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Bioinformatics Research and Applications

9th International Symposium, ISBRA 2013, Charlotte, NC, USA, May 20-22, 2013, Proceedings

  • Conference proceedings
  • © 2013

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Editors:
  1. Zhipeng Cai

    1. Computer Science, Georgia State University, Atlanta, USA

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  2. Oliver Eulenstein

    1. Computer Science, Iowa State University, Ames, USA

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  3. Daniel Janies

    1. Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, USA

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  4. Daniel Schwartz

    1. Physiology and Neurobiology, University of Connecticut, Storrs, USA

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Part of the book series: Lecture Notes in Computer Science (LNCS, volume 7875)

Part of the book sub series: Lecture Notes in Bioinformatics (LNBI)

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Conference proceedings info: ISBRA 2013.

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Table of contents (29 papers)

  1. Front Matter

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  2. Peptide Identification from Mass Spectrometry

    • Bin Ma
    Pages 1-1

  3. Identifying Critical Transitions of Biological Processes by Dynamical Network Biomarkers

    • Luonan Chen
    Pages 2-2

  4. Computational Behavioral Ecology

    • Tanya Berger-Wolf
    Pages 3-3

  5. Unusual RNA Structures: Information Content in RNAs from the “Prebiotic Ribosome” to Modern Viruses

    • Stephen C. Harvey
    Pages 4-4

  6. The Radiation Hybrid Map Construction Problem Is FPT

    • Iyad Kanj, Ge Xia, Binhai Zhu
    Pages 5-16

  7. Reconstructing Ancestral Genomic Orders Using Binary Encoding and Probabilistic Models

    • Fei Hu, Lingxi Zhou, Jijun Tang
    Pages 17-27

  8. Computational Methods for the Parallel 3D Simulation of Biochemical Kinetics at the Microscopic Scale

    • Laurent Crépin, Fabrice Harrouet, Sébastien Kerdélo, Jacques Tisseau, Pascal Redou
    Pages 28-39

  9. A Tool for Non-binary Tree Reconciliation

    • Yu Zheng, Louxin Zhang
    Pages 40-51

  10. Patterns of Chromatin-Modifications Discriminate Different Genomic Features in Arabidopsis

    • Anuj Srivastava, Xiaoyu Zhang, Sal LaMarca, Liming Cai, Russell L. Malmberg
    Pages 52-63

  11. Inferring Time-Delayed Gene Regulatory Networks Using Cross-Correlation and Sparse Regression

    • Piyushkumar A. Mundra, Jie Zheng, Mahesan Niranjan, Roy E. Welsch, Jagath C. Rajapakse
    Pages 64-75

  12. A Simulation of Synthetic agr System in E.coli

    • Xiangmiao Zeng, Ke Liu, Fangping Xie, Ying Zhang, Lei Qiao, Cuihong Dai et al.
    Pages 76-86

  13. Gene Regulatory Networks from Gene Ontology

    • Wenting Liu, Kuiyu Chang, Jie Zheng, Jain Divya, Jung-Jae Kim, Jagath C. Rajapakse
    Pages 87-98

  14. Partitioning Biological Networks into Highly Connected Clusters with Maximum Edge Coverage

    • Falk Hüffner, Christian Komusiewicz, Adrian Liebtrau, Rolf Niedermeier
    Pages 99-111

  15. Reconstructing k-Reticulated Phylogenetic Network from a Set of Gene Trees

    • Hoa Vu, Francis Chin, W. K. Hon, Henry Leung, K. Sadakane, Ken W. K. Sung et al.
    Pages 112-124

  16. LCR_Finder: A de Novo Low Copy Repeat Finder for Human Genome

    • Xuan Liu, David Wai-lok Cheung, Hing-Fung Ting, Tak-Wah Lam, Siu-Ming Yiu
    Pages 125-136

  17. Heuristic Algorithms for the Protein Model Assignment Problem

    • Jörg Hauser, Kassian Kobert, Fernando Izquierdo-Carrasco, Karen Meusemann, Bernhard Misof, Michael Gertz et al.
    Pages 137-148

  18. Alignment of DNA Mass-Spectral Profiles Using Network Flows

    • Pavel Skums, Olga Glebova, Alex Zelikovsky, Zoya Dimitrova, David Stiven Campo Rendon, Lilia Ganova-Raeva et al.
    Pages 149-160

  19. A Context-Driven Gene Prioritization Method for Web-Based Functional Genomics

    • Jeremy J. Jay, Erich J. Baker, Elissa J. Chesler
    Pages 161-172

  20. Exploiting Dependencies of Patterns in Gene Expression Analysis Using Pairwise Comparisons

    • Nam S. Vo, Vinhthuy Phan
    Pages 173-184
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  1. Bioinformatics Research and Applications

Keywords

About this book

This book constitutes the refereed proceedings of the 9th International Symposium on Bioinformatics Research and Applications, ISBRA 2013, held in Charlotte, NC, USA, in May 2013. The 25 revised full papers presented together with 4 invited talks were carefully reviewed and selected from 46 submissions. The papers cover a wide range of biomedical databases and data integration, high-performance bio-computing, biomolecular imaging, high-throughput sequencing data analysis, bio-ontologies, molecular evolution, comparative genomics and phylogenomics, molecular modeling and simulation, pattern discovery and classification, computational proteomics, population genetics, data mining and visualization, software tools and applications.

Editors and Affiliations

  • Computer Science, Georgia State University, Atlanta, USA

    Zhipeng Cai

  • Computer Science, Iowa State University, Ames, USA

    Oliver Eulenstein

  • Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, USA

    Daniel Janies

  • Physiology and Neurobiology, University of Connecticut, Storrs, USA

    Daniel Schwartz

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