Martin Steinegger
Associate Professor
Seoul Incheon Metropolitan Area South Korea
Summary
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Rockstar🎓
Top SchoolMartin Steinegger is an associate professor and computational biologist with 14 years of experience building high-performance algorithms for sequence search, clustering, and metagenome analysis. He leads method development that combines big-data algorithms and machine learning to mine microbial diversity, and his lab produced widely used tools such as MMseqs2 and Foldseek that dramatically accelerate homology and structure searches. A hands-on back-end developer and build engineer, he regularly contributes performance and correctness fixes across major open-source projects (MMseqs2, HH-suite, Kraken2, ColabFold) and improves reproducible packaging via bioconda. His background spans academia and industry—from scalable cloud/HPC implementations at the Max Planck Söding Lab to production-facing pipelines—giving him an uncommon blend of deep algorithmic insight and pragmatic software engineering.
14 years of coding experience
13 years of employment as a software developer
Doctor of Philosophy (PhD), Computer Science, Doctor of Philosophy (PhD), Computer Science at Technical University MunichLudwig Maximilian University of MunichBachelor of Science (B.Sc.), Bioinformatics, passed with merit, Bachelor of Science (B.Sc.), Bioinformatics, passed with merit at Technische Universität MünchenComputer Engineering, Computer Engineering at HTL BraunauBusiness Informatics, Software Engineering, Business Informatics, Software Engineering at Edvschule Plattling
Stackoverflow
1,121reputation
70kreached
5answers
26questions
Github Skills (37)
algorithm10
debugging10
algorithms10
debug10
c-language10
python10
package-management10
scripting10
conda10
cmake10
data-structure10
script10
performance-optimization10
bioinformatics10
sh10
Programming languages (9)
Github contributions (5)
steineggerlab/foldseek
Sep 2018 - Jan 2023
Foldseek enables fast and sensitive comparisons of large structure sets.
Role in this project:
Back-end Developer
Back-end DeveloperContributions:5 releases, 2 reviews, 346 commits in 4 years 4 months
Contributions summary:Martin appears to have been actively involved in the development and maintenance of the Foldseek project's core code. Their commits focus on modifying and enhancing existing algorithms like TM-align and NN-based alignment. The user also made efforts to optimize the code for performance and added support for features.
protein-structurealignmentssensitivecomparisonsbioinformatics
soedinglab/MMseqs2
Mar 2013 - Dec 2022
MMseqs2: ultra fast and sensitive search and clustering suite
Role in this project:Back-end Developer
Back-end DeveloperContributions:26 releases, 6 reviews, 1982 commits in 9 years 10 months
Contributions summary:Martin contributed primarily to the MMseqs2 codebase through bug fixes and improvements to existing functionality. Their commits focused on addressing data type inconsistencies, integrating a touch function within the prefiltering module, and correcting coordinate calculations within the alignment process. Moreover, they were also involved in merging changes from the master branch. Their work involved changes to various source files like QueryMatcher.cpp, QueryMatcher.h and also contributions to the core algorithm in src/alignment.
profile-searchmetagenomicsalignmentultrammseqs
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