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  1. The String Barcoding (SBC) problem, introduced by Rash and Gusfield (RECOMB, 2002), consists in finding a minimum set of substrings that can be used to distinguish between all members of a set of given strings...

    Authors: Giuseppe Lancia and Romeo Rizzi

    Citation: Algorithms for Molecular Biology 2006 1:12

    Content type: Research

    Published on:

  2. Bifurcation analysis has proven to be a powerful method for understanding the qualitative behavior of gene regulatory networks. In addition to the more traditional forward problem of determining the mapping from ...

    Authors: James Lu, Heinz W Engl and Peter Schuster

    Citation: Algorithms for Molecular Biology 2006 1:11

    Content type: Research

    Published on:

  3. Two important and not yet solved problems in bacterial genome research are the identification of horizontally transferred genes and the prediction of gene expression levels. Both problems can be addressed by m...

    Authors: Peter Meinicke, Thomas Brodag, Wolfgang Florian Fricke and Stephan Waack

    Citation: Algorithms for Molecular Biology 2006 1:10

    Content type: Research

    Published on:

  4. Given a set S of n locally aligned sequences, it is a needed prerequisite to partition it into groups of very similar sequences to facilitate subsequent computations, such as the generation of a phylogenetic tree...

    Authors: Katharina A Lehmann, Michael Kaufmann, Stephan Steigele and Kay Nieselt

    Citation: Algorithms for Molecular Biology 2006 1:9

    Content type: Research

    Published on:

  5. Recently, we performed an assessment of 13 popular computational tools for discovery of transcription factor binding sites (M. Tompa, N. Li, et al., "Assessing Computational Tools for the Discovery of Transcri...

    Authors: Nan Li and Martin Tompa

    Citation: Algorithms for Molecular Biology 2006 1:8

    Content type: Research

    Published on:

  6. Most cellular processes are carried out by multi-protein complexes, groups of proteins that bind together to perform a specific task. Some proteins form stable complexes, while other proteins form transient as...

    Authors: Elena Zotenko, Katia S Guimarães, Raja Jothi and Teresa M Przytycka

    Citation: Algorithms for Molecular Biology 2006 1:7

    Content type: Research

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  7. Automated software tools for multiple alignment often fail to produce biologically meaningful results. In such situations, expert knowledge can help to improve the quality of alignments.

    Authors: Burkhard Morgenstern, Sonja J Prohaska, Dirk Pöhler and Peter F Stadler

    Citation: Algorithms for Molecular Biology 2006 1:6

    Content type: Research

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  8. Motif patterns of maximal saturation emerged originally in contexts of pattern discovery in biomolecular sequences and have recently proven a valuable notion also in the design of data compression schemes. Inf...

    Authors: Alberto Apostolico, Matteo Comin and Laxmi Parida

    Citation: Algorithms for Molecular Biology 2006 1:4

    Content type: Research

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  9. RNA has been recognized as a key player in cellular regulation in recent years. In many cases, non-coding RNAs exert their function by binding to other nucleic acids, as in the case of microRNAs and snoRNAs. T...

    Authors: Stephan H Bernhart, Hakim Tafer, Ulrike Mückstein, Christoph Flamm, Peter F Stadler and Ivo L Hofacker

    Citation: Algorithms for Molecular Biology 2006 1:3

    Content type: Research

    Published on:

  10. This editorial announces Algorithms for Molecular Biology, a new online open access journal published by BioMed Central. By launching the first open access journal on algorithmic bioinformatics, we provide a foru...

    Authors: Burkhard Morgenstern and Peter F Stadler

    Citation: Algorithms for Molecular Biology 2006 1:1

    Content type: Editorial

    Published on: