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Algorithms in Bioinformatics

7th International Workshop, WABI 2007, Philadelphia, PA, USA, September 8-9, 2007, Proceedings

  • Conference proceedings
  • © 2007

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Editors:
  1. Raffaele Giancarlo
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  2. Sridhar Hannenhalli
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Part of the book series: Lecture Notes in Computer Science (LNCS, volume 4645)

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

Included in the following conference series:

Conference proceedings info: WABI 2007.

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Table of contents (39 papers)

  1. Front Matter

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  2. Shotgun Protein Sequencing

    • Pavel A. Pevzner
    Pages 1-1

  3. Locality Kernels for Protein Classification

    • Evgeni Tsivtsivadze, Jorma Boberg, Tapio Salakoski
    Pages 2-11

  4. When Less Is More: Improving Classification of Protein Families with a Minimal Set of Global Features

    • Roy Varshavsky, Menachem Fromer, Amit Man, Michal Linial
    Pages 12-24

  5. Fault Tolerance for Large Scale Protein 3D Reconstruction from Contact Maps

    • Marco Vassura, Luciano Margara, Pietro Di Lena, Filippo Medri, Piero Fariselli, Rita Casadio
    Pages 25-37

  6. Bringing Folding Pathways into Strand Pairing Prediction

    • Jieun K. Jeong, Piotr Berman, Teresa M. Przytycka
    Pages 38-48

  7. A Fast and Accurate Heuristic for the Single Individual SNP Haplotyping Problem with Many Gaps, High Reading Error Rate and Low Coverage

    • Loredana M. Genovese, Filippo Geraci, Marco Pellegrini
    Pages 49-60

  8. Two Birds, One Stone: Selecting Functionally Informative Tag SNPs for Disease Association Studies

    • Phil Hyoun Lee, Hagit Shatkay
    Pages 61-72

  9. Genotype Error Detection Using Hidden Markov Models of Haplotype Diversity

    • Justin Kennedy, Ion Măndoiu, Bogdan PaÅŸaniuc
    Pages 73-84

  10. Haplotype Inference Via Hierarchical Genotype Parsing

    • Pasi Rastas, Esko Ukkonen
    Pages 85-97

  11. Seeded Tree Alignment and Planar Tanglegram Layout

    • Antoni Lozano, Ron Y. Pinter, Oleg Rokhlenko, Gabriel Valiente, Michal Ziv-Ukelson
    Pages 98-110

  12. Inferring Models of Rearrangements, Recombinations, and Horizontal Transfers by the Minimum Evolution Criterion

    • Hadas Birin, Zohar Gal-Or, Isaac Elias, Tamir Tuller
    Pages 111-123

  13. An Ω(n 2/logn) Speed-Up of Heuristics for the Gene-Duplication Problem

    • Mukul S. Bansal, Oliver Eulenstein
    Pages 124-135

  14. Incremental Discovery of Irredundant Motif Bases in Time O(|Σ|n 2 logn)

    • Alberto Apostolico, Claudia Tagliacollo
    Pages 136-148

  15. A Graph Clustering Approach to Weak Motif Recognition

    • Christina Boucher, Daniel G. Brown, Paul Church
    Pages 149-160

  16. Informative Motifs in Protein Family Alignments

    • Hatice Gulcin Ozer, William C. Ray
    Pages 161-170

  17. Topology Independent Protein Structural Alignment

    • Joe Dundas, T. A. Binkowski, Bhaskar DasGupta, Jie Liang
    Pages 171-182

  18. Generalized Pattern Search and Mesh Adaptive Direct Search Algorithms for Protein Structure Prediction

    • Giuseppe Nicosia, Giovanni Stracquadanio
    Pages 183-193

  19. Alignment-Free Local Structural Search by Writhe Decomposition

    • Degui Zhi, Maxim Shatsky, Steven E. Brenner
    Pages 194-195

  20. Defining and Computing Optimum RMSD for Gapped Multiple Structure Alignment

    • Xueyi Wang, Jack Snoeyink
    Pages 196-207
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Other volumes

  1. Algorithms in Bioinformatics

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About this book

This book constitutes the refereed proceedings of the 7th International Workshop on Algorithms in Bioinformatics, WABI 2007, held in Philadelphia, PA, USA in September 2007.

The 38 revised full papers presented together with the abstract of a keynote talk were carefully reviewed and selected from 133 submissions. All current issues of algorithms in bioinformatics are addressed, ranging from mathematical tools to experimental studies of approximation algorithms and reports on significant computational analyses. Numerous biological problems are dealt with, including genetic mapping, sequence alignment and sequence analysis, phylogeny, comparative genomics, and protein structure. Furthermore the papers feature high-performance computing approaches to computationally hard learning and optimization problems in bioinformatics and cover methods, software and dataset repositories for development and testing of such algorithms and their underlying models.

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