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  1. Content type: Research

    In recent years, quartet-based phylogeny reconstruction methods have received considerable attentions in the computational biology community. Traditionally, the accuracy of a phylogeny reconstruction method is...

    Authors: Gang Wu, Ming-Yang Kao, Guohui Lin and Jia-Huai You

    Citation: Algorithms for Molecular Biology 2008 3:1

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  2. Content type: Research

    cis-Regulatory modules (CRMs) of eukaryotic genes often contain multiple binding sites for transcription factors. The phenomenon that binding sites form clusters in CRMs is exploited in many algorithms to locate ...

    Authors: Valentina Boeva, Julien Clément, Mireille Régnier, Mikhail A Roytberg and Vsevolod J Makeev

    Citation: Algorithms for Molecular Biology 2007 2:13

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  3. Content type: Research

    Some amino acid residues functionally interact with each other. This interaction will result in an evolutionary co-variation between these residues – coevolution. Our goal is to find these coevolving residues.

    Authors: Rodrigo Gouveia-Oliveira and Anders G Pedersen

    Citation: Algorithms for Molecular Biology 2007 2:12

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  4. Content type: Research

    We present the N-map method, a pairwise and asymmetrical approach which allows us to compare sequences by taking into account evolutionary events that produce shuffled, reversed or repeated elements. Basically, t...

    Authors: Gilles Didier and Carito Guziolowski

    Citation: Algorithms for Molecular Biology 2007 2:11

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  5. Content type: Software article

    This paper presents a software library, nicknamed BATS, for some basic sequence analysis tasks. Namely, local alignments, via approximate string matching, and global alignments, via longest common subsequence ...

    Authors: Raffaele Giancarlo, Alessandro Siragusa, Enrico Siragusa and Filippo Utro

    Citation: Algorithms for Molecular Biology 2007 2:10

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  6. Content type: Research

    The optimal score for ungapped local alignments of infinitely long random sequences is known to follow a Gumbel extreme value distribution. Less is known about the important case, where gaps are allowed. For t...

    Authors: Stefan Wolfsheimer, Bernd Burghardt and Alexander K Hartmann

    Citation: Algorithms for Molecular Biology 2007 2:9

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  7. Content type: Research

    Neighbor-Net is a novel method for phylogenetic analysis that is currently being widely used in areas such as virology, bacteriology, and plant evolution. Given an input distance matrix, Neighbor-Net produces ...

    Authors: David Bryant, Vincent Moulton and Andreas Spillner

    Citation: Algorithms for Molecular Biology 2007 2:8

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  8. Content type: Research

    Transcriptional regulatory network (TRN) discovery from one method (e.g. microarray analysis, gene ontology, phylogenic similarity) does not seem feasible due to lack of sufficient information, resulting in th...

    Authors: Jingjun Sun, Kagan Tuncay, Alaa Abi Haidar, Lisa Ensman, Frank Stanley, Michael Trelinski and Peter Ortoleva

    Citation: Algorithms for Molecular Biology 2007 2:2

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  9. Content type: Research

    When transcription factor binding sites are known for a particular transcription factor, it is possible to construct a motif model that can be used to scan sequences for additional sites. However, few statisti...

    Authors: C Steven Carmack, Lee Ann McCue, Lee A Newberg and Charles E Lawrence

    Citation: Algorithms for Molecular Biology 2007 2:1

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  10. Content type: Research

    The sparse connectivity of protein-protein interaction data sets makes identification of functional modules challenging. The purpose of this study is to critically evaluate a novel clustering technique for clu...

    Authors: Woochang Hwang, Young-Rae Cho, Aidong Zhang and Murali Ramanathan

    Citation: Algorithms for Molecular Biology 2006 1:24

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  11. Content type: Research

    A structured motif allows variable length gaps between several components, where each component is a simple motif, which allows either no gaps or only fixed length gaps. The motif can either be represented as a p...

    Authors: Yongqiang Zhang and Mohammed J Zaki

    Citation: Algorithms for Molecular Biology 2006 1:22

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  12. Content type: Research

    Extracting motifs from sequences is a mainstay of bioinformatics. We look at the problem of mining structured motifs, which allow variable length gaps between simple motif components. We propose an efficient a...

    Authors: Yongqiang Zhang and Mohammed J Zaki

    Citation: Algorithms for Molecular Biology 2006 1:21

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  13. Content type: Research

    The performance of alignment programs is traditionally tested on sets of protein sequences, of which a reference alignment is known. Conclusions drawn from such protein benchmarks do not necessarily hold for t...

    Authors: Andreas Wilm, Indra Mainz and Gerhard Steger

    Citation: Algorithms for Molecular Biology 2006 1:19

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  14. Content type: Research

    A number of algorithms have been developed for calculating the quartet distance between two evolutionary trees on the same set of species. The quartet distance is the number of quartets – sub-trees induced by ...

    Authors: Chris Christiansen, Thomas Mailund, Christian NS Pedersen, Martin Randers and Martin Stig Stissing

    Citation: Algorithms for Molecular Biology 2006 1:16

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  15. Content type: Research

    Biclustering has emerged as a powerful algorithmic tool for analyzing measurements of gene expression. A number of different methods have emerged for computing biclusters in gene expression data. Many of these...

    Authors: Gregory A Grothaus, Adeel Mufti and TM Murali

    Citation: Algorithms for Molecular Biology 2006 1:15

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  16. Content type: Research

    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

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  17. Content type: Research

    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

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  18. Content type: Research

    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

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  19. Content type: Research

    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

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  20. Content type: Research

    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

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  21. Content type: Research

    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

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  22. Content type: Research

    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

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  23. Content type: Research

    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

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  24. Content type: Research

    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

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  25. Content type: Editorial

    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

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