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Bioinformatics Research and Applications

Fourth International Symposium, ISBRA 2008, Atlanta, GA, USA, May 6-9, 2008, Proceedings

  • Conference proceedings
  • © 2008

Overview

Editors:
  1. Ion Măndoiu
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  2. Raj Sunderraman
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  3. Alexander Zelikovsky
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Part of the book series: Lecture Notes in Computer Science (LNCS, volume 4983)

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

Included in the following conference series:

Conference proceedings info: ISBRA 2008.

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Table of contents (47 papers)

  1. Front Matter

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  2. Invited Keynote Talk: Set-Level Analyses for Genome-Wide Association Data

    • Dan L. Nicolae, Omar De la Cruz, William Wen, Baoguan Ke, Minsun Song
    Pages 1-1

  3. Hierarchical Clustering Using Constraints

    • Mariana Kant, Maurice LeBon, David Sankoff
    Pages 2-13

  4. The Gene-Duplication Problem: Near-Linear Time Algorithms for NNI Based Local Searches

    • Mukul S. Bansal, Oliver Eulenstein
    Pages 14-25

  5. A Distance-Based Method for Detecting Horizontal Gene Transfer in Whole Genomes

    • Xintao Wei, Lenore Cowen, Carla Brodley, Arthur Brady, D. Sculley, Donna K. Slonim
    Pages 26-37

  6. An Approach for Determining Evolutionary Distance in Network-Based Phylogenetic Analysis

    • Tingting Zhou, Keith C. C. Chan, Yi Pan, Zhenghua Wang
    Pages 38-49

  7. Pairwise Statistical Significance Versus Database Statistical Significance for Local Alignment of Protein Sequences

    • Ankit Agrawal, Volker Brendel, Xiaoqiu Huang
    Pages 50-61

  8. Estimating Pairwise Statistical Significance of Protein Local Alignments Using a Clustering-Classification Approach Based on Amino Acid Composition

    • Ankit Agrawal, Arka Ghosh, Xiaoqiu Huang
    Pages 62-73

  9. Gapped Extension for Local Multiple Alignment of Interspersed DNA Repeats

    • Todd J. Treangen, Aaron E. Darling, Mark A. Ragan, Xavier Messeguer
    Pages 74-86

  10. Improved Alignment of Protein Sequences Based on Common Parts

    • David Hoksza
    Pages 87-99

  11. Invited Keynote Talk: Computing P-Values for Peptide Identifications in Mass Spectrometry

    • Nikita Arnold, Tema Fridman, Robert M. Day, Andrey A. Gorin
    Pages 100-109

  12. PFP: A Computational Framework for Phylogenetic Footprinting in Prokaryotic Genomes

    • Dongsheng Che, Guojun Li, Shane T. Jensen, Jun S. Liu, Ying Xu
    Pages 110-121

  13. Accelerating the Neighbor-Joining Algorithm Using the Adaptive Bucket Data Structure

    • Leonid Zaslavsky, Tatiana A. Tatusova
    Pages 122-133

  14. Generalized Gene Adjacencies, Graph Bandwidth and Clusters in Yeast Evolution

    • Qian Zhu, Zaky Adam, Vicky Choi, David Sankoff
    Pages 134-145

  15. Physicochemical Correlation between Amino Acid Sites in Short Sequences under Selective Pressure

    • David Campo, Zoya Dimitrova, Yuri Khudyakov
    Pages 146-158

  16. HCV Quasispecies Assembly Using Network Flows

    • Kelly Westbrooks, Irina Astrovskaya, David Campo, Yury Khudyakov, Piotr Berman, Alex Zelikovsky
    Pages 159-170

  17. A Dynamic Programming Algorithm for De Novo Peptide Sequencing with Variable Scoring

    • Matthew A. Goto, Eric J. Schwabe
    Pages 171-182

  18. Invited Keynote Talk: Haplotype Sharing for Genome-Wide Case-Control Association Studies

    • Andrew S. Allen
    Pages 183-183

  19. Incorporating Literature Knowledge in Bayesian Network for Inferring Gene Networks with Gene Expression Data

    • Eyad Almasri, Peter Larsen, Guanrao Chen, Yang Dai
    Pages 184-195

  20. Integrative Network Component Analysis for Regulatory Network Reconstruction

    • Chen Wang, Jianhua Xuan, Li Chen, Po Zhao, Yue Wang, Robert Clarke et al.
    Pages 196-207
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  1. Bioinformatics Research and Applications

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About this book

This book constitutes the refereed proceedings of the Fourth International Symposium on Bioinformatics Research and Applications, ISBRA 2008, held in Atlanta, GA, USA in May 2008. The 35 revised full papers presented together with 6 workshop papers and 6 invited papers were carefully reviewed and selected from a total of 94 submissions. The papers cover a wide range of topics, including clustering and classification, gene expression analysis, gene networks, genome analysis, motif finding, pathways, protein structure prediction, protein domain interactions, phylogenetics, and software tools.

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