Undergraduate Research & Scholarships

Pooja Agarwal

Archaeal Transcription Factor Homology Search With Protein Classifiers

A novel transcription factor, which controls when genes are turned on and off, has been identified in archaea, a domain of species that eukaryotes like humans evolved from. I aim to find homologs, or proteins with a similar function in different species, of the portion of this transcription factor that binds to DNA and has a similar structure to a part of proteins in eukaryotes. To do this, I aim to use embeddings, or simpler representations of proteins with numbers, generated from protein classifiers like ESM and ProtCNN to determine whether a protein contains our DNA binding domain. Understanding this DNA binding domain better can help us understand the evolution of and eukaryotic gene regulation from archaeal machinery.

Message To Sponsor

Your support for the URAP research program has been invaluable in allowing me and other undergrads to grow as researchers. This experience has allowed me to work independently on my own research project, strengthening my commitment to attend graduate school and exposing me to new experiences and challenges that I've been able to learn from. Without your support, none of this would be possible, and I am endlessly grateful for your generosity towards this program!