Research Journey

Protein Structure Biology and Drug Design: Started my research career as a fan of protein structure and grew a keen interest in understanding their mechanism of action in molecular level. In my PhD started with viral protein structure [link] and my PhD supervisors taught me how to feel the data flowing inside biological incidents and how to tell a story simply from letters and numbers. Started with the structures of neuraminidase protein of Influenza virus and later my flow of my interest helped me explore the proteins from other viruses, leishmania, etc. and finally to mammals like mouse and human. I had an excellent training during my postdoctoral research at Saha Institute of Nuclear Physics on how to extract interesting biological information from protein crystallography data. Attached to the same string, in-silico design of small molecule based drug I applied first time in Leishmania genome through comparative genomics strategy [link]. Later applied these structural biology knowledge to publish papers in the domain of peptide drug candidate, molecular dynamics simulation [link].

Genomics & Sequence Motifs: After spending a long research path in structural bioinformatics, from 2015, my curiosity started to incline towards the field of genomics and a deeper molecular origin of protein structure. Since then I explored genomics in different domains of biology: Viral genomics, mouse and human genomics, immunogenomics and other levels in molecular genomics. Particularly secondary structural motifs in DNA and their regulatory roles is a specific area of interest for me [link]. Tools and skills of Next generation sequence analyses are the domains I always projected in my career skill and feel comfortable with. IBS, POSTECH, South Korea with immunology, I had a chance to explore the gut microbiome and their interaction with immune cells [link]. Prediction of epitopes & immunogenic peptides is also a great area of interest to me. Currently as a Marie Curie Career-FIT fellow at University College Dublin I am working on food proteolysis and biologically active peptides obtained from food proteins like proteins from Milk.

Viral genomics and Bioinformatics: Starting with genomics and structural biology of neuraminidase protein of influenza virus, I have explored different viral models to investigate antiviral strategies. My first attempt was to predict conserved epitopic regions of neuraminidase protein, which can be used as a vaccine [link]. Later applied the same algorithm on rotaviral protein VP7 [link] and proposed vaccine candidates. With time, after growing interest in genomics and structure biology, I became involved with the DNA secondary structure mediated regulatory genomics of cytomegalovirus [link].

Algorithms and Bioinformatics Pipelines: For running bioinformatics analysis I have created several pipelines in domains of Bioinformatics where I worked and published paper. Initially, I started with 20D-algorithm [link] based number crunching pipelines and applied to the detection of viral vaccine/epitopic candidates. Later, when I was working with drug design pipelines, had a chance to develop the comparative-genomics to small molecule drug design pipeline which one was really exciting [link]. Later I extended the drug design pipeline to the world of molecular dynamics simulations with both small molecules and peptides [link]. When I started to integrate myself towards genomics several areas I have explored like pipelines related to genome to: secondary structural motif prediction, microbiome analysis, RNAseq, ChIP-seq, ATAC-seq, mutation analysis and many other in the stream. Among algorithms, I worked on two algorithms related to 20D euclidean space: one is for predicting peptide variability along protein sequence and the second one is to predict phylogenetic relationship within a bunch of proteins [link].

Online resources

From the knowledge and experiences that I earned from my research career, I made and attempt here to construct (& still constructing) a repository of educational resources for learning. This will be including a comprehensive list of tools, software and learning materials covering different domains of Bioinformatics and Computational Biology like: Drug Design tools and protocols, Software & tools molecular structure biology, databases and browsers in Genomics, stable & useful NGS pipelines and tools, repositories for viral genome information, resource for personalized food and Nutrition, Resource for Mass Spectrometry Data analysis & many more. This repository will be curated & updated in timely manner. Please go to the link to visit the resource page.