Uniclust databases of clustered and deeply annotated protein sequences and alignments. - Milot Mirdita; Lars von den Driesch; Clovis Galiez; Maria Jesus Martin; Johannes Söding; Martin Steinegger (Nucleic Acids Res., 2017)

MMseqs2 desktop and local web server app for fast, interactive sequence searches. - Milot Mirdita; Martin Steinegger; Johannes Söding (Bioinform., 2019)

HH-suite3 for fast remote homology detection and deep protein annotation. - Martin Steinegger; Markus Meier; Milot Mirdita; Harald Vöhringer; Stephan J. Haunsberger; Johannes Söding (BMC Bioinform., 2019)

Fast and sensitive taxonomic assignment to metagenomic contigs. - Milot Mirdita; Martin Steinegger; Florian P. Breitwieser; Johannes Söding; Eli Levy Karin (Bioinform., 2021)

SpacePHARER: sensitive identification of phages from CRISPR spacers in prokaryotic hosts. - Ruoshi Zhang; Milot Mirdita; Eli Levy Karin; Clovis Norroy; Clovis Galiez; Johannes Söding (Bioinform., 2021)

PredictProtein - Predicting Protein Structure and Function for 29 Years. - Michael Bernhofer; Christian Dallago; Timothy Karl; Venkata P. Satagopam; Michael Heinzinger; Maria Littmann; Tobias Olenyi; Jiajun Qiu; Konstantin Schütze; Guy Yachdav; Haim Ashkenazy; Nir Ben-Tal; et al. (Nucleic Acids Res., 2021)

DescribePROT: database of amino acid-level protein structure and function predictions. - Bi Zhao; Akila Katuwawala; Christopher J. Oldfield; A. Keith Dunker; Eshel Faraggi; Jörg Gsponer; Andrzej Kloczkowski; Nawar Malhis; Milot Mirdita; Zoran Obradovic; Johannes Söding; Martin Steinegger; et al. (Nucleic Acids Res., 2021)

Foldcomp: a library and format for compressing and indexing large protein structure sets. - Hyunbin Kim; Milot Mirdita; Martin Steinegger (Bioinform., 2023)

The OMG dataset: An Open MetaGenomic corpus for mixed-modality genomic language modeling. - Andre Cornman; Jacob West-Roberts; Antonio Pedro Camargo; Simon Roux; Martin Beracochea; Milot Mirdita; Sergey Ovchinnikov; Yunha Hwang (ICLR, 2025)