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Computational Biology and Bioinformatics, IEEE/ACM Transactions on

Issue 4 • Date Oct.-Dec. 2010

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Displaying Results 1 - 25 of 25
  • [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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  • Guest Editors' Introduction to the Special Section on Bioinformatics Research and Applications

    Publication Year: 2010 , Page(s): 577 - 578
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  • Rearrangement Phylogeny of Genomes in Contig Form

    Publication Year: 2010 , Page(s): 579 - 587
    Cited by:  Papers (1)
    Save to Project icon | Request Permissions | Click to expandAbstract | PDF file iconPDF (800 KB) |  | HTML iconHTML  

    There has been a trend in increasing the phylogenetic scope of genome sequencing while decreasing the quality of the published sequence for each genome. With reduced finishing effort, there is an increasing number of genomes being published in contig form. Rearrangement algorithms, including gene order-based phylogenetic tools, require whole genome data on gene order, segment order, or some other ... View full abstract»

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  • Untangling Tanglegrams: Comparing Trees by Their Drawings

    Publication Year: 2010 , Page(s): 588 - 597
    Save to Project icon | Request Permissions | Click to expandAbstract | PDF file iconPDF (994 KB) |  | HTML iconHTML  

    A tanglegram is a pair of trees on the same set of leaves with matching leaves in the two trees joined by an edge. Tanglegrams are widely used in biology-to compare evolutionary histories of host and parasite species and to analyze genes of species in the same geographical area. We consider optimization problems in tanglegram drawings. We show a linear time algorithm to decide if a tanglegram admi... View full abstract»

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  • Pure Parsimony Xor Haplotyping

    Publication Year: 2010 , Page(s): 598 - 610
    Save to Project icon | Request Permissions | Click to expandAbstract | PDF file iconPDF (1458 KB) |  | HTML iconHTML  

    The haplotype resolution from xor-genotype data has been recently formulated as a new model for genetic studies. The xor-genotype data is a cheaply obtainable type of data distinguishing heterozygous from homozygous sites without identifying the homozygous alleles. In this paper, we propose a formulation based on a well-known model used in haplotype inference: pure parsimony. We exhibit exact solu... View full abstract»

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  • Exact Computation of Coalescent Likelihood for Panmictic and Subdivided Populations under the Infinite Sites Model

    Publication Year: 2010 , Page(s): 611 - 618
    Save to Project icon | Request Permissions | Click to expandAbstract | PDF file iconPDF (1164 KB) |  | HTML iconHTML  

    Coalescent likelihood is the probability of observing the given population sequences under the coalescent model. Computation of coalescent likelihood under the infinite sites model is a classic problem in coalescent theory. Existing methods are based on either importance sampling or Markov chain Monte Carlo and are inexact. In this paper, we develop a simple method that can compute the exact coale... View full abstract»

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  • Improved Algorithms for Parsing ESLTAGs: A Grammatical Model Suitable for RNA Pseudoknots

    Publication Year: 2010 , Page(s): 619 - 627
    Save to Project icon | Request Permissions | Click to expandAbstract | PDF file iconPDF (1392 KB) |  | HTML iconHTML  

    Formal grammars have been employed in biology to solve various important problems. In particular, grammars have been used to model and predict RNA structures. Two such grammars are Simple Linear Tree Adjoining Grammars (SLTAGs) and Extended SLTAGs (ESLTAGs). Performances of techniques that employ grammatical formalisms critically depend on the efficiency of the underlying parsing algorithms. In th... View full abstract»

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  • Querying Graphs in Protein-Protein Interactions Networks Using Feedback Vertex Set

    Publication Year: 2010 , Page(s): 628 - 635
    Cited by:  Papers (4)
    Save to Project icon | Request Permissions | Click to expandAbstract | PDF file iconPDF (1187 KB) |  | HTML iconHTML  

    Recent techniques increase rapidly the amount of our knowledge on interactions between proteins. The interpretation of these new information depends on our ability to retrieve known substructures in the data, the Protein-Protein Interactions (PPIs) networks. In an algorithmic point of view, it is an hard task since it often leads to NP-hard problems. To overcome this difficulty, many authors have ... View full abstract»

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  • A Sparse Learning Machine for High-Dimensional Data with Application to Microarray Gene Analysis

    Publication Year: 2010 , Page(s): 636 - 646
    Cited by:  Papers (2)
    Save to Project icon | Request Permissions | Click to expandAbstract | PDF file iconPDF (739 KB) |  | HTML iconHTML  

    Extracting features from high-dimensional data is a critically important task for pattern recognition and machine learning applications. High-dimensional data typically have much more variables than observations, and contain significant noise, missing components, or outliers. Features extracted from high-dimensional data need to be discriminative, sparse, and can capture essential characteristics ... View full abstract»

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  • A Survey of Spatial Defects in Homo Sapiens Affymetrix GeneChips

    Publication Year: 2010 , Page(s): 647 - 653
    Cited by:  Papers (1)
    Multimedia
    Save to Project icon | Request Permissions | Click to expandAbstract | PDF file iconPDF (3470 KB) |  | HTML iconHTML  

    Modern biology has moved from a science of individual measurements to a science where data are collected on an industrial scale. Foremost, among the new tools for biochemistry are chip arrays which, in one operation, measure hundreds of thousands or even millions of DNA sequences or RNA transcripts. While this is impressive, increasingly sophisticated analysis tools have been required to convert g... View full abstract»

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  • A Cluster Refinement Algorithm for Motif Discovery

    Publication Year: 2010 , Page(s): 654 - 668
    Cited by:  Papers (1)
    Multimedia
    Save to Project icon | Request Permissions | Click to expandAbstract | PDF file iconPDF (3000 KB)  

    Finding Transcription Factor Binding Sites, i.e., motif discovery, is crucial for understanding the gene regulatory relationship. Motifs are weakly conserved and motif discovery is an NP-hard problem. We propose a new approach called Cluster Refinement Algorithm for Motif Discovery (CRMD). CRMD employs a flexible statistical motif model allowing a variable number of motifs and motif instances. CRM... View full abstract»

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  • Finding the Nearest Neighbors in Biological Databases Using Less Distance Computations

    Publication Year: 2010 , Page(s): 669 - 680
    Cited by:  Papers (1)
    Save to Project icon | Request Permissions | Click to expandAbstract | PDF file iconPDF (2509 KB) |  | HTML iconHTML  

    Modern biological applications usually involve the similarity comparison between two objects, which is often computationally very expensive, such as whole genome pairwise alignment and protein 3D structure alignment. Nevertheless, being able to quickly identify the closest neighboring objects from very large databases for a newly obtained sequence or structure can provide timely hints to its funct... View full abstract»

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  • Human-Readable Rule Generator for Integrating Amino Acid Sequence Information and Stability of Mutant Proteins

    Publication Year: 2010 , Page(s): 681 - 687
    Cited by:  Papers (1)
    Save to Project icon | Request Permissions | Click to expandAbstract | PDF file iconPDF (1508 KB) |  | HTML iconHTML  

    Most of the bioinformatics tools developed for predicting mutant protein stability appear as a black box and the relationship between amino acid sequence/structure and stability is hidden to the users. We have addressed this problem and developed a human-readable rule generator for integrating the knowledge of amino acid sequence and experimental stability change upon single mutation. Using inform... View full abstract»

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  • Quantifying the Degree of Self-Nestedness of Trees: Application to the Structural Analysis of Plants

    Publication Year: 2010 , Page(s): 688 - 703
    Multimedia
    Save to Project icon | Request Permissions | Click to expandAbstract | PDF file iconPDF (3453 KB) |  | HTML iconHTML  

    In this paper, we are interested in the problem of approximating trees by trees with a particular self-nested structure. Self-nested trees are such that all their subtrees of a given height are isomorphic. We show that these trees present remarkable compression properties, with high compression rates. In order to measure how far a tree is from being a self-nested tree, we then study how to quantif... View full abstract»

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  • Quartets MaxCut: A Divide and Conquer Quartets Algorithm

    Publication Year: 2010 , Page(s): 704 - 718
    Cited by:  Papers (1)
    Save to Project icon | Request Permissions | Click to expandAbstract | PDF file iconPDF (3006 KB) |  | HTML iconHTML  

    Accurate phylogenetic reconstruction methods are currently limited to a maximum of few dozens of taxa. Supertree methods construct a large tree over a large set of taxa, from a set of small trees over overlapping subsets of the complete taxa set. Hence, in order to construct the tree of life over a million and a half different species, the use of a supertree method over the product of accurate met... View full abstract»

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  • RDCurve: A Nonparametric Method to Evaluate the Stability of Ranking Procedures

    Publication Year: 2010 , Page(s): 719 - 726
    Cited by:  Papers (1)
    Save to Project icon | Request Permissions | Click to expandAbstract | PDF file iconPDF (1727 KB) |  | HTML iconHTML  

    Great concerns have been raised about the reproducibility of gene signatures based on high-throughput techniques such as microarray. Studies analyzing similar samples often report poorly overlapping results, and the p-value usually lacks biological context. We propose a nonparametric ReDiscovery Curve (RDCurve) method, to estimate the frequency of rediscovery of gene signature identified. Given a ... View full abstract»

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  • SARNA-Predict: Accuracy Improvement of RNA Secondary Structure Prediction Using Permutation-Based Simulated Annealing

    Publication Year: 2010 , Page(s): 727 - 740
    Cited by:  Papers (7)
    Save to Project icon | Request Permissions | Click to expandAbstract | PDF file iconPDF (3909 KB) |  | HTML iconHTML  

    Ribonucleic acid (RNA), a single-stranded linear molecule, is essential to all biological systems. Different regions of the same RNA strand will fold together via base pair interactions to make intricate secondary and tertiary structures that guide crucial homeostatic processes in living organisms. Since the structure of RNA molecules is the key to their function, algorithms for the prediction of ... View full abstract»

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  • Using Gaussian Process with Test Rejection to Detect T-Cell Epitopes in Pathogen Genomes

    Publication Year: 2010 , Page(s): 741 - 751
    Save to Project icon | Request Permissions | Click to expandAbstract | PDF file iconPDF (2520 KB) |  | HTML iconHTML  

    A major challenge in the development of peptide-based vaccines is finding the right immunogenic element, with efficient and long-lasting immunization effects, from large potential targets encoded by pathogen genomes. Computer models are convenient tools for scanning pathogen genomes to preselect candidate immunogenic peptides for experimental validation. Current methods predict many false positive... View full abstract»

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  • VARUN: Discovering Extensible Motifs under Saturation Constraints

    Publication Year: 2010 , Page(s): 752 - 726
    Cited by:  Papers (2)
    Multimedia
    Save to Project icon | Request Permissions | Click to expandAbstract | PDF file iconPDF (2537 KB) |  | HTML iconHTML  

    The discovery of motifs in biosequences is frequently torn between the rigidity of the model on one hand and the abundance of candidates on the other hand. In particular, motifs that include wild cards or “don't cares” escalate exponentially with their number, and this gets only worse if a don't care is allowed to stretch up to some prescribed maximum length. In this paper, a notion ... View full abstract»

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  • The Metropolized Partial Importance Sampling MCMC Mixes Slowly on Minimum Reversal Rearrangement Paths

    Publication Year: 2010 , Page(s): 763 - 767
    Save to Project icon | Request Permissions | Click to expandAbstract | PDF file iconPDF (315 KB) |  | HTML iconHTML  

    Markov chain Monte Carlo has been the standard technique for inferring the posterior distribution of genome rearrangement scenarios under a Bayesian approach. We present here a negative result on the rate of convergence of the generally used Markov chains. We prove that the relaxation time of the Markov chains walking on the optimal reversal sorting scenarios might grow exponentially with the size... View full abstract»

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  • IEEE Computer Society - Stay Connected [advertisement]

    Publication Year: 2010 , Page(s): 768
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  • IEEE/ACM TCBB: Information for authors

    Publication Year: 2010 , Page(s): c3
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  • [Back cover]

    Publication Year: 2010 , Page(s): c4
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  • 2010 TCBB Annual Index

    Publication Year: 2010 , Page(s): Notinrint
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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