Algorithms in Bioinformatics

10th International Workshop, WABI 2010, Liverpool, UK, September 6-8, 2010. Proceedings

  • Vincent Moulton
  • Mona Singh
Conference proceedings WABI 2010
Part of the Lecture Notes in Computer Science book series (LNCS, volume 6293)

Table of contents

  1. Front Matter
    PDF

  2. Biomolecular Structure: RNA, Protein and Molecular Comparison

    1. A Worst-Case and Practical Speedup for the RNA Co-folding Problem Using the Four-Russians Idea
      Yelena Frid, Dan Gusfield
      Pages 1-12
    2. Sparse Estimation for Structural Variability
      Raghavendra Hosur, Rohit Singh, Bonnie Berger
      Pages 13-27
    3. Data Structures for Accelerating Tanimoto Queries on Real Valued Vectors
      Thomas G. Kristensen, Christian N. S. Pedersen
      Pages 28-39
    4. Sparsification of RNA Structure Prediction Including Pseudoknots
      Mathias Möhl, Raheleh Salari, Sebastian Will, Rolf Backofen, S. Cenk Sahinalp
      Pages 40-51
    5. Prediction of RNA Secondary Structure Including Kissing Hairpin Motifs
      Corinna Theis, Stefan Janssen, Robert Giegerich
      Pages 52-64
    6. Reducing the Worst Case Running Times of a Family of RNA and CFG Problems, Using Valiant’s Approach
      Shay Zakov, Dekel Tsur, Michal Ziv-Ukelson
      Pages 65-77

  3. Comparative Genomics

    1. Reconstruction of Ancestral Genome Subject to Whole Genome Duplication, Speciation, Rearrangement and Loss
      Denis Bertrand, Yves Gagnon, Mathieu Blanchette, Nadia El-Mabrouk
      Pages 78-89
    2. Genomic Distance with DCJ and Indels
      Marília D. V. Braga, Eyla Willing, Jens Stoye
      Pages 90-101
    3. Listing All Sorting Reversals in Quadratic Time
      Krister M. Swenson, Ghada Badr, David Sankoff
      Pages 102-110

  4. Haplotype and Genotype Analysis

    1. Discovering Kinship through Small Subsets
      Daniel G. Brown, Tanya Berger-Wolf
      Pages 111-123
    2. Fixed-Parameter Algorithm for Haplotype Inferences on General Pedigrees with Small Number of Sites
      Duong D. Doan, Patricia A. Evans
      Pages 124-135
    3. Haplotypes versus Genotypes on Pedigrees
      Bonnie Kirkpatrick
      Pages 136-147
    4. Haplotype Inference on Pedigrees with Recombinations and Mutations
      Yuri Pirola, Paola Bonizzoni, Tao Jiang
      Pages 148-161

  5. High-throughput Data Analysis: Next Generation Sequencing and Flow Cytometry

    1. Identifying Rare Cell Populations in Comparative Flow Cytometry
      Ariful Azad, Johannes Langguth, Youhan Fang, Alan Qi, Alex Pothen
      Pages 162-175
    2. Fast Mapping and Precise Alignment of AB SOLiD Color Reads to Reference DNA
      Miklós Csűrös, Szilveszter Juhos, Attila Bérces
      Pages 176-188
    3. Design of an Efficient Out-of-Core Read Alignment Algorithm
      Arun S. Konagurthu, Lloyd Allison, Thomas Conway, Bryan Beresford-Smith, Justin Zobel
      Pages 189-201
    4. Estimation of Alternative Splicing isoform Frequencies from RNA-Seq Data
      Marius Nicolae, Serghei Mangul, Ion Măndoiu, Alex Zelikovsky
      Pages 202-214

  6. Networks

    1. Improved Orientations of Physical Networks
      Iftah Gamzu, Danny Segev, Roded Sharan
      Pages 215-225
    2. Enumerating Chemical Organisations in Consistent Metabolic Networks: Complexity and Algorithms
      Paulo Vieira Milreu, Vicente Acuña, Etienne Birmelé, Pierluigi Crescenzi, Alberto Marchetti-Spaccamela, Marie-France Sagot et al.
      Pages 226-237

About these proceedings

Keywords

algorithms bioinformatics complexity data structures functional genomics genetic mapping metagenomics ncrna sequencing sorting

Editors and affiliations

  • Vincent Moulton
    • 1
  • Mona Singh
    • 2
  1. 1.School of Computing SciencesUniversity of East AngliaNorwichUK
  2. 2.Lewis-Sigler Institute for Integrative Genomics, Department of Computer SciencePrinceton UniversityPrincetonUSA

Bibliographic information

  • DOI https://doi.org/10.1007/978-3-642-15294-8
  • Copyright Information Springer-Verlag Heidelberg 2010
  • Publisher Name Springer, Berlin, Heidelberg
  • eBook Packages Computer Science
  • Print ISBN 978-3-642-15293-1
  • Online ISBN 978-3-642-15294-8
  • Series Print ISSN 0302-9743
  • Series Online ISSN 1611-3349