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IEEE/ACM Transactions on Computational Biology and Bioinformatics

Issue 1 • Date Jan.-March 2006

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Displaying Results 1 - 14 of 14
  • [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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  • State of the Journal

    Publication Year: 2006, Page(s): 1
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  • Jointly analyzing gene expression and copy number data in breast cancer using data reduction models

    Publication Year: 2006, Page(s):2 - 16
    Cited by:  Papers (18)
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (3859 KB) | HTML iconHTML

    With the growing surge of biological measurements, the problem of integrating and analyzing different types of genomic measurements has become an immediate challenge for elucidating events at the molecular level. In order to address the problem of integrating different data types, we present a framework that locates variation patterns in two biological inputs based on the generalized singular valu... View full abstract»

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  • Spatio-temporal analysis of constitutive exocytosis in epithelial cells

    Publication Year: 2006, Page(s):17 - 32
    Cited by:  Papers (14)  |  Patents (1)
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (9405 KB) | HTML iconHTML

    Exocytosis is an essential cellular trafficking process integral to the proper distribution and function of a plethora of molecules, including transporters, receptors, and enzymes. Moreover, incorrect protein targeting can lead to pathological conditions. Recently, the application of evanescent wave microscopy has allowed us to image the final steps of exocytosis. However, spatio-temporal analysis... View full abstract»

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  • Statistical analysis of RNA backbone

    Publication Year: 2006, Page(s):33 - 46
    Cited by:  Papers (16)
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (3180 KB) | HTML iconHTML

    Local conformation is an important determinant of RNA catalysis and binding. The analysis of RNA conformation is particularly difficult due to the large number of degrees of freedom (torsion angles) per residue. Proteins, by comparison, have many fewer degrees of freedom per residue. In this work, we use and extend classical tools from statistics and signal processing to search for clusters in RNA... View full abstract»

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  • Gene mapping and marker clustering using Shannon's mutual information

    Publication Year: 2006, Page(s):47 - 56
    Cited by:  Papers (32)
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (1242 KB) | HTML iconHTML

    Finding the causal genetic regions underlying complex traits is one of the main aims in human genetics. In the context of complex diseases, which are believed to be controlled by multiple contributing loci of largely unknown effect and position, it is especially important to develop general yet sensitive methods for gene mapping. We discuss the use of Shannon's information theory for population-ba... View full abstract»

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  • A hidden Markov model for transcriptional regulation in single cells

    Publication Year: 2006, Page(s):57 - 71
    Cited by:  Papers (8)
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (2924 KB) | HTML iconHTML

    We discuss several issues pertaining to the use of stochastic biochemical systems for modeling transcriptional regulation in single cells. By appropriately choosing the system state, we can model transcriptional regulation by a hidden Markov model (HMM). This opens the possibility of using well-known techniques for the statistical analysis and stochastic control of HMMs to mathematically and compu... View full abstract»

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  • A hill-climbing approach for automatic gridding of cDNA microarray images

    Publication Year: 2006, Page(s):72 - 83
    Cited by:  Papers (18)  |  Patents (5)
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (6723 KB) | HTML iconHTML

    Image and statistical analysis are two important stages of cDNA microarrays. Of these, gridding is necessary to accurately identify the location of each spot while extracting spot intensities from the microarray images and automating this procedure permits high-throughput analysis. Due to the deficiencies of the equipment used to print the arrays, rotations, misalignments, high contamination with ... View full abstract»

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  • Unicyclic networks: compatibility and enumeration

    Publication Year: 2006, Page(s):84 - 91
    Cited by:  Papers (5)
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (503 KB) | HTML iconHTML

    Graphs obtained from a binary leaf labeled ("phylogenetic") tree by adding an edge so as to introduce a cycle provide a useful representation of hybrid evolution in molecular evolutionary biology. This class of graphs (which we call "unicyclic networks") also has some attractive combinatorial properties, which we present. We characterize when a set of binary phylogenetic trees is displayed by a un... View full abstract»

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  • A short proof that phylogenetic tree reconstruction by maximum likelihood is hard

    Publication Year: 2006, Page(s):92 - 94
    Cited by:  Papers (34)
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (90 KB) | HTML iconHTML

    Maximum likelihood is one of the most widely used techniques to infer evolutionary histories. Although it is thought to be intractable, a proof of its hardness has been lacking. Here, we give a short proof that computing the maximum likelihood tree is NP-hard by exploiting a connection between likelihood and parsimony observed by Tuffley and Steel View full abstract»

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  • 2005 Reviewers List

    Publication Year: 2006, Page(s):95 - 96
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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