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Algorithms in Bioinformatics

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

  • Conference proceedings
  • © 2005

Overview

Editors:
  1. Rita Casadio

    1. Biocomputing Group, University of Bologna, Italy

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    You can also search for this editor in PubMed   Google Scholar

  2. Gene Myers

    1. Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, USA

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    You can also search for this editor in PubMed   Google Scholar

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

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

Included in the following conference series:

Conference proceedings info: WABI 2005.

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Keywords

Table of contents (35 papers)

  1. Front Matter

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  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
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Other volumes

  1. Algorithms in Bioinformatics

Editors and Affiliations

  • Biocomputing Group, University of Bologna, Italy

    Rita Casadio

  • Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, USA

    Gene Myers

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