Forthcoming and Online First Articles

International Journal of Bioinformatics Research and Applications

International Journal of Bioinformatics Research and Applications (IJBRA)

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International Journal of Bioinformatics Research and Applications (5 papers in press)

Regular Issues

  • Bioinformatic analysis of post-transcriptional regulation of Endoplasmic reticulum stress genes by alternative polyadenylation and microRNA.   Order a copy of this article
    by Neha Singh, Srishti Shriya, Farhat Afza, Padmini Bisoyi, Arun K. Kashyap, Kundan K. Chaubey, Buddhi Prakash Jain 
    Abstract: Various post-transcriptional regulation processes modulate the Endoplasmic reticulum stress response. Alternative polyadenylation is one post-transcriptional regulatory mechanism which generates transcript with alternate 3'end. The transcript with different 3'UTR differentially modulated by various cis-regulator elements and miRNAs. Present work aims to characterize CPE in 16 ER stress associated genes. Canonical AAUAAA PAS is present in 13 out of total 24 sites (53%). Alternative polyadenylation was found in five genes (HSPA5, HSPA9, ATF6, SHQ1, and VLDLR) in NCBI and EST database. Further insilico analysis was done using computational tools as well as experimentally validated databases to find out miRNAs which target the ER stress associated genes. The information about the alternative polyadenylation and the microRNA sites in the ER stress associated genes might be useful for further study of regulation of ER stress response and its associated molecular and pathological processes.
    Keywords: Alternative polyadenylation; core polyadenylation element; miRNA; Endoplasmic reticulum stress; polyadenylation signal.

  • A Comprehensive In-Silico characterization of Gasdermin superfamily genes regulating pyroptosis linked diseases   Order a copy of this article
    by Suman Rani, Praveen P. Balgir, Nandini , Bhagwant Singh, Husandeep Kaur 
    Abstract: Pyroptosis is a lytic form of inflammatory cell death. Non-Synonymous Single Nucleotide Polymorphism (nsSNPs) have been accepted as biomarkers of disease susceptibility. In the present study nsSNPs of Gasdermin Super family Genes, presently proven to be involved in pyroptosis and consequently in etiology of many diseases, were screened for their functional and structural effects. 3 nsSNPs of GSDMA, 2 each of GSDMB, GSDMC and GSDMD, 6 nsSNPs of GSDME and 2 nsSNPs of DFNB59 gene were predicted to be deleterious; showing decrease in structural stability by in silico tools. Further in silico analysis of post translationally modified Phosphorylation sites of members of gene family were checked for presence of SNPs which may influence the PTM and consequently the protein function. Current study has comprehensively tried to analyze all Gasdermin family gene variants with different in-silico algorithms combined with already available literature of wet lab experiments, to propose a list of nsSNPs that are the potential targets for future functional genetic analysis.
    Keywords: nsSNPs; SIFT; PolyPhen; PROVEAN; MuPro; I-Mutant; SNP&Go;I-TASSER; STRUM; Accelrys Discovery Studio 4.0; Gasdermin family.

  • Diabetic Retinopathy Detection Method Using Artificial Neural Network   Order a copy of this article
    by Israa Odeh, Mouhammd Al-kasassbeh, Mohammad Almseidin 
    Abstract: Diabetic retinopathy (DR) is one of the leading causes of vision loss in diabetics worldwide. DR is a microvascular disease that affects the eye's retina, leading to vascular blockage and thus disrupting the primary source of nourishment for the retinal tissue. This paper merged a considerable range of known classification algorithms into a sophisticated diagnostic model and a new multilayer perceptron (MLP)-based classifier. The latter achieved the highest accuracy rates among all other classifiers, including the previously introduced ensemble model. 4 sub-datasets were generated by WrapperSubsetEval. and InfoGainEval. Feature selection algorithms achieved 75.8% and 70.7% accuracy rates on the best performing subdataset (InfoGainEval. top 5) by the ensemble model and the new MLP-based classifier. The results express the splendid performance of the partial dataset with the MLP artificial neural network, which contributes significantly to a less complex classification process than the original full Messidor dataset.
    Keywords: Diabetic Retinopathy; Ensemble learning; Machine learning; Neural Networks; MLP.
    DOI: 10.1504/IJBRA.2022.10050964
  • Identification of Putative Therapeutic Candidates of Plasmodium falciparum by In-Silico Comparative Genomics Analysis   Order a copy of this article
    by Arun Kumar Kashyap, Sujit Shah, Ajay Kumar, Buddhi Prakash Jain, Nikita Kashyap 
    Abstract: Malaria is an endemic disease causing millions of death worldwide People from many countries are at the risk of being infected from malaria The treatments available today are limited and there is a need of better therapeutics The methods for vaccine candidate identification and drug candidates are time consuming and laborious However the recent advancement and development in genomics provide efficient alternative technique for identification of Drug and vaccine candidates in combination with computational biology In present study comparative genomic approach was used for identification of the novel therapeutic candidate including vaccine candidate and drug candidates for Plasmodium falciparum on the basis of essentiality of protein for the organism By homology from known essential genes of different eukaryotic organism 579 essential genes are identified in Plasmodium falciparum By metabolic pathway analysis the identified proteins were classified in different metabolic pathway proteins Further the different parameters of the essentiality were checked
    Keywords: Plasmodium; Comparative Genomics; Therepeutic candidate; Vaccine candidate; In silico.
    DOI: 10.1504/IJBRA.2022.10051063
    by Luiz Philipi Calegari, Diego Fettermann 
    Abstract: Despite the relevant amount of studies in the literature about e-health technologies, it is necessary organized the information about the theme in a clear structure within the technological context. The present study aims to gather information about applications of e-health technologies from a systematic literature review. The search obtaining 130 entries considered in this research. The studies were grouped in relation to the technologies and to the health area of the technological application, according to International Statistical Classification of Diseases and Related health problems. Among the technologies present in the literature, most (62) did not focus on a specific technology, covering more than one e-health technology. In a more focused way, there are studies regarding m-health, telemedicine and wearables technologies. About technological application health area, Endocrine, nutritional and metabolic diseases area presented most of the studies. The present study gathers information about the e-health technology, providing guidance for future research.
    Keywords: m-health; information technology; internet of things; telemedicine; bioinformatics; healthcare.
    DOI: 10.1504/IJBRA.2022.10051065