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Computational Biology and Bioinformatics, IEEE/ACM Transactions on

Issue 4 • Date Oct.-Dec. 2009

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Displaying Results 1 - 22 of 22
  • [Front cover]

    Publication Year: 2009 , Page(s): c1
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  • [Inside front cover]

    Publication Year: 2009 , Page(s): c2
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  • A Statistical Change Point Model Approach for the Detection of DNA Copy Number Variations in Array CGH Data

    Publication Year: 2009 , Page(s): 529 - 541
    Cited by:  Papers (7)
    Save to Project icon | Request Permissions | Click to expandAbstract | PDF file iconPDF (3657 KB) |  | HTML iconHTML  

    Array comparative genomic hybridization (aCGH) provides a high-resolution and high-throughput technique for screening of copy number variations (CNVs) within the entire genome. This technique, compared to the conventional CGH, significantly improves the identification of chromosomal abnormalities. However, due to the random noise inherited in the imaging and hybridization process, identifying stat... View full abstract»

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  • Assessing the Discordance of Multiple Sequence Alignments

    Publication Year: 2009 , Page(s): 542 - 551
    Save to Project icon | Request Permissions | Click to expandAbstract | PDF file iconPDF (843 KB) |  | HTML iconHTML  

    Multiple sequence alignments have wide applicability in many areas of computational biology, including comparative genomics, functional annotation of proteins, gene finding, and modeling evolutionary processes. Because of the computational difficulty of multiple sequence alignment and the availability of numerous tools, it is critical to be able to assess the reliability of multiple alignments. We... View full abstract»

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  • Comparison of Tree-Child Phylogenetic Networks

    Publication Year: 2009 , Page(s): 552 - 569
    Cited by:  Papers (8)
    Save to Project icon | Request Permissions | Click to expandAbstract | PDF file iconPDF (1907 KB) |  | HTML iconHTML  

    Phylogenetic networks are a generalization of phylogenetic trees that allow for the representation of non-tree-like evolutionary events, like recombination, hybridization, or lateral gene transfer. While much progress has been made to find practical algorithms for reconstructing a phylogenetic network from a set of sequences, all attempts to endorse a class of phylogenetic networks (strictly exten... View full abstract»

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  • Heuristic Reusable Dynamic Programming: Efficient Updates of Local Sequence Alignment

    Publication Year: 2009 , Page(s): 570 - 582
    Cited by:  Papers (1)  |  Patents (1)
    Save to Project icon | Request Permissions | Click to expandAbstract | PDF file iconPDF (2391 KB) |  | HTML iconHTML  

    Recomputation of the previously evaluated similarity results between biological sequences becomes inevitable when researchers realize errors in their sequenced data or when the researchers have to compare nearly similar sequences, e.g., in a family of proteins. We present an efficient scheme for updating local sequence alignments with an affine gap model. In principle, using the previous matching ... View full abstract»

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  • Evaluating Protein Similarity from Coarse Structures

    Publication Year: 2009 , Page(s): 583 - 593
    Cited by:  Papers (3)
    Multimedia
    Save to Project icon | Request Permissions | Click to expandAbstract | PDF file iconPDF (2613 KB) |  | HTML iconHTML  

    To unscramble the relationship between protein function and protein structure, it is essential to assess the protein similarity from different aspects. Although many methods have been proposed for protein structure alignment or comparison, alternative similarity measures are still strongly demanded due to the requirement of fast screening and query in large-scale structure databases. In this paper... View full abstract»

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  • Inferential Clustering Approach for Microarray Experiments with Replicated Measurements

    Publication Year: 2009 , Page(s): 594 - 604
    Cited by:  Papers (1)
    Save to Project icon | Request Permissions | Click to expandAbstract | PDF file iconPDF (2079 KB) |  | HTML iconHTML  

    Cluster analysis has proven to be a useful tool for investigating the association structure among genes in a microarray data set. There is a rich literature on cluster analysis and various techniques have been developed. Such analyses heavily depend on an appropriate (dis)similarity measure. In this paper, we introduce a general clustering approach based on the confidence interval inferential meth... View full abstract»

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  • Laplacian Linear Discriminant Analysis Approach to Unsupervised Feature Selection

    Publication Year: 2009 , Page(s): 605 - 614
    Cited by:  Papers (9)
    Save to Project icon | Request Permissions | Click to expandAbstract | PDF file iconPDF (1811 KB) |  | HTML iconHTML  

    Until recently, numerous feature selection techniques have been proposed and found wide applications in genomics and proteomics. For instance, feature/gene selection has proven to be useful for biomarker discovery from microarray and mass spectrometry data. While supervised feature selection has been explored extensively, there are only a few unsupervised methods that can be applied to exploratory... View full abstract»

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  • Modeling and Visualizing Uncertainty in Gene Expression Clusters Using Dirichlet Process Mixtures

    Publication Year: 2009 , Page(s): 615 - 628
    Cited by:  Papers (4)
    Multimedia
    Save to Project icon | Request Permissions | Click to expandAbstract | PDF file iconPDF (4420 KB) |  | HTML iconHTML  

    Although the use of clustering methods has rapidly become one of the standard computational approaches in the literature of microarray gene expression data, little attention has been paid to uncertainty in the results obtained. Dirichlet process mixture (DPM) models provide a nonparametric Bayesian alternative to the bootstrap approach to modeling uncertainty in gene expression clustering. Most pr... View full abstract»

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  • On Nakhleh's Metric for Reduced Phylogenetic Networks

    Publication Year: 2009 , Page(s): 629 - 638
    Cited by:  Papers (2)
    Save to Project icon | Request Permissions | Click to expandAbstract | PDF file iconPDF (1031 KB) |  | HTML iconHTML  

    We prove that Nakhleh's metric for reduced phylogenetic networks is also a metric on the classes of tree-child phylogenetic networks, semibinary tree-sibling time consistent phylogenetic networks, and multilabeled phylogenetic trees. We also prove that it separates distinguishable phylogenetic networks. In this way, it becomes the strongest dissimilarity measure for phylogenetic networks available... View full abstract»

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  • Protein Structure Classification Based on Conserved Hydrophobic Residues

    Publication Year: 2009 , Page(s): 639 - 651
    Cited by:  Papers (3)
    Save to Project icon | Request Permissions | Click to expandAbstract | PDF file iconPDF (3632 KB) |  | HTML iconHTML  

    Protein folding is frequently guided by local residue interactions that form clusters in the protein core. The interactions between residue clusters serve as potential nucleation sites in the folding process. Evidence postulates that the residue interactions are governed by the hydrophobic propensities that the residues possess. An array of hydrophobicity scales has been developed to determine the... View full abstract»

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  • A Positive Detecting Code and Its Decoding Algorithm for DNA Library Screening

    Publication Year: 2009 , Page(s): 652 - 666
    Cited by:  Papers (1)
    Save to Project icon | Request Permissions | Click to expandAbstract | PDF file iconPDF (3802 KB) |  | HTML iconHTML  

    The study of gene functions requires high-quality DNA libraries. However, a large number of tests and screenings are necessary for compiling such libraries. We describe an algorithm for extracting as much information as possible from pooling experiments for library screening. Collections of clones are called pools, and a pooling experiment is a group test for detecting all positive clones. The pro... View full abstract»

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  • Constructing Level-2 Phylogenetic Networks from Triplets

    Publication Year: 2009 , Page(s): 667 - 681
    Cited by:  Papers (16)
    Multimedia
    Save to Project icon | Request Permissions | Click to expandAbstract | PDF file iconPDF (1453 KB)  

    Jansson and Sung showed that, given a dense set of input triplets T (representing hypotheses about the local evolutionary relationships of triplets of taxa), it is possible to determine in polynomial time whether there exists a level-1 network consistent with T, and if so, to construct such a network. Here, we extend this work by showing that this problem is even polynomial time solvable for the c... View full abstract»

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  • On the Approximation of Optimal Structures for RNA-RNA Interaction

    Publication Year: 2009 , Page(s): 682 - 688
    Cited by:  Papers (4)
    Save to Project icon | Request Permissions | Click to expandAbstract | PDF file iconPDF (970 KB) |  | HTML iconHTML  

    The interaction of two RNA molecules is a common mechanism for many biological processes. Small interfering RNAs represent a simple example of such an interaction. But other more elaborate instances of RNA-RNA interaction exist. Therefore, algorithms that predict the structure of the RNA complex thus formed are of great interest. Most of the proposed algorithms are based on dynamic programming. RN... View full abstract»

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  • Evaluation of Geometric Complementarity between Molecular Surfaces Using Compactly Supported Radial Basis Functions

    Publication Year: 2009 , Page(s): 689 - 694
    Cited by:  Papers (1)
    Save to Project icon | Request Permissions | Click to expandAbstract | PDF file iconPDF (1329 KB) |  | HTML iconHTML  

    One of the challenges faced by all molecular docking algorithms is that of being able to discriminate between correct results and false positives obtained in the simulations. The scoring or energetic function is the one that must fulfill this task. Several scoring functions have been developed and new methodologies are still under development. In this paper, we have employed the compactly supporte... View full abstract»

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  • Machine Learning Techniques for the Automated Classification of Adhesin-Like Proteins in the Human Protozoan Parasite Trypanosoma cruzi

    Publication Year: 2009 , Page(s): 695 - 702
    Save to Project icon | Request Permissions | Click to expandAbstract | PDF file iconPDF (953 KB) |  | HTML iconHTML  

    This paper reports on the evaluation of different machine learning techniques for the automated classification of coding gene sequences obtained from several organisms in terms of their functional role as adhesins. Diverse, biologically-meaningful, sequence-based features were extracted from the sequences and used as inputs to the in silico prediction models. Another contribution of this work is t... View full abstract»

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  • Call for Papers: Special Issue of Transactions in Computational Biology and Bioinformatics: Special Issue on BioCreative II.5

    Publication Year: 2009 , Page(s): 703
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    Freely Available from IEEE
  • New Title from Wiley and CS Press: Too Soon to Tell

    Publication Year: 2009 , Page(s): 704
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    Freely Available from IEEE
  • IEEE/ACM TCBB: Information for authors

    Publication Year: 2009 , Page(s): c3
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    Freely Available from IEEE
  • [Back cover]

    Publication Year: 2009 , Page(s): c4
    Save to Project icon | Request Permissions | PDF file iconPDF (397 KB)  
    Freely Available from IEEE
  • 2009 TCBB Annual Index

    Publication Year: 2009 , Page(s): Not in Print
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    Freely Available from IEEE

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