Milot Mirdita
Assistant Professor at Sungkyunkwan University
South Korea
Summary
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Rockstar🎓
Top SchoolMilot Mirdita is an assistant professor and bioinformatician with 14 years of experience at the intersection of protein science and software engineering, currently based in South Korea. He combines academic research (PhD-level bioinformatics) with deep hands-on engineering from roles at Max Planck and Sungkyunkwan, building performant tools for protein structure and homology analysis. A prolific open-source contributor, he has improved major projects like ColabFold (making protein folding more accessible), Foldseek and HH-suite, and helped port SIMD-optimized code across architectures to boost performance. His background spans full-stack, backend, and build-system work—evident in Bioconda packaging and cross-platform fixes—so he fluently bridges research algorithms and production-ready tooling. Notably, he often focuses on practical usability and reproducibility, adding features like Google Drive export and automatic BibTeX citation generation to streamline scientific workflows.
14 years of coding experience
15 years of employment as a software developer
Master of Science Computer Science, Master of Science Computer Science at Ludwig-Maximilians-Universität MünchenBachelor of Science Bioinformatics, Bachelor of Science Bioinformatics at Technical University of MunichDr. rer. nat. Bioinformatics, Dr. rer. nat. Bioinformatics at The University of Göttingen
German, English, Albanian, Latin
Stackoverflow
701reputation
25kreached
7answers
5questions
Github Skills (46)
algorithm10
code-optimization10
algorithms10
c-language10
package-management10
python10
avx10
conda10
bash10
cmake10
google-colab10
sse10
optimisation10
neon10
bioinformatics10
Programming languages (13)
Github contributions (5)
soedinglab/hh-suite
Jun 2014 - May 2022
Remote protein homology detection suite.
Role in this project:
Back-end Developer
Back-end DeveloperContributions:1 release, 228 commits, 17 PRs in 8 years
Contributions summary:Milot's contributions primarily focused on improving the codebase for the HH-suite software suite, specifically optimizing performance through SIMD instructions and fixing bugs. They addressed issues in core files related to the Viterbi algorithm, prefiltering, and alignment procedures. Furthermore, the user fixed a typo and addressed an issue affecting compressed PDB databases within the scripts, ensuring that the software suite correctly handled various input data formats.
simdcppprofile-searchviterbialignment
steineggerlab/foldseek
Dec 2021 - Dec 2022
Foldseek enables fast and sensitive comparisons of large structure sets.
Role in this project:Back-end Developer
Back-end DeveloperContributions:5 releases, 12 reviews, 88 commits in 1 year
Contributions summary:Milot's contributions primarily focus on enhancing the functionality of the `foldseek` tool. They added a `--db-output` parameter to the `easy-search` workflow, enabling the use of the query database after the search. The user also contributed to the `appenddbtoindex` functionality, adding the ability to append precomputed indices from sub-projects. These changes indicate a focus on improving the tool's database management and search capabilities.
protein-structurealignmentssensitivecomparisonsbioinformatics
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