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Complementary DNA (cDNA) microarrays are a well established technology for studying gene expression. A microarray image is obtained by laser scanning a hybridized cDNA microarray, which consists of thousands o...
Genome sequencing and post-genomics projects such as structural genomics are extending the frontier of the study of sequence-structure-function relationship of genes and their products. Although many sequence/...
The clustered heat map is the most popular means of visualizing genomic data. It compactly displays a large amount of data in an intuitive format that facilitates the detection of hidden structures and relatio...
High-throughput flow cytometry experiments produce hundreds of large multivariate samples of cellular characteristics. These samples require specialized processing to obtain clinically meaningful measurements....
Co-evolution is the process in which two (or more) sets of orthologs exhibit a similar or correlative pattern of evolution. Co-evolution is a powerful way to learn about the functional interdependencies betwee...
While in principle a seemingly infinite variety of combinations of mutations could result in tumor development, in practice it appears that most human cancers fall into a relatively small number of "sub-types,...
The binding of peptide fragments of extracellular peptides to class II MHC is a crucial event in the adaptive immune response. Each MHC allotype generally binds a distinct subset of peptides and the enormous n...
In recent years, Data Mining technology has been applied more than ever before in the field of traditional Chinese medicine (TCM) to discover regularities from the experience accumulated in the past thousands ...
Bacterial infections represent a global health challenge. The identification of novel antibacterial targets for both therapy and vaccination is needed on a constant basis because resistance continues to spread...
High-throughput automated sequencing has enabled an exponential growth rate of sequencing data. This requires increasing sequence quality and reliability in order to avoid database contamination with artefactu...
Maturation inhibitors are a new class of antiretroviral drugs. Bevirimat (BVM) was the first substance in this class of inhibitors entering clinical trials. While the inhibitory function of BVM is well establi...
The availability of various "omics" datasets creates a prospect of performing the study of genome-wide genetic regulatory networks. However, one of the major challenges of using mathematical models to infer ge...
While microarrays are the predominant method for gene expression profiling, probe signal variation is still an area of active research. Probe signal is sequence dependent and affected by probe-target binding s...
Protein sorting is the process that newly synthesized proteins are transported to their target locations within or outside of the cell. This process is precisely regulated by protein sorting signals in differe...
This article is part of a Supplement: Volume 11 Supplement 1
One of key issues in the post-genomic era is to assign functions to uncharacterized proteins. Since proteins seldom act alone; rather, they must interact with other biomolecular units to execute their function...
This article is part of a Supplement: Volume 11 Supplement 1
Conserved gene clusters are groups of genes that are located close to one another in the genomes of several species. They tend to code for proteins that have a functional interaction. The identification of conser...
This article is part of a Supplement: Volume 11 Supplement 1
As the size of the known human interactome grows, biologists increasingly rely on computational tools to identify patterns that represent protein complexes and pathways. Previous studies have shown that densel...
This article is part of a Supplement: Volume 11 Supplement 1
Increasing amount of data from comparative genomics, and newly developed technologies producing accurate gene expression data facilitate the study of the expression divergence of homologous genes. Previous stu...
This article is part of a Supplement: Volume 11 Supplement 1
MHC/HLA class II molecules are important components of the immune system and play a critical role in processes such as phagocytosis. Understanding peptide recognition properties of the hundreds of MHC class II...
This article is part of a Supplement: Volume 11 Supplement 1
The rapidly increasing availability of whole-genome sequences has enabled the study of whole-genome evolution. Evolutionary mechanisms based on genome rearrangements have attracted much attention and given ris...
This article is part of a Supplement: Volume 11 Supplement 1
An explosive global spreading of multidrug resistant Mycobacterium tuberculosis (Mtb) is a catastrophe, which demands an urgent need to design or develop novel/potent antitubercular agents. The Lysine/DAP biosynt...
This article is part of a Supplement: Volume 11 Supplement 1
MicroRNAs (miRNAs) are short non-coding RNA molecules, which play an important role in post-transcriptional regulation of gene expression. There have been many efforts to discover miRNA precursors (pre-miRNAs)...
This article is part of a Supplement: Volume 11 Supplement 1
Prostaglandin H2 (PGH2) is a common precursor for the synthesis of five different Prostanoids via specific Prostanoid Synthases. The binding of this substrate with these Synthases is not properly understood. More...
This article is part of a Supplement: Volume 11 Supplement 1
This paper compares the most common digital signal processing methods of exon prediction in eukaryotes, and also proposes a technique for noise suppression in exon prediction. The specimen used here which has ...
This article is part of a Supplement: Volume 11 Supplement 1
Thermophilic proteins sustain themselves and function at higher temperatures. Despite their structural and functional similarities with their mesophilic homologues, they show enhanced stability. Various compar...
This article is part of a Supplement: Volume 11 Supplement 1
Flavin binding proteins (FBP) plays a critical role in several biological functions such as electron transport system (ETS). These flavoproteins contain very tightly bound, sometimes covalently, flavin adenine...
This article is part of a Supplement: Volume 11 Supplement 1
Protein structure comparison is a fundamental task in structural biology. While the number of known protein structures has grown rapidly over the last decade, searching a large database of protein structures i...
This article is part of a Supplement: Volume 11 Supplement 1
The current advances in electron cryo-microscopy technique have made it possible to obtain protein density maps at about 6-10 Å resolution. Although it is hard to derive the protein chain directly from such a ...
This article is part of a Supplement: Volume 11 Supplement 1
In the yeast Saccharomyces cerevisiae, interactions between galactose, Gal3p, Gal80p, and Gal4p determine the transcriptional status of the genes required for the galactose utilization. Increase in the cellular g...
This article is part of a Supplement: Volume 11 Supplement 1
Glycobiology pertains to the study of carbohydrate sugar chains, or glycans, in a particular cell or organism. Many computational approaches have been proposed for analyzing these complex glycan structures, wh...
This article is part of a Supplement: Volume 11 Supplement 1
Pathways in biological system often cooperate with each other to function. Changes of interactions among pathways tightly associate with alterations in the properties and functions of the cell and hence altera...
This article is part of a Supplement: Volume 11 Supplement 1
Understanding of secondary metabolic pathway in plant is essential for finding druggable candidate enzymes. However, there are many enzymes whose functions are not yet discovered in organism-specific metabolic...
This article is part of a Supplement: Volume 11 Supplement 1
It has been apparent in the last few years that small non coding RNAs (ncRNA) play a very significant role in biological regulation. Among these microRNAs (miRNAs), 22-23 nucleotide small regulatory RNAs, have...
This article is part of a Supplement: Volume 11 Supplement 1
Traditional algorithms for hidden Markov model decoding seek to maximize either the probability of a state path or the number of positions of a sequence assigned to the correct state. These algorithms provide ...
This article is part of a Supplement: Volume 11 Supplement 1
Human Immunodeficiency Virus type 1 (HIV-1), the causative agent of Acquired Immune Deficiency Syndrome (AIDS), exhibits very high genetic diversity with different variants or subtypes prevalent in different p...
This article is part of a Supplement: Volume 11 Supplement 1
Folding of a protein into its three dimensional structure is influenced by both local and global interactions within a protein. Higher order residue interactions, like pairwise, triplet and quadruplet ones, pl...
This article is part of a Supplement: Volume 11 Supplement 1
Keyword matching or ID matching is the most common searching method in a large database of protein-protein interactions. They are purely syntactic methods, and retrieve the records in the database that contain...
This article is part of a Supplement: Volume 11 Supplement 1
MicroRNA (miRNA) expression profiling data has recently been found to be particularly important in cancer research and can be used as a diagnostic and prognostic tool. Current approaches of tumor classificatio...
This article is part of a Supplement: Volume 11 Supplement 1
Identifying disease gene from a list of candidate genes is an important task in bioinformatics. The main strategy is to prioritize candidate genes based on their similarity to known disease genes. Most of exis...
This article is part of a Supplement: Volume 11 Supplement 1
Antibacterial peptides are one of the effecter molecules of innate immune system. Over the last few decades several antibacterial peptides have successfully approved as drug by FDA, which has prompted an inter...
This article is part of a Supplement: Volume 11 Supplement 1
Prediction of protein localization in subnuclear organelles is more challenging than general protein subcelluar localization. There are only three computational models for protein subnuclear localization thus ...
This article is part of a Supplement: Volume 11 Supplement 1
The classification of protein sequences using string algorithms provides valuable insights for protein function prediction. Several methods, based on a variety of different patterns, have been previously propo...
This article is part of a Supplement: Volume 11 Supplement 1
Small non-coding RNAs (21 to 24 nucleotides) regulate a number of developmental processes in plants and animals by silencing genes using multiple mechanisms. Among these, the most conserved classes are microRN...
This article is part of a Supplement: Volume 11 Supplement 1
This article has been withdrawn from the public domain because of significant plagiarism. In the light of this situation, BioMed Central regrets that this article is no longer available. The authors apologise ...
This article is part of a Supplement: Volume 11 Supplement 1
The Retraction Note to this article has been published in BMC Bioinformatics 2010 11:258
The large amount of high-throughput genomic data has facilitated the discovery of the regulatory relationships between transcription factors and their target genes. While early methods for discovery of transcr...
This article is part of a Supplement: Volume 11 Supplement 1
Defensins comprise a group of antimicrobial peptides, widely recognized as important elements of the innate immune system in both animals and plants. Cationicity, rather than the secondary structure, is believ...
This article is part of a Supplement: Volume 11 Supplement 1
In supervised learning, traditional approaches to building a classifier use two sets of examples with pre-defined classes along with a learning algorithm. The main limitation of this approach is that examples fro...
This article is part of a Supplement: Volume 11 Supplement 1
Tandem mass spectrometry (MS/MS) has become the primary way for protein identification in proteomics. A good score function for measuring the match quality between a peptide and an MS/MS spectrum is instrument...
This article is part of a Supplement: Volume 11 Supplement 1
As a novel cancer diagnostic paradigm, mass spectroscopic serum proteomic pattern diagnostics was reported superior to the conventional serologic cancer biomarkers. However, its clinical use is not fully valid...
This article is part of a Supplement: Volume 11 Supplement 1
This article is part of a Supplement: Volume 11 Supplement 1
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