# IEEE/ACM Transactions on Computational Biology and Bioinformatics

## Filter Results

Displaying Results 1 - 21 of 21
• ### front cover

Publication Year: 2014, Page(s): C1
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• ### IEEE/ACM Transactions on Computational Biology and Bioinformatics Editorial Board

Publication Year: 2014, Page(s): C2
| PDF (386 KB)
• ### Reviewer Appreciation Editorial

Publication Year: 2014, Page(s): 613
| PDF (34 KB) | HTML
• ### Guest editorial for the 12th Asia Pacific Bioinformatics Conference

Publication Year: 2014, Page(s):614 - 615
| PDF (82 KB) | HTML
• ### From Function to Interaction: A New Paradigm for Accurately Predicting Protein Complexes Based on Protein-to-Protein Interaction Networks

Publication Year: 2014, Page(s):616 - 627
Cited by:  Papers (7)
| | PDF (1200 KB) | HTML

Identification of protein complexes is critical to understand complex formation and protein functions. Recent advances in high-throughput experiments have provided large data sets of protein-protein interactions (PPIs). Many approaches, based on the assumption that complexes are dense subgraphs of PPI networks (PINs in short), have been proposed to predict complexes using graph clustering methods.... View full abstract»

• ### A Novel Wavelet-Based Approach for Predicting Nucleosome Positions Using DNA Structural Information

Publication Year: 2014, Page(s):638 - 647
Cited by:  Papers (1)
| | PDF (652 KB) | HTML

Nucleosomes are basic elements of chromatin structure. The positioning of nucleosomes along a genome is very important to dictate eukaryotic DNA compaction and access. Current computational methods have focused on the analysis of nucleosome occupancy and the positioning of well-positioned nucleosomes. However, fuzzy nucleosomes require more complex configurations and are more difficult to predict ... View full abstract»

• ### Beyond Fixed-Resolution Alignment-Free Measures for Mammalian Enhancers Sequence Comparison

Publication Year: 2014, Page(s):628 - 637
Cited by:  Papers (5)
| | PDF (783 KB) | HTML

The cell-type diversity is to a large degree driven by transcription regulation, i.e., enhancers. It has been recently shown that in high-level eukaryotes enhancers rarely work alone, instead they collaborate by forming clusters of cis-regulatory modules (CRMs). Even if the binding of transcription factors is sequence-specific, the identification of functionally similar enhancers is very difficult... View full abstract»

• ### An Improved Ensemble Learning Method for Classifying High-Dimensional and Imbalanced Biomedicine Data

Publication Year: 2014, Page(s):657 - 666
Cited by:  Papers (12)
| | PDF (1260 KB) | HTML

Training classifiers on skewed data can be technically challenging tasks, especially if the data is high-dimensional simultaneously, the tasks can become more difficult. In biomedicine field, skewed data type often appears. In this study, we try to deal with this problem by combining asymmetric bagging ensemble classifier (asBagging) that has been presented in previous work and an improved random ... View full abstract»

• ### SeeSite: Characterizing Relationships between Splice Junctions and Splicing Enhancers

Publication Year: 2014, Page(s):648 - 656
| | PDF (683 KB) | HTML

RNA splicing is a cellular process driven by the interaction between numerous regulatory sequences and binding sites, however, such interactions have been primarily explored by laboratory methods since computational tools largely ignore the relationship between different splicing elements. Current computational methods identify either splice sites or other regulatory sequences, such as enhancers a... View full abstract»

• ### Maximum Likelihood Estimation of GEVD: Applications in Bioinformatics

Publication Year: 2014, Page(s):673 - 680
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We propose a method, maximum likelihood estimation of generalized eigenvalue decomposition (MLGEVD) that employs a well known technique relying on the generalization of singular value decomposition (SVD). The main aim of the work is to show the tight equivalence between MLGEVD and generalized ridge regression. This relationship reveals an important mathematical property of GEVD in which the second... View full abstract»

• ### A Simple but Powerful Heuristic Method for Accelerating $k$ -Means Clustering of Large-Scale Data in Life Science

Publication Year: 2014, Page(s):681 - 692
Cited by:  Papers (3)
| | PDF (1611 KB) | HTML

K-means clustering has been widely used to gain insight into biological systems from large-scale life science data. To quantify the similarities among biological data sets, Pearson correlation distance and standardized Euclidean distance are used most frequently; however, optimization methods have been largely unexplored. These two distance measurements are equivalent in the sense that they yield ... View full abstract»

• ### Probabilistic Reconstruction of Ancestral Gene Orders with Insertions and Deletions

Publication Year: 2014, Page(s):667 - 672
Cited by:  Papers (13)
| | PDF (406 KB) | HTML

Changes of gene orderings have been extensively used as a signal to reconstruct phylogenies and ancestral genomes. Inferring the gene order of an extinct species has a wide range of applications, including the potential to reveal more detailed evolutionary histories, to determine gene content and ordering, and to understand the consequences of structural changes for organismal function and species... View full abstract»

• ### A High-Throughput Zebrafish Screening Method for Visual Mutants by Light-Induced Locomotor Response

Publication Year: 2014, Page(s):693 - 701
Cited by:  Papers (6)
| | PDF (1212 KB) | HTML Media

Normal and visually-impaired zebrafish larvae have differentiable light-induced locomotor response (LLR), which is composed of visual and non-visual components. It is recently demonstrated that differences in the acute phase of the LLR, also known as the visual motor response (VMR), can be utilized to evaluate new eye drugs. However, most of the previous studies focused on the average LLR activity... View full abstract»

• ### Automatic Myonuclear Detection in Isolated Single Muscle Fibers Using Robust Ellipse Fitting and Sparse Representation

Publication Year: 2014, Page(s):714 - 726
Cited by:  Papers (8)
| | PDF (1715 KB) | HTML

Accurate and robust detection of myonuclei in isolated single muscle fibers is required to calculate myonuclear domain size. However, this task is challenging because: 1) shape and size variations of the nuclei, 2) overlapping nuclear clumps, and 3) multiple z-stack images with out-of-focus regions. In this paper, we have proposed a novel automatic detection algorithm to robustly quantify myonucle... View full abstract»

• ### A Novel Synthesizing Genetic Logic Circuit: Frequency Multiplier

Publication Year: 2014, Page(s):702 - 713
Cited by:  Papers (3)
| | PDF (2070 KB) | HTML

This paper presents a novel synthesizing genetic logic circuit design based on an existing synthetic genetic oscillator, which provides a function of frequency multiplier to synthesize a clock signal whose frequency is a multiple of that of the genetic oscillator. In the renowned literature, the synthetic genetic oscillator, known as a repressilator, has been successfully built in Escherichia coli... View full abstract»

• ### Noise Resistant Generalized Parametric Validity Index of Clustering for Gene Expression Data

Publication Year: 2014, Page(s):741 - 752
Cited by:  Papers (3)
| | PDF (1274 KB) | HTML

Validity indices have been investigated for decades. However, since there is no study of noise-resistance performance of these indices in the literature, there is no guideline for determining the best clustering in noisy data sets, especially microarray data sets. In this paper, we propose a generalized parametric validity (GPV) index which employs two tunable parameters α and β to c... View full abstract»

• ### Predicting Protein Relationships to Human Pathways through a Relational Learning Approach Based on Simple Sequence Features

Publication Year: 2014, Page(s):753 - 765
| | PDF (777 KB) | HTML Media

Biological pathways are important elements of systems biology and in the past decade, an increasing number of pathway databases have been set up to document the growing understanding of complex cellular processes. Although more genome-sequence data are becoming available, a large fraction of it remains functionally uncharacterized. Thus, it is important to be able to predict the mapping of poorly ... View full abstract»

• ### Double Selection Based Semi-Supervised Clustering Ensemble for Tumor Clustering from Gene Expression Profiles

Publication Year: 2014, Page(s):727 - 740
Cited by:  Papers (21)
| | PDF (1134 KB) | HTML

Tumor clustering is one of the important techniques for tumor discovery from cancer gene expression profiles, which is useful for the diagnosis and treatment of cancer. While different algorithms have been proposed for tumor clustering, few make use of the expert's knowledge to better the performance of tumor discovery. In this paper, we first view the expert's knowledge as constraints in the proc... View full abstract»

• ### Biomarker Signature Discovery from Mass Spectrometry Data

Publication Year: 2014, Page(s):766 - 772
Cited by:  Papers (2)
| | PDF (513 KB) | HTML

Mass spectrometry based high throughput proteomics are used for protein analysis and clinical diagnosis. Many machine learning methods have been used to construct classifiers based on mass spectrometry data, for discrimination between cancer stages. However, the classifiers generated by machine learning such as SVM techniques typically lack biological interpretability. We present an innovative tec... View full abstract»

• ### IEEE/ACM Transactions on Computational Biology and Bioinformatics Information for Authors

Publication Year: 2014, Page(s): C3
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Publication Year: 2014, 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
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