I am a postdoctoral researcher at Seoul National University, where I work with Martin Steinegger. My expertise includes bioinformatics, metagenomics, protein structure prediction and machine learning. I’m a developer and maintainer of many open-source tools like ColabFold, MMseqs2 and Foldseek. I hold a PhD from the University of Göttingen and the MPI-NAT, where I worked with Johannes Söding.
Education
Ph.D. (Dr. rer. nat, summa cum laude)
M.Sc. in Computer Science
B.Sc. in Bioinformatics
Projects
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ColabFold accelerates protein structure and complex prediction by utilizing the fast homology search of MMseqs2 and the advanced folding model of AlphaFold2.
Foldseek is a free open-source software and webserver that enables fast and sensitive comparisons of large sets of publicly available protein structures, with sensitivities similar to state-of-the-art structural aligners but four to five orders of magnitude faster.
MMseqs2 is open-source software for protein and nucleotide sequence search and clustering, offering profile searches with PSI-BLAST-like sensitivity at 400x the speed, fast metagenomic contig taxonomic labeling, and it includes a desktop and server app.
Plass is an open-source assembler that can recover 2-10 times more protein sequences from complex metagenomes, and has been used to assemble some of the largest free collections of protein sequences.
Publications
(2025).
De novo discovery of conserved gene clusters in microbial genomes with Spacedust.
Nature Methods.
(2025).
GPU-accelerated homology search with MMseqs2.
Nature Methods.
(2025).
AlphaFold Protein Structure Database and 3D-Beacons: new data and capabilities.
Journal of Molecular Biology.
(2025).
Easy and accurate protein structure prediction using ColabFold.
Nature Protocols.
(2025).
Easy and interactive taxonomic profiling with Metabuli App.
bioRxiv.
Contact
- milot@mirdita.de
- 1 Gwanak-ro, Gwanak-gu, Seoul, 08826
- Enter Building 502 and take the elevator to office 407
- BlueSky
- Mastodon