Volume 9 Supplement 6
Edited by Guoqing Lu, Jun Ni, Thomas L Casavant and Brian Athey
Symposium of Computations in Bioinformatics and Bioscience (SCBB07). Go to conference site.
Iowa City, Iowa, USA13-15 August 2007
The Second Symposium on Computations in Bioinformatics and Bioscience (SCBB07) was held in Iowa City, Iowa, USA, on August 13–15, 2007. This annual event attracted dozens of bioinformatics professionals and st...
Localization of complex traits by genetic linkage analysis may involve exploration of a vast multidimensional parameter space. The posterior probability of linkage (PPL), a class of statistics for complex trai...
DNA-binding proteins are of utmost importance to gene regulation. The identification of DNA-binding domains is useful for understanding the regulation mechanisms of DNA-binding proteins. In this study, we prop...
Inference of evolutionary trees using the maximum likelihood principle is NP-hard. Therefore, all practical methods rely on heuristics. The topological transformations often used in heuristics are Nearest Neig...
A protein structural class (PSC) belongs to the most basic but important classification in protein structures. The prediction technique of protein structural class has been developing for decades. Two popular ...
Graphs and networks are common analysis representations for biological systems. Many traditional graph algorithms such as k-clique, k-coloring, and subgraph matching have great potential as analysis techniques...
Activities of drug molecules can be predicted by QSAR (quantitative structure activity relationship) models, which overcomes the disadvantages of high cost and long cycle by employing the traditional experimen...
Analysis of gene expression data for tumor classification is an important application of bioinformatics methods. But it is hard to analyse gene expression data from DNA microarray experiments by commonly used ...
Orthologous genes with deep phylogenetic histories are likely to retain similar regulatory features. In this report we utilize orthology assignments for pairs of genes co-regulated by bidirectional promoters t...
Genetic association studies have been used to map disease-causing genes. A newly introduced statistical method, called exhaustive haplotype association study, analyzes genetic information consisting of differe...
In accordance with the increasing amount of information concerning individual differences in drug response and molecular interaction, the role of in silico prediction of drug interaction on the pathway level is b...
The traditional (unweighted) k-means is one of the most popular clustering methods for analyzing gene expression data. However, it suffers three major shortcomings. It is sensitive to initial partitions, its r...
Tandem mass spectrometry has emerged as a cornerstone of high throughput proteomic studies owing in part to various high throughput search engines which are used to interpret these tandem mass spectra. However...
In DNA microarray gene expression profiling studies, a fundamental task is to extract statistically significant genes that meet certain research hypothesis. Currently, Venn diagram is a frequently used method ...
Historically, two categories of computational algorithms (alignment-based and alignment-free) have been applied to sequence comparison–one of the most fundamental issues in bioinformatics. Multiple sequence al...
Gene pathway can be defined as a group of genes that interact with each other to perform some biological processes. Along with the efforts to identify the individual genes that play vital roles in a particular...
This article provides guidelines for selecting optimal numerical solvers for biomolecular system models. Because various parameters of the same system could have drastically different ranges from 10-15 to 1010, t...
A survey of microarray databases reveals that most of the repository contents and data models are heterogeneous (i.e., data obtained from different chip manufacturers), and that the repositories provide only b...
Data clustering is a powerful technique for identifying data with similar characteristics, such as genes with similar expression patterns. However, not all implementations of clustering algorithms yield the sa...
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