How I got started
I earned my undergraduate degree in biotechnology from Vellore Institute of Technology (VIT), India and then changed fields to pursue Bioinformatics in graduate school from San Diego State University. My interest has always been in microbiology, and now I am more focused on microbial community structure and functions. In graduate school, I worked in Dr. Dinsdale's lab, which studies the ecological and evolutionary relationships of microbial communities in marine environments. My research project focused on developing and optimizing bioinformatics workflows for shotgun sequencing metagenomes, a technique that is commonly applied to study microbial communities. After graduating, I started working with NCGAS, where I continue to work on developing workflows to analyze metagenomes or microbiome datasets to make them available to the research community.
My projects at NCGAS include:
- Developing and maintaining a workflow to reconstruct genomes (metagenome-assembled genomes) from metagenomic datasets, which is taught at the NCGAS metagenomics workshop.
- Developing a workflow to assemble and annotate metatranscriptome datasets. Current metatranscriptome pipelines skip the assembly step altogether and use the short-read sequences directly to run differential gene expression analysis. Assembling the short reads to longer sequences (contigs) increases the chances of having a whole gene represented as one long sequence, instead of fragments.
- Mining the Sequence Read Archive (SRA) as part of the Center of Excellence for Women & Technology REU I am working with undergraduate students to develop a workflow to mine the Sequence Read Archive (SRA). The workflow would allow users to look for other datasets that potentially have the gene or genome of interest in the SRA. This workflow will help researchers add more relevant datasets to their studies, which can potentially add statistical significance to their findings. It can also help researchers with limited funding add more datasets to their projects.
I also work on several collaborative projects, including:
- Genome analysis to study gene family evolution in tapeworm species. This work will allow scientists to identify gene families that have evolved to cause infection in mammals. An ongoing collaborative project with the University of Arkansas, Fayetteville, it can potentially sponsor improvements to tapeworm treatment and control.
- Reference-based analysis to identify the differential expressed genes that are playing a role in the maturation process in the Tetrahymena species, a unicellular eukaryote that reproduces sexually. This is an ongoing collaborative project with Albion College in Michigan.
- Metagenome analysis to study the microbial community structure and function in the kelp forest ecosystem, the coral reef ecosystem, and in whale shark data. These projects are in collaboration with Dinsdale lab at San Diego State University.
Favorite part of the job
My favorite task at NCGAS is helping users who, like me, are moving from a biology background to bioinformatics.
I like to hide away and read any chance I get. I also started going to school again to get my PhD, so I spend a good chunk of my time working on assignments and my thesis.