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IEEE/ACM Transactions on Computational Biology and Bioinformatics

Issue 1 • Date Jan.-March 2008

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Displaying Results 1 - 20 of 20
  • [Front cover]

    Publication Year: 2008, Page(s): c1
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  • [Inside front cover]

    Publication Year: 2008, Page(s): c2
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  • An Evaluation of Information Content as a Metric for the Inference of Putative Conserved Noncoding Regions in DNA Sequences Using a Genetic Algorithms Approach

    Publication Year: 2008, Page(s):1 - 14
    Cited by:  Papers (13)
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (2460 KB) | HTML iconHTML

    In previous work, we presented GAMI [1], an approach to motif inference that uses a genetic algorithms search. GAMI is designed specifically to find putative conserved regulatory motifs in noncoding regions of divergent species and is designed to allow for analysis of long nucleotide sequences. In this work, we compare GAMI's performance when run with its original fitness function (a simple count ... View full abstract»

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  • An Information Theoretic Exploratory Method for Learning Patterns of Conditional Gene Coexpression from Microarray Data

    Publication Year: 2008, Page(s):15 - 24
    Cited by:  Papers (6)
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (629 KB) | HTML iconHTML

    In this paper, we introduce an exploratory framework for learning patterns of conditional coexpression in gene expression data. The main idea behind the proposed approach consists of estimating how the information content shared by a set of M nodes in a network (where each node is associated to an expression profile) varies upon conditioning on a set of L conditioning variables (in the simplest ca... View full abstract»

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  • RnaPredict—An Evolutionary Algorithm for RNA Secondary Structure Prediction

    Publication Year: 2008, Page(s):25 - 41
    Cited by:  Papers (23)
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (4059 KB) | HTML iconHTML

    This paper presents two in-depth studies on RnaPredict, an evolutionary algorithm for RNA secondary structure prediction. The first study is an analysis of the performance of two thermodynamic models, Individual Nearest Neighbor (INN) and Individual Nearest Neighbor Hydrogen Bond (INN-HB). The correlation between the free energy of predicted structures and the sensitivity is analyzed for 19 RNA se... View full abstract»

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  • Statistical Characterization of Protein Ensembles

    Publication Year: 2008, Page(s):42 - 55
    Cited by:  Papers (4)
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (2192 KB) | HTML iconHTML

    When accounting for structural fluctuations or measurement errors, a single rigid structure may not be sufficient to represent a protein. One approach to solve this problem is to represent the possible conformations as a discrete set of observed conformations, an ensemble. In this work, we follow a different richer approach and introduce a framework for estimating probability density functions in ... View full abstract»

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  • A (1.5 + ε)-Approximation Algorithm for Unsigned Translocation Distance

    Publication Year: 2008, Page(s):56 - 66
    Cited by:  Papers (3)
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (2003 KB) | HTML iconHTML

    Genome rearrangement is an important area in computational biology and bioinformatics. The translocation operation is one of the popular operations for genome rearrangement. It was proved that computing the unsigned translocation distance is NP-hard. In this paper, we present a (1.5+epsiv)-approximation algorithm for computing the unsigned translocation distance that improves upon the best known 1... View full abstract»

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  • A Novel Biologically and Psychologically Inspired Fuzzy Decision Support System: Hierarchical Complementary Learning

    Publication Year: 2008, Page(s):67 - 79
    Cited by:  Papers (3)
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (3008 KB) | HTML iconHTML

    A computational intelligent system that models the human cognitive abilities may promise significant performance in problem learning because a human is effective in learning and problem solving. Functionally modeling the human cognitive abilities not only avoids the details of the underlying neural mechanisms performing the tasks but also reduces the complexity of the system. The complementary lea... View full abstract»

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  • An Automatic Translation of SBML into Beta-Binders

    Publication Year: 2008, Page(s):80 - 90
    Cited by:  Papers (2)
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (1324 KB) | HTML iconHTML

    A translation of systems biology markup language (SBML) into a process algebra is proposed in order to allow the formal specification, the simulation, and the formal analysis of biological models. Beta-binders, a language with a quantitative stochastic extension, is chosen for the translation. The proposed translation focuses on the main components of SBML models, as species and reactions. Further... View full abstract»

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  • Combinatorial Approaches for Mass Spectra Recalibration

    Publication Year: 2008, Page(s):91 - 100
    Cited by:  Papers (3)
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (806 KB) | HTML iconHTML

    Mass spectrometry has become one of the most popular analysis techniques in Proteomics and Systems Biology. With the creation of larger data sets, the automated recalibration of mass spectra becomes important to ensure that every peak in the sample spectrum is correctly assigned to some peptide and protein. Algorithms for recalibrating mass spectra have to be robust with respect to wrongly assigne... View full abstract»

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  • Computational Problems in Perfect Phylogeny Haplotyping: Typing without Calling the Allele

    Publication Year: 2008, Page(s):101 - 109
    Cited by:  Papers (2)
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (610 KB) | HTML iconHTML

    A haplotype is an m-long binary vector. The XOR-genotype of two haplotypes is the m-vector of their coordinate-wise XOR. We study the following problem: Given a set of XOR-genotypes, reconstruct their haplotypes so that the set of resulting haplotypes can be mapped onto a perfect phylogeny (PP) tree. The question is motivated by studying population evolution in human genetics and is a variant of t... View full abstract»

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  • DNA Motif Representation with Nucleotide Dependency

    Publication Year: 2008, Page(s):110 - 119
    Cited by:  Papers (3)
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (1107 KB) | HTML iconHTML

    The problem of discovering novel motifs of binding sites is important to the understanding of gene regulatory networks. Motifs are generally represented by matrices (position weight matrix (PWM) or position specific scoring matrix (PSSM)) or strings. However, these representations cannot model biological binding sites well because they fail to capture nucleotide interdependence. It has been pointe... View full abstract»

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  • Novel Algorithm for Coexpression Detection in Time-Varying Microarray Datasets

    Publication Year: 2008, Page(s):120 - 135
    Cited by:  Papers (5)
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (5516 KB) | HTML iconHTML

    When analyzing the results of microarray experiments, biologists generally use unsupervised categorization tools. However, such tools regard each time point as an independent dimension and utilize the euclidean distance to compute the similarities between expressions. Furthermore, some of these methods require the number of clusters to be determined in advance, which is clearly impossible in the c... View full abstract»

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  • Progressive Tree Neighborhood applied to the Maximum Parsimony Problem

    Publication Year: 2008, Page(s):136 - 145
    Cited by:  Papers (14)
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (2482 KB) | HTML iconHTML

    The Maximum Parsimony (MP) problem aims at reconstructing a phylogenetic tree from DNA sequences while minimizing the number of genetic transformations. To solve this NP-complete problem, heuristic methods have been developed, often based on local search. In this paper, we focus on the influence of the neighborhood relations. After analyzing the advantages and drawbacks of the well-known Nearest N... View full abstract»

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  • 2007 Reviewers List

    Publication Year: 2008, Page(s):146 - 147
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  • 2007 Annual Index

    Publication Year: 2008, Page(s):148 - 158
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  • Call for Applications for Editor-in-Chief

    Publication Year: 2008, Page(s): 159
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  • Join the IEEE Computer Society today! [advertisement]

    Publication Year: 2008, Page(s): 160
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  • IEEE/ACM TCBB: Information for authors

    Publication Year: 2008, Page(s): c3
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  • [Back cover]

    Publication Year: 2008, 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