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A Foundation to Tackle Anything

A tool created by a doctor for his master's in health informatics Capstone Project finds applications across clinical research.

Written by Philip Baker
A scientist in a lab studies lab results.

A typical challenge for clinical researchers today arises when their research generates potentially useful data that their lack of clinical informatics skills makes impossible to analyze.

A typical challenge for clinical researchers today arises when their research generates potentially useful data that their lack of clinical informatics skills makes impossible to analyze.

Matthew Stutz, MD, currently an attending physician at Cook County Health, worked with UChicago’s Duchossois Family Institute (DFI) for his Capstone project as part of the Master of Science in Biomedical Informatics (MScBMI) program to create a solution to this problem. 

With a subspecialty in pulmonary critical care, Stutz arrived at the University of Chicago as a critical care research fellow eager to do clinically focused research while deepening his knowledge of biomedical informatics. 

“The biomedical informatics degree was the perfect way for me to expand my knowledge and understanding of health informatics,” Stutz says. “My goal was to conduct meaningful research that would ideally lead to real improvements in patient care and patient care delivery, and that’s what the diverse curriculum of the MScBMI program made possible. 

“The biomedical informatics program allows you to craft your path in a way that fits your needs, and then you take what you learn to your next step and continue to grow.”

Matthew Stutz, Biomedical informatics student

The biomedical informatics program allows you to craft your path in a way that fits your needs, and then you take what you learn to your next step and continue to grow.

Matthew Stutz, MD, MScBMI’22

Published research

As part of the Pulmonary Critical Care team, Stutz worked with the DFI for his Capstone Project to create a data acquisition tool able to merge clinical and microbiologic data to generate data sets for investigators. DFI was integral to the success of his project, which used the Institute’s technical infrastructure and expertise to study the metabolic and chemical composition of microbial samples from the gut.

“We created a tool that gives researchers who lack skills in clinical informatics the ability to generate data tables that elucidate both the clinical and microbiologic features of their patients,” he says. “Bringing highly complex databases of genomic data together with clinical research through coding and data science was what I came to the biomedical informatics degree program to learn.”

The tool that emerged from his project has set numerous clinical research projects in motion relating to liver disease, liver and heart transplants, critically ill patients, and more. One such project, on which Stutz was a co-author, emerged from the Pulmonary and Critical Care team as part of his fellowship. Its findings were published in Nature Communications Journal in November 2022.

The study, which suggested a link between microbiota health and patient outcomes, sought to understand why patients who enter the ICU with similar symptoms follow different clinical courses. Using data taken from the fecal samples of 71 patients with COVID-19 admitted to the medical ICU at UChicago Medicine, the work showed that the composition of gut microbiota and the metabolites they produce could predict the trajectory of respiratory function and death in patients with severe COVID-19. 

“The biomedical informatics coursework gave me the skillset to work with large data sets and perform the analysis needed to complete the work that went into that publication,” Stutz says. “Even if part of my journey at the University of Chicago involved realizing that I wanted to move into doing more clinical work than the research-oriented work I arrived to do, the BMI program’s curriculum served me perfectly since the classes in clinical decision support and healthcare delivery science made that a seamless transition. 

“Now I can use big data sets and do meaningful research, but I can also step into the clinical informatics space and become more of a clinician informaticist. The program gives you the foundation to tackle anything.”


The Graham School will not be admitting new students to the Master of Science in Biomedical Informatics (MScBMI) in Autumn 2024. The University will take this opportunity to consider future programming in the Biological Sciences Division (BSD). Please see the BSD website for more information about their offerings.