BMC Bioinformatics - Volume 11, issue Preprint

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Electronic ISSN
1471-2105

Abstract

Background

In water-soluble proteins it is energetically favorable to bury hydrophobic residues and to expose polar and charged residues. In contrast to water soluble proteins, transmembrane proteins face three distinct environments; a hydrophobic lipid environment inside the membrane, a hydrophil

Journal: BMC Bioinformatics, vol. 11, no. Preprint, 2010

Abstract

Background

Nonnegative Matrix Factorization (NMF) is an unsupervised learning technique that has been applied successfully in several fields, including signal processing, face recognition and text mining. Recent applications of NMF in bioinformatics have demonstrated its ability to extract meaning

Journal: BMC Bioinformatics, vol. 11, no. Preprint, 2010

Abstract

Background

A common approach to understanding the genetic basis of complex traits is through identification of associated quantitative trait loci (QTL). Fine mapping QTLs requires several generations of backcrosses and analysis of large populations, which is time-consuming and costly effort. Furth

Journal: BMC Bioinformatics, vol. 11, no. Preprint, 2010

Abstract

Background

Candida albicans is a commonly encountered fungal pathogen in humans. The formation of biofilm is a major virulence factor in C. albicans pathogenesis and is related to antidrug resistance of this organism. Although many factors affecting biofilm have been analyzed, molecu

Journal: BMC Bioinformatics, vol. 11, no. Preprint, 2010

Abstract

Background

Different microarray studies have compiled gene lists for predicting outcomes of a range of treatments and diseases. These have produced gene lists that have little overlap, indicating that the results from any one study are unstable. It has been suggested that the underlying pathways a

Journal: BMC Bioinformatics, vol. 11, no. Preprint, 2010

Abstract

Background

Protein-protein interaction (PPI) plays essential roles in cellular functions. The cost, time and other limitations associated with the current experimental methods have motivated the development of computational methods for predicting PPIs. As protein interactions generally occur via d

Journal: BMC Bioinformatics, vol. 11, no. Preprint, 2010

Abstract

Background

Precise and efficient methods for gene targeting are critical for detailed functional analysis of genomes and regulatory networks and for potentially improving the efficacy and safety of gene therapies. Oligomerized Pool ENgineering (OPEN) is a recently developed method for engineering

Journal: BMC Bioinformatics, vol. 11, no. Preprint, 2010

Abstract

Background

Time-course microarray experiments can produce useful data which can help in understanding the underlying dynamics of the system. Clustering is an important stage in microarray data analysis where the data is grouped together according to certain characteristics. The majority of cluster

Journal: BMC Bioinformatics, vol. 11, no. Preprint, 2010

Abstract

Background

The opportunities for bacterial population genomics that are being realised by the application of parallel nucleotide sequencing require novel bioinformatics platforms. These must be capable of the storage, retrieval, and analysis of linked phenotypic and genotypic information in an acc

Journal: BMC Bioinformatics, vol. 11, no. Preprint, 2010

Abstract

Background

Multiplex Ligation-Dependent Probe Amplification (MLPA) is an application that can be used for the detection of multiple chromosomal aberrations in a single experiment. In one reaction, up to 50 different genomic sequences can be analysed. For a reliable work-flow, tools are needed for

Journal: BMC Bioinformatics, vol. 11, no. Preprint, 2010