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Computational Biology and Bioinformatics, IEEE/ACM Transactions on

Issue 2 • Date April-June 2010

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Displaying Results 1 - 25 of 27
  • [Front cover]

    Publication Year: 2010 , Page(s): c1
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  • [Inside front cover]

    Publication Year: 2010 , Page(s): c2
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  • EIC Editorial

    Publication Year: 2010 , Page(s): 193 - 194
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  • Data Mining in Bioinformatics: Selected Papers from BIOKDD

    Publication Year: 2010 , Page(s): 195 - 196
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  • GPD: A Graph Pattern Diffusion Kernel for Accurate Graph Classification with Applications in Cheminformatics

    Publication Year: 2010 , Page(s): 197 - 207
    Cited by:  Papers (1)
    Request Permissions | Click to expandAbstract | PDF file iconPDF (1807 KB) |  | HTML iconHTML  

    Graph data mining is an active research area. Graphs are general modeling tools to organize information from heterogeneous sources and have been applied in many scientific, engineering, and business fields. With the fast accumulation of graph data, building highly accurate predictive models for graph data emerges as a new challenge that has not been fully explored in the data mining community. In ... View full abstract»

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  • Molecular Function Prediction Using Neighborhood Features

    Publication Year: 2010 , Page(s): 208 - 217
    Cited by:  Papers (5)
    Request Permissions | Click to expandAbstract | PDF file iconPDF (1613 KB) |  | HTML iconHTML  

    The recent advent of high-throughput methods has generated large amounts of gene interaction data. This has allowed the construction of genomewide networks. A significant number of genes in such networks remain uncharacterized and predicting the molecular function of these genes remains a major challenge. A number of existing techniques assume that genes with similar functions are topologically cl... View full abstract»

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  • A Metric on the Space of Reduced Phylogenetic Networks

    Publication Year: 2010 , Page(s): 218 - 222
    Cited by:  Papers (3)
    Request Permissions | Click to expandAbstract | PDF file iconPDF (285 KB) |  | HTML iconHTML  

    Phylogenetic networks are leaf-labeled, rooted, acyclic, and directed graphs that are used to model reticulate evolutionary histories. Several measures for quantifying the topological dissimilarity between two phylogenetic networks have been devised, each of which was proven to be a metric on certain restricted classes of phylogenetic networks. A biologically motivated class of phylogenetic networ... View full abstract»

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  • Automated Hierarchical Density Shaving: A Robust Automated Clustering and Visualization Framework for Large Biological Data Sets

    Publication Year: 2010 , Page(s): 223 - 237
    Cited by:  Papers (3)
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    Request Permissions | Click to expandAbstract | PDF file iconPDF (2702 KB) |  | HTML iconHTML  

    A key application of clustering data obtained from sources such as microarrays, protein mass spectroscopy, and phylogenetic profiles is the detection of functionally related genes. Typically, only a small number of functionally related genes cluster into one or more groups, and the rest need to be ignored. For such situations, we present Automated Hierarchical Density Shaving (Auto-HDS), a framewo... View full abstract»

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  • Automated Isolation of Translational Efficiency Bias That Resists the Confounding Effect of GC(AT)-Content

    Publication Year: 2010 , Page(s): 238 - 250
    Cited by:  Papers (2)
    Request Permissions | Click to expandAbstract | PDF file iconPDF (4562 KB) |  | HTML iconHTML  

    Genomic sequencing projects are an abundant source of information for biological studies ranging from the molecular to the ecological in scale; however, much of the information present may yet be hidden from casual analysis. One such information domain, trends in codon usage, can provide a wealth of information about an organism's genes and their expression. Degeneracy in the genetic code allows m... View full abstract»

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  • Gene Association Networks from Microarray Data Using a Regularized Estimation of Partial Correlation Based on PLS Regression

    Publication Year: 2010 , Page(s): 251 - 262
    Cited by:  Papers (2)
    Request Permissions | Click to expandAbstract | PDF file iconPDF (1651 KB) |  | HTML iconHTML  

    Reconstruction of gene-gene interactions from large-scale data such as microarrays is a first step toward better understanding the mechanisms at work in the cell. Two main issues have to be managed in such a context: 1) choosing which measures have to be used to distinguish between direct and indirect interactions from high-dimensional microarray data and 2) constructing networks with a low propor... View full abstract»

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  • Identification of Full and Partial Class Relevant Genes

    Publication Year: 2010 , Page(s): 263 - 277
    Cited by:  Papers (8)
    Request Permissions | Click to expandAbstract | PDF file iconPDF (4863 KB) |  | HTML iconHTML  

    Multiclass cancer classification on microarray data has provided the feasibility of cancer diagnosis across all of the common malignancies in parallel. Using multiclass cancer feature selection approaches, it is now possible to identify genes relevant to a set of cancer types. However, besides identifying the relevant genes for the set of all cancer types, it is deemed to be more informative to bi... View full abstract»

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  • Model Composition for Macromolecular Regulatory Networks

    Publication Year: 2010 , Page(s): 278 - 287
    Cited by:  Papers (1)
    Request Permissions | Click to expandAbstract | PDF file iconPDF (1570 KB) |  | HTML iconHTML  

    Models of regulatory networks become more difficult to construct and understand as they grow in size and complexity. Large models are usually built up from smaller models, representing subsets of reactions within the larger network. To assist modelers in this composition process, we present a formal approach for model composition, a wizard-style program for implementing the approach, and suggested... View full abstract»

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  • Reassortment Networks for Investigating the Evolution of Segmented Viruses

    Publication Year: 2010 , Page(s): 288 - 298
    Cited by:  Papers (1)
    Request Permissions | Click to expandAbstract | PDF file iconPDF (3150 KB) |  | HTML iconHTML  

    Many viruses of interest, such as influenza A, have distinct segments in their genome. The evolution of these viruses involves mutation and reassortment, where segments are interchanged between viruses that coinfect a host. Phylogenetic trees can be constructed to investigate the mutation-driven evolution of individual viral segments. However, reassortment events among viral genomes are not well d... View full abstract»

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  • Signal Quality Measurements for cDNA Microarray Data

    Publication Year: 2010 , Page(s): 299 - 308
    Cited by:  Papers (1)
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    Request Permissions | Click to expandAbstract | PDF file iconPDF (2649 KB) |  | HTML iconHTML  

    Concerns about the reliability of expression data from microarrays inspire ongoing research into measurement error in these experiments. Error arises at both the technical level within the laboratory and the experimental level. In this paper, we will focus on estimating the spot-specific error, as there are few currently available models. This paper outlines two different approaches to quantify th... View full abstract»

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  • Alignments of RNA Structures

    Publication Year: 2010 , Page(s): 309 - 322
    Cited by:  Papers (1)
    Request Permissions | Click to expandAbstract | PDF file iconPDF (3403 KB) |  | HTML iconHTML  

    We describe a theoretical unifying framework to express the comparison of RNA structures, which we call alignment hierarchy. This framework relies on the definition of common supersequences for arc-annotated sequences and encompasses the main existing models for RNA structure comparison based on trees and arc-annotated sequences with a variety of edit operations. It also gives rise to edit models ... View full abstract»

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  • Approximation Algorithms for Predicting RNA Secondary Structures with Arbitrary Pseudoknots

    Publication Year: 2010 , Page(s): 323 - 332
    Request Permissions | Click to expandAbstract | PDF file iconPDF (659 KB) |  | HTML iconHTML  

    We study three closely related problems motivated by the prediction of RNA secondary structures with arbitrary pseudoknots: the problem 2-lnterval Pattern proposed by Vialette, the problem Maximum Base Pair Stackings proposed by Leong et al., and the problem Maximum Stacking Base Pairs proposed by Lyngso. For the 2-lnterval Pattern, we present polynomial-time approximation algorithms for the probl... View full abstract»

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  • Fast Hinge Detection Algorithms for Flexible Protein Structures

    Publication Year: 2010 , Page(s): 333 - 341
    Cited by:  Papers (1)
    Request Permissions | Click to expandAbstract | PDF file iconPDF (3843 KB) |  | HTML iconHTML  

    Analysis of conformational changes is one of the keys to the understanding of protein functions and interactions. For the analysis, we often compare two protein structures, taking flexible regions like hinge regions into consideration. The Root Mean Square Deviation (RMSD) is the most popular measure for comparing two protein structures, but it is only for rigid structures without hinge regions. I... View full abstract»

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  • Fixed-Parameter Tractability of the Maximum Agreement Supertree Problem

    Publication Year: 2010 , Page(s): 342 - 353
    Cited by:  Papers (1)
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    Request Permissions | Click to expandAbstract | PDF file iconPDF (1563 KB) |  | HTML iconHTML  

    Given a set L of labels and a collection of rooted trees whose leaves are bijectively labeled by some elements of L, the Maximum Agreement Supertree (SMAST) problem is given as follows: find a tree T on a largest label set L' ?? L that homeomorphically contains every input tree restricted to L'. The problem has phylogenetic applications to infer supertrees and perform tree congruence analyses. In ... View full abstract»

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  • Modeling Protein Interacting Groups by Quasi-Bicliques: Complexity, Algorithm, and Application

    Publication Year: 2010 , Page(s): 354 - 364
    Cited by:  Papers (2)
    Request Permissions | Click to expandAbstract | PDF file iconPDF (2577 KB) |  | HTML iconHTML  

    Protein-protein interactions (PPIs) are one of the most important mechanisms in cellular processes. To model protein interaction sites, recent studies have suggested to find interacting protein group pairs from large PPI networks at the first step and then to search conserved motifs within the protein groups to form interacting motif pairs. To consider the noise effect and the incompleteness of bi... View full abstract»

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  • Sorting Genomes by Reciprocal Translocations, Insertions, and Deletions

    Publication Year: 2010 , Page(s): 365 - 374
    Cited by:  Papers (2)
    Request Permissions | Click to expandAbstract | PDF file iconPDF (661 KB) |  | HTML iconHTML  

    The problem of sorting by reciprocal translocations (abbreviated as SBT) arises from the field of comparative genomics, which is to find a shortest sequence of reciprocal translocations that transforms one genome ?? into another genome ??, with the restriction that ?? and ?? contain the same genes. SBT has been proved to be polynomial-time solvable, and several polynomial algorithms have been deve... View full abstract»

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  • Linear Separability of Gene Expression Data Sets

    Publication Year: 2010 , Page(s): 375 - 381
    Cited by:  Papers (2)
    Request Permissions | Click to expandAbstract | PDF file iconPDF (1119 KB) |  | HTML iconHTML  

    We study simple geometric properties of gene expression data sets, where samples are taken from two distinct classes (e.g., two types of cancer). Specifically, the problem of linear separability for pairs of genes is investigated. If a pair of genes exhibits linear separation with respect to the two classes, then the joint expression level of the two genes is strongly correlated to the phenomena o... View full abstract»

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  • IEEE Computer Society Career Center

    Publication Year: 2010 , Page(s): 382
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  • IEEE Computer Society CSDA Certification [advertisement]

    Publication Year: 2010 , Page(s): 383
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  • IEEE CS Press Too Soon to Tell

    Publication Year: 2010 , Page(s): 384
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  • Fixed-Parameter Tractability of the Maximum Agreement Supertree Problem

    Publication Year: 2010 , Page(s): 342 - 353
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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