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Bioinformatics Research and Applications

11th International Symposium, ISBRA 2015 Norfolk, USA, June 7-10, 2015 Proceedings

  • Robert Harrison
  • Yaohang Li
  • Ion Măndoiu
Conference proceedings ISBRA 2015

Part of the Lecture Notes in Computer Science book series (LNCS, volume 9096)

Also part of the Lecture Notes in Bioinformatics book sub series (LNBI, volume 9096)

Table of contents

  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
  21. Diploid Alignments and Haplotyping
    Veli Mäkinen, Daniel Valenzuela
    Pages 235-246
  22. Structural Comparative Analysis of Ecto- NTPDase Models from S. Mansoni and H. Sapiens
    Vinicius Schmitz Nunes, Eveline Gomes Vasconcelos, Priscila Faria-Pinto, Carlos Cristiano H. Borges, Priscila V. S. Z. Capriles
    Pages 247-259
  23. Assessing the Robustness of Parsimonious Predictions for Gene Neighborhoods from Reconciled Phylogenies: Supplementary Material
    Ashok Rajaraman, Cedric Chauve, Yann Ponty
    Pages 260-271
  24. Sorting Signed Circular Permutations by Super Short Reversals
    Gustavo Rodrigues Galvão, Christian Baudet, Zanoni Dias
    Pages 272-283
  25. Multiple Alignment of Structures Using Center Of ProTeins
    Kaushik Roy, Satish Chandra Panigrahi, Asish Mukhopadhyay
    Pages 284-296
  26. NRRC: A Non-referential Reads Compression Algorithm
    Subrata Saha, Sanguthevar Rajasekaran
    Pages 297-308
  27. New Heuristics for Clustering Large Biological Networks
    Md. Kishwar Shafin, Kazi Lutful Kabir, Iffatur Ridwan, Tasmiah Tamzid Anannya, Rashid Saadman Karim, Mohammad Mozammel Hoque et al.
    Pages 309-319
  28. A Novel Algorithm for Glycan de novo Sequencing Using Tandem Mass Spectrometry
    Weiping Sun, Gilles A. Lajoie, Bin Ma, Kaizhong Zhang
    Pages 320-330
  29. Community Detection-Based Feature Construction for Protein Sequence Classification
    Karthik Tangirala, Nic Herndon, Doina Caragea
    Pages 331-342
  30. Curvilinear Triangular Discretization of Biomedical Images
    Jing Xu, Andrey N. Chernikov
    Pages 343-354
  31. The Role of miRNAs in Cisplatin-Resistant HeLa Cells
    Yubo Yang, Cuihong Dai, Zhipeng Cai, Aiju Hou, Dayou Cheng, Dechang Xu
    Pages 355-365
  32. DNA AS X: An Information-Coding-Based Model to Improve the Sensitivity in Comparative Gene Analysis
    Ning Yu, Xuan Guo, Feng Gu, Yi Pan
    Pages 366-377
  33. A Distance-Based Method for Inferring Phylogenetic Networks in the Presence of Incomplete Lineage Sorting
    Yun Yu, Luay Nakhleh
    Pages 378-389
  34. Predicting Protein Functions Based on Dynamic Protein Interaction Networks
    Bihai Zhao, Jianxin Wang, Fang-Xiang Wu, Yi Pan
    Pages 390-401
  35. An Iterative Approach for Phylogenetic Analysis of Tumor Progression Using FISH Copy Number
    Jun Zhou, Yu Lin, William Hoskins, Jijun Tang
    Pages 402-412
  36. Back Matter
    Pages 413-445
    PDF

About these proceedings

Introduction

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.

Keywords

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

Editors and affiliations

  • Robert Harrison
    • 1
  • Yaohang Li
    • 2
  • Ion Măndoiu
    • 3
  1. 1.Georgia State UniversityAtlantaUSA
  2. 2.Old Dominion UniversityNorfolkUSA
  3. 3.University of ConnecticutStorrsUSA

Bibliographic information

  • DOI https://doi.org/10.1007/978-3-319-19048-8
  • Copyright Information Springer International Publishing Switzerland 2015
  • Publisher Name Springer, Cham
  • eBook Packages Computer Science
  • Print ISBN 978-3-319-19047-1
  • Online ISBN 978-3-319-19048-8
  • Series Print ISSN 0302-9743
  • Series Online ISSN 1611-3349
  • Buy this book on publisher's site
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