Milot Mirdita

Milot Mirdita

Postdoc in Bioinformatics

Seoul National University

I’m 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

 
 
 
 
 
Postdoc
August 2022 – Present Seoul, Korea
 
 
 
 
 
Ph.D. (Dr. rer. nat, summa cum laude)
July 2017 – April 2022 Göttingen, Germany
 
 
 
 
 
M.Sc. in Computer Science
April 2014 – August 2016 Munich, Germany
 
 
 
 
 
B.Sc. in Bioinformatics
October 2010 – March 2014 Munich, Germany

Projects

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ColabFold: making protein folding accessible to all
ColabFold accelerates protein structure and complex prediction by utilizing the fast homology search of MMseqs2 and the advanced folding model of AlphaFold2.
ColabFold: making protein folding accessible to all
Foldseek: fast and accurate protein structure search
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.
Foldseek: fast and accurate protein structure search
Plass: Protein-level assembly increases protein sequence recovery from metagenomic samples manyfol
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.
Plass: Protein-level assembly increases protein sequence recovery from metagenomic samples manyfol

Publications

(2023). Beyond sequence similarity: cross-phyla protein annotation by structural prediction and alignment. bioRxiv.

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(2022). ColabFold: making protein folding accessible to all. Nature Methods.

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(2022). Foldseek: fast and accurate protein structure search. bioRxiv.

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(2021). SpacePHARER: sensitive identification of phages from CRISPR spacers in prokaryotic hosts. Bioinformatics.

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(2021). Fast and sensitive taxonomic assignment to metagenomic contigs. Bioinformatics.

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