Biology subjects

Hasan, S.

Publications and source records attributed to Hasan, S..

3 recordsLinked to original sources

bioRxiv2018

Differentiating Genomic SNPs Using Allele Depth and Predicted Genotype

Differentiating between genomic SNPs and other types of single nucleotide variants becomes a key issue in research aimed at studying the importance of these variants of a particular type in biological processes. Here we present an R based method for differentiating between genomic single nucleotide polymorphisms (SNPs) and RNA editing sites. We use data from an earlier study of ours and target only the known dbsnp SNPs that we found in our study. Our method involves calculating the ratio of allele depth for ref and alt alleles and comparing that to the predicted genotype. We use the concept that editing levels should be different for each allele and thus should not reflect the ratio predicted by the genotype. The study yielded an accuracy rate ranging from 86 to over 90 percent at successfully predicted dbsnp entries as SNPs. Albeit this is in the absence of known RNA editing site vcf data to compare as a reference.

genomics↗

bioRxiv2018

Identifying Changes in RNA Editome Unique to Major Depressive Disorder

Major Depressive Disorder (MDD) is one of the most significant psychiatric disorders in the world today. Its incidence is widespread in society and its heavy adverse impact on the quality of life is well documented. Previously genetic studies on MDD had identified a hereditary component of the disease as well as crediting RNA editing with a role in its development. The later due to an overexpression of a heavily edited isoform of the Serotonin 2c receptor. Here we used publicly available RNA sequence data from suicide patients diagnosed with MDD as well as controls for identifying RNA editing sites unique to MDD. After variant calling and several steps of filtering, we identified 142 unique RNA editing sites in the MDD patients. These included intronic, downstream, UTR3 and exonic edits. The latter comprising several amino acid changes in the encoded protein. The genes implicated to be uniquely edited in MDD included the aforementioned and previously implicated Serotonin 2c receptor, others involved in functions that play roles in depression and suicide such as Cannabinoid Receptor 1, Frizzled Class 3 Receptor, Neuroligin 3 and others.

genomics↗

bioRxiv2017

Designing an intuitive web application for drug discovery scientists

Although a scientific web application that is intuitive can help scientists utilize data more easily and advance their research, there is little guidance on how to design such an application in the academic literature. We discuss how we designed an intuitive application for bench scientists working in drug discovery following an approach that can be applied to the design and development of scientific resources in a broad range of disciplines.

bioinformatics↗