Volume 11 Supplement 1
Edited by Laxmi Parida and Gene Myers
The Eighth Asia Pacific Bioinformatics Conference (APBC 2010). Go to conference site.
Bangalore, India18-21 January 2010
Page 1 of 2
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...
MicroRNAs (miRNAs) play an essential task in gene regulatory networks by inhibiting the expression of target mRNAs. As their mRNA targets are genes involved in important cell functions, there is a growing inte...
Many biological functions involve various protein-protein interactions (PPIs). Elucidating such interactions is crucial for understanding general principles of cellular systems. Previous studies have shown the...
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...
Feature selection techniques are critical to the analysis of high dimensional datasets. This is especially true in gene selection from microarray data which are commonly with extremely high feature-to-sample r...
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...
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...
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...
Prediction of protein structural classes (α, β, α + β and α/β) from amino acid sequences is of great importance, as it is beneficial to study protein function, regulation and interactions. Many methods have been ...
Post-translational modifications (PTMs) have a key role in regulating cell functions. Consequently, identification of PTM sites has a significant impact on understanding protein function and revealing cellular...
Improving the accuracy and efficiency of motif recognition is an important computational challenge that has application to detecting transcription factor binding sites in genomic data. Closely related to motif...
Metagenomics is the study of environmental samples using sequencing. Rapid advances in sequencing technology are fueling a vast increase in the number and scope of metagenomics projects. Most metagenome sequen...
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 ...
The Retraction Note to this article has been published in BMC Bioinformatics 2010 11:258
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...
MapReduce is a parallel framework that has been used effectively to design large-scale parallel applications for large computing clusters. In this paper, we evaluate the viability of the MapReduce framework fo...
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...
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 ...
Single nucleotide polymorphism (SNP) based association studies aim at identifying SNPs associated with phenotypes, for example, complex diseases. The associated SNPs may influence the disease risk individually...
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...
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...
Recombinant protein production is a useful biotechnology to produce a large quantity of highly soluble proteins. Currently, the most widely used production system is to fuse a target protein into different vec...
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...
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...
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...
Many research results show that the biological systems are composed of functional modules. Members in the same module usually have common functions. This is useful information to understand how biological syst...
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...
Finding sequences of evolutionary operations that transform one genome into another is a classical problem in comparative genomics. While most of the genome rearrangement algorithms assume that there is exactl...
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 ...
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...
The study of genome rearrangements has become a mainstay of phylogenetics and comparative genomics. Fundamental in such a study is the median problem: given three genomes find a fourth that minimizes the sum o...
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...
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...
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...
Proteins show a great variety of 3D conformations, which can be used to infer their evolutionary relationship and to classify them into more general groups; therefore protein structure alignment algorithms are...
Analyzing interaction networks for functional characterization poses significant challenges arising from the noisy, incomplete, and generic nature of both the interaction data as well as functional annotation ...
RNA structure prediction problem is a computationally complex task, especially with pseudo-knots. The problem is well-studied in existing literature and predominantly uses highly coupled Dynamic Programming (D...
Introduction of spaced speeds opened a way of sensitivity improvement in homology search without loss of search speed. Since then, the efforts of finding optimal seed which maximizes the sensitivity have been ...
Pathways provide topical descriptions of cellular circuitry. Comparing analogous pathways reveals intricate insights into individual functional differences among species. While previous works in the field perf...
The protein folding problem remains one of the most challenging open problems in computational biology. Simplified models in terms of lattice structure and energy function have been proposed to ease the comput...
Existing hidden Markov model decoding algorithms do not focus on approximately identifying the sequence feature boundaries.
One important goal of structural bioinformatics is to recognize and predict the interactions between protein binding sites and RNA. Recently, a comprehensive analysis of ribosomal proteins and their interactio...
Genomic data provide a wealth of new information for phylogenetic analysis. Yet making use of this data requires phylogenetic methods that can efficiently analyze extremely large data sets and account for proc...
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...
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 ...
Haplotype-based approaches have been extensively studied for case-control association mapping in recent years. It has been shown that haplotype methods can provide more consistent results comparing to single-l...
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...
Type III secretion system (T3SS) is a specialized protein delivery system in gram-negative bacteria that injects proteins (called effectors) directly into the eukaryotic host cytosol and facilitates bacterial ...
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...
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...
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