Publications by authors named "Martin Steinegger"

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Cross-phyla protein annotation by structural prediction and alignment.
Fabian Ruperti, Nikolaos Papadopoulos, Jacob M Musser, Milot Mirdita, Martin Steinegger, Detlev Arendt

Genome Biol· May 2023

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ColabFold: making protein folding accessible to all.
Milot Mirdita, Konstantin Schütze, Yoshitaka Moriwaki, Lim Heo, Sergey Ovchinnikov, Martin Steinegger

Nat Methods· June 2022

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Structural phylogenetics unravels the evolutionary diversification of communication systems in gram-positive bacteria and their viruses.
David Moi, Charles Bernard, Martin Steinegger, Yannis Nevers, Mauricio Langleib

Nat Struct Mol Biol· December 2025

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Evolutionary characterization of antiviral SAMD9/9L across kingdoms supports ancient convergence and lineage-specific adaptations.
Alexandre Legrand, Rémi Demeure, Amandine Chantharath, Carine Rey, Julie Baltenneck, Martin Steinegger

Nat Ecol Evol· December 2025

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AlphaFold Protein Structure Database 2025: a redesigned interface and updated structural coverage.
Damian Bertoni, Maxim Tsenkov, Paulyna Magana, Sreenath Nair, Ivanna Pidruchna, Martin Steinegger

Nucleic Acids Res· November 2025

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GPU-accelerated homology search with MMseqs2.
Felix Kallenborn, Alejandro Chacon, Christian Hundt, Hassan Sirelkhatim, Kieran Didi, Martin Steinegger

Nat Methods· October 2025

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Easy and interactive taxonomic profiling with Metabuli App.
SunJae Lee, Jaebeom Kim, Milot Mirdita, Cameron L M Gilchrist, Martin Steinegger

Bioinformatics· October 2025

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Democratizing protein language model training, sharing and collaboration.
Jin Su, Zhikai Li, Tianli Tao, Chenchen Han, Yan He, Martin Steinegger

Nat Biotechnol· October 2025

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CarpeDeam: a de novo metagenome assembler for heavily damaged ancient datasets.
Louis Kraft, Johannes Söding, Martin Steinegger, Annika Jochheim, Peter Wad Sackett

Genome Biol· October 2025

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An nf-core framework for the systematic comparison of alternative modeling tools: the multiple sequence alignment case study.
Luisa Santus, Jose Espinosa-Carrasco, Leon Rauschning, Júlia Mir-Pedrol, Igor Trujnara, Martin Steinegger

NAR Genom Bioinform· September 2025

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Logan: Planetary-Scale Genome Assembly Surveys Life's Diversity.
Rayan Chikhi, Téo Lemane, Raphaël Loll-Krippleber, Mercè Montoliu-Nerin, Brice Raffestin, Martin Steinegger

bioRxiv· September 2025

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AlphaFold Protein Structure Database and 3D-Beacons: New Data and Capabilities.
Jennifer Fleming, Paulyna Magana, Sreenath Nair, Maxim Tsenkov, Damian Bertoni, Martin Steinegger

J Mol Biol· August 2025

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Cutting-edge deep-learning based tools for metagenomic research.
Eli Levy Karin, Martin Steinegger

Natl Sci Rev· June 2025

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Structural basis of the catalytic and allosteric mechanism of bacterial acetyltransferase PatZ.
Jun Bae Park, Gwanwoo Lee, Yu-Yeon Han, Dongwook Kim, Kyoo Heo, Martin Steinegger

Proc Natl Acad Sci U S A· June 2025

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Unicore Enables Scalable and Accurate Phylogenetic Reconstruction with Structural Core Genes.
Dongwook Kim, Sukhwan Park, Martin Steinegger

Genome Biol Evol· May 2025

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Ancient convergence with prokaryote defense and recent adaptations to lentiviruses in primates characterize the ancestral immune factors SAMD9s.
Alexandre Legrand, Rémi Demeure, Amandine Chantharath, Carine Rey, Julie Baltenneck, Martin Steinegger

bioRxiv· May 2025

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FunVIP: Fungal Validation and Identification Pipeline based on phylogenetic analysis.
Chang Wan Seo, Shinnam Yoo, Yoonhee Cho, Ji Seon Kim, Martin Steinegger

J Microbiol· April 2025

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Easy and accurate protein structure prediction using ColabFold.
Gyuri Kim, Sewon Lee, Eli Levy Karin, Hyunbin Kim, Yoshitaka Moriwaki, Martin Steinegger

Nat Protoc· March 2025

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Rapid and sensitive protein complex alignment with Foldseek-Multimer.
Woosub Kim, Milot Mirdita, Eli Levy Karin, Cameron L M Gilchrist, Hugo Schweke, Martin Steinegger

Nat Methods· March 2025

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Molecular Display of the Animal Meta-Venome for Discovery of Novel Therapeutic Peptides.
Meng-Hsuan Hsiao, Yang Miao, Zixing Liu, Konstantin Schütze, Nathachit Limjunyawong, Martin Steinegger

Mol Cell Proteomics· February 2025

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BFVD-a large repository of predicted viral protein structures.
Rachel Seongeun Kim, Eli Levy Karin, Milot Mirdita, Rayan Chikhi, Martin Steinegger

Nucleic Acids Res· January 2025

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Discovery of highly active kynureninases for cancer immunotherapy through protein language model.
Hyunuk Eom, Sukhwan Park, Kye Soo Cho, Jihyeon Lee, Hyunbin Kim, Martin Steinegger

Nucleic Acids Res· January 2025

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Bilingual language model for protein sequence and structure.
Michael Heinzinger, Konstantin Weissenow, Joaquin Gomez Sanchez, Adrian Henkel, Milot Mirdita, Martin Steinegger

NAR Genom Bioinform· December 2024

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Strain-resolved de-novo metagenomic assembly of viral genomes and microbial 16S rRNAs.
Annika Jochheim, Florian A Jochheim, Alexandra Kolodyazhnaya, Étienne Morice, Martin Steinegger

Microbiome· October 2024

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Author Correction: Metagenome analysis using the Kraken software suite.
Jennifer Lu, Natalia Rincon, Derrick E Wood, Florian P Breitwieser, Christopher Pockrandt, Martin Steinegger

Nat Protoc· August 2024

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Mutation-induced LZTR1 polymerization provokes cardiac pathology in recessive Noonan syndrome.
Alexandra Viktoria Busley, Óscar Gutiérrez-Gutiérrez, Elke Hammer, Fabian Koitka, Amin Mirzaiebadizi, Martin Steinegger

Cell Rep· July 2024

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Molecular Display of the Animal Meta-Venome for Discovery of Novel Therapeutic Peptides.
Meng-Hsuan Hsiao, Yang Miao, Zixing Liu, Konstantin Schütze, Nathachit Limjunyawong, Martin Steinegger

bioRxiv· May 2024

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