Josh Noonan ’22

University of North Carolina at Charlotte, Fodor Lab, Charlotte, NC

Over the summer, I had the pleasure of working in Dr. Anthony Fodor’s bioinformatics lab at the University of North Carolina at Charlotte. Bioinformatics lies at the intersection of computer science, statistics, and biology, and focuses on the enormous amount of data created by the genome. Dr. Fodor’s lab focuses on applying bioinformatics to the human gut microbiota, and the research produced in his lab has been integral in improving our knowledge of the gut microbiome. In the lab, we use traditional wet lab techniques to sequence DNA through 16S ribosomal RNA sequencing and whole genome sequencing. These sequencing techniques generate extremely long strings of A, T, C, and G DNA base pairs, and we then use open-source bioinformatics pipelines to identify microbiota present in the sample.

Josh Noonan
Synthesizing my research into a comprehensive document with figures.

My research primarily focused on comparing differences in the outcomes of various popular bioinformatics pipelines. Each pipeline has a unique way of classifying microbiota present from genetic data, and thus using a particular pipeline can have a specific effect on your analysis and interpretation of taxa present. My work began by considering five different classifiers, but I ultimately narrowed my scope down to an in-depth analysis of two metagenomic classifiers: Kraken and Metaphlan2. I found some stark differences in the performance of the two classifiers, and my work helped to reinforce the argument that a graduate student in the lab was attempting to make in his dissertation.

I entered this summer knowing very little about bioinformatics. I am a mathematics major, and while I have taken classes in computer science and statistics, I had not seen any biology material since I was in high school. However, Dr. Fodor and the members of his lab were eager to help me learn more about bioinformatics, and welcomed me into the group as if I was a fellow postdoc or Ph.D. student at UNCC.

While my research was unfortunately remote due to the Covid-19 pandemic, I still had a great experience and could not be happier with the way that it ended up. I learned a lot about a field new to me and got to hone my skills in R and Python. I entered the summer thinking that I wanted to pursue graduate education in mathematics, 
but my exposure in Dr. Fodor’s lab sparked an interest in biology and the human body systems. I realized that while there was some cool math happening that made all the software and pipelines work, I was most interested in the mechanisms of the gut that we were trying to capture. I am now planning on pursuing a career in medicine, and I plan to incorporate research into my future.

A huge thank you to both the ’68 Center 
for Career Exploration for organizing 
this amazing ability to pursue an unpaid internship, and the Class of 1966 for providing this opportunity. Without the generosity of the best alumni in the world, this summer would not have been possible for me!