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.

A new greedy randomised adaptive search procedure for multiple sequence alignment.
Abstract The Multiple Sequence Alignment (MSA) is one of the most challenging tasks in bioinformatics. It consists of aligning several sequences to show the fundamental relationship and the common characteristics between a set of protein or nucleic sequences; this problem has been shown to be NP-complete if the number of sequences is >2. In this paper, a new incomplete algorithm based on a Greedy Randomised Adaptive Search Procedure (GRASP) is presented to deal with the MSA problem. The first GRASP's phase is a new greedy algorithm based on the application of a new random progressive method and a hybrid...
Source: International Journal of Bioinformatics Research and Applications - June 29, 2013 Category: Bioinformatics Authors: Layeb A, Selmane M, Elhoucine MB Tags: Int J Bioinform Res Appl Source Type: research

Exploitation of in silico potential in prediction, validation and elucidation of mechanism of anti-angiogenesis by novel compounds: comparative correlation between wet lab and in silico data.
This study describes in silico validation of the wet lab data from aeroplysinin-1, curcumin and halofuginone using Autodock Tools 4.0. The inhibition patterns of the vascular endothelial cell differentiation and capillary tube formation mediated by anti-angiogenic growth factors from these test compounds were found quite comparable with the in silico results using angiogenic targets (EFGR, bFGF and VEGFR-1). Successful validation of the wet lab results of the selected angiogenic targets by in silico method has led to exploit the hidden potential of in silico tools in preliminary screening of the unknown compounds for anti-...
Source: International Journal of Bioinformatics Research and Applications - June 29, 2013 Category: Bioinformatics Authors: Arif JM, Siddiqui MH, Akhtar S, Al-Sagair OA Tags: Int J Bioinform Res Appl Source Type: research

In silico analysis of putative miRNAs and their target genes in sorghum (Sorghum bicolor).
Abstract MicroRNAs (miRNAs) are small endogenous genes regulators which regulate different processes underlying plant adaptation to abiotic stresses. To gain a deep understanding of role of miRNAs in plants, in the present study, we computationally analyzed different sorghum miRNAs in the drought-induced gene sequences. Homologous miRNA were identified using different plant miRNA databases. Using previously established genes databases, various targets of sorghum miRNAs were predicted viz: transcription factors, chaperonins, metabolic enzymes and other gene targets necessary for proper plant development. An...
Source: International Journal of Bioinformatics Research and Applications - June 29, 2013 Category: Bioinformatics Authors: Ram G, Sharma AD Tags: Int J Bioinform Res Appl Source Type: research

Identifying radiation exposure biomarkers from mouse blood transcriptome.
Abstract Ionising radiation is a pleiotropic stress agent that may induce a variety of adverse effects. Molecular biomarker approaches possess promise to assess radiation exposure, however, the pleiotropic nature of ionising radiation induced transcriptional responses and the historically poor inter-laboratory performance of omics-derived biomarkers serve as barriers to identification of unequivocal biomarker sets. Here, we present a whole-genome survey of the murine transcriptomic response to physiologically relevant radiation doses, 2 Gy and 8 Gy. We used this dataset with the Random Forest algorithm to ...
Source: International Journal of Bioinformatics Research and Applications - June 29, 2013 Category: Bioinformatics Authors: Hyduke DR, Laiakis EC, Li HH, Jr AJ Tags: Int J Bioinform Res Appl Source Type: research

Serial fusion of random subspace ensemble for subcellular phenotype images classification.
Abstract Subcellular localisation is a key functional characteristic of proteins. In this paper, we apply Haralick texture analysis and Curvelet Transform for feature description and propose a cascade Random Subspace (RS) ensemble with rejection options for subcellular phenotype classification. Serial fusions of RS classifier ensembles much improve classification reliability. The rejection option is implemented by relating the consensus degree from majority voting to a confidence measure and abstaining to classify ambiguous samples if the consensus degree is lower than a threshold. Using the public 2D HeLa...
Source: International Journal of Bioinformatics Research and Applications - June 29, 2013 Category: Bioinformatics Authors: Zhang B, Pham TD Tags: Int J Bioinform Res Appl Source Type: research

Efficient calculation of compound similarity based on maximum common subgraphs and its application to prediction of gene transcript levels.
Abstract Properties of a chemical entity, both physical and biological, are related to its structure. Since compound similarity can be used to infer properties of novel compounds, in chemoinformatics much attention has been paid to ways of calculating structural similarity. A useful metric to capture the structural similarity between compounds is the relative size of the Maximum Common Subgraph (MCS). The MCS is the largest substructure present in a pair of compounds, when represented as graphs. However, in practice it is difficult to employ such a metric, since calculation of the MCS becomes computational...
Source: International Journal of Bioinformatics Research and Applications - June 29, 2013 Category: Bioinformatics Authors: Berlo RJ, Winterbach W, Groot MJ, Bender A, Verheijen PJ, Reinders MJ, Ridder DD Tags: Int J Bioinform Res Appl Source Type: research

Meropenem: a potent drug against superbug as unveiled through bioinformatics approaches.
This study revealed that meropenem has good interaction with the active sites of the receptor that could retard the spread of antibiotic resistant bacteria. PMID: 23467058 [PubMed - in process] (Source: International Journal of Bioinformatics Research and Applications)
Source: International Journal of Bioinformatics Research and Applications - May 23, 2013 Category: Bioinformatics Authors: Mallick M, Odedra D, Vidyarthi AS, Shankaracharya Tags: Int J Bioinform Res Appl Source Type: research

The family based variability in protein family expansion.
Abstract In this paper we propose an automatic protein family expansion approach for recruitment of new members among the protein-coding genes in newly sequenced genomes. The criteria for adding a new member to a family depends on the structure of each individual family versus being globally uniform. The detection of a threshold in the ROC space of all sorted iterative profile sets defines the alignments selection criteria for each family. Furthermore, the statistical estimation of most-frequent optimal sorting criteria generates the optimal filtering strategy in a learning-parameter set for profile-based ...
Source: International Journal of Bioinformatics Research and Applications - May 23, 2013 Category: Bioinformatics Authors: Sarkar A, Nikolski M, Durrens P Tags: Int J Bioinform Res Appl Source Type: research

A parallel strategy for predicting the secondary structure of polycistronic microRNAs.
Abstract The biogenesis of a functional microRNA is largely dependent on the secondary structure of the microRNA precursor (pre-miRNA). Recently, it has been shown that microRNAs are present in the genome as the form of polycistronic transcriptional units in plants and animals. It will be important to design efficient computational methods to predict such structures for microRNA discovery and its applications in gene silencing. In this paper, we propose a parallel algorithm based on the master-slave architecture to predict the secondary structure from an input sequence. We conducted some experiments to ver...
Source: International Journal of Bioinformatics Research and Applications - May 23, 2013 Category: Bioinformatics Authors: Han D, Tang G, Zhang J Tags: Int J Bioinform Res Appl Source Type: research

Identification of motor imagery tasks through CC-LR algorithm in brain computer interface.
This study focuses on the identification of Motor Imagery (MI) tasks for the development of Brain Computer Interface (BCI) technologies combining Cross-Correlation and Logistic Regression (CC-LR) techniques. The proposed method is tested on two benchmark data sets, IVa and IVb of BCI Competition III, and the performance is evaluated through a 3-fold cross-validation procedure. The experimental outcomes are compared with two recently reported algorithms, R-Common Spatial Pattern (CSP) with aggregation and Clustering Technique (CT)-based Least Square Support Vector Machine (LS-SVM) and also other four algorithms using data s...
Source: International Journal of Bioinformatics Research and Applications - May 23, 2013 Category: Bioinformatics Authors: Siuly, Li Y, Wen P Tags: Int J Bioinform Res Appl Source Type: research

Evaluation of gene ontology semantic similarities on protein interaction datasets.
CONCLUSIONS: For the identification of interacted proteins, CoutoEnriched is the best definition of the similarity between GO terms, and there is no significant difference between most methods calculating the semantic similarity between two sets of GO terms. PMID: 23467062 [PubMed - in process] (Source: International Journal of Bioinformatics Research and Applications)
Source: International Journal of Bioinformatics Research and Applications - May 23, 2013 Category: Bioinformatics Authors: Chen G, Li J, Wang J Tags: Int J Bioinform Res Appl Source Type: research

Discovering novel carriers for oral insulin tablets: a pharmacoinformatics approach.
This study is a prospect of oral insulin tablet through pharmacoinformatics approach. PMID: 23467063 [PubMed - in process] (Source: International Journal of Bioinformatics Research and Applications)
Source: International Journal of Bioinformatics Research and Applications - May 23, 2013 Category: Bioinformatics Authors: Seenivasagam R, Hemavathi K, Sivakumar G, Niranjan V Tags: Int J Bioinform Res Appl Source Type: research

Prediction of protein secondary structure using Large Margin Nearest Neighbour classification.
Abstract In this paper, we introduce a novel method for protein secondary structure prediction by using Position-Specific Scoring Matrices (PSSM) profiles and Large Margin Nearest Neighbour (LMNN) classification. Since the PSSM profiles are not specifically designed for protein secondary structure prediction, the traditional nearest neighbour method could not achieve satisfactory prediction accuracy. To address this problem, we first use a LMNN model to learn a Mahalanobis distance metric for nearest neighbour classification. Then, an energy-based rule is invoked to assign secondary structure. Tests show t...
Source: International Journal of Bioinformatics Research and Applications - May 23, 2013 Category: Bioinformatics Authors: Yang W, Wang K, Zuo W Tags: Int J Bioinform Res Appl Source Type: research

ASFinder: a tool for genome-wide identification of alternatively splicing transcripts from EST-derived sequences.
Abstract Expressed Sequence Tags (ESTs) are a rich resource for identifying Alternatively Splicing (AS) genes. The ASFinder webserver is designed to identify AS isoforms from EST-derived sequences. Two approaches are implemented in ASFinder. If no genomic sequences are provided, the server performs a local BLASTN to identify AS isoforms from ESTs having both ends aligned but an internal segment unaligned. Otherwise, ASFinder uses SIM4 to map ESTs to the genome, then the overlapping ESTs that are mapped to the same genomic locus and have internal variable exon/intron boundaries are identified as AS isoforms...
Source: International Journal of Bioinformatics Research and Applications - May 23, 2013 Category: Bioinformatics Authors: Min XJ Tags: Int J Bioinform Res Appl Source Type: research

Analysis of non-synonymous single-nucleotide polymorphisms and population variability of PLD2 gene associated with hypertension.
Abstract We have determined the non-synonymous Single-Nucleotide Polymorphisms (nsSNPs) of PLD2 gene and its variations in different populations to understand its role in hypertension. Out of 350 SNPs, six are found to be non-synonymous, of which two showed significant damaging effect and SNP variability with large differences among the Minor Allele Frequency (MAF) observed in various populations. The amino acid change found for rs2286672 is from arginine to cysteine, i.e., from largest amino acid containing guanidino group to a small amino acid containing sulfhydryl group, and for rs3764897, it is from gl...
Source: International Journal of Bioinformatics Research and Applications - May 23, 2013 Category: Bioinformatics Authors: Kundu A, Ramakrishnan P, Rajendran A, Dharwar NV, Anbarasu A Tags: Int J Bioinform Res Appl Source Type: research