APBC 2010. The Eighth Asia Pacific Bioinformatics Conference Bangalore, India, 18-21 January 2010

Authors: Laxmi Parida and Gene Myers

Nonnegative principal component analysis for mass spectral serum profiles and biomarker discovery

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...

Authors: Henry Han

MTar: a computational microRNA target prediction architecture for human transcriptome

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...

Authors: Vinod Chandra, Reshmi Girijadevi, Achuthsankar S Nair, Sreenadhan S Pillai and Radhakrishna M Pillai

Predicting the protein-protein interactions using primary structures with predicted protein surface

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...

Authors: Darby Tien-Hao Chang, Yu-Tang Syu and Po-Chang Lin

Better score function for peptide identification with ETD MS/MS spectra

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...

Authors: Xiaowen Liu, Baozhen Shan, Lei Xin and Bin Ma

A multi-filter enhanced genetic ensemble system for gene selection and sample classification of microarray data

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...

Authors: Pengyi Yang, Bing B Zhou, Zili Zhang and Albert Y Zomaya

Genome-wide sequence-based prediction of peripheral proteins using a novel semi-supervised learning technique

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...

Authors: Nitin Bhardwaj, Mark Gerstein and Hui Lu

Molecular dynamics simulation studies and in vitro site directed mutagenesis of avian beta-defensin Apl_AvBD2

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...

Authors: Soja Saghar Soman, Krishnankutty Chandrika Sivakumar and Easwaran Sreekumar

Knowledge-based analysis of microarrays for the discovery of transcriptional regulation relationships

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...

Authors: Junhee Seok, Amit Kaushal, Ronald W Davis and Wenzhong Xiao

Prediction of protein structural classes for low-homology sequences based on predicted secondary structure

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 ...

Authors: Jian-Yi Yang, Zhen-Ling Peng and Xin Chen

PostMod: sequence based prediction of kinase-specific phosphorylation sites with indirect relationship

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...

Authors: Inkyung Jung, Akihisa Matsuyama, Minoru Yoshida and Dongsup Kim

Fast motif recognition via application of statistical thresholds

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...

Authors: Christina Boucher and James King

Short clones or long clones? A simulation study on the use of paired reads in metagenomics

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...

Authors: Suparna Mitra, Max Schubach and Daniel H Huson

In silico screening of herbal and nanoparticle lead compounds for effectivity against H5N1, H1N1 neuraminidase and telomerase

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 ...

Authors: Sayak Ganguli, Manjita Mazumder, Protip Basu, Paushali Roy, Sayani Mitra and Abhijit Datta

Prediction of novel miRNAs and associated target genes in Glycine max

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...

Authors: Trupti Joshi, Zhe Yan, Marc Libault, Dong-Hoon Jeong, Sunhee Park, Pamela J Green, D Janine Sherrier, Andrew Farmer, Greg May, Blake C Meyers, Dong Xu and Gary Stacey

MrsRF: an efficient MapReduce algorithm for analyzing large collections of evolutionary trees

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...

Authors: Suzanne J Matthews and Tiffani L Williams

Classification of protein sequences by means of irredundant patterns

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...

Authors: Matteo Comin and Davide Verzotto

Amino acid classification based spectrum kernel fusion for protein subnuclear localization

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 ...

Authors: Suyu Mei and Wang Fei

Identifying main effects and epistatic interactions from large-scale SNP data via adaptive group Lasso

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...

Authors: Can Yang, Xiang Wan, Qiang Yang, Hong Xue and Weichuan Yu

AntiBP2: improved version of antibacterial peptide prediction

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...

Authors: Sneh Lata, Nitish K Mishra and Gajendra PS Raghava