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IEEE/ACM Transactions on Computational Biology and Bioinformatics

Issue 4 • Date Oct.-Dec. 2004

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Displaying Results 1 - 11 of 11
  • [Front cover]

    Publication Year: 2004, Page(s): c1
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  • [Inside front cover]

    Publication Year: 2004, Page(s): c2
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  • Guest Editorial: WABI Special Section Part 1

    Publication Year: 2004, Page(s):137 - 138
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  • Maximum-scoring segment sets

    Publication Year: 2004, Page(s):139 - 150
    Cited by:  Papers (2)
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (940 KB) | HTML iconHTML

    We examine the problem of finding maximum-scoring sets of disjoint segments in a sequence of scores. The problem arises in DNA and protein segmentation and in postprocessing of sequence alignments. Our key result states a simple recursive relationship between maximum-scoring segment sets. The statement leads to fast algorithms for finding such segment sets. We apply our methods to the identificati... View full abstract»

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  • Phylogenetic super-networks from partial trees

    Publication Year: 2004, Page(s):151 - 158
    Cited by:  Papers (50)
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (808 KB) | HTML iconHTML

    In practice, one is often faced with incomplete phylogenetic data, such as a collection of partial trees or partial splits. This paper poses the problem of inferring a phylogenetic super-network from such data and provides an efficient algorithm for doing so, called the Z-closure method. Additionally, the questions of assigning lengths to the edges of the network and how to restrict the "dimension... View full abstract»

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  • An O(N2) algorithm for discovering optimal Boolean pattern pairs

    Publication Year: 2004, Page(s):159 - 170
    Cited by:  Papers (3)
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (1043 KB) | HTML iconHTML

    We consider the problem of finding the optimal combination of string patterns, which characterizes a given set of strings that have a numeric attribute value assigned to each string. Pattern combinations are scored based on the correlation between their occurrences in the strings and the numeric attribute values. The aim is to find the combination of patterns which is best with respect to an appro... View full abstract»

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  • A polynomial-time algorithm for the matching of crossing contact-map patterns

    Publication Year: 2004, Page(s):171 - 180
    Cited by:  Papers (5)
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (649 KB) | HTML iconHTML

    Contact maps are a model to capture the core information in the structure of biological molecules, e.g., proteins. A contact map consists of an ordered set S of elements (representing a protein's sequence of amino acids), and a set A of element pairs of S, called arcs (representing amino acids which are closely neighbored in the structure). Given two contact maps (S, A) and (Sp, A... View full abstract»

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  • Using uncorrelated discriminant analysis for tissue classification with gene expression data

    Publication Year: 2004, Page(s):181 - 190
    Cited by:  Papers (36)  |  Patents (2)
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (960 KB) | HTML iconHTML

    The classification of tissue samples based on gene expression data is an important problem in medical diagnosis of diseases such as cancer. In gene expression data, the number of genes is usually very high (in the thousands) compared to the number of data samples (in the tens or low hundreds); that is, the data dimension is large compared to the number of data points (such data is said to be under... View full abstract»

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  • Annual Index

    Publication Year: 2004, Page(s):191 - 192
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  • IEEE/ACM TCBB: Information for authors

    Publication Year: 2004, Page(s): c3
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  • [Back cover]

    Publication Year: 2004, 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