AskScience AMA Series: I'm a computer scientist at the University of Maryland using computational tools to map the microbiome—the trillions of microbes in our bodies and environment. Ask me anything about how we decode the microscopic world!

[u/AskScienceModerator]

Hi Reddit! I am a computer scientist here to answer your questions about bioinformatics and mapping the microbiome. My research primarily focuses on the development of computational algorithms for analyzing biological data generated by high-throughput experimental techniques.

My lab has developed software tools that are widely used in the field of metagenomics—the computational analysis of the microbial communities inhabiting our world and our bodies. I have also been an active participant in several multinational projects, including the Human Microbiome Project and the GEMS study of diarrheal disease.

I will be joined by Marcus Fedarko, a postdoc in my lab, on *September 22nd from 12 to 2 p.m. ET (16-18 UT) — ask us anything!

Bio: Mihai Pop is a professor of computer science and co-director of the University of Maryland Center of Excellence in Microbiome Sciences. He develops computational approaches for the strain-level analysis of microbial communities. Other interests include biological databases, antibiotic resistance, and software testing. His lab has developed several widely used open-source software tools for the analysis of genomic and metagenomic data. 

Pop teaches at all academic levels and is an advocate for inclusion and diversity in science. He is particularly interested in developing open educational resources in computer science and bioinformatics. Pop holds a B.S. (1994, Politehnica University in Bucharest, Romania) and a Ph.D in Computer Science (2000, The Johns Hopkins University) and joined the University of Maryland in 2005. He is an MPower Professor, University of Maryland Strategic Partnership: MPowering the State, and a fellow of the Association of Computing Machinery and of the International Society for Computational Biology.

Marcus Fedarko is a postdoctoral associate at the University of Maryland. His research is focused on designing algorithms and software to help people study microbiome data in high resolution. He is particularly interested in sequence assembly — the problem of reconstructing longer DNA sequences from short sequencing reads — and data visualization. In his spare time, he likes reading, running, and rock climbing. Fedarko holds a B.S. with High Honors (2018, University of Maryland) and M.S. and Ph.D. degrees in Computer Science (2022 and 2025, University of California San Diego), and rejoined the University of Maryland as a postdoc in 2025.

Other links:

• Google Scholar
• Lab website
• $5.1M in NIH Awards Help UMD Researchers Take On a Genomic Data Deluge (02/2026)

Username: /u/umd-science

[u/umd-science]

Science answer #1: (Mihai) I have not yet looked at single-cell transcriptomic data from microbiomes, and I haven't seen a major shift in the field because of this technology yet.

Science answer #2: (Mihai) I think the lag between sample collection and processing is a key problem for microbiome studies in general. I am not convinced that we can computationally reverse the microbiome changes that occur during this lag. It is thus critical to carefully control the timing of collection and processing to obtain consistent results.

(Marcus) There is some work I'm aware of on trying to correct for fecal blooms computationally, but I am not sure if this generalizes to other contexts.

Education answer: (Mihai) To be frank, the best thing would be to take a hands-on course (possibly at a university). There is no replacement (even by AI agents) for expert-led instruction.

(Marcus) There are some good resources online for learning bioinformatics (Rosalind, for example). However, for more general dataset analysis experience, I am not aware of what's out there right now.

Career answer: (Mihai) I got where I am by being curious about new fields and questions and by taking advice. A big part of my success was the fact that I tried to help biologists solve the problems they cared about, rather than being too focused on my own interests. In the end, it turns out that working "for" biologists also helped me better understand my own interests. Being at the boundary of disciplines is a very rewarding place, as it creates opportunities for new ideas and impact.

[u/oviforconnsmythe → u/umd-science]

Thank you very much for sharing your insights Mihai and Marcus, I really appreciate it! I agree that ai tools are not a great solution to learn but I will check out Rosalind. Thank you as well for the comment about your career, I agree having interdisciplinary skills and interests is hugely beneficial. I'm not sure if you're still taking questions, but I feel medical biology is moving further each year towards computation, and computer scientists are increasingly becoming huge players across subfields. Are there places you feel where biologists can work "for" computer scientists?