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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)

Also part of the Lecture Notes in Bioinformatics book sub series (LNBI, volume 6293)

Table of contents

  1. Front Matter
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  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
    3. Efficient Subgraph Frequency Estimation with G-Tries
      Pedro Ribeiro, Fernando Silva
      Pages 238-249

  7. Phylogenetics

    1. Accuracy Guarantees for Phylogeny Reconstruction Algorithms Based on Balanced Minimum Evolution
      Magnus Bordewich, Radu Mihaescu
      Pages 250-261
    2. The Complexity of Inferring a Minimally Resolved Phylogenetic Supertree
      Jesper Jansson, Richard S. Lemence, Andrzej Lingas
      Pages 262-273
    3. Reducing Multi-state to Binary Perfect Phylogeny with Applications to Missing, Removable, Inserted, and Deleted Data
      Kristian Stevens, Dan Gusfield
      Pages 274-287
    4. An Experimental Study of Quartets MaxCut and Other Supertree Methods
      M. Shel Swenson, Rahul Suri, C. Randal Linder, Tandy Warnow
      Pages 288-299
    5. An Efficient Method for DNA-Based Species Assignment via Gene Tree and Species Tree Reconciliation
      Louxin Zhang, Yun Cui
      Pages 300-311

  8. Sequences, Strings and Motifs

    1. Effective Algorithms for Fusion Gene Detection
      Dan He, Eleazar Eskin
      Pages 312-324
    2. Swiftly Computing Center Strings
      Franziska Hufsky, Léon Kuchenbecker, Katharina Jahn, Jens Stoye, Sebastian Böcker
      Pages 325-336
    3. Speeding Up Exact Motif Discovery by Bounding the Expected Clump Size
      Tobias Marschall, Sven Rahmann
      Pages 337-349
    4. Pair HMM Based Gap Statistics for Re-evaluation of Indels in Alignments with Affine Gap Penalties
      Alexander Schönhuth, Raheleh Salari, S. Cenk Sahinalp
      Pages 350-361
    5. Quantifying the Strength of Natural Selection of a Motif Sequence
      Chen-Hsiang Yeang
      Pages 362-373
  9. Back Matter
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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
  • Buy this book on publisher's site