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Computational Biology and Bioinformatics, IEEE/ACM Transactions on

Issue 3 • Date July-Sept. 2009

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Displaying Results 1 - 19 of 19
  • [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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  • EIC Editorial: Introducing New Associate Editors

    Publication Year: 2009 , Page(s): 369
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  • A Monte Carlo EM Algorithm for De Novo Motif Discovery in Biomolecular Sequences

    Publication Year: 2009 , Page(s): 370 - 386
    Cited by:  Papers (2)
    Save to Project icon | Request Permissions | Click to expandAbstract | PDF file iconPDF (2670 KB) |  | HTML iconHTML  

    Motif discovery methods play pivotal roles in deciphering the genetic regulatory codes (i.e., motifs) in genomes as well as in locating conserved domains in protein sequences. The Expectation Maximization (EM) algorithm is one of the most popular methods used in de novo motif discovery. Based on the position weight matrix (PWM) updating technique, this paper presents a Monte Carlo version of the E... View full abstract»

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  • A Unified Approach for Reconstructing Ancient Gene Clusters

    Publication Year: 2009 , Page(s): 387 - 400
    Cited by:  Papers (4)
    Save to Project icon | Request Permissions | Click to expandAbstract | PDF file iconPDF (2500 KB) |  | HTML iconHTML  

    The order of genes in genomes provides extensive information. In comparative genomics, differences or similarities of gene orders are determined to predict functional relations of genes or phylogenetic relations of genomes. For this purpose, various combinatorial models can be used to identify gene clusters-groups of genes that are colocated in a set of genomes. We introduce a unified approach to ... View full abstract»

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  • An Approximation Algorithm for the Minimum Breakpoint Linearization Problem

    Publication Year: 2009 , Page(s): 401 - 409
    Cited by:  Papers (3)
    Save to Project icon | Request Permissions | Click to expandAbstract | PDF file iconPDF (609 KB) |  | HTML iconHTML  

    In the recent years, there has been a growing interest in inferring the total order of genes or markers on a chromosome, since current genetic mapping efforts might only suffice to produce a partial order. Many interesting optimization problems were thus formulated in the framework of genome rearrangement. As an important one among them, the minimum breakpoint linearization (MBL) problem is to fin... View full abstract»

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  • An Extended Kalman Filtering Approach to Modeling Nonlinear Dynamic Gene Regulatory Networks via Short Gene Expression Time Series

    Publication Year: 2009 , Page(s): 410 - 419
    Cited by:  Papers (23)
    Save to Project icon | Request Permissions | Click to expandAbstract | PDF file iconPDF (3081 KB) |  | HTML iconHTML  

    In this paper, the extended Kalman filter (EKF) algorithm is applied to model the gene regulatory network from gene time series data. The gene regulatory network is considered as a nonlinear dynamic stochastic model that consists of the gene measurement equation and the gene regulation equation. After specifying the model structure, we apply the EKF algorithm for identifying both the model paramet... View full abstract»

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  • Computing the Distribution of a Tree Metric

    Publication Year: 2009 , Page(s): 420 - 426
    Cited by:  Papers (3)
    Save to Project icon | Request Permissions | Click to expandAbstract | PDF file iconPDF (336 KB) |  | HTML iconHTML  

    The Robinson-Foulds (RF) distance is by far the most widely used measure of dissimilarity between trees. Although the distribution of these distances has been investigated for 20 years, an algorithm that is explicitly polynomial time has yet to be described for computing the distribution for trees around a given tree. In this paper, we derive a polynomial-time algorithm for this distribution. We s... View full abstract»

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  • Evolutionary Optimization of Kernel Weights Improves Protein Complex Comembership Prediction

    Publication Year: 2009 , Page(s): 427 - 437
    Cited by:  Papers (5)
    Multimedia
    Save to Project icon | Request Permissions | Click to expandAbstract | PDF file iconPDF (3017 KB) |  | HTML iconHTML  

    In recent years, more and more high-throughput data sources useful for protein complex prediction have become available (e.g., gene sequence, mRNA expression, and interactions). The integration of these different data sources can be challenging. Recently, it has been recognized that kernel-based classifiers are well suited for this task. However, the different kernels (data sources) are often comb... View full abstract»

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  • Improved Approximation Algorithms for Reconstructing the History of Tandem Repeats

    Publication Year: 2009 , Page(s): 438 - 453
    Save to Project icon | Request Permissions | Click to expandAbstract | PDF file iconPDF (1167 KB) |  | HTML iconHTML  

    Some genetic diseases in human beings are dominated by short sequences repeated consecutively called tandem repeats. Once a region containing tandem repeats is found, it is of great interest to study the history of creating the repeats. The computational problem of reconstructing the duplication history of tandem repeats has been studied extensively in the literature. Almost all previous studies f... View full abstract»

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  • Metrics for Phylogenetic Networks II: Nodal and Triplets Metrics

    Publication Year: 2009 , Page(s): 454 - 469
    Cited by:  Papers (11)
    Save to Project icon | Request Permissions | Click to expandAbstract | PDF file iconPDF (778 KB) |  | HTML iconHTML  

    The assessment of phylogenetic network reconstruction methods requires the ability to compare phylogenetic networks. This is the second in a series of papers devoted to the analysis and comparison of metrics for tree-child time consistent phylogenetic networks on the same set of taxa. In this paper, we generalize to phylogenetic networks two metrics that have already been introduced in the literat... View full abstract»

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  • Model Reduction of Multiscale Chemical Langevin Equations: A Numerical Case Study

    Publication Year: 2009 , Page(s): 470 - 482
    Cited by:  Papers (9)
    Save to Project icon | Request Permissions | Click to expandAbstract | PDF file iconPDF (2230 KB) |  | HTML iconHTML  

    Two very important characteristics of biological reaction networks need to be considered carefully when modeling these systems. First, models must account for the inherent probabilistic nature of systems far from the thermodynamic limit. Often, biological systems cannot be modeled with traditional continuous-deterministic models. Second, models must take into consideration the disparate spectrum o... View full abstract»

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  • On Subset Seeds for Protein Alignment

    Publication Year: 2009 , Page(s): 483 - 494
    Cited by:  Papers (2)
    Save to Project icon | Request Permissions | Click to expandAbstract | PDF file iconPDF (2183 KB) |  | HTML iconHTML  

    We apply the concept of subset seeds proposed in [1] to similarity search in protein sequences. The main question studied is the design of efficient seed alphabets to construct seeds with optimal sensitivity/selectivity trade-offs. We propose several different design methods and use them to construct several alphabets. We then perform a comparative analysis of seeds built over those alphabets and ... View full abstract»

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  • Parsimony Score of Phylogenetic Networks: Hardness Results and a Linear-Time Heuristic

    Publication Year: 2009 , Page(s): 495 - 505
    Cited by:  Papers (6)
    Save to Project icon | Request Permissions | Click to expandAbstract | PDF file iconPDF (895 KB) |  | HTML iconHTML  

    Phylogenies-the evolutionary histories of groups of organisms-play a major role in representing the interrelationships among biological entities. Many methods for reconstructing and studying such phylogenies have been proposed, almost all of which assume that the underlying history of a given set of species can be represented by a binary tree. Although many biological processes can be effectively ... View full abstract»

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  • Protein Design by Sampling an Undirected Graphical Model of Residue Constraints

    Publication Year: 2009 , Page(s): 506 - 516
    Cited by:  Papers (2)
    Save to Project icon | Request Permissions | Click to expandAbstract | PDF file iconPDF (732 KB) |  | HTML iconHTML  

    This paper develops an approach for designing protein variants by sampling sequences that satisfy residue constraints encoded in an undirected probabilistic graphical model. Due to evolutionary pressures on proteins to maintain structure and function, the sequence record of a protein family contains valuable information regarding position-specific residue conservation and coupling (or covariation)... View full abstract»

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  • RNA Search with Decision Trees and Partial Covariance Models

    Publication Year: 2009 , Page(s): 517 - 527
    Cited by:  Papers (3)
    Save to Project icon | Request Permissions | Click to expandAbstract | PDF file iconPDF (3409 KB) |  | HTML iconHTML  

    The use of partial covariance models to search for RNA family members in genomic sequence databases is explored. The partial models are formed from contiguous subranges of the overall RNA family multiple alignment columns. A binary decision-tree framework is presented for choosing the order to apply the partial models and the score thresholds on which to make the decisions. The decision trees are ... View full abstract»

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  • IEEE Computer Society Career Center

    Publication Year: 2009 , Page(s): 528
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    Freely Available from IEEE
  • IEEE/ACM TCBB: Information for authors

    Publication Year: 2009 , Page(s): c3
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  • [Back cover]

    Publication Year: 2009 , 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