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Microarray studies provide a way of linking variations of phenotypes with their genetic causations. Constructing predictive models using high dimensional microarray measurements usually consists of three steps...
Protein-protein interaction (PPI) databases have become a major resource for investigating biological networks and pathways in cells. A number of publicly available repositories for human PPIs are currently av...
This article is part of a Supplement: Volume 7 Supplement 5
Proteins control and mediate many biological activities of cells by interacting with other protein partners. This work presents a statistical model to predict protein interaction networks of Drosophila melanogast...
This article is part of a Supplement: Volume 7 Supplement 5
Defensins are antimicrobial peptides of innate immunity functioning by non-specific binding to anionic phospholipids in bacterial membranes. Their cationicity, amphipathicity and ability to oligomerize are con...
This article is part of a Supplement: Volume 7 Supplement 5
Recent advances and automation in DNA sequencing technology has created a vast amount of DNA sequence data. This increasing growth of sequence data demands better and efficient analysis methods. Identifying ge...
This article is part of a Supplement: Volume 7 Supplement 5
The Erratum to this article has been published in BMC Bioinformatics 2007 8:241
Caspases belong to a class of cysteine proteases which function as critical effectors in apoptosis and inflammation by cleaving substrates immediately after unique sites. Prediction of such cleavage sites will...
This article is part of a Supplement: Volume 7 Supplement 5
Metal-binding proteins play important roles in structural stability, signaling, regulation, transport, immune response, metabolism control, and metal homeostasis. Because of their functional and sequence diver...
This article is part of a Supplement: Volume 7 Supplement 5
Whole genome sequence data is a step towards generating the 'parts list' of life to understand the underlying principles of Biocomplexity. Genome sequencing initiatives of human and model organisms are targete...
This article is part of a Supplement: Volume 7 Supplement 5
Biomedical named entity recognition (Bio-NER) is a challenging problem because, in general, biomedical named entities of the same category (e.g., proteins and genes) do not follow one standard nomenclature. Th...
This article is part of a Supplement: Volume 7 Supplement 5
Mammalian antimicrobial peptides (AMPs) are effectors of the innate immune response. A multitude of signals coming from pathways of mammalian pathogen/pattern recognition receptors and other proteins affect th...
This article is part of a Supplement: Volume 7 Supplement 5
Pemphigus vulgaris (PV) is a severe autoimmune blistering skin disorder that is strongly associated with major histocompatibility complex class II alleles DRB1*0402 and DQB1*0503. The target antigen of PV, des...
This article is part of a Supplement: Volume 7 Supplement 5
Knowledge of protein domain boundaries is critical for the characterisation and understanding of protein function. The ability to identify domains without the knowledge of the structure – by using sequence inf...
This article is part of a Supplement: Volume 7 Supplement 5
In recent times, there has been an exponential rise in the number of protein structures in databases e.g. PDB. So, design of fast algorithms capable of querying such databases is becoming an increasingly impor...
This article is part of a Supplement: Volume 7 Supplement 5
Antigenic diversity in dengue virus strains has been studied, but large-scale and detailed systematic analyses have not been reported. In this study, we report a bioinformatics method for analyzing viral antig...
This article is part of a Supplement: Volume 7 Supplement 5
Automatic annotation of sequenced eukaryotic genomes integrates a combination of methodologies such as ab-initio methods and alignment of homologous genes and/or proteins. For example, annotation of the zebrafish...
This article is part of a Supplement: Volume 7 Supplement 5
User-scripts are programs stored in Web browsers that can manipulate the content of websites prior to display in the browser. They provide a novel mechanism by which users can conveniently gain increased contr...
DNA microarray technology provides a powerful tool for characterizing gene expression on a genome scale. While the technology has been widely used in discovery-based medical and basic biological research, its ...
The proliferation of data repositories in bioinformatics has resulted in the development of numerous interfaces that allow scientists to browse, search and analyse the data that they contain. Interfaces typica...
Anatomical studies of neural circuitry describing the basic wiring diagram of the brain produce intrinsically spatial, highly complex data of great value to the neuroscience community. Published neuroanatomica...
With the advent of metabolomics as a powerful tool for both functional and biomarker discovery, the identification of specific differences between complex metabolite profiles is becoming a major challenge in t...
An important step in understanding the conditions that specify gene expression is the recognition of gene regulatory elements. Due to high diversity of different types of transcription factors and their DNA bi...
This article is part of a Supplement: Volume 7 Supplement 4
DNA microarrays are a powerful tool for monitoring the expression of tens of thousands of genes simultaneously. With the advance of microarray technology, the challenge issue becomes how to analyze a large amo...
This article is part of a Supplement: Volume 7 Supplement 4
Graphical user interface (GUI) software promotes novelty by allowing users to extend the functionality. SVM Classifier is a cross-platform graphical application that handles very large datasets well. The purpo...
This article is part of a Supplement: Volume 7 Supplement 4
The problem of inferring the evolutionary history and constructing the phylogenetic tree with high performance has become one of the major problems in computational biology.
This article is part of a Supplement: Volume 7 Supplement 4
Quantitative simultaneous monitoring of the expression levels of thousands of genes under various experimental conditions is now possible using microarray experiments. However, there are still gaps toward whol...
This article is part of a Supplement: Volume 7 Supplement 4
Cell culture systems are useful in studying toxicological effects of chemicals such as Hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX), however little is known as to how accurately isolated cells reflect respons...
This article is part of a Supplement: Volume 7 Supplement 4
As more and more genomes are sequenced, comparative genomics approaches provide a methodology for identifying conserved regulatory elements that may be involved in gene regulations.
This article is part of a Supplement: Volume 7 Supplement 4
Spatio-temporal dynamics within cells can now be visualized at appropriate resolution, due to the advances in molecular imaging technologies. Even single-particle tracking (SPT) and single fluorophore video im...
This article is part of a Supplement: Volume 7 Supplement 4
DNA Microarray technology is an innovative methodology in experimental molecular biology, which has produced huge amounts of valuable data in the profile of gene expression. Many clustering algorithms have bee...
This article is part of a Supplement: Volume 7 Supplement 4
Comparative genomics has become an essential approach for identifying homologous gene candidates and their functions, and for studying genome evolution. There are many tools available for genome comparisons. U...
This article is part of a Supplement: Volume 7 Supplement 4
Cluster analysis is an integral part of high dimensional data analysis. In the context of large scale gene expression data, a filtered set of genes are grouped together according to their expression profiles u...
This article is part of a Supplement: Volume 7 Supplement 4
Hydrophobins are fungal proteins that can turn into amphipathic membranes at hydrophilic/hydrophobic interfaces by self-assembly. The assemblages by Class I hydrophobins are extremely stable and possess the re...
This article is part of a Supplement: Volume 7 Supplement 4
Multicategory Support Vector Machines (MC-SVM) are powerful classification systems with excellent performance in a variety of data classification problems. Since the process of generating models in traditional...
This article is part of a Supplement: Volume 7 Supplement 4
Protein secondary structure prediction is a fundamental and important component in the analytical study of protein structure and functions. The prediction technique has been developed for several decades. The ...
This article is part of a Supplement: Volume 7 Supplement 4
One type of DNA microarray experiment is discovery of gene expression patterns for a cell line undergoing a biological process over a series of time points. Two important issues with such an experiment are the...
This article is part of a Supplement: Volume 7 Supplement 4
The problem of finding a Shortest Common Supersequence (SCS) of a set of sequences is an important problem with applications in many areas. It is a key problem in biological sequences analysis. The SCS problem...
This article is part of a Supplement: Volume 7 Supplement 4
One main research challenge in the post-genomic era is to understand the relationship between protein sequences and their biological functions. In recent years, several automated annotation systems have been d...
This article is part of a Supplement: Volume 7 Supplement 4
Protein sequence clustering has been widely used as a part of the analysis of protein structure and function. In most cases single linkage or graph-based clustering algorithms have been applied. OPTICS (Orderi...
This article is part of a Supplement: Volume 7 Supplement 4
The amplification of variable regions of immunoglobulins has become a major challenge in the cloning of antibody genes, whether from hybridoma cell lines or splenic B cells. Using conventional protocols, the h...
This article is part of a Supplement: Volume 7 Supplement 4
Recently several statistical methods have been proposed to identify genes with differential expression between two conditions. However, very few studies consider the problem of sample imbalance and there is no...
This article is part of a Supplement: Volume 7 Supplement 4
Microarray techniques have revolutionized genomic research by making it possible to monitor the expression of thousands of genes in parallel. As the amount of microarray data being produced is increasing at an...
This article is part of a Supplement: Volume 7 Supplement 4
Structure matching plays an important part in understanding the functional role of biological structures. Bioinformatics assists in this effort by reformulating this process into a problem of finding a maximum...
This article is part of a Supplement: Volume 7 Supplement 4
Haplotype analysis has gained increasing attention in the context of association studies of disease genes and drug responsivities over the last years. The potential use of haplotypes has led to the initiation ...
This article is part of a Supplement: Volume 7 Supplement 4
Searching for the longest common sequence (LCS) of multiple biosequences is one of the most fundamental tasks in bioinformatics. In this paper, we present a parallel algorithm named FAST_LCS to speedup the com...
This article is part of a Supplement: Volume 7 Supplement 4
Ant colony algorithm has emerged recently as a new meta-heuristic method, which is inspired from the behaviours of real ants for solving NP-hard problems. However, the classical ant colony algorithm also has i...
This article is part of a Supplement: Volume 7 Supplement 4
TATA box is one of the most important transcription factor binding sites. But the exact sequences of TATA box are still not very clear.
This article is part of a Supplement: Volume 7 Supplement 4
The first symposium of computations in bioinformatics and bioscience (SCBB06) was held in Hangzhou, China on June 21–22, 2006. Twenty-six peer-reviewed papers were selected for publication in this special issu...
This article is part of a Supplement: Volume 7 Supplement 4
The estimation of the difference between two evolutionary distances within a triplet of homologs is a common operation that is used for example to determine which of two sequences is closer to a third one. The...
The process of transcription is controlled by systems of transcription factors, which bind to specific patterns of binding sites in the transcriptional control regions of genes, called cis-regulatory modules (CRM...
Studies on the distribution of indel sizes have consistently found that they obey a power law. This finding has lead several scientists to propose that logarithmic gap costs, G (k) = a + c ln k, are more biologic...
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