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Selected papers from WABI 09

Edited by Tandy Warnow and Steven Salzberg

View all collections published in Algorithms for Molecular Biology.

  1. Proteins have evolved subject to energetic selection pressure for stability and flexibility. Structural similarity between proteins that have gone through conformational changes can be captured effectively if ...

    Authors: Saeed Salem, Mohammed J Zaki and Chris Bystroff
    Citation: Algorithms for Molecular Biology 2010 5:12
  2. Segmental duplications, or low-copy repeats, are common in mammalian genomes. In the human genome, most segmental duplications are mosaics comprised of multiple duplicated fragments. This complex genomic organ...

    Authors: Crystal L Kahn, Shay Mozes and Benjamin J Raphael
    Citation: Algorithms for Molecular Biology 2010 5:11
  3. This paper considers the problem of identifying pathways through metabolic networks that relate to a specific biological response. Our proposed model, HME3M, first identifies frequently traversed network paths...

    Authors: Timothy Hancock and Hiroshi Mamitsuka
    Citation: Algorithms for Molecular Biology 2010 5:10
  4. The fingerprint of a molecule is a bitstring based on its structure, constructed such that structurally similar molecules will have similar fingerprints. Molecular fingerprints can be used in an initial phase ...

    Authors: Thomas G Kristensen, Jesper Nielsen and Christian NS Pedersen
    Citation: Algorithms for Molecular Biology 2010 5:9
  5. Supertree methods comprise one approach to reconstructing large molecular phylogenies given multi-marker datasets: trees are estimated on each marker and then combined into a tree (the "supertree") on the enti...

    Authors: M Shel Swenson, François Barbançon, Tandy Warnow and C Randal Linder
    Citation: Algorithms for Molecular Biology 2010 5:8
  6. Regulatory antisense RNAs are a class of ncRNAs that regulate gene expression by prohibiting the translation of an mRNA by establishing stable interactions with a target sequence. There is great demand for eff...

    Authors: Raheleh Salari, Rolf Backofen and S Cenk Sahinalp
    Citation: Algorithms for Molecular Biology 2010 5:5
  7. Functionally related genes tend to be correlated in their expression patterns across multiple conditions and/or tissue-types. Thus co-expression networks are often used to investigate functional groups of gene...

    Authors: Matthew Hansen, Logan Everett, Larry Singh and Sridhar Hannenhalli
    Citation: Algorithms for Molecular Biology 2010 5:4
  8. Recent high throughput sequencing technologies are capable of generating a huge amount of data for bacterial genome sequencing projects. Although current sequence assemblers successfully merge the overlapping ...

    Authors: Peter Husemann and Jens Stoye
    Citation: Algorithms for Molecular Biology 2010 5:3
  9. Supertree methods combine the phylogenetic information from multiple partially-overlapping trees into a larger phylogenetic tree called a supertree. Several supertree construction methods have been proposed to...

    Authors: Jianrong Dong, David Fernández-Baca and FR McMorris
    Citation: Algorithms for Molecular Biology 2010 5:2