Bioinformatics Research and Applications

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

  • Editors
  • Ion Măndoiu
  • Raj Sunderraman
  • Alexander Zelikovsky
Conference proceedings ISBRA 2008

Part of the Lecture Notes in Computer Science book series (LNCS, volume 4983)

Also part of the Lecture Notes in Bioinformatics book sub series (LNBI, volume 4983)

Table of contents

  1. Front Matter
    PDF
  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

About these proceedings

Introduction

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.

Keywords

bioinformatics biological systems analysis cellular systems classification complexity computational biology computational life scienc computational systems biology data mining evolutionary biology feature selection genome genome analysis machine lear

Bibliographic information

  • DOI https://doi.org/10.1007/978-3-540-79450-9
  • Copyright Information Springer-Verlag Berlin Heidelberg 2008
  • Publisher Name Springer, Berlin, Heidelberg
  • eBook Packages Computer Science
  • Print ISBN 978-3-540-79449-3
  • Online ISBN 978-3-540-79450-9
  • Series Print ISSN 0302-9743
  • Series Online ISSN 1611-3349
  • About this book