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.

BioInt: an integrative biological object-oriented application framework and interpreter.
Abstract BioInt, a biological programming application framework and interpreter, is an attempt to equip the researchers with seamless integration, efficient extraction and effortless analysis of the data from various biological databases and algorithms. Based on the type of biological data, algorithms and related functionalities, a biology-specific framework was developed which has nine modules. The modules are a compilation of numerous reusable BioADTs. This software ecosystem containing more than 450 biological objects underneath the interpreter makes it flexible, integrative and comprehensive. Similar t...
Source: International Journal of Bioinformatics Research and Applications - November 13, 2015 Category: Bioinformatics Authors: Desai S, Burra P Tags: Int J Bioinform Res Appl Source Type: research

Impact of pixel intensity correlations on statistical inferences of expression levels in cDNA microarray experiments.
The objective of the present study is to estimate the uncertainty associated with the final intensity ratio at each spot in cDNA microarray chips and also to explore the role of pixel intensity correlations in statistical inferences of gene expression levels. We estimate uncertainty at each spot using the theory of error propagation under two different situations: (1) when there is no correlation between pixel intensities and (2) when the pixel intensities are positively correlated. The inverses of these estimated uncertainties are used as weights in downstream analysis to test the significance of each gene. The analysis w...
Source: International Journal of Bioinformatics Research and Applications - November 13, 2015 Category: Bioinformatics Authors: Binu VS, Nair NS, Manjunatha PK, Kalesh MK Tags: Int J Bioinform Res Appl Source Type: research

Analysing extremely small sized ratio datasets.
Abstract The naïve use of expression ratios in high-throughput biological studies can greatly limit analytical outcome especially when sample size is small. In the worst-case scenario, with only one reference and one test state each (often due to the severe lack of study material); such limitations make it difficult to perform statistically meaningful analysis. Workarounds include the single sample Z-test or through network inference. Here, we describe a complementary plot-based approach for analysing such extremely small sized ratio (ESSR) data - a generalisation of the Bland-Altman plot, which we shall ...
Source: International Journal of Bioinformatics Research and Applications - November 13, 2015 Category: Bioinformatics Authors: Ricchiuto P, Sng JC, Goh WW Tags: Int J Bioinform Res Appl Source Type: research

A cohesive analysis of DNA/RNA sequences via entropy, energetics and spectral-domain methods to assess genomic features across single viral diversity.
Abstract In virology context, a particular virus may prevail in different forms of serotypes (as in the case of dengue 1-4 viral strains) with common and distinct genomic features. Finding such genomic details of a serogroup is useful in knowing related information for unique vaccine designs compatible for immunity across the viral diversity. For robust comparison of genomes of serovars of a virus in order to decide on their common and differential genomic details, proposed here is a set of sequence analyses exercised side-by-side via entropy, energetic and spectral-domain methods. Results obtained thereof...
Source: International Journal of Bioinformatics Research and Applications - November 13, 2015 Category: Bioinformatics Authors: Neelakanta PS, Chatterjee S, Pavlovic M Tags: Int J Bioinform Res Appl Source Type: research

Classification of PCR-SSCP bands in T2DM by probabilistic neural network: a reliable tool.
This study proves to be very reliable and gives accurate and fast detection for mutation analysis in diabetes. This method could be extended for analysis in other human diseases. PMID: 26561316 [PubMed - in process] (Source: International Journal of Bioinformatics Research and Applications)
Source: International Journal of Bioinformatics Research and Applications - November 13, 2015 Category: Bioinformatics Authors: Badarinath AR, Das AR, Mazumder S, Banerjee R, Chakraborty P, Saraswathy R Tags: Int J Bioinform Res Appl Source Type: research

An interactomic approach for identification of putative drug targets in Listeria monocytogenes.
Abstract A wide variety of human population is infected with Listeria monocytogenes, which causes listeriosis, a deadly disease with mortality rate of about 30%. The major hindrance to cure listeriosis is the unavailability of specific or selectable drug targets. At present, antibiotics used to cure the disease are not specific and insufficient to manage the disease efficiently. Therefore, in order to search specific drugs, here, we used interactome analysis to search specific drug targets which may provide novel templates for drug designing having better efficacy without any potential adverse effects. The...
Source: International Journal of Bioinformatics Research and Applications - November 13, 2015 Category: Bioinformatics Authors: Chordia N, Sharma NK, Kumar A Tags: Int J Bioinform Res Appl Source Type: research

Receptor-based 3D-QSAR approach to find selectivity features of flexible similar binding sites: case study on MMP-12/MMP-13.
Abstract Design of selective matrix metalloproteinases (MMPs) inhibitors is still a challenging task because of binding pocket similarities and flexibility among MMPs family. To overcome this issue we try to generate a (three-dimensional quantitative structure activity relationship) 3D-QSAR model that might reflect, at least in part, the differential properties of MMP-12 and MMP-13 active sites compared to each other. The different alignment rules were applied for CoMFA/CoMSIA model development. In an approach the best docked poses were followed by alignment based on their zinc binding group. As it was sug...
Source: International Journal of Bioinformatics Research and Applications - November 13, 2015 Category: Bioinformatics Authors: Hadizadeh F, Shamsara J Tags: Int J Bioinform Res Appl Source Type: research

Opposite nucleotide usage biases in different parts of the Corynebacterium diphtheriae spaC gene.
Abstract In this work we described a bacterial open reading frame with two different directions of nucleotide usage biases in its two parts. The level of GC-content in third codon positions (3GC) is equal to 40.17 ± 0.22% during the most of the length of Corynebacterium diphtheriae spaC gene. However, in the 3'-end of the same gene (from codon #1600 to codon #1873) 3GC level is equal to 64.61 ± 0.91%. Using original methodology ('VVTAK Sliding window' and 'VVTAK VarInvar') we approved that there is an ongoing mutational AT-pressure during the most of the length of spaC gene (up to codon #1599), and there...
Source: International Journal of Bioinformatics Research and Applications - November 13, 2015 Category: Bioinformatics Authors: Khrustalev VV, Barkovsky EV, Kolodkina VL, Khrustaleva TA Tags: Int J Bioinform Res Appl Source Type: research

Is HNF4A a candidate to study zinc finger protein slug?
Abstract Protein-Protein Interactions (PPI) play a crucial role in deciphering function besides identifying candidates. While the experimental analysis is often time consuming involving number of experiments like pulldown assays, they are not necessarily limiting the ability to detect novel protein interactors. In this work, we discuss the role and putative interactors of SNAI2, a slug protein which is involved in the development of cancer progression. The protein interactions have been deciphered by domain pair exclusion method which gives confidence to already precluded interaction pairs. Additionally, c...
Source: International Journal of Bioinformatics Research and Applications - November 13, 2015 Category: Bioinformatics Authors: Suravajhala P, Singh TR Tags: Int J Bioinform Res Appl Source Type: research

Proteins involved in more domain types tend to be more essential.
In this study, we investigate what kind of proteins is inclined to be essential from a new perspective. The investigation implies that protein essentiality is correlated with protein domains, which are functional, structural and evolutionary units of proteins. Proteins with a larger Number of Domain Types (NDT) tend to be essential. The analyses on 22 species show that essential proteins identified by NDT are much more than those identified by ten random identifications. The consideration of the structural feature makes us less dependent on network data and thus enables us to investigate protein essentiality of more specie...
Source: International Journal of Bioinformatics Research and Applications - March 21, 2015 Category: Bioinformatics Authors: Chen L, Cheng Y, Li M, Wang J Tags: Int J Bioinform Res Appl Source Type: research

Classification methods for the analysis of LH-PCR data associated with inflammatory bowel disease patients.
In this study we analyse the microbial communities within the human gut and their role in Inflammatory Bowel Disease (IBD). The bacterial communities were interrogated using Length Heterogeneity PCR (LH-PCR) fingerprinting of mucosal and luminal associated microbial communities for a class of healthy and diseases patients. PMID: 25786791 [PubMed - in process] (Source: International Journal of Bioinformatics Research and Applications)
Source: International Journal of Bioinformatics Research and Applications - March 21, 2015 Category: Bioinformatics Authors: Wisittipanit N, Rangwala H, Sikaroodi M, Keshavarzian A, Mutlu EA, Gillevet P Tags: Int J Bioinform Res Appl Source Type: research

Looking into the genome of Thermosynechococcus elongatus (thermophilic cyanobacteria) with codon selection and usage perspective.
Abstract Genome analysis of thermophilic cyanobacterium, Thermosynechococcus elongatus BP-1 revealed factors ruling choices of codons in this organism. Multiple parameters like Nc, GC3s, RSCU, Codon Adaptation Index (CAI), optimal and rare codons, codon-pair context and amino acid usage were analysed and compositional constraint was identified as major factor. Wide range of Nc values for the same GC3 content suggested the role of translational selection. Mutational bias is suggested at synonymous position. Among optimal codons for translation, most were GC-ending. Seven codons (AGA, AGG, AUA, UAA, UAG, UCA...
Source: International Journal of Bioinformatics Research and Applications - March 21, 2015 Category: Bioinformatics Authors: Prabha R, Singh DP, Rai A Tags: Int J Bioinform Res Appl Source Type: research

Preclinical evaluation and molecular docking of 2,5-di-tert-butyl-1,4-benzoquinone (DTBBQ) from Streptomyces sp. VITVSK1 as a potent antibacterial agent.
Abstract The incidence of bacterial disease has increased tremendously in the last decade, because of the emergence of drug resistance strains within the bacterial pathogens. The present study was to investigate the antibacterial compound 2,5-di-tert-butyl-1,4-benzoquinone (DTBBQ) isolated from marine Streptomyces sp. VITVSK1 as a potent antibacterial agent. The antibacterial potential of DTBBQ was investigated against RNA Polymerase (PDB ID-1I6V) by in silico molecular docking tools. Results of our study showed the high affinity interaction between DTBBQ and RNA polymerase and also confirmed the drug like...
Source: International Journal of Bioinformatics Research and Applications - March 21, 2015 Category: Bioinformatics Authors: Jannu VG, Sanjenbam P, Kannabiran K Tags: Int J Bioinform Res Appl Source Type: research

Artificial neural networks for dihedral angles prediction in enzyme loops: a novel approach.
Abstract Structure prediction of proteins is considered a limiting step and determining factor in drug development and in the introduction of new therapies. Since the 3D structures of proteins determine their functionalities, prediction of dihedral angles remains an open and important problem in bioinformatics, as well as a major step in discovering tertiary structures. This work presents a method that predicts values of the dihedral angles φ and ψ for enzyme loops based on data derived from amino acid sequences. The prediction of dihedral angles is implemented through a neural network based mining mecha...
Source: International Journal of Bioinformatics Research and Applications - March 21, 2015 Category: Bioinformatics Authors: Al-Gharabli SI, Al-Agtash S, Rawashdeh NA, Barqawi KR Tags: Int J Bioinform Res Appl Source Type: research

HDVDB: a data warehouse for hepatitis delta virus.
Abstract Hepatitis Delta Virus (HDV) is an RNA virus and causes delta hepatitis in humans. Although a lot of data is available for HDV, but retrieval of information is a complicated task. Current web database 'HDVDB' provides a comprehensive web-resource for HDV. The database is basically concerned with basic information about HDV and disease caused by this virus, genome structure, pathogenesis, epidemiology, symptoms and prevention, etc. Database also supplies sequence data and bibliographic information about HDV. A tool 'siHDV Predict' to design the effective siRNA molecule to control the activity of HDV...
Source: International Journal of Bioinformatics Research and Applications - March 21, 2015 Category: Bioinformatics Authors: Singh S, Gupta SK, Nischal A, Pant KK, Seth PK Tags: Int J Bioinform Res Appl Source Type: research