ming Zhao

• Institute for Computing and Information Sciences, Radboud University, Nijmegen, The Netherlands

  Twan Laarhoven

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