Selected articles from the Eighth Asia-Pacific Bioinformatics Conference (APBC 2010)

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

Integration of multiple data sources to prioritize candidate genes using discounted rating system

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...

Authors: Yongjin Li and Jagdish C Patra

Learning to predict expression efficacy of vectors in recombinant protein production

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...

Authors: Wen-Ching Chan, Po-Huang Liang, Yan-Ping Shih, Ueng-Cheng Yang, Wen-chang Lin and Chun-Nan Hsu

SFSSClass: an integrated approach for miRNA based tumor classification

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...

Authors: Ramkrishna Mitra, Sanghamitra Bandyopadhyay, Ujjwal Maulik and Michael Q Zhang

An ontology-based search engine for protein-protein interactions

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...

Authors: Byungkyu Park and Kyungsook Han

HORI: a web server to compute Higher Order Residue Interactions in protein structures

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...

Authors: Pandurangan Sundaramurthy, Khader Shameer, Raashi Sreenivasan, Sunita Gakkhar and Ramanathan Sowdhamini

A hub-attachment based method to detect functional modules from confidence-scored protein interactions and expression profiles

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...

Authors: Chia-Hao Chin, Shu-Hwa Chen, Chin-Wen Ho, Ming-Tat Ko and Chung-Yen Lin

Using genomic signatures for HIV-1 sub-typing

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...

Authors: Aridaman Pandit and Somdatta Sinha

Genome rearrangements with duplications

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...

Authors: Martin Bader

Decoding HMMs using the k best paths: algorithms and applications

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 ...

Authors: Daniel G Brown and Daniil Golod

Prediction of novel precursor miRNAs using a context-sensitive hidden Markov model (CSHMM)

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...

Authors: Sumeet Agarwal, Candida Vaz, Alok Bhattacharya and Ashwin Srinivasan

Heuristics for the inversion median problem

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...

Authors: Vaibhav Rajan, Andrew Wei Xu, Yu Lin, Krister M Swenson and Bernard ME Moret

Reaction graph kernels predict EC numbers of unknown enzymatic reactions in plant secondary metabolism

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...

Authors: Hiroto Saigo, Masahiro Hattori, Hisashi Kashima and Koji Tsuda

Detection of characteristic sub pathway network for angiogenesis based on the comprehensive pathway network

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...

Authors: Yezhou Huang and Shao Li

A weighted q-gram method for glycan structure classification

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...

Authors: Limin Li, Wai-Ki Ching, Takako Yamaguchi and Kiyoko F Aoki-Kinoshita

Efficient protein alignment algorithm for protein search

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...

Authors: Zaixin Lu, Zhiyu Zhao and Bin Fu

Functional characterization and topological modularity of molecular interaction networks

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 ...

Authors: Jayesh Pandey, Mehmet Koyutürk and Ananth Grama

Towards high performance computing for molecular structure prediction using IBM Cell Broadband Engine - an implementation perspective

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...

Authors: SPT Krishnan, Sim Sze Liang and Bharadwaj Veeravalli

Hit integration for identifying optimal spaced seeds

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 ...

Authors: Won-Hyoung Chung and Seong-Bae Park

Comparative classification of species and the study of pathway evolution based on the alignment of metabolic pathways

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...

Authors: Adi Mano, Tamir Tuller, Oded Béjà and Ron Y Pinter

A hybrid approach to protein folding problem integrating constraint programming with local search

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...

Authors: Abu Dayem Ullah and Kathleen Steinhöfel

New decoding algorithms for Hidden Markov Models using distance measures on labellings

Existing hidden Markov model decoding algorithms do not focus on approximately identifying the sequence feature boundaries.

Authors: Daniel G Brown and Jakub Truszkowski

Analysis of interactions between ribosomal proteins and RNA structural motifs

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...

Authors: Giovanni Ciriello, Claudio Gallina and Concettina Guerra

Efficient genome-scale phylogenetic analysis under the duplication-loss and deep coalescence cost models

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...

Authors: Mukul S Bansal, J Gordon Burleigh and Oliver Eulenstein

Stability analysis of the GAL regulatory network in Saccharomyces cerevisiae and Kluyveromyces lactis

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...

Authors: Vishwesh V Kulkarni, Venkatesh Kareenhalli, Pushkar Malakar, Lucy Y Pao, Michael G Safonov and Ganesh A Viswanathan

Structure prediction for the helical skeletons detected from the low resolution protein density map

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 ...

Authors: Kamal Al Nasr, Weitao Sun and Jing He

A novel approach for haplotype-based association analysis using family data

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...

Authors: Yixuan Chen, Xin Li and Jing Li

A fast indexing approach for protein structure comparison

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...

Authors: Lei Zhang, James Bailey, Arun S Konagurthu and Kotagiri Ramamohanarao

Computational prediction of type III secreted proteins from gram-negative bacteria

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 ...

Authors: Yang Yang, Jiayuan Zhao, Robyn L Morgan, Wenbo Ma and Tao Jiang

Prediction of FAD interacting residues in a protein from its primary sequence using evolutionary information

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...

Authors: Nitish K Mishra and Gajendra PS Raghava

Comparative analysis of thermophilic and mesophilic proteins using Protein Energy Networks

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...

Authors: MS Vijayabaskar and Saraswathi Vishveshwara