International Journal of Bioinformatics Research and Applications This is an RSS file. You can use it to subscribe to this data in your favourite RSS reader or to display this data on your own website or blog.

Diversity and evolution of the envelope gene of dengue virus type 1 circulating in India in recent times.
Abstract Dengue viral attacks have been reported in various parts of India in recent years. In this paper we report on our studies of the characterisation and evolutionary aspects of gene sequences of the envelope glycoprotein of the prevalent Indian dengue virus type 1. Comparison with sequences from other countries shows that the envelope genes identified in India are closely related to strains from Malaysia. From the evolutionary point of view the envelope gene sequences of this dengue virus of India for past few years show that a marked mutational shift in the nucleotide sequences of the envelope gene ...
Source: International Journal of Bioinformatics Research and Applications - December 9, 2015 Category: Bioinformatics Authors: Dey S, Nandy A, Nandy P, Das S Tags: Int J Bioinform Res Appl Source Type: research

On the interconnection of stable protein complexes: inter-complex hubs and their conservation in Saccharomyces cerevisiae and Homo sapiens networks.
Abstract Protein complexes are key molecular entities that perform a variety of essential cellular functions. The connectivity of proteins within a complex has been widely investigated with both experimental and computational techniques. We developed a computational approach to identify and characterise proteins that play a role in interconnecting complexes. We computed a measure of inter-complex centrality, the crossroad index, based on disjoint paths connecting proteins in distinct complexes and identified inter-complex hubs as proteins with a high value of the crossroad index. We applied the approach to...
Source: International Journal of Bioinformatics Research and Applications - December 9, 2015 Category: Bioinformatics Authors: Guerra C Tags: Int J Bioinform Res Appl Source Type: research

Neural network and rough set hybrid scheme for prediction of missing associations.
Abstract Currently, internet is the best tool for distributed computing, which involves spreading of data geographically. But, retrieving information from huge data is critical and has no relevance unless it provides certain information. Prediction of missing associations can be viewed as fundamental problems in machine learning where the main objective is to determine decisions for the missing associations. Mathematical models such as naive Bayes structure, human composed network structure, Bayesian network modelling, etc., were developed to this end. But, it has certain limitations and failed to include ...
Source: International Journal of Bioinformatics Research and Applications - December 9, 2015 Category: Bioinformatics Authors: Anitha A, Acharjya DP Tags: Int J Bioinform Res Appl Source Type: research

Automatic segmentation of Potyviridae family polyproteins.
We describe an automatic segmentation method for polyproteins of the viruses belonging to the Potyviridae family. It uses machine learning techniques in order to predict the cleavage site which define the segments in which said polyproteins are cut in their process of functional maturation. The segmentation application is publicly available for use on a website and it can be accessed through the web service interface too. The prediction models have an average sensitivity of 0.79 and a Matthews correlation coefficient average of 0.23. This method is capable of predicting correctly (coinciding with previously published segme...
Source: International Journal of Bioinformatics Research and Applications - December 9, 2015 Category: Bioinformatics Authors: Vargas JF, Velasco JA, Alvarez GI, Linares DL, Bravo E Tags: Int J Bioinform Res Appl Source Type: research

Docking analysis of gallic acid derivatives as HIV-1 protease inhibitors.
Abstract HIV-1 Protease (HIV-1 PR) enzymes are essential for accurate assembly and maturation of infectious HIV retroviruses. The significant role of HIV-1 protease in viral replication has made it a potential drug target. In the recent past, phytochemical Gallic Acid (GA) derivatives have been screened for protease inhibitor activity. The present work aims to design and evaluate potential GA-based HIV-1 PR phytoinhibitors by docking approach. The ligands were prepared by ChemDraw and docking was performed in HEX software. In this present study, one of the GA analogues (GA4) emerged as a potent drug candid...
Source: International Journal of Bioinformatics Research and Applications - December 9, 2015 Category: Bioinformatics Authors: Singh A, Pal TK Tags: Int J Bioinform Res Appl Source Type: research

In silico analysis, annotation and characterisation of putative ESTs from Sorghum bicolor associated with heat stress.
Abstract Owing to their sessile nature, plants experience a variety of environmental stresses, but tolerance to these adverse conditions is a very complex phenomenon. Among all stresses, heat stress is the most important constraint that affects plant yield in rain-fed areas. To shed some light on candidate genes involved in heat stress, sequences potentially associated with heat shock resistance were retrieved and identified by in silico analysis using the public sequence database of various plants. A total of 30,000 EST sequences were mined and 24 putative ESTs associated with heat stress were picked up f...
Source: International Journal of Bioinformatics Research and Applications - December 9, 2015 Category: Bioinformatics Authors: Ram G, Sharma AD Tags: Int J Bioinform Res Appl Source Type: research

A permutation based simulated annealing algorithm to predict pseudoknotted RNA secondary structures.
Abstract Pseudoknots are RNA tertiary structures which perform essential biological functions. This paper discusses SARNA-Predict-pk, a RNA pseudoknotted secondary structure prediction algorithm based on Simulated Annealing (SA). The research presented here extends previous work of SARNA-Predict and further examines the effect of the new algorithm to include prediction of RNA secondary structure with pseudoknots. An evaluation of the performance of SARNA-Predict-pk in terms of prediction accuracy is made via comparison with several state-of-the-art prediction algorithms using 20 individual known structures...
Source: International Journal of Bioinformatics Research and Applications - November 13, 2015 Category: Bioinformatics Authors: Tsang HH, Wiese KC Tags: Int J Bioinform Res Appl Source Type: research

A comprehensive evaluation of machine learning techniques for cancer class prediction based on microarray data.
Abstract Prostate cancer is among the most common cancer in males and its heterogeneity is well known. The genomic level changes can be detected in gene expression data and those changes may serve as standard model for any random cancer data for class prediction. Various techniques were implied on prostate cancer data set in order to accurately predict cancer class including machine learning techniques. Large number of attributes but few numbers of samples in microarray data leads to poor training; therefore, the most challenging part is attribute reduction or non-significant gene reduction. In this work, ...
Source: International Journal of Bioinformatics Research and Applications - November 13, 2015 Category: Bioinformatics Authors: Raza K, Hasan AN Tags: Int J Bioinform Res Appl Source Type: research

Acoustic analysis of speech under stress.
Abstract When a person is emotionally charged, stress could be discerned in his voice. This paper presents a simplified and a non-invasive approach to detect psycho-physiological stress by monitoring the acoustic modifications during a stressful conversation. Voice database consists of audio clips from eight different popular FM broadcasts wherein the host of the show vexes the subjects who are otherwise unaware of the charade. The audio clips are obtained from real-life stressful conversations (no simulated emotions). Analysis is done using PRAAT software to evaluate mean fundamental frequency (F0) and fo...
Source: International Journal of Bioinformatics Research and Applications - November 13, 2015 Category: Bioinformatics Authors: Sondhi S, Khan M, Vijay R, Salhan AK, Chouhan S Tags: Int J Bioinform Res Appl Source Type: research

A combination of dual-tree discrete wavelet transform and minimum redundancy maximum relevance method for diagnosis of Alzheimer's disease.
Abstract In this paper, we propose a three-phased method for diagnosis of Alzheimer's disease using the structural magnetic resonance imaging (MRI). In first phase, gray matter tissue probability map is obtained from every brain MRI volume. Further, five regions of interest (ROIs) are extracted as per prior knowledge. In second phase, features are extracted from each ROI using 3D dual-tree discrete wavelet transform. In third phase, relevant features are selected using minimum redundancy maximum relevance features selection technique. The decision model is built with features so obtained, using a classifie...
Source: International Journal of Bioinformatics Research and Applications - November 13, 2015 Category: Bioinformatics Authors: Aggarwal N, Rana B, Agrawal RK, Kumaran S Tags: Int J Bioinform Res Appl Source Type: research

Bioinformatics: promises and progress.
Abstract Bioinformatics is a multidisciplinary science that solves and analyzes biological problems. With the quantum explosion in biomedical data, the demand of bioinformatics has increased gradually. Present paper provides an overview of various ways through which the biologists or biological researchers in the domain of neurology, structural and functional biology, evolutionary biology, clinical science, etc., use bioinformatics applications for data analysis to summarise their research. A new perspective is used to classify the knowledge available in the field thus will help general audience to underst...
Source: International Journal of Bioinformatics Research and Applications - November 13, 2015 Category: Bioinformatics Authors: Gupta S, Misra G, Khurana SM Tags: Int J Bioinform Res Appl Source Type: research

Understanding the virulence of the entero-aggregative E. coli O104:H4.
Abstract O104:H4 is a new strain of E. coli that has caused an outbreak in Germany. It was isolated from patients with bloody diarrhoea and Haemolytic Uremic Syndrome (HUS). BGI (www.genomics.cn) sequenced and assembled this new strain. It was reported to show resistance to a number of drugs that are toxic to other E. coli and causes serious complications during infections, which ultimately lead to death. Multi-drug resistance and high virulence of this strain is thought to be acquired from different sources, by horizontal gene transfer. A total of 38 prophage elements were detected from the new strain by ...
Source: International Journal of Bioinformatics Research and Applications - November 13, 2015 Category: Bioinformatics Authors: Kesavan B, Srividhya KV, Krishnaswamy S, Raja M, Vidya N, Mohan AV Tags: Int J Bioinform Res Appl Source Type: research

Predicting DNA mutations during cancer evolution.
Abstract Bio-systems are inherently complex information processing systems. Their physiological complexities limit the formulation and testing of a hypothesis for their behaviour. Our goal here was to test a computational framework utilising published data from a longitudinal study of patients with acute myeloid leukaemia (AML), whose DNA from both normal and malignant tissues were subjected to NGS analysis at various points in time. By processing the sequencing data before relapse time, we tested our framework by predicting the regions of the genome to be mutated at relapse time and, later, by comparing o...
Source: International Journal of Bioinformatics Research and Applications - November 13, 2015 Category: Bioinformatics Authors: Martinez JC, Lopez-Jimenez N, Meng T, Iyengar SS Tags: Int J Bioinform Res Appl Source Type: research

Mining amino acid association patterns in class B GPCRs.
Abstract Class B GPCR family is a small group of receptors which are activated by peptides of intermediate length that range from 30 to 40 amino acid residues including hormones, neuropeptides and autocrine factors that mediate diverse physiological functions. They are involved in physiological processes like glucose homeostasis (glucagon and glucagon-like peptide-1), calcium homeostasis and bone turnover (parathyroid hormone and calcitonin), and control of the stress axis (corticotropin-releasing factor). Most of the GPCR structures and their functions are still unknown. Thus, the study of amino acid asso...
Source: International Journal of Bioinformatics Research and Applications - November 13, 2015 Category: Bioinformatics Authors: Kumari T, Pardasani KR Tags: Int J Bioinform Res Appl Source Type: research

Mining nutrigenetics patterns related to obesity: use of parallel multifactor dimensionality reduction.
Abstract This paper aims to enlighten the complex etiology beneath obesity by analysing data from a large nutrigenetics study, in which nutritional and genetic factors associated with obesity were recorded for around two thousand individuals. In our previous work, these data have been analysed using artificial neural network methods, which identified optimised subsets of factors to predict one's obesity status. These methods did not reveal though how the selected factors interact with each other in the obtained predictive models. For that reason, parallel Multifactor Dimensionality Reduction (pMDR) was use...
Source: International Journal of Bioinformatics Research and Applications - November 13, 2015 Category: Bioinformatics Authors: Karayianni KN, Grimaldi KA, Nikita KS, Valavanis IK Tags: Int J Bioinform Res Appl Source Type: research