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Selected papers from WABI 10

  1. Research

    Sparse estimation for structural variability

    Proteins are dynamic molecules that exhibit a wide range of motions; often these conformational changes are important for protein function. Determining biologically relevant conformational changes, or true var...

    Raghavendra Hosur, Rohit Singh and Bonnie Berger

    Algorithms for Molecular Biology 2011 6:12

    Published on: 19 April 2011

  2. Research

    Haplotypes versus genotypes on pedigrees

    Genome sequencing will soon produce haplotype data for individuals. For pedigrees of related individuals, sequencing appears to be an attractive alternative to genotyping. However, methods for pedigree analysi...

    Bonnie B Kirkpatrick

    Algorithms for Molecular Biology 2011 6:10

    Published on: 19 April 2011

  3. Research

    Estimation of alternative splicing isoform frequencies from RNA-Seq data

    Massively parallel whole transcriptome sequencing, commonly referred as RNA-Seq, is quickly becoming the technology of choice for gene expression profiling. However, due to the short read length delivered by c...

    Marius Nicolae, Serghei Mangul, Ion I Măndoiu and Alex Zelikovsky

    Algorithms for Molecular Biology 2011 6:9

    Published on: 19 April 2011

  4. Research

    An experimental study of Quartets MaxCut and other supertree methods

    Supertree methods represent one of the major ways by which the Tree of Life can be estimated, but despite many recent algorithmic innovations, matrix representation with parsimony (MRP) remains the main algori...

    M Shel Swenson, Rahul Suri, C Randal Linder and Tandy Warnow

    Algorithms for Molecular Biology 2011 6:7

    Published on: 19 April 2011

  5. Research

    An FPT haplotyping algorithm on pedigrees with a small number of sites

    Genetic disease studies investigate relationships between changes in chromosomes and genetic diseases. Single haplotypes provide useful information for these studies but extracting single haplotypes directly b...

    Duong D Doan and Patricia A Evans

    Algorithms for Molecular Biology 2011 6:8

    Published on: 19 April 2011

  6. Research

    Listing all sorting reversals in quadratic time

    We describe an average-case O(n2) algorithm to list all reversals on a signed permutation π that, when applied to π, produce a permutation that is closer to the identity. This algorithm is optimal in the sense th...

    Krister M Swenson, Ghada Badr and David Sankoff

    Algorithms for Molecular Biology 2011 6:11

    Published on: 19 April 2011

  7. Research

    Sparsification of RNA structure prediction including pseudoknots

    Although many RNA molecules contain pseudoknots, computational prediction of pseudoknotted RNA structure is still in its infancy due to high running time and space consumption implied by the dynamic programmin...

    Mathias Möhl, Raheleh Salari, Sebastian Will, Rolf Backofen and S Cenk Sahinalp

    Algorithms for Molecular Biology 2010 5:39

    Published on: 31 December 2010