Bioinformatics Research and Applications

1. Front Matter

   Pages 1-19

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2. Deriving Protein Backbone Using Traces Extracted from Density Maps at Medium Resolutions

   • Kamal Al Nasr, Jing He

   Pages 1-11

3. Binary Contingency Table Method for Analyzing Gene Mutation in Cancer Genome

   • Emi Ayada, Atsushi Niida, Takanori Hasegawa, Satoru Miyano, Seiya Imoto

   Pages 12-23

4. A Filter-Based Approach for Approximate Circular Pattern Matching

   • Md. Aashikur Rahman Azim, Costas S. Iliopoulos, M. Sohel Rahman, M. Samiruzzaman

   Pages 24-35

5. Fast Algorithms for Inferring Gene-Species Associations

   • Arkadiusz Betkier, Paweł Szczęsny, Paweł Górecki

   Pages 36-47

6. Couplet Supertree Based Species Tree Estimation

   • Sourya Bhattacharyya, Jayanta Mukhopadhyay

   Pages 48-59

7. A Novel Computational Method for Deriving Protein Secondary Structure Topologies Using Cryo-EM Density Maps and Multiple Secondary Structure Predictions

   • Abhishek Biswas, Desh Ranjan, Mohammad Zubair, Jing He

   Pages 60-71

8. Managing Reproducible Computational Experiments with Curated Proteins in KINARI-2

   • John C. Bowers, Rose Tharail John, Ileana Streinu

   Pages 72-83

9. Protein Crystallization Screening Using Associative Experimental Design

   • İmren Dinç, Marc L. Pusey, Ramazan S. Aygün

   Pages 84-95

10. DAM: A Bayesian Method for Detecting Genome-wide Associations on Multiple Diseases

    • Xuan Guo, Jing Zhang, Zhipeng Cai, Ding-Zhu Du, Yi Pan

    Pages 96-107

11. MINED: An Efficient Mutual Information Based Epistasis Detection Method to Improve Quantitative Genetic Trait Prediction

    • Dan He, Zhanyong Wang, Laxmi Parada

    Pages 108-124

12. Domain Adaptation with Logistic Regression for the Task of Splice Site Prediction

    • Nic Herndon, Doina Caragea

    Pages 125-137

13. A Stacking-Based Approach to Identify Translated Upstream Open Reading Frames in Arabidopsis Thaliana

    • Qiwen Hu, Catharina Merchante, Anna N. Stepanova, Jose M. Alonso, Steffen Heber

    Pages 138-149

14. PRESS-PLOT: An Online Server for Protein Structural Analysis and Evaluation with Residue-level Virtual Angle Correlation Plots

    • Yuanyuan Huang, Kejue Jia, Robert Jernigan, Zhijun Wu

    Pages 150-161

15. Calcium Ion Fluctuations Alter Channel Gating in a Stochastic Luminal Calcium Release Site Model

    • Hao Ji, Yaohang Li, Seth H. Weinberg

    Pages 162-174

16. Interleaving Global and Local Search for Protein Motion Computation

    • Kevin Molloy, Amarda Shehu

    Pages 175-186

17. On the Complexity of Duplication-Transfer-Loss Reconciliation with Non-binary Gene Trees

    • Misagh Kordi, Mukul S. Bansal

    Pages 187-198

18. On the Near-Linear Correlation of the Eigenvalues Across BLOSUM Matrices

    • Jin Li, Yen Kaow Ng, Xingwu Liu, Shuai Cheng Li

    Pages 199-210

19. Predicting RNA Secondary Structures: One-grammar-fits-all Solution

    • Menglu Li, Micheal Cheng, Yongtao Ye, Wk Hon, Hf Ting, Tw Lam et al.

    Pages 211-222

20. An Approach for Matching Mixture MS/MS Spectra with a Pair of Peptide Sequences in a Protein Database

    • Yi Liu, Weiping Sun, Gilles Lajoie, Bin Ma, Kaizhong Zhang

    Pages 223-234

This book constitutes the refereed proceedings of the 11th International Symposium on Bioinformatics Research and Applications, ISBRA 2015, held in Norfolk, VA, USA, in June 2015. The 34 revised full papers and 14 two-page papers included in this volume were carefully reviewed and selected from 98 submissions. The papers cover a wide range of topics in bioinformatics and computational biology and their applications.

• RNA
• bioinformatics
• biological networks
• biomedical image processing
• cancer genomics
• computational biology
• data mining
• dynamic programming
• functional genomics
• gene prediction
• graph algorithms
• interaction networks
• machine learning
• miRNA
• pathway
• protein database
• protein structure prediction
• sequence analysis
• supervised learning
• transformation

• Georgia State University, Atlanta, USA

  Robert Harrison

• Old Dominion University, Norfolk, USA

  Yaohang Li

• University of Connecticut, Storrs, USA

  Ion Măndoiu

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