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Algorithms in Bioinformatics

5th International Workshop, WABI 2005, Mallorca, Spain, October 3-6, 2005. Proceedings

  • Rita Casadio
  • Gene Myers
Conference proceedings WABI 2005

Part of the Lecture Notes in Computer Science book series (LNCS, volume 3692)

Also part of the Lecture Notes in Bioinformatics book sub series (LNBI, volume 3692)

Table of contents

  1. Front Matter
    PDF

  2. Expression

    1. Hybrid Methods

      1. Spectral Clustering Gene Ontology Terms to Group Genes by Function
        Nora Speer, Christian Spieth, Andreas Zell
        Pages 1-12
      2. Dynamic De-Novo Prediction of microRNAs Associated with Cell Conditions: A Search Pruned by Expression
        Chaya Ben-Zaken Zilberstein, Michal Ziv-Ukelson
        Pages 13-26

    2. Time Patterns

      1. Clustering Gene Expression Series with Prior Knowledge
        Laurent Bréhélin
        Pages 27-38
      2. A Linear Time Biclustering Algorithm for Time Series Gene Expression Data
        Sara C. Madeira, Arlindo L. Oliveira
        Pages 39-52
      3. Time-Window Analysis of Developmental Gene Expression Data with Multiple Genetic Backgrounds
        Tamir Tuller, Efrat Oron, Erez Makavy, Daniel A. Chamovitz, Benny Chor
        Pages 53-64

  3. Phylogeny

    1. Quartets

      1. A Lookahead Branch-and-Bound Algorithm for the Maximum Quartet Consistency Problem
        Gang Wu, Jia-Huai You, Guohui Lin
        Pages 65-76
      2. Computing the Quartet Distance Between Trees of Arbitrary Degree
        Chris Christiansen, Thomas Mailund, Christian N. S. Pedersen, Martin Randers
        Pages 77-88

    2. Tree Reconciliation

      1. Using Semi-definite Programming to Enhance Supertree Resolvability
        Shlomo Moran, Satish Rao, Sagi Snir
        Pages 89-103
      2. An Efficient Reduction from Constrained to Unconstrained Maximum Agreement Subtree
        Z. S. Peng, H. F. Ting
        Pages 104-115

    3. Clades and Haplotypes

      1. Pattern Identification in Biogeography
        Ganeshkumar Ganapathy, Barbara Goodson, Robert Jansen, Vijaya Ramachandran, Tandy Warnow
        Pages 116-127
      2. On the Complexity of Several Haplotyping Problems
        Rudi Cilibrasi, Leo van Iersel, Steven Kelk, John Tromp
        Pages 128-139
      3. A Hidden Markov Technique for Haplotype Reconstruction
        Pasi Rastas, Mikko Koivisto, Heikki Mannila, Esko Ukkonen
        Pages 140-151
      4. Algorithms for Imperfect Phylogeny Haplotyping (IPPH) with a Single Homoplasy or Recombination Event
        Yun S. Song, Yufeng Wu, Dan Gusfield
        Pages 152-164

  4. Networks

    1. A Faster Algorithm for Detecting Network Motifs
      Sebastian Wernicke
      Pages 165-177
    2. Reaction Motifs in Metabolic Networks
      Vincent Lacroix, Cristina G. Fernandes, Marie-France Sagot
      Pages 178-191
    3. Reconstructing Metabolic Networks Using Interval Analysis
      Warwick Tucker, Vincent Moulton
      Pages 192-203

  5. Genome Rearrangements

    1. Trasposition Model

      1. A 1.375-Approximation Algorithm for Sorting by Transpositions
        Isaac Elias, Tzvika Hartman
        Pages 204-215
      2. A New Tight Upper Bound on the Transposition Distance
        Anthony Labarre
        Pages 216-227

    2. Other Models

      1. Perfect Sorting by Reversals Is Not Always Difficult
        Sèverine Bérard, Anne Bergeron, Cedric Chauve, Christophe Paul
        Pages 228-238
      2. Minimum Recombination Histories by Branch and Bound
        Rune B. Lyngsø, Yun S. Song, Jotun Hein
        Pages 239-250

  6. Sequences

    1. Strings

      1. A Unifying Framework for Seed Sensitivity and Its Application to Subset Seeds
        Gregory Kucherov, Laurent Noé, Mikhail Roytberg
        Pages 251-263
      2. Generalized Planted (l,d)-Motif Problem with Negative Set
        Henry C. M. Leung, Francis Y. L. Chin
        Pages 264-275
      3. Alignment of Tandem Repeats with Excision, Duplication, Substitution and Indels (EDSI)
        Michael Sammeth, Thomas Weniger, Dag Harmsen, Jens Stoye
        Pages 276-290
      4. The Peres-Shields Order Estimator for Fixed and Variable Length Markov Models with Applications to DNA Sequence Similarity
        Daniel Dalevi, Devdatt Dubhashi
        Pages 291-302

    2. Multi-alignment and Clustering

      1. Multiple Structural RNA Alignment with Lagrangian Relaxation
        Markus Bauer, Gunnar W. Klau, Knut Reinert
        Pages 303-314
      2. Faster Algorithms for Optimal Multiple Sequence Alignment Based on Pairwise Comparisons
        Pankaj K. Agarwal, Yonatan Bilu, Rachel Kolodny
        Pages 315-327
      3. Ortholog Clustering on a Multipartite Graph
        Akshay Vashist, Casimir Kulikowski, Ilya Muchnik
        Pages 328-340

    3. Clustering and Representation

      1. Linear Time Algorithm for Parsing RNA Secondary Structure
        Baharak Rastegari, Anne Condon
        Pages 341-352
      2. A Compressed Format for Collections of Phylogenetic Trees and Improved Consensus Performance
        Robert S. Boyer, Warren A. Hunt Jr, Serita M. Nelesen
        Pages 353-364

  7. Structure

    1. Threading

      1. Optimal Protein Threading by Cost-Splitting
        P. Veber, N. Yanev, R. Andonov, V. Poirriez
        Pages 365-375
      2. Efficient Parameterized Algorithm for Biopolymer Structure-Sequence Alignment
        Yinglei Song, Chunmei Liu, Xiuzhen Huang, Russell L. Malmberg, Ying Xu, Liming Cai
        Pages 376-388

    2. Folding

      1. Rotamer-Pair Energy Calculations Using a Trie Data Structure
        Andrew Leaver-Fay, Brian Kuhlman, Jack Snoeyink
        Pages 389-400
      2. Improved Maintenance of Molecular Surfaces Using Dynamic Graph Connectivity
        Eran Eyal, Dan Halperin
        Pages 401-413
      3. The Main Structural Regularities of the Sandwich Proteins
        Alexander Kister
        Pages 414-422
      4. Discovery of Protein Substructures in EM Maps
        Keren Lasker, Oranit Dror, Ruth Nussinov, Haim Wolfson
        Pages 423-434
  8. Back Matter
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About these proceedings

Keywords

Alignment algorithm algorithmics algorithms approximation algorithms bioinformatics clustering computational biology data analysis data mining discrete mathematics genetic mapping genome genome analysis pattern searching

Editors and affiliations

  • Rita Casadio
    • 1
  • Gene Myers
    • 2
  1. 1.Biocomputing GroupUniversity of BolognaItaly
  2. 2.Janelia Farm Research Campus, Howard Hughes Medical InstituteAshburnUSA

Bibliographic information

  • DOI https://doi.org/10.1007/11557067
  • Copyright Information Springer-Verlag Berlin Heidelberg 2005
  • Publisher Name Springer, Berlin, Heidelberg
  • eBook Packages Computer Science
  • Print ISBN 978-3-540-29008-7
  • Online ISBN 978-3-540-31812-5
  • Series Print ISSN 0302-9743
  • Series Online ISSN 1611-3349
  • Buy this book on publisher's site