Milot Mirdita

21.4k total citations · 9 hit papers
29 papers, 9.0k citations indexed

About

Milot Mirdita is a scholar working on Molecular Biology, Ecology and Materials Chemistry. According to data from OpenAlex, Milot Mirdita has authored 29 papers receiving a total of 9.0k indexed citations (citations by other indexed papers that have themselves been cited), including 26 papers in Molecular Biology, 10 papers in Ecology and 5 papers in Materials Chemistry. Recurrent topics in Milot Mirdita's work include Genomics and Phylogenetic Studies (19 papers), Machine Learning in Bioinformatics (14 papers) and Protein Structure and Dynamics (10 papers). Milot Mirdita is often cited by papers focused on Genomics and Phylogenetic Studies (19 papers), Machine Learning in Bioinformatics (14 papers) and Protein Structure and Dynamics (10 papers). Milot Mirdita collaborates with scholars based in South Korea, Germany and United States. Milot Mirdita's co-authors include Martin Steinegger, Sergey Ovchinnikov, Yoshitaka Moriwaki, Konstantin Schütze, Lim Heo, Johannes Söding, Cameron L. M. Gilchrist, Charlotte Tumescheit, Stephanie Kim and Michel van Kempen and has published in prestigious journals such as Nature, Science and Nucleic Acids Research.

In The Last Decade

Milot Mirdita

24 papers receiving 8.9k citations

Hit Papers

5 papers align trajectories

What are hit papers?

Hit papers significantly outperform the citation benchmark for their cohort. A paper qualifies if it has ≥500 total citations, achieves ≥1.5× the top-1% citation threshold for papers in the same subfield and year (this is the minimum needed to enter the top 1%, not the average within it), or reaches the top citation threshold in at least one of its specific research topics.

ColabFold: making protein folding accessible to all

2022 5.0k citations Milot Mirdita, Konstantin Schütze et al. Nature Methods profile →
Fast and accurate protein structure search with Foldseek

2023 956 citations Michel van Kempen, Stephanie Kim et al. Nature Biotechnology profile →
HH-suite3 for fast remote homology detection and deep protein annotation

2019 667 citations Martin Steinegger, Markus Meier et al. BMC Bioinformatics profile →
Protein Sequence Analysis Using the MPI Bioinformatics Toolkit

2020 466 citations Milot Mirdita, Martin Steinegger et al. profile →
Uniclust databases of clustered and deeply annotated protein sequences and alignments

2016 446 citations Milot Mirdita, Clovis Galiez et al. Nucleic Acids Research profile →
MMseqs2 desktop and local web server app for fast, interactive sequence searches

2019 341 citations Milot Mirdita, Martin Steinegger et al. Bioinformatics profile →
Protein-level assembly increases protein sequence recovery from metagenomic samples manyfold

2019 264 citations Martin Steinegger, Milot Mirdita et al. Nature Methods profile →
Clustering predicted structures at the scale of the known protein universe

2023 160 citations Inigo Barrio‐Hernandez, Jürgen Jänes et al. Nature profile →
Bilingual language model for protein sequence and structure

2024 74 citations Michael Heinzinger, Konstantin Weißenow et al. NAR Genomics and Bioinformatics profile →

Peers

Milot Mirdita

ECOLO

GENET

Sergey Ovchinnikov United States

Lim Heo United States

Haim Ashkenazy Israel

Martin Steinegger South Korea

Mark N. Wass United Kingdom

James B Procter United Kingdom

Gerardo Tauriello Switzerland

Rafal Gumienny Switzerland

John‐Marc Chandonia United States

Christine Rempfer Germany

Sergey Ovchinnikov United States

Milot Mirdita

7.9k ×1.3

751 ×0.6

ECOLO

766 ×0.8

1.2k ×1.3

GENET

1.5k ×1.8

Citations per year, relative to Milot Mirdita Milot Mirdita (= 1×) peers Sergey Ovchinnikov

Countries citing papers authored by Milot Mirdita

Since Specialization

Citations

This map shows the geographic impact of Milot Mirdita's research. It shows the number of citations coming from papers published by authors working in each country. You can also color the map by specialization and compare the number of citations received by Milot Mirdita with the expected number of citations based on a country's size and research output (numbers larger than one mean the country cites Milot Mirdita more than expected).

Fields of papers citing papers by Milot Mirdita

Since Specialization

Physical SciencesHealth SciencesLife SciencesSocial Sciences

This network shows the impact of papers produced by Milot Mirdita. Nodes represent research fields, and links connect fields that are likely to share authors. Colored nodes show fields that tend to cite the papers produced by Milot Mirdita. The network helps show where Milot Mirdita may publish in the future.

Co-authorship network of co-authors of Milot Mirdita

This figure shows the co-authorship network connecting the top 25 collaborators of Milot Mirdita. A scholar is included among the top collaborators of Milot Mirdita based on the total number of citations received by their joint publications. Widths of edges represent the number of papers authors have co-authored together. Node borders signify the number of papers an author published with Milot Mirdita. Milot Mirdita is excluded from the visualization to improve readability, since they are connected to all nodes in the network.

All Works

Sort: Min cites: Since: Top N: Style:

20 of 20 papers shown

Mirdita, Milot, et al.. (2026). Multiple protein structure alignment at scale with FoldMason. Science. 391(6784). 485–488.

Mirdita, Milot, et al.. (2025). Easy and interactive taxonomic profiling with Metabuli App. Bioinformatics. 41(10).

Mirdita, Milot, et al.. (2025). De novo discovery of conserved gene clusters in microbial genomes with Spacedust. Nature Methods. 22(10). 2065–2073.

Karin, Eli Levy, et al.. (2024). BFVD—a large repository of predicted viral protein structures. Nucleic Acids Research. 53(D1). D340–D347. 30 indexed citations

Karin, Eli Levy, Milot Mirdita, Rayan Chikhi, et al.. (2024). Petabase-Scale Homology Search for Structure Prediction. Cold Spring Harbor Perspectives in Biology. 16(5). a041465–a041465. 4 indexed citations

Heinzinger, Michael, et al.. (2024). Bilingual language model for protein sequence and structure. NAR Genomics and Bioinformatics. 6(4). lqae150–lqae150. 74 indexed citations breakdown →

Karin, Eli Levy, Hyunbin Kim, Yoshitaka Moriwaki, et al.. (2024). Easy and accurate protein structure prediction using ColabFold. Nature Protocols. 20(3). 620–642. 44 indexed citations

Kim, Hyunbin, Milot Mirdita, & Martin Steinegger. (2023). Foldcomp: a library and format for compressing and indexing large protein structure sets. Bioinformatics. 39(4). 9 indexed citations

Basu, Sushmita, Bi Zhao, Eshel Faraggi, et al.. (2023). DescribePROT in 2023: more, higher-quality and experimental annotations and improved data download options. Nucleic Acids Research. 52(D1). D426–D433. 7 indexed citations

10.

Barrio‐Hernandez, Inigo, Jürgen Jänes, Milot Mirdita, et al.. (2023). Clustering predicted structures at the scale of the known protein universe. Nature. 622(7983). 637–645. 160 indexed citations breakdown →

11.

Kempen, Michel van, Stephanie Kim, Charlotte Tumescheit, et al.. (2023). Fast and accurate protein structure search with Foldseek. Nature Biotechnology. 42(2). 243–246. 956 indexed citations breakdown →

12.

Παπαδόπουλος, Νικόλαος, et al.. (2023). Cross-phyla protein annotation by structural prediction and alignment. Genome biology. 24(1). 113–113. 13 indexed citations

13.

Olenyi, Tobias, Michael Heinzinger, Michael Bernhofer, et al.. (2022). LambdaPP : Fast and accessible protein‐specific phenotype predictions. Protein Science. 32(1). e4524–e4524. 10 indexed citations

14.

Mirdita, Milot, et al.. (2021). SpacePHARER: sensitive identification of phages from CRISPR spacers in prokaryotic hosts. Bioinformatics. 37(19). 3364–3366. 56 indexed citations

15.

Mirdita, Milot, Martin Steinegger, Florian P. Breitwieser, Johannes Söding, & Eli Levy Karin. (2021). Fast and sensitive taxonomic assignment to metagenomic contigs. Bioinformatics. 37(18). 3029–3031. 150 indexed citations

16.

Karin, Eli Levy, Milot Mirdita, & Johannes Söding. (2020). MetaEuk—sensitive, high-throughput gene discovery, and annotation for large-scale eukaryotic metagenomics. Microbiome. 8(1). 48–48. 159 indexed citations

17.

Mirdita, Milot, Martin Steinegger, & Johannes Söding. (2019). MMseqs2 desktop and local web server app for fast, interactive sequence searches. Bioinformatics. 35(16). 2856–2858. 341 indexed citations breakdown →

18.

Steinegger, Martin, et al.. (2019). HH-suite3 for fast remote homology detection and deep protein annotation. BMC Bioinformatics. 20(1). 473–473. 667 indexed citations breakdown →

19.

Mirdita, Milot, et al.. (2016). Uniclust databases of clustered and deeply annotated protein sequences and alignments. Nucleic Acids Research. 45(D1). D170–D176. 446 indexed citations breakdown →

20.

Kaján, László, Guy Yachdav, Esmeralda Vicedo, et al.. (2013). Cloud Prediction of Protein Structure and Function with PredictProtein for Debian. BioMed Research International. 2013. 1–6. 9 indexed citations

Rankless uses publication and citation data sourced from OpenAlex, an open and comprehensive bibliographic database. While OpenAlex provides broad and valuable coverage of the global research landscape, it—like all bibliographic datasets—has inherent limitations. These include incomplete records, variations in author disambiguation, differences in journal indexing, and delays in data updates. As a result, some metrics and network relationships displayed in Rankless may not fully capture the entirety of a scholar's output or impact.

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