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IEEE/ACM Transactions on Computational Biology and Bioinformatics

Issue 1 • Jan.-March 2005

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Displaying Results 1 - 15 of 15
  • [Front cover]

    Publication Year: 2005, Page(s): c1
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  • [Inside front cover]

    Publication Year: 2005, Page(s): c2
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  • Guest Editorial: WABI Special Section Part II

    Publication Year: 2005, Page(s):1 - 2
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  • A new distance for high level RNA secondary structure comparison

    Publication Year: 2005, Page(s):3 - 14
    Cited by:  Papers (11)
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (1346 KB) | HTML iconHTML

    We describe an algorithm for comparing two RNA secondary structures coded in the form of trees that introduces two new operations, called node fusion and edge fusion, besides the tree edit operations of deletion, insertion, and relabeling classically used in the literature. This allows us to address some serious limitations of the more traditional tree edit operations when the trees represent RNAs... View full abstract»

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  • Topological rearrangements and local search method for tandem duplication trees

    Publication Year: 2005, Page(s):15 - 28
    Cited by:  Papers (7)
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (949 KB) | HTML iconHTML

    The problem of reconstructing the duplication history of a set of tandemly repeated sequences was first introduced by Fitch (1977). Many recent studies deal with this problem, showing the validity of the unequal recombination model proposed by Fitch, describing numerous inference algorithms, and exploring the combinatorial properties of these new mathematical objects, which are duplication trees. ... View full abstract»

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  • Optimizing multiple seeds for protein homology search

    Publication Year: 2005, Page(s):29 - 38
    Cited by:  Papers (2)  |  Patents (7)
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (412 KB) | HTML iconHTML

    We present a framework for improving local protein alignment algorithms. Specifically, we discuss how to extend local protein aligners to use a collection of vector seeds or ungapped alignment seeds to reduce noise hits. We model picking a set of seed models as an integer programming problem and give algorithms to choose such a set of seeds. While the problem is NP-hard, and Quasi-NP-hard to appro... View full abstract»

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  • State of the transaction [IEEE/ACM Transactions on Computational Biology and Bioinformatics]

    Publication Year: 2005
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (38 KB) | HTML iconHTML

    Reviews the first year of publication and outlines plans for the second year. View full abstract»

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  • Bases of motifs for generating repeated patterns with wild cards

    Publication Year: 2005, Page(s):40 - 50
    Cited by:  Papers (24)
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (252 KB) | HTML iconHTML

    Motif inference represents one of the most important areas of research in computational biology, and one of its oldest ones. Despite this, the problem remains very much open in the sense that no existing definition is fully satisfying, either in formal terms, or in relation to the biological questions that involve finding such motifs. Two main types of motifs have been considered in the literature... View full abstract»

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  • Multiseed lossless filtration

    Publication Year: 2005, Page(s):51 - 61
    Cited by:  Papers (22)
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (420 KB) | HTML iconHTML

    We study a method of seed-based lossless filtration for approximate string matching and related bioinformatics applications. The method is based on a simultaneous use of several spaced seeds rather than a single seed as studied by Burkhardt and Karkkainen. We present algorithms to compute several important parameters of seed families, study their combinatorial properties, and describe several tech... View full abstract»

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  • Text Mining Biomedical Literature for Discovering Gene-to-Gene Relationships: A Comparative Study of Algorithms

    Publication Year: 2005, Page(s):62 - 76
    Cited by:  Papers (14)
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (1768 KB) | HTML iconHTML

    Partitioning closely related genes into clusters has become an important element of practically all statistical analyses of microarray data. A number of computer algorithms have been developed for this task. Although these algorithms have demonstrated their usefulness for gene clustering, some basic problems remain. This paper describes our work on extracting functional keywords from MEDLINE for a... View full abstract»

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  • 2004 Reviewers list

    Publication Year: 2005, Page(s): 77
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  • [Advertisement]

    Publication Year: 2005, Page(s): 79
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  • [Advertisement]

    Publication Year: 2005, Page(s): 80
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  • IEEE/ACM TCBB: Information for authors

    Publication Year: 2005, Page(s): c3
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  • [Back cover]

    Publication Year: 2005, Page(s): c4
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Aims & Scope

This bimonthly publishes archival research results related to the algorithmic, mathematical, statistical, and computational methods that are central in bioinformatics and computational biology.

Full Aims & Scope

Meet Our Editors

Editor-in-Chief
Ying Xu
University of Georgia
xyn@bmb.uga.edu

Associate Editor-in-Chief
Dong Xu
University of Missouri
xudong@missouri.edu