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IEEE/ACM Transactions on Computational Biology and Bioinformatics

Issue 4 • Date Oct.-Dec. 2006

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

    Publication Year: 2006, Page(s): c1
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  • [Inside front cover]

    Publication Year: 2006, Page(s): c2
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  • Guest Editor's Introduction to the Special Issue on Computational Biology and Bioinformatics - Part 1

    Publication Year: 2006, Page(s):321 - 322
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  • Using Max Cut to Enhance Rooted Trees Consistency

    Publication Year: 2006, Page(s):323 - 333
    Cited by:  Papers (17)
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (1844 KB) | HTML iconHTML

    Supertree methods are used to construct a large tree over a large set of taxa from a set of small trees over overlapping subsets of the complete taxa set. Since accurate reconstruction methods are currently limited to a maximum of a few dozen taxa, the use of a supertree method in order to construct the tree of life is inevitable. Supertree methods are broadly divided according to the input trees:... View full abstract»

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  • Pattern Identification in Biogeography

    Publication Year: 2006, Page(s):334 - 346
    Cited by:  Papers (7)
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (864 KB) | HTML iconHTML

    Identifying common patterns among area cladograms that arise in historical biogeography is an important tool for biogeographical inference. We develop the first rigorous formalization of these pattern-identification problems. We develop metrics to compare area cladograms. We define the maximum agreement area cladogram (MAAC) and we develop efficient algorithms for finding the MAAC of two area clad... View full abstract»

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  • Efficient Detection of Network Motifs

    Publication Year: 2006, Page(s):347 - 359
    Cited by:  Papers (87)  |  Patents (1)
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (2462 KB) | HTML iconHTML

    Motifs in a given network are small connected subnetworks that occur in significantly higher frequencies than would be expected in random networks. They have recently gathered much attention as a concept to uncover structural design principles of complex networks. Kashtan et al. [Bioinformatics, 2004] proposed a sampling algorithm for performing the computationally challenging task of detecting ne... View full abstract»

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  • Motif Search in Graphs: Application to Metabolic Networks

    Publication Year: 2006, Page(s):360 - 368
    Cited by:  Papers (47)
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (632 KB) | HTML iconHTML

    The classic view of metabolism as a collection of metabolic pathways is being questioned with the currently available possibility of studying whole networks. Novel ways of decomposing the network into modules and motifs that could be considered as the building blocks of a network are being suggested. In this work, we introduce a new definition of motif in the context of metabolic networks. Unlike ... View full abstract»

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  • A 1.375-Approximation Algorithm for Sorting by Transpositions

    Publication Year: 2006, Page(s):369 - 379
    Cited by:  Papers (35)
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (1542 KB) | HTML iconHTML

    Sorting permutations by transpositions is an important problem in genome rearrangements. A transposition is a rearrangement operation in which a segment is cut out of the permutation and pasted in a different location. The complexity of this problem is still open and it has been a 10-year-old open problem to improve the best known 1.5-approximation algorithm. In this paper, we provide a 1.375-appr... View full abstract»

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  • New Bounds and Tractable Instances for the Transposition Distance

    Publication Year: 2006, Page(s):380 - 394
    Cited by:  Papers (11)
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (2161 KB) | HTML iconHTML

    The problem of sorting by transpositions asks for a sequence of adjacent interval exchanges that sorts a permutation and is of the shortest possible length. The distance of the permutation is defined as the length of such a sequence. Despite the apparently intuitive nature of this problem, introduced in 1995 by Bafna and Pevzner, the complexity of both finding an optimal sequence and computing the... View full abstract»

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  • Comparing Tandem Repeats with Duplications and Excisions of Variable Degree

    Publication Year: 2006, Page(s):395 - 407
    Cited by:  Papers (7)
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (1447 KB) | HTML iconHTML

    Traditional sequence comparison by alignment employs a mutation model comprised of two events, substitutions and indels (insertions or deletions) of single positions. However, modern genetic analysis knows a variety of more complex mutation events (e.g., duplications, excisions, and rearrangements), especially regarding DNA. With ever more DNA sequence data becoming available, the need to accurate... View full abstract»

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  • Faster Algorithms for Optimal Multiple Sequence Alignment Based on Pairwise Comparisons

    Publication Year: 2006, Page(s):408 - 422
    Cited by:  Papers (3)
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (1878 KB) | HTML iconHTML

    Multiple sequence alignment (MSA) is one of the most fundamental problems in computational molecular biology. The running time of the best known scheme for finding an optimal alignment, based on dynamic programming, increases exponentially with the number of input sequences. Hence, many heuristics were suggested for the problem. We consider a version of the MSA problem where the goal is to find an... View full abstract»

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  • Efficient Parameterized Algorithms for Biopolymer Structure-Sequence Alignment

    Publication Year: 2006, Page(s):423 - 432
    Cited by:  Papers (5)
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (781 KB) | HTML iconHTML

    Computational alignment of a biopolymer sequence (e.g., an RNA or a protein) to a structure is an effective approach to predict and search for the structure of new sequences. To identify the structure of remote homologs, the structure-sequence alignment has to consider not only sequence similarity, but also spatially conserved conformations caused by residue interactions and, consequently, is comp... View full abstract»

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  • Annual index

    Publication Year: 2006, Page(s): Not in print
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  • IEEE/ACM TCBB: Information for authors

    Publication Year: 2006, Page(s): c3
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  • [Back cover]

    Publication Year: 2006, 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