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Computational Biology and Bioinformatics, IEEE/ACM Transactions on

Issue 2 • Date April-June 2008

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Displaying Results 1 - 21 of 21
  • [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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  • Consensus Genetic Maps as Median Orders from Inconsistent Sources

    Publication Year: 2008, Page(s):161 - 171
    Cited by:  Papers (7)
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (1765 KB) | HTML iconHTML

    A genetic map is an ordering of genetic markers calculated from a population of known lineage. Although, traditionally, a map has been generated from a single population for each species, recently, researchers have created maps from multiple populations. In the face of these new data, we address the need to find a consensus map - a map that combines the information from multiple partial and possib... View full abstract»

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  • Extracting Dynamics from Static Cancer Expression Data

    Publication Year: 2008, Page(s):172 - 182
    Cited by:  Papers (2)
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (721 KB) | HTML iconHTML

    Static expression experiments analyze samples from many individuals. These samples are often snapshots of the progression of a certain disease such as cancer. This raises an intriguing question: Can we determine a temporal order for these samples? Such an ordering can lead to better understanding of the dynamics of the disease and to the identification of genes associated with its progression. In ... View full abstract»

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  • Graphical Models of Residue Coupling in Protein Families

    Publication Year: 2008, Page(s):183 - 197
    Cited by:  Papers (15)
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (1609 KB) | HTML iconHTML

    Many statistical measures and algorithmic techniques have been proposed for studying residue coupling in protein families. Generally speaking, two residue positions are considered coupled if, in the sequence record, some of their amino acid type combinations are significantly more common than others. While the proposed approaches have proven useful in finding and describing coupling, a significant... View full abstract»

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  • Identification of Protein Coding Regions Using the Modified Gabor-Wavelet Transform

    Publication Year: 2008, Page(s):198 - 207
    Cited by:  Papers (27)
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (2203 KB) | HTML iconHTML

    An important topic in genomic sequence analysis is the identification of protein coding regions. In this context, several coding DNA model-independent methods based on the occurrence of specific patterns of nucleotides at coding regions have been proposed. Nonetheless, these methods have not been completely suitable due to their dependence on an empirically predefined window length required for a ... View full abstract»

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  • Search for Steady States of Piecewise-Linear Differential Equation Models of Genetic Regulatory Networks

    Publication Year: 2008, Page(s):208 - 222
    Cited by:  Papers (17)
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (2907 KB) | HTML iconHTML

    The analysis of the attractors of a genetic regulatory network gives a good indication of the possible functional modes of the system. In this paper, we are concerned with the problem of finding all steady states of genetic regulatory networks described by piecewise-linear differential equation (PLDE) models. We show that the problem is NP-hard and translate it into the problem of finding all valu... View full abstract»

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  • Toward Verified Biological Models

    Publication Year: 2008, Page(s):223 - 234
    Cited by:  Papers (5)
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (2164 KB) | HTML iconHTML

    The last several decades have witnessed a vast accumulation of biological data and data analysis. Many of these data sets represent only a small fraction of the system's behavior, making the visualization of full system behavior difficult. A more complete understanding of a biological system is gained when different types of data (and/or conclusions drawn from the data) are integrated into a large... View full abstract»

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  • Computing Phylogenetic Diversity for Split Systems

    Publication Year: 2008, Page(s):235 - 244
    Cited by:  Papers (6)
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (862 KB) | HTML iconHTML

    In conservation biology, it is a central problem to measure, predict, and preserve biodiversity as species face extinction. In 1992, Faith proposed measuring the diversity of a collection of species in terms of their relationships on a phylogenetic tree and using this information to identify collections of species with high diversity. Here, we are interested in some variants of the resulting optim... View full abstract»

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  • Haplotyping for Disease Association: A Combinatorial Approach

    Publication Year: 2008, Page(s):245 - 251
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (728 KB) | HTML iconHTML

    We consider a combinatorial problem derived from haplotyping a population with respect to a , either recessive or dominant. Given a set of individuals, partitioned into healthy and diseased, and the corresponding sets of genotypes, we want to infer "bad" and "good" haplotypes to account for these genotypes and for the disease. Assume, for example, that the disease is recessive. Then, the resolving... View full abstract»

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  • Highly Scalable Genotype Phasing by Entropy Minimization

    Publication Year: 2008, Page(s):252 - 261
    Cited by:  Papers (6)
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (3485 KB) | HTML iconHTML

    A single nucleotide polymorphism (SNP) is a position in the genome at which two or more of the possible four nucleotides occur in a large percentage of the population. SNPs account for most of the genetic variability between individuals and mapping SNPs in the human population has become the next high priority in genomics after the completion of the Human Genome Project. In diploid organisms such ... View full abstract»

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  • Inferring Connectivity of Genetic Regulatory Networks Using Information-Theoretic Criteria

    Publication Year: 2008, Page(s):262 - 274
    Cited by:  Papers (13)  |  Patents (1)
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (2598 KB) | HTML iconHTML

    Recently, the concept of mutual information has been proposed for inferring the structure of genetic regulatory networks from gene expression profiling. After analyzing the limitations of mutual information in inferring the gene-to-gene interactions, this paper introduces the concept of conditional mutual information and, based on this, proposes two novel algorithms to infer the connectivity struc... View full abstract»

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  • Nature Reserve Selection Problem: A Tight Approximation Algorithm

    Publication Year: 2008, Page(s):275 - 280
    Cited by:  Papers (6)
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (424 KB) | HTML iconHTML

    The nature reserve selection problem is a problem that arises in the context of studying biodiversity conservation. Subject to budgetary constraints, the problem is to select a set of regions to be conserved so that the phylogenetic diversity of the set of species contained within those regions is maximized. Recently, it has been shown in a paper by Moulton et al. that this problem is NP-hard. In ... View full abstract»

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  • Optimal Algorithms for the Interval Location Problem with Range Constraints on Length and Average

    Publication Year: 2008, Page(s):281 - 290
    Cited by:  Papers (3)
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (927 KB) | HTML iconHTML

    Let A be a sequence of n real numbers, L1 and L2 be two integers such that L1 les L2, and let R1 and R2 be two real numbers such that R1 les R2. An interval of A is feasible if its length is between L1 and L2, and its average is between R1 and R2. In this paper, we st... View full abstract»

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  • Prediction of R5, X4, and R5X4 HIV-1 Coreceptor Usage with Evolved Neural Networks

    Publication Year: 2008, Page(s):291 - 300
    Cited by:  Papers (4)
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (2424 KB) | HTML iconHTML

    The HIV-1 genome is highly heterogeneous. This variation affords the virus a wide range of molecular properties, including the ability to infect cell types, such as macrophages and lymphocytes, expressing different chemokine receptors on the cell surface. In particular, R5 HIV-1 viruses use CCR5 as a coreceptor for viral entry, X4 viruses use CXCR4, whereas some viral strains, known as R5X4 or D-t... View full abstract»

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  • Shorelines of Islands of Tractability: Algorithms for Parsimony and Minimum Perfect Phylogeny Haplotyping Problems

    Publication Year: 2008, Page(s):301 - 312
    Cited by:  Papers (4)
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (483 KB) | HTML iconHTML

    The problem parsimony haplotyping (PH) asks for the smallest set of haplotypes that can explain a given set of genotypes, and the problem minimum perfect phylogeny haplotyping (MPPH) asks for the smallest such set that also allows the haplotypes to be embedded in a perfect phylogeny, an evolutionary tree with biologically motivated restrictions. For PH, we extend recent work by further mapping the... View full abstract»

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  • 2SNP: Scalable Phasing Method for Trios and Unrelated Individuals

    Publication Year: 2008, Page(s):313 - 318
    Cited by:  Papers (4)
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (1778 KB) | HTML iconHTML

    Emerging microarray technologies allow affordable typing of very long genome sequences. A key challenge in analyzing such a huge amount of data is scalable and accurate computational inferring of haplotypes (that is, splitting of each genotype into a pair of corresponding haplotypes). In this paper, we first phase genotypes consisting only of two SNPs using genotypes frequencies adjusted to the ra... View full abstract»

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  • IEEE Computer Society Digital Library [advertisement]

    Publication Year: 2008, Page(s): 319
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  • Build Your Career in Computing [advertisement]

    Publication Year: 2008, Page(s): 320
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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