Training Grant is Equipping Future Leaders in Biomedical Data Sciences

Greg Medlock shares his experience

By Charles Feigenoff charliefeigenoff@gmail.com

It’s not necessarily intuitive, but successful biomedical data science is as much about people skills as it is about the latest algorithm or statistical technique. “As a data scientist, you need to be able to coordinate with all members of a research team,” said Gregory Medlock, a 2019 graduate of the University of Virginia Department of Biomedical Engineering’s Ph.D. program and an expert in computational modeling and machine learning. “Being an effective collaborator helps you use your skills for greater impact.”

Medlock honed his collaborative abilities during his two years as a participant in a National Institutes of Health training grant led by his doctoral thesis advisor, Jason Papin, professor of biomedical engineering. Papin’s ability to enlist some of the most eminent faculty at the University as co-directors on the training grant is an indication of the importance of this initiative. They are Donald Brown, professor in the UVA Engineering School’s Department of Engineering Systems and Environment and the former director of the UVA Data Science Institute; Dr. Thomas Loughran, director of the UVA Cancer Center; and Kevin Skadron, Harry Douglas Forsyth Professor and chair of UVA Engineering’s Department of Computer Science.

Greg Medlock with Jason Papin — Greg Medlock (right) with his PhD mentor Dr. Jason Papin.

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Finding Common Ground Between Experimentation and Data Science

A critical element in the grant is cross-disciplinary co-mentorship. “We want students in experimental labs to feel comfortable working in labs that do heavy computational work and vice versa,” Papin said.

As a graduate student in Papin’s lab, Medlock had been developing data-driven methods and computational modeling approaches to better understand metabolism in the microbiome. He chose Dr. William Petri, a specialist in infectious medicine and international health, as his co-mentor. Petri is working with researchers in Bangladesh to better understand conditions that lead to environmental enteric dysfunction, which can limit patients’ ability to absorb nutrition from the food they eat. In children, it can produce stunting. Medlock applied his expertise in data science to determine whether there was a signature in the microbiome of children who developed diarrhea when exposed to a particular pathogen.

“I am a very hands-on learner,” Medlock said. “My experience in the Petri Lab made me more conscious of the challenges associated with field research.”

Medlock is now applying the knowledge he gained as a postdoctoral fellow in a lab led by Dr. Sean Moore, a pediatric gastroenterologist at UVA. Moore is working with collaborators in Pakistan to develop treatments for environmental enteric dysfunction, and Medlock is using a variety of data sciences techniques to try to better understand host-microbe and microbe-to-microbe interactions.

Applying Lessons Learned

In addition to the co-mentoring experience, training-grant students participate in a variety of activities that build collaborative skills and technical expertise. Each year, all training grant recipients come together for an intense two-day hackathon that focuses on a big data challenge. One year, the group developed a method to predict instances of sepsis using vital signs and other measurements taken from a large patient database. Another year, the students combined single-cell RNA sequencing data with other cell profiling techniques to predict cell types. Students also organize a monthly journal club and arrange guest presentations on such topics as clinical data management, data visualization and biomedical data sciences in industry.

Medlock is drawing on these collaborative experiences as he begins working with new colleagues. Within a month of joining Moore’s Lab, he went to Dubai to meet with the clinical team from Pakistan. Among his first tasks was to organize a mini-hackathon for the Dubai meeting. “It was a great way for me to introduce myself to the group,” Medlock said. “The training grant has enabled me to be much more thoughtful about how I can become an accepted member of an existing team.”