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Selected papers from WABI 09

Edited by Tandy Warnow and Steven Salzberg

Collection published: 4 January 2010

  1. Research

    A tree-based method for the rapid screening of chemical fingerprints

    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 ...

    Thomas G Kristensen, Jesper Nielsen and Christian NS Pedersen

    Algorithms for Molecular Biology 2010 5:9

    Published on: 4 January 2010

  2. Research

    Constructing majority-rule supertrees

    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...

    Jianrong Dong, David Fernández-Baca and FR McMorris

    Algorithms for Molecular Biology 2010 5:2

    Published on: 4 January 2010

  3. Research

    A markov classification model for metabolic pathways

    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...

    Timothy Hancock and Hiroshi Mamitsuka

    Algorithms for Molecular Biology 2010 5:10

    Published on: 4 January 2010

  4. Research

    FlexSnap: Flexible Non-sequential Protein Structure Alignment

    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 ...

    Saeed Salem, Mohammed J Zaki and Chris Bystroff

    Algorithms for Molecular Biology 2010 5:12

    Published on: 4 January 2010

  5. Research

    Phylogenetic comparative assembly

    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 ...

    Peter Husemann and Jens Stoye

    Algorithms for Molecular Biology 2010 5:3

    Published on: 4 January 2010

  6. Research

    Fast prediction of RNA-RNA interaction

    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...

    Raheleh Salari, Rolf Backofen and S Cenk Sahinalp

    Algorithms for Molecular Biology 2010 5:5

    Published on: 4 January 2010

  7. Research

    Linear-time protein 3-D structure searching with insertions and deletions

    Two biomolecular 3-D structures are said to be similar if the RMSD (root mean square deviation) between the two molecules' sequences of 3-D coordinates is less than or equal to some given constant bound. Tools...

    Tetsuo Shibuya, Jesper Jansson and Kunihiko Sadakane

    Algorithms for Molecular Biology 2010 5:7

    Published on: 4 January 2010

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