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Selected papers from WABI 10

Edited by Vincent Moulton and Mona Singh

View all collections published in Algorithms for Molecular Biology.

  1. 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...

    Authors: Raghavendra Hosur, Rohit Singh and Bonnie Berger
    Citation: Algorithms for Molecular Biology 2011 6:12
  2. 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...

    Authors: Krister M Swenson, Ghada Badr and David Sankoff
    Citation: Algorithms for Molecular Biology 2011 6:11
  3. 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...

    Authors: Bonnie B Kirkpatrick
    Citation: Algorithms for Molecular Biology 2011 6:10
  4. 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...

    Authors: Marius Nicolae, Serghei Mangul, Ion I Măndoiu and Alex Zelikovsky
    Citation: Algorithms for Molecular Biology 2011 6:9
  5. 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...

    Authors: M Shel Swenson, Rahul Suri, C Randal Linder and Tandy Warnow
    Citation: Algorithms for Molecular Biology 2011 6:7
  6. 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...

    Authors: Mathias Möhl, Raheleh Salari, Sebastian Will, Rolf Backofen and S Cenk Sahinalp
    Citation: Algorithms for Molecular Biology 2010 5:39