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In individually dye-balanced microarray designs, each biological sample is hybridized on two different slides, once with Cy3 and once with Cy5. While this strategy ensures an automatic correction of the gene-spec...
Preparedness for a possible global pandemic caused by viruses such as the highly pathogenic influenza A subtype H5N1 has become a global priority. In particular, it is critical to monitor the appearance of any...
This article is part of a Supplement: Volume 9 Supplement 1
The Potato type II (Pot II) family of proteinase inhibitors plays critical roles in the defense system of plants from Solanaceae family against pests. To better understand the evolution of this family, we investi...
This article is part of a Supplement: Volume 9 Supplement 1
Network Component Analysis (NCA) has shown its effectiveness in discovering regulators and inferring transcription factor activities (TFAs) when both microarray data and ChIP-on-chip data are available. Howeve...
This article is part of a Supplement: Volume 9 Supplement 1
Cyanobacteria are model organisms for studying photosynthesis, carbon and nitrogen assimilation, evolution of plant plastids, and adaptability to environmental stresses. Despite many studies on cyanobacteria, ...
This article is part of a Supplement: Volume 9 Supplement 1
T-cell epitopes that promiscuously bind to multiple alleles of a human leukocyte antigen (HLA) supertype are prime targets for development of vaccines and immunotherapies because they are relevant to a large p...
This article is part of a Supplement: Volume 9 Supplement 1
The identification of mutations that confer unique properties to a pathogen, such as host range, is of fundamental importance in the fight against disease. This paper describes a novel method for identifying a...
This article is part of a Supplement: Volume 9 Supplement 1
The tumour suppressor protein p53 protein has a core domain that binds DNA and is the site for most oncogenic mutations. This domain is quite unstable compared to its homologs p63 and p73. Two key residues in ...
This article is part of a Supplement: Volume 9 Supplement 1
Metabotropic glutamate receptors (mGluRs) are G protein coupled receptors that play important roles in synaptic plasticity and other neuro-physiological and pathological processes. Allosteric mGluR ligands are...
This article is part of a Supplement: Volume 9 Supplement 1
Type I signal peptidases (SPases) are essential membrane-bound serine proteases responsible for the cleavage of signal peptides from proteins that are translocated across biological membranes. The crystal stru...
This article is part of a Supplement: Volume 9 Supplement 1
G protein-coupled receptors (GPCRs) are abundant, activate complex signalling and represent the targets for up to ~60% of pharmaceuticals but there is a paucity of structural data. Bovine rhodopsin is the firs...
This article is part of a Supplement: Volume 9 Supplement 1
The prediction of protein structure can be facilitated by the use of constraints based on a knowledge of functional sites. Without this information it is still possible to predict which residues are likely to ...
This article is part of a Supplement: Volume 9 Supplement 1
Protein domains present some of the most useful information that can be used to understand protein structure and functions. Recent research on protein domain boundary prediction has been mainly based on widely...
This article is part of a Supplement: Volume 9 Supplement 1
The analysis of expressed sequence tags (EST) offers a rapid and cost effective approach to elucidate the transcriptome of an organism, but requires several computational methods for assembly and annotation. R...
This article is part of a Supplement: Volume 9 Supplement 1
Identification of differentially expressed genes is a typical objective when analyzing gene expression data. Recently, Bayesian hierarchical models have become increasingly popular to solve this type of proble...
This article is part of a Supplement: Volume 9 Supplement 1
Nucleic acid hybridization, a fundamental technique in molecular biology, can be modified into very effective and sensitive methods for detecting particular targets mixed with millions of non-target sequences....
This article is part of a Supplement: Volume 9 Supplement 1
The explosive growth of biological data provides opportunities for new statistical and comparative analyses of large information sets, such as alignments comprising tens of thousands of sequences. In such stud...
This article is part of a Supplement: Volume 9 Supplement 1
The most renowned biological ontology, Gene Ontology (GO) is widely used for annotations of genes and gene products of different organisms. However, there are shortcomings in the Resource Description Framework...
This article is part of a Supplement: Volume 9 Supplement 1
The indexing of scientific literature and content is a relevant and contemporary requirement within life science information systems. Navigating information available in legacy formats continues to be a challe...
This article is part of a Supplement: Volume 9 Supplement 1
Prediction of transmembrane (TM) helices by statistical methods suffers from lack of sufficient training data. Current best methods use hundreds or even thousands of free parameters in their models which are t...
This article is part of a Supplement: Volume 9 Supplement 1
Experimentally verified protein-protein interactions (PPI) cannot be easily retrieved by researchers unless they are stored in PPI databases. The curation of such databases can be made faster by ranking newly-...
This article is part of a Supplement: Volume 9 Supplement 1
Analysis of single nucleotide polymorphism (SNP) is becoming a key research in genomics fields. Many functional analyses of SNPs have been carried out for coding regions and splicing sites that can alter prote...
This article is part of a Supplement: Volume 9 Supplement 1
We provide a 2007 update on the bioinformatics research in the Asia-Pacific from the Asia Pacific Bioinformatics Network (APBioNet), Asia's oldest bioinformatics organisation set up in 1998. From 2002, APBioNe...
This article is part of a Supplement: Volume 9 Supplement 1
A logical model of the known metabolic processes in S. cerevisiae was constructed from iFF708, an existing Flux Balance Analysis (FBA) model, and augmented with information from the KEGG online pathway database. ...
Modern omics research involves the application of high-throughput technologies that generate vast volumes of data. These data need to be pre-processed, analyzed and integrated with existing knowledge through t...
In real-time PCR, it is necessary to consider the efficiency of amplification (EA) of amplicons in order to determine initial target levels properly. EAs can be deduced from standard curves, but these involve ...
We present a novel method of protein fold decoy discrimination using machine learning, more specifically using neural networks. Here, decoy discrimination is represented as a machine learning problem, where ne...
Array-based comparative genome hybridization (aCGH) is commonly used to determine the genomic content of bacterial strains. Since prokaryotes in general have less conserved genome sequences than eukaryotes, se...
Clustering is a popular data exploration technique widely used in microarray data analysis. Most conventional clustering algorithms, however, generate only one set of clusters independent of the biological con...
Inferring gene regulatory networks from data requires the development of algorithms devoted to structure extraction. When only static data are available, gene interactions may be modelled by a Bayesian Network...
Structural analysis of biochemical networks is a growing field in bioinformatics and systems biology. The availability of an increasing amount of biological data from molecular biological networks promises a d...
Motif finding algorithms have developed in their ability to use computationally efficient methods to detect patterns in biological sequences. However the posterior classification of the output still suffers fr...
Mass spectrometry for biological data analysis is an active field of research, providing an efficient way of high-throughput proteome screening. A popular variant of mass spectrometry is SELDI, which is often ...
Recent years have seen the development of various pathway-based methods for the analysis of microarray gene expression data. These approaches have the potential to bring biological insights into microarray stu...
High-throughput genome biological experiments yield large and multifaceted datasets that require flexible and user-friendly analysis tools to facilitate their interpretation by life scientists. Many solutions ...
Illumina bead-based arrays are becoming increasingly popular due to their high degree of replication and reported high data quality. However, little attention has been paid to the pre-processing of Illumina da...
Single Nucleotide Polymorphisms, among other type of sequence variants, constitute key elements in genetic epidemiology and pharmacogenomics. While sequence data about genetic variation is found at databases s...
Viruses of the Bunyaviridae have segmented negative-stranded RNA genomes and several of them cause significant disease. Many partial sequences have been obtained from the segments so that GenBank searches give co...
The performance of different programming languages has previously been benchmarked using abstract mathematical algorithms, but not using standard bioinformatics algorithms. We compared the memory usage and spe...
The expansion of automatic imaging technologies has created a need to be able to efficiently compare and review large sets of image data. To enable comparisons of image data between samples we need to define t...
Gene Ontology (GO) annotation, which describes the function of genes and gene products across species, has recently been used to predict protein subcellular and subnuclear localization. Existing GO-based predi...
Chromosomal replication is the central event in the bacterial cell cycle. Identification of replication origins (oriC s) is necessary for almost all newly sequenced bacterial genomes. Given the increasing pace of...
Information extraction (IE) efforts are widely acknowledged to be important in harnessing the rapid advance of biomedical knowledge, particularly in areas where important factual information is published in a ...
Population structure analysis is important to genetic association studies and evolutionary investigations. Parametric approaches, e.g. STRUCTURE and L-POP, usually assume Hardy-Weinberg equilibrium (HWE) and l...
Microarray gene expression data are often analyzed together with corresponding physiological response and clinical metadata of biological subjects, e.g. patients' residual tumor sizes after chemotherapy or glu...
The reconstruction of genetic regulatory networks from microarray gene expression data has been a challenging task in bioinformatics. Various approaches to this problem have been proposed, however, they do not...
Formal classification of a large collection of protein structures aids the understanding of evolutionary relationships among them. Classifications involving manual steps, such as SCOP and CATH, face the challe...
Many programs have been developed to identify transcription factor binding sites. However, most of them are not able to infer two-word motifs with variable spacer lengths. This case is encountered for RNA poly...
Most methods available to predict protein epitopes are sequence based. There is a need for methods using 3D information for prediction of discontinuous epitopes and derived immunogenic peptides.
The recent explosion in biological and other real-world network data has created the need for improved tools for large network analyses. In addition to well established global network properties, several new math...
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