Harun Mustafa

Harun Mustafa

Assistant research scientist in the Salzberg Lab at the Center for Computational Biology

About me

I am an assistant research scientist in the Salzberg Lab at the Center for Computational Biology at Johns Hopkins University. My main research interests are in computational biology, genomics, and metagenomics.

I work primarily in the development and application of algorithms for large-scale sequence comparisons and analysis. This includes scalable methods for indexing and efficient algorithms for querying massive biological sequence databases, with applications in taxonomic profiling and antimicrobial resistance tracing. I also develop novel sequence alignment algorithms that better model complex genomic rearrangements, and allow for missing sequence imputation.

Brief History

I completed my Honours B.Sc. with High Distinction at the University of Toronto, dual majoring in computational biology and mathematics. Under the supervision of Michael Brudno, I developed methods for assembling the sequences of novel Alu insertions detected in second-generation sequencing data.

I completed my M.Sc. in computational biology at the ETH Zürich, where I developed a classification method for determining internal sites in proteins permissive to tag insertion under the joint supervision of Sven Panke and Jörg Stelling.

I joined the Biomedical Informatics Group in 2017 as a Ph.D. student, working with Gunnar Rätsch and André Kahles, and completed my Ph.D. at the end of 2022. I was subsequently a postdoctoral fellow in the same group from 2023 until 2025.

Since October 2025, I have been working in the Salzberg Lab at Johns Hopkins University.

Selected Publications

* equal contribution

See the publications page for the full list.