Algorithms in Bioinformatics

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

Editors:

ISBN: 978-3-642-15293-1 (Print) 978-3-642-15294-8 (Online)

Table of contents (30 chapters)

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  1. Front Matter

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  2. Biomolecular Structure: RNA, Protein and Molecular Comparison

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      Pages 1-12

      A Worst-Case and Practical Speedup for the RNA Co-folding Problem Using the Four-Russians Idea

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      Pages 13-27

      Sparse Estimation for Structural Variability

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      Pages 28-39

      Data Structures for Accelerating Tanimoto Queries on Real Valued Vectors

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      Pages 40-51

      Sparsification of RNA Structure Prediction Including Pseudoknots

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      Pages 52-64

      Prediction of RNA Secondary Structure Including Kissing Hairpin Motifs

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      Pages 65-77

      Reducing the Worst Case Running Times of a Family of RNA and CFG Problems, Using Valiant’s Approach

  3. Comparative Genomics

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      Pages 78-89

      Reconstruction of Ancestral Genome Subject to Whole Genome Duplication, Speciation, Rearrangement and Loss

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      Pages 90-101

      Genomic Distance with DCJ and Indels

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      Pages 102-110

      Listing All Sorting Reversals in Quadratic Time

  4. Haplotype and Genotype Analysis

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      Pages 111-123

      Discovering Kinship through Small Subsets

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      Pages 124-135

      Fixed-Parameter Algorithm for Haplotype Inferences on General Pedigrees with Small Number of Sites

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      Pages 136-147

      Haplotypes versus Genotypes on Pedigrees

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      Pages 148-161

      Haplotype Inference on Pedigrees with Recombinations and Mutations

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

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      Pages 162-175

      Identifying Rare Cell Populations in Comparative Flow Cytometry

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      Pages 176-188

      Fast Mapping and Precise Alignment of AB SOLiD Color Reads to Reference DNA

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      Pages 189-201

      Design of an Efficient Out-of-Core Read Alignment Algorithm

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      Pages 202-214

      Estimation of Alternative Splicing isoform Frequencies from RNA-Seq Data

  6. Networks

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      Pages 215-225

      Improved Orientations of Physical Networks

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      Pages 226-237

      Enumerating Chemical Organisations in Consistent Metabolic Networks: Complexity and Algorithms

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      Pages 238-249

      Efficient Subgraph Frequency Estimation with G-Tries

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