# IEEE/ACM Transactions on Computational Biology and Bioinformatics

## Filter Results

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

Publication Year: 2007, Page(s): c1
Cited by:  Papers (6)
| |PDF (2186 KB)
• ### [Inside front cover]

Publication Year: 2007, Page(s): c2
| |PDF (88 KB)
• ### State of the Journal

Publication Year: 2007, Page(s): 1
Cited by:  Papers (1)
| |PDF (35 KB)
• ### Associate Editor Appreciation and Welcome

Publication Year: 2007, Page(s): 2
| |PDF (75 KB) | HTML
• ### Guest Editor's Introduction to the Special Section on Computational Biology and Bioinformatics (WABI) -- Part 2

Publication Year: 2007, Page(s): 3
| |PDF (31 KB) | HTML
• ### Perfect Sorting by Reversals Is Not Always Difficult

Publication Year: 2007, Page(s):4 - 16
Cited by:  Papers (23)
| |PDF (1011 KB) | HTML

We propose new algorithms for computing pairwise rearrangement scenarios that conserve the combinatorial structure of genomes. More precisely, we investigate the problem of sorting signed permutations by reversals without breaking common intervals. We describe a combinatorial framework for this problem that allows us to characterize classes of signed permutations for which one can compute, in poly... View full abstract»

• ### Ortholog Clustering on a Multipartite Graph

Publication Year: 2007, Page(s):17 - 27
Cited by:  Papers (7)
| |PDF (982 KB) | HTML

We present a method for automatically extracting groups of orthologous genes from a large set of genomes by a new clustering algorithm on a weighted multipartite graph. The method assigns a score to an arbitrary subset of genes from multiple genomes to assess the orthologous relationships between genes in the subset. This score is computed using sequence similarities between the member genes and t... View full abstract»

• ### EMatch: Discovery of High Resolution Structural Homologues of Protein Domains in Intermediate Resolution Cryo-EM Maps

Publication Year: 2007, Page(s):28 - 39
Cited by:  Papers (20)
| |PDF (1516 KB) | HTML

Cryo-EM has become an increasingly powerful technique for elucidating the structure, dynamics, and function of large flexible macromolecule assemblies that cannot be determined at atomic resolution. However, due to the relatively low resolution of cryo-EM data, a major challenge is to identify components of complexes appearing in cryo-EM maps. Here, we describe EMatch, a novel integrated approach ... View full abstract»

• ### Accurate Cancer Classification Using Expressions of Very Few Genes

Publication Year: 2007, Page(s):40 - 53
Cited by:  Papers (94)  |  Patents (2)
| |PDF (3292 KB) | HTML

We aim at finding the smallest set of genes that can ensure highly accurate classification of cancers from microarray data by using supervised machine learning algorithms. The significance of finding the minimum gene subsets is three-fold: 1) it greatly reduces the computational burden and "noise" arising from irrelevant genes. In the examples studied in this paper, finding the minimum gene subset... View full abstract»

• ### Correcting Base-Assignment Errors in Repeat Regions of Shotgun Assembly

Publication Year: 2007, Page(s):54 - 64
Cited by:  Papers (4)
| |PDF (2599 KB) | HTML

Accurate base-assignment in repeat regions of a whole genome shotgun assembly is an unsolved problem. Since reads in repeat regions cannot be easily attributed to a unique location in the genome, current assemblers may place these reads arbitrarily. As a result, the base-assignment error rate in repeats is likely to be much higher than that in the rest of the genome. We developed an iterative algo... View full abstract»

• ### Multiclass Cancer Classification Using Semisupervised Ellipsoid ARTMAP and Particle Swarm Optimization with Gene Expression Data

Publication Year: 2007, Page(s):65 - 77
Cited by:  Papers (27)
| |PDF (3615 KB) | HTML

It is crucial for cancer diagnosis and treatment to accurately identify the site of origin of a tumor. With the emergence and rapid advancement of DNA microarray technologies, constructing gene expression profiles for different cancer types has already become a promising means for cancer classification. In addition to research on binary classification such as normal versus tumor samples, which att... View full abstract»

• ### Predicting Protein-Protein Interactions from Protein Domains Using a Set Cover Approach

Publication Year: 2007, Page(s):78 - 87
Cited by:  Papers (29)
| |PDF (1105 KB) | HTML

One goal of contemporary proteome research is the elucidation of cellular protein interactions. Based on currently available protein-protein interaction and domain data, we introduce a novel method, maximum specificity set cover (MSSC), for the prediction of protein-protein interactions. In our approach, we map the relationship between interactions of proteins and their corresponding domain archit... View full abstract»

• ### Accuracy Assessment of Diploid Consensus Sequences

Publication Year: 2007, Page(s):88 - 97
Cited by:  Papers (6)  |  Patents (2)
| |PDF (1847 KB) | HTML

If the origins of fragments are known in genome sequencing projects, it is straightforward to reconstruct diploid consensus sequences. In reality, however, this is not true. Although there are proposed methods to reconstruct haplotypes from genome sequencing projects, an accuracy assessment is required to evaluate the confidence of the estimated diploid consensus sequences. In this paper, we defin... View full abstract»

• ### Colored de Bruijn Graphs and the Genome Halving Problem

Publication Year: 2007, Page(s):98 - 107
Cited by:  Papers (16)
| |PDF (1400 KB) | HTML

Breakpoint graph analysis is a key algorithmic technique in studies of genome rearrangements. However, breakpoint graphs are defined only for genomes without duplicated genes, thus limiting their applications in rearrangement analysis. We discuss a connection between the breakpoint graphs and de Bruijn graphs that leads to a generalization of the notion of breakpoint graph for genomes with duplica... View full abstract»

• ### Distorted Metrics on Trees and Phylogenetic Forests

Publication Year: 2007, Page(s):108 - 116
Cited by:  Papers (15)
| |PDF (245 KB) | HTML

We study distorted metrics on binary trees in the context of phylogenetic reconstruction. Given a binary tree T on n leaves with a path metric d, consider the pairwise distances {d(u,v)} between leaves. It is well known that these determine the tree and the d length of all edges. Here, we consider distortions d of d such that, for all leaves u and v, it holds that |d(u,v)-dmacr(u,v)|<f/2 if eit... View full abstract»

• ### DNA Deformation Energy as an Indirect Recognition Mechanism in Protein-DNA Interactions

Publication Year: 2007, Page(s):117 - 125
Cited by:  Papers (3)
| |PDF (1993 KB) | HTML

Proteins that bind to specific locations in genomic DNA control many basic cellular functions. Proteins detect their binding sites using both direct and indirect recognition mechanisms. Deformation energy, which models the energy required to bend DNA from its native shape to its shape when bound to a protein, has been shown to be an indirect recognition mechanism for one particular protein, integr... View full abstract»

• ### Metabolic Flux Estimation-A Self-Adaptive Evolutionary Algorithm with Singular Value Decomposition

Publication Year: 2007, Page(s):126 - 138
Cited by:  Papers (7)
| |PDF (3585 KB) | HTML

Metabolic flux analysis is important for metabolic system regulation and intracellular pathway identification. A popular approach for intracellular flux estimation involves using 13C tracer experiments to label states that can be measured by nuclear magnetic resonance spectrometry or gas chromatography mass spectrometry. However, the bilinear balance equations derived from 13... View full abstract»

• ### Quartet-Based Phylogeny Reconstruction with Answer Set Programming

Publication Year: 2007, Page(s):139 - 152
Cited by:  Papers (5)
| |PDF (1497 KB) | HTML

In this paper, a new representation is presented for the maximum quartet consistency (MQC) problem, where solving the MQC problem becomes searching for an ultrametric matrix that satisfies a maximum number of given quartet topologies. A number of structural properties of the MQC problem in this new representation are characterized through formulating into answer set programming, a recent powerful ... View full abstract»

• ### On the Length of the Longest Exact Position Match in a Random Sequence

Publication Year: 2007, Page(s):153 - 156
Cited by:  Papers (1)
| |PDF (346 KB) | HTML

A mixed Poisson approximation and a Poisson approximation for the length of the longest exact match of a random sequence across another sequence are provided, where the match is required to start at position 1 in the first sequence. This problem arises when looking for suitable anchors in whole genome alignments. View full abstract»

• ### Correction to "Attribute Clustering for Grouping, Selection, and Classification of Gene Expression Data"

Publication Year: 2007, Page(s): 157
Cited by:  Papers (3)
| |PDF (42 KB) | HTML

This is a correction to a typographical error in (11) in [1] which present the calculation of the sum of the multiple significant interdependence redundancy measure. Equation (11) in [1] should be: $$k=argmaxnolimits_{kin{2,ldots,p}}sum_{r=1}^k sum_{A_iin{C_r-eta_r}}R(A_i:eta_r).$$(11)We remark that the experimental results reported in [1] are based on (11) above not (11) in [1]. View full abstract»

• ### 2006 reviewers list

Publication Year: 2007, Page(s):158 - 160
Cited by:  Papers (7)
| |PDF (28 KB)
• ### [Back cover]

Publication Year: 2007, Page(s): c4
| |PDF (2186 KB)

## 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
Aidong Zhang, PhD, IEEE Fellow
Dept. of Computer Science and Engineering
State University of New York at Buffalo
Buffalo, New York 14260 USA
azhang@buffalo.edu

Associate Editor-in-Chief
Dong Xu
University of Missouri
xudong@missouri.edu