Computational Intelligence Methods for Bioinformatics and Biostatistics

1. Front Matter

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2. Relativistic Heavy Ions and DNA Damage

   1. A Theoretical Analysis of Visual Distributions of Ionizing-Radiation-Induced Foci in Human Cells by Heavy Ions

      • Artem L. Ponomarev, Francis A. Cucinotta

      Pages 1-11

   2. Multiple CPU Computing: The Example of the Code RITRACKS

      • Ianik Plante, Francis A. Cucinotta

      Pages 12-25

   3. Modeling the Depressed Hematopoietic Cells for Immune System under Chronic Radiation

      • Shaowen Hu, Francis A. Cucinotta

      Pages 26-36

3. Image Segmentation

   1. Feature-Based Medical Image Registration Using a Fuzzy Clustering Segmentation Approach

      • Hassan Mahmoud, Francesco Masulli, Stefano Rovetta

      Pages 37-47

   2. A Novel Approach Based on Joint Optimization of Alignment and Statistical Surface Representation with Wavelet Transform for CBCT Segmentation

      • Yu-Bing Chang, Peng Yuan, Tai-Hong Kuo, Zixiang Xiong, Jaime Gateno, James J. Xia et al.

      Pages 48-56

4. Proteomics

   1. Searching Structural Blocks by SS Exhaustive Matching

      • Virginio Cantoni, Alessio Ferone, Ozlem Ozbudak, Alfredo Petrosino

      Pages 57-69

   2. Characterizing Intermediate Conformations in Protein Conformational Space

      • Rosanne Vetro, Nurit Haspel, Dan Simovici

      Pages 70-80

   3. A Method of Extracting Sentences Containing Protein Function Information from Articles by Iterative Learning with Feature Update

      • Kazunori Miyanishi, Takenao Ohkawa

      Pages 81-94

5. RNA and DNA Sequence Analysis

   1. Non-coding RNA Covariance Model Combination Using Mixed Primary-Secondary Structure Alignment

      • Jennifer A. Smith

      Pages 95-104

   2. A Study of Compression–Based Methods for the Analysis of Barcode Sequences

      • Massimo La Rosa, Antonino Fiannaca, Riccardo Rizzo, Alfonso Urso

      Pages 105-116

6. RNA, DNA, and SNP Microarrays

   1. Assessing Agreement between microRNA Microarray Platforms via Linear Measurement Error Models

      • Niccolò Bassani, Federico Ambrogi, Elia Biganzoli

      Pages 117-131

   2. Extracting Key Pathways from Gene Signature and Genetic Aberrations in Subtypes of Cancer

      • Peikai Chen, Yubo Fan, Tsz-kwong Man, Ching C. Lau, Y. S. Hung, Stephen T. -C. Wong

      Pages 132-146

7. Semi-Supervised/Unsupervised Cluster Analysis

   1. Investigating Distance Metrics in Semi-supervised Fuzzy c-Means for Breast Cancer Classification

      • Daphne Teck Ching Lai, Jonathan M. Garibaldi

      Pages 147-157

   2. Two Covariances Harnessing Fuzzy Clustering Based PCA for Discrimination of Microarray Data

      • Mika Sato-Ilic

      Pages 158-172

   3. Random Matrix Theory and Covariance Matrix Filtering for Cancer Gene Expression

      • Leif E. Peterson, Charles E. Ford

      Pages 173-184

8. Back Matter

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This book constitutes the refereed proceedings of the 9th International Meeting on Computational Intelligence Methods for Bioinformatics and Biostatistics, CIBB 2012, held in Houston, TX, USA during in July 2012. The 16 revised full papers presented were carefully reviewed and selected from 23 submissions. The papers are organized in topical sections on relativistic heavy ions and DNA damage; image segmentation; proteomics; RNA and DNA sequence analysis; RNA, DNA, and SNP microarrays; semi-supervised/unsupervised cluster analysis.

• evolutionary computational methods
• fuzzy logic
• gene expression
• machine learning
• neural networks
• algorithm analysis and problem complexity

• Center for Biostatistics, TMHRI, Weill Cornell Medical College, ll,, Cornell University,, Houston, USA

  Leif E. Peterson

• DIBRIS, University of Genova, Genova, Italy

  Francesco Masulli

• Sbarro Institute for Cancer Research and Moleculare Medicine, Center for Biotechnology, Temple University, Philadelphia, USA

  Giuseppe Russo

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