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IEEE/ACM Transactions on Computational Biology and Bioinformatics

Issue 1 • Date Jan.-March 2009

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Displaying Results 1 - 25 of 27
  • [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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  • Final, Five-Year End, Editorial

    Publication Year: 2009, Page(s):1 - 2
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  • New EIC Editorial

    Publication Year: 2009, Page(s): 3
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  • Special Section: Phylogenetics

    Publication Year: 2009, Page(s):4 - 6
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  • Barking Up The Wrong Treelength: The Impact of Gap Penalty on Alignment and Tree Accuracy

    Publication Year: 2009, Page(s):7 - 21
    Cited by:  Papers (12)
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (4223 KB) | HTML iconHTML Multimedia Media

    The current technique for estimating phylogenies from sequence data uses two phases: first, the sequences are aligned, and then the tree is estimated using the obtained alignment. More recently, however, several computational methods have been developed for simultaneous estimation of the alignment and the tree, of which POY (a heuristic for the NP-hard "minimum treelength" problem, which extends m... View full abstract»

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  • Budgeted Phylogenetic Diversity on Circular Split Systems

    Publication Year: 2009, Page(s):22 - 29
    Cited by:  Papers (3)
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (449 KB) | HTML iconHTML

    In the last 15 years, phylogenetic diversity (PD) has gained interest in the community of conservation biologists as a surrogate measure for assessing biodiversity. We have recently proposed two approaches to select taxa for maximizing PD, namely PD with budget constraints and PD on split systems. In this paper, we will unify these two strategies and present a dynamic programming algorithm to solv... View full abstract»

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  • Hybridization in Nonbinary Trees

    Publication Year: 2009, Page(s):30 - 45
    Cited by:  Papers (14)
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (990 KB) | HTML iconHTML

    Reticulate evolution - the umbrella term for processes like hybridization, horizontal gene transfer, and recombination - plays an important role in the history of life of many species. Although the occurrence of such events is widely accepted, approaches to calculate the extent to which reticulation has influenced evolution are relatively rare. In this paper, we show that the NP-hard problem of ca... View full abstract»

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  • Metrics for Phylogenetic Networks I: Generalizations of the Robinson-Foulds Metric

    Publication Year: 2009, Page(s):46 - 61
    Cited by:  Papers (17)
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (1286 KB) | HTML iconHTML

    The assessment of phylogenetic network reconstruction methods requires the ability to compare phylogenetic networks. This is the first 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 study three metrics that have already been introduced in the literature: the Robinson-Foulds dist... View full abstract»

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  • Robustness of Topological Supertree Methods for Reconciling Dense Incompatible Data

    Publication Year: 2009, Page(s):62 - 75
    Cited by:  Papers (1)
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (522 KB) | HTML iconHTML

    Given a collection of rooted phylogenetic trees with overlapping sets of leaves, a compatible supertree S is a single tree whose set of leaves is the union of the input sets of leaves and such that S agrees with each input tree when restricted to the leaves of the input tree. Typically with trees from real data, no compatible supertree exists, and various methods may be utilized to r... View full abstract»

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  • The Identifiability of Covarion Models in Phylogenetics

    Publication Year: 2009, Page(s):76 - 88
    Cited by:  Papers (6)
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (253 KB) | HTML iconHTML

    Covarion models of character evolution describe inhomogeneities in substitution processes through time. In phylogenetics, such models are used to describe changing functional constraints or selection regimes during the evolution of biological sequences. In this work the identifiability of such models for generic parameters on a known phylogenetic tree is established, provided the number of covario... View full abstract»

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  • Fourier Transform Inequalities for Phylogenetic Trees

    Publication Year: 2009, Page(s):89 - 95
    Cited by:  Papers (1)
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (193 KB) | HTML iconHTML

    Phylogenetic invariants are not the only constraints on site-pattern frequency vectors for phylogenetic trees. A mutation matrix, by its definition, is the exponential of a matrix with non-negative off-diagonal entries; this positivity requirement implies non-trivial constraints on the site-pattern frequency vectors. We call these additional constraints "edge-parameter inequalities." In this paper... View full abstract»

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  • Outgoing EIC Editorial for this Special Section of TCBB with the Theme of Phylogenetics

    Publication Year: 2009, Page(s): 96
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  • Maximum Parsimony for Tree Mixtures

    Publication Year: 2009, Page(s):97 - 102
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (503 KB) | HTML iconHTML

    With the number of sequenced genomes growing ever larger, it is now common practice to concatenate sequence alignments from several genomic loci as a first step to phylogenetic tree inference. However, as different loci may support different trees due to processes such as gene duplication and lineage sorting, it is important to better understand how commonly used phylogenetic inference methods beh... View full abstract»

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  • Drawing Rooted Phylogenetic Networks

    Publication Year: 2009, Page(s):103 - 109
    Cited by:  Papers (5)
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (916 KB) | HTML iconHTML

    The evolutionary history of a collection of species is usually represented by a phylogenetic tree. Sometimes, phylogenetic networks are used as a means of representing reticulate evolution or of showing uncertainty and incompatibilities in evolutionary datasets. This is often done using unrooted phylogenetic networks such as split networks, due in part, to the availability of software (SplitsTree)... View full abstract»

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  • REGULAR PAPERS 
  • Consistency of Topological Moves Based on the Balanced Minimum Evolution Principle of Phylogenetic Inference

    Publication Year: 2009, Page(s):110 - 117
    Cited by:  Papers (10)
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (478 KB) | HTML iconHTML

    Many phylogenetic algorithms search the space of possible trees using topological rearrangements and some optimality criterion. FastME is such an approach that uses the balanced minimum evolution (BME) principle, which computer studies have demonstrated to have high accuracy. FastME includes two variants: balanced subtree prune and regraft (BSPR) and balanced nearest neighbor interchange (BNNI). T... View full abstract»

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  • Refining Phylogenetic Trees Given Additional Data: An Algorithm Based on Parsimony

    Publication Year: 2009, Page(s):118 - 125
    Cited by:  Papers (2)
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (695 KB) | HTML iconHTML

    Given a set X of taxa, a phylogenetic X-tree T that is only partially resolved, and a collection of characters on X, we consider the problem of finding a resolution (refinement) of T that minimizes the parsimony score of the given characters. Previous work has shown that this problem has a polynomial time solution provided certain strong constraints are imposed on the input. In this paper we provi... View full abstract»

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  • Shrinkage Effect in Ancestral Maximum Likelihood

    Publication Year: 2009, Page(s):126 - 133
    Cited by:  Papers (3)
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (357 KB) | HTML iconHTML

    Ancestral maximum likelihood (AML) is a method that simultaneously reconstructs a phylogenetic tree and ancestral sequences from extant data (sequences at the leaves). The tree and ancestral sequences maximize the probability of observing the given data under a Markov model of sequence evolution, in which branch lengths are also optimized but constrained to take the same value on any edge across a... View full abstract»

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  • Gene Classification Using Codon Usage and Support Vector Machines

    Publication Year: 2009, Page(s):134 - 143
    Cited by:  Papers (17)
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (1147 KB) | HTML iconHTML

    A novel approach for gene classification, which adopts codon usage bias as input feature vector for classification by support vector machines (SVM) is proposed. The DNA sequence is first converted to a 59-dimensional feature vector where each element corresponds to the relative synonymous usage frequency of a codon. As the input to the classifier is independent of sequence length and variance, our... View full abstract»

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  • Initializing Partition-Optimization Algorithms

    Publication Year: 2009, Page(s):144 - 157
    Cited by:  Papers (30)
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (1994 KB) | HTML iconHTML

    Clustering datasets is a challenging problem needed in a wide array of applications. Partition-optimization approaches, such as k-means or expectation-maximization (EM) algorithms, are sub-optimal and find solutions in the vicinity of their initialization. This paper proposes a staged approach to specifying initial values by finding a large number of local modes and then obtaining representatives ... View full abstract»

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  • Structural Properties of Gene Regulatory Networks: Definitions and Connections

    Publication Year: 2009, Page(s):158 - 170
    Cited by:  Papers (4)
    Request permission for commercial reuse | Click to expandAbstract | PDF file iconPDF (950 KB) | HTML iconHTML

    The study of gene regulatory networks is a significant problem in systems biology. Of particular interest is the problem of determining the unknown or hidden higher level regulatory signals by using gene expression data from DNA microarray experiments. Several studies in this area have demonstrated the critical aspect of the network structure in tackling the network modelling problem. Structural a... View full abstract»

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  • 2008 Reviewers List

    Publication Year: 2009, Page(s):171 - 173
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  • IEEE Computer Society Certified Software Development Professional

    Publication Year: 2009, Page(s): 174
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  • IEEE Computer Society Career Center

    Publication Year: 2009, Page(s): 175
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  • Build Your Career in Computing [advertisement]

    Publication Year: 2009, Page(s): 176
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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