This fall, 20 ɫ students published a peer-reviewed scientific paper — the culmination of work done during a semester-long laboratory course. During the semester, students analyzed genomes sequenced from marine samples collected in Key West, Florida — doing hands-on original bioinformatics research on par with graduate students and working with bioinformatics tools to explore drug discovery potential.
The course, BIOS 4590, is a research project lab for senior biology majors that provides an opportunity for professors to share their expertise with students in a hands-on environment. In his class, Associate Professor , who holds joint appointments in the and, aimed to introduce undergraduates to advanced bioinformatics tools through applied research using new-to-science raw data.
The resulting paper, “,” which was recently published in ACS Chemical Biology, involves the historically understudied genus of Microbulbifer, a type of bacteria often associated with sponges and corals. These microbial communities are rich sources of natural products, small biological molecules often associated with medicine and drug discovery.
"This class, and the resulting research, is a testament to the transformative power of hands-on learning,” says Susan Lozier, dean of the College of Sciences, Betsy Middleton and John Clark Sutherland Chair, and professor in the School of Earth and Atmospheric Sciences. “The success of this course — and the students’ remarkable achievement — reflects ɫ's commitment to fostering curiosity, collaboration, and scientific rigor and to empowering the next generation of scientists and leaders."
Funded by Agarwal’s 2023 and , the class also received support from leadership in the College of Sciences, School of Biological Sciences, and School Chemistry and Biochemistry. The study’s lead author, graduate student Yifan (Grace) Tang, served as the class teaching assistant, and was funded in part by a .
“The students in this class are working on important, novel work — this cohort worked with real genomic data that had never been sequenced before,” she says. “Typically, researchers might work with one or two genome sequences, but we provided students with 42 — this might be the first time anyone has looked at Microbulbifer at such a wide scope.”
From classroom to publication
To prepare for the class, Tang worked alongside Laboratory Manager , who manages the School of Biological Sciences teaching laboratory spaces, to sequence the Key West bacterial genomes.
“Our work in the Agarwal Lab is in natural product discovery. We focus on finding new pharmaceutical drugs through marine bacteria — but with a bioinformatics spin,” Tang explains. “We wanted to bring this type of experience to undergraduates, so we gave fully sequenced genomes to students and asked them to look for potential properties.”
Throughout the class, students learned different techniques for analyzing bacterial genome sequences and extracting data with various tools — gaining both lab and computational skills through hands-on experiences, live demos, and troubleshooting sessions.
“The highlight was showing students just how much we can learn about a bacterial genus, especially one that hasn’t been studied at this scale before,” Tang shares. “This is a growing field, so there are so many opportunities for students to make meaningful contributions while learning new skills.”
Empowering future students
For many students, it was their first time using these types of tools, but Agarwal says that it’s something they'll likely encounter in both industry and research. He sees this type of research experience as especially helpful for seniors, who are often deciding between entering the workforce or continuing their education.
“Bioinformatics is increasingly important for analyzing big data. Students need the ability to manipulate and understand data using computational tools, and this class plays an important role in familiarizing them with this process,” he shares. “Our goal is to demystify research and give students the confidence and tools for both graduate school and for the workforce after graduation.”
The class will be offered for a third time in Fall 2026. While the exact course of research hasn’t yet been decided, “we always aim for something new that can produce publication-quality research — students don’t repeat past year’s work,” Agarwal says. This recent cohort of students built on the success of 18 undergraduates who took the class in 2023, who . “This course truly underscores ɫ’s commitment to pioneering meaningful undergraduate experiences — no other peer institution I know of is exposing undergraduates to bioinformatics at this level.”
Funding: NSF CAREER and the Dreyfus Foundation
