BMC Bioinformatics - Volume 7, issue Preprint

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Electronic ISSN
1471-2105

Abstract

Background

Phytochromes are photoreceptors, discovered in plants, that control a wide variety of developmental processes. They have also been found in bacteria and fungi, but for many species their biological role remains obscure. This work concentrates on the phytochrome system of Agrobacteriu

Journal: BMC Bioinformatics, vol. 7, no. Preprint, 2006

Abstract

Background

Intensity values measured by Affymetrix microarrays have to be both normalized, to be able to compare different microarrays by removing non-biological variation, and summarized, generating the final probe set expression values. Various pre-processing techniques, such as dChip, GCRMA, RM

Journal: BMC Bioinformatics, vol. 7, no. Preprint, 2006

Abstract

Background

A large number of genes usually show differential expressions in a microarray experiment with two types of tissues, and the p-values of a proper statistical test are often used to quantify the significance of these differences. The genes with small p-values are then picked

Journal: BMC Bioinformatics, vol. 7, no. Preprint, 2006

Abstract

Background

Metagenomics, sequence analyses of genomic DNA isolated directly from the environments, can be used to identify organisms and model community dynamics of a particular ecosystem. Metagenomics also has the potential to identify significantly different metabolic potential in different envi

Journal: BMC Bioinformatics, vol. 7, no. Preprint, 2006

Abstract

Background

The automation of many common molecular biology techniques has resulted in the accumulation of vast quantities of experimental data. One of the major challenges now facing researchers is how to process this data to yield useful information about a biological system (e.g. knowledge of ge

Journal: BMC Bioinformatics, vol. 7, no. Preprint, 2006

Abstract

Background

Quantification of the metabolic network of an organism offers insights into possible ways of developing mutant strain for better productivity of an extracellular metabolite. The first step in this quantification is the enumeration of stoichiometries of all reactions occurring in a metab

Journal: BMC Bioinformatics, vol. 7, no. Preprint, 2006

Abstract

Background

The use of exogenous small interfering RNAs (siRNAs) for gene silencing has quickly become a widespread molecular tool providing a powerful means for gene functional study and new drug target identification. Although considerable progress has been made recently in understanding how the

Journal: BMC Bioinformatics, vol. 7, no. Preprint, 2006

Abstract

Background

Experimental verification of gene products has not kept pace with the rapid growth of microbial sequence information. However, existing annotations of gene locations contain sufficient information to screen for probable errors. Furthermore, comparisons among genomes become more informat

Journal: BMC Bioinformatics, vol. 7, no. Preprint, 2006

Abstract

Background

Trait heterogeneity, which exists when a trait has been defined with insufficient specificity such that it is actually two or more distinct traits, has been implicated as a confounding factor in traditional statistical genetics of complex human disease. In the absence of detailed phenot

Journal: BMC Bioinformatics, vol. 7, no. Preprint, 2006

Abstract

Background:

In class prediction problems using microarray data, gene selection is essential to improve the prediction accuracy and to identify potential marker genes for a disease. Among numerous existing methods for gene selection, support vector machine-based recursive feature elimination (SVM-R

Journal: BMC Bioinformatics, vol. 7, no. Preprint, 2006