Martin Steinegger

21 papers C 1Journal 20
YearRankTypeTitle / Venue / Authors
2026 J jnl
Scaling Atomistic Protein Binder Design with Generative Pretraining and Test-Time Compute.
CoRR
Kieran Didi, Zuobai Zhang, Guoqing Zhou, Danny Reidenbach, Zhonglin Cao, Sooyoung Cha, Tomas Geffner, Christian Dallago, Jian Tang, Michael M. Bronstein, Martin Steinegger, Emine Küçükbenli, Arash Vahdat, Karsten Kreis
2025 J jnl
Easy and interactive taxonomic profiling with Metabuli App.
Bioinform.
Sunjae Lee, Jaebeom Kim, Milot Mirdita, Cameron L. M. Gilchrist, Martin Steinegger
2024 J jnl
BioNeMo Framework: a modular, high-performance library for AI model development in drug discovery.
CoRR
Peter St. John, Dejun Lin, Polina Binder, Malcolm Greaves, Vega Shah, John St. John, Adrian Lange, Patrick D. Hsu, Rajesh Illango, Arvind Ramanathan, Anima Anandkumar, David H. Brookes, Akosua Busia, Abhishaike Mahajan, Stephen Malina, Neha Prasad, Sam Sinai, Lindsay Edwards, Thomas Gaudelet, Cristian Regep, Martin Steinegger, Burkhard Rost, Alexander Brace, Kyle Hippe, Luca Naef, Keisuke Kamata, George Armstrong, Kevin Boyd, Zhonglin Cao, Han-Yi Chou, Simon Chu, Allan dos Santos Costa, Sajad Darabi, Eric Dawson, Kieran Didi, Cong Fu, Mario Geiger, Michelle Gill, Darren Hsu, Gagan Kaushik, Maria Korshunova, Steven Kothen-Hill, Youhan Lee, Meng Liu, Micha Livne, Zachary McClure, Jonathan Mitchell, Alireza Moradzadeh, Ohad Mosafi, Youssef Nashed, Saee Paliwal, Yuxing Peng, Sara Rabhi, Farhad Ramezanghorbani, Danny Reidenbach, Camir Ricketts, Brian Roland, Kushal Shah, Tyler Shimko, Hassan Sirelkhatim, Savitha Srinivasan, Abraham C. Stern, Dorota Toczydlowska, Srimukh Prasad Veccham, Niccolò Alberto Elia Venanzi, Anton Vorontsov, Jared Wilber, Isabel Wilkinson, Wei Jing Wong, Eva Xue, Cory Ye, Xin Yu, Yang Zhang, Guoqing Zhou, Becca Zandstein, Christian Dallago, Bruno Trentini, Emine Küçükbenli, Timur Rvachov, Eddie Calleja, Johnny Israeli, Harry Clifford, Risto Haukioja, Nicholas Haemel, Kyle Tretina, Neha Tadimeti, Anthony B. Costa
2023 J jnl
Block Aligner: an adaptive SIMD-accelerated aligner for sequences and position-specific scoring matrices.
Bioinform.
Daniel Liu, Martin Steinegger
2023 J jnl
Foldcomp: a library and format for compressing and indexing large protein structure sets.
Bioinform.
Hyunbin Kim, Milot Mirdita, Martin Steinegger
2023 J jnl
UFCG: database of universal fungal core genes and pipeline for genome-wide phylogenetic analysis of fungi.
Nucleic Acids Res.
Dongwook Kim, Cameron L. M. Gilchrist, Jongsik Chun, Martin Steinegger
2022 J jnl
Nearest neighbor search on embeddings rapidly identifies distant protein relations.
Frontiers Bioinform.
Konstantin Schütze, Michael Heinzinger, Martin Steinegger, Burkhard Rost
2022 J jnl
PhyloCSF++: a fast and user-friendly implementation of PhyloCSF with annotation tools.
Bioinform.
Christopher Pockrandt, Martin Steinegger, Steven L. Salzberg
2022 J jnl
ProtTrans: Toward Understanding the Language of Life Through Self-Supervised Learning.
IEEE Trans. Pattern Anal. Mach. Intell.
Ahmed Elnaggar, Michael Heinzinger, Christian Dallago, Ghalia Rehawi, Yu Wang, Llion Jones, Tom Gibbs, Tamas Feher, Christoph Angerer, Martin Steinegger, Debsindhu Bhowmik, Burkhard Rost
2021 J jnl
DescribePROT: database of amino acid-level protein structure and function predictions.
Nucleic Acids Res.
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, Yaoqi Zhou, Lukasz A. Kurgan
2021 J jnl
Fast and sensitive taxonomic assignment to metagenomic contigs.
Bioinform.
Milot Mirdita, Martin Steinegger, Florian P. Breitwieser, Johannes Söding, Eli Levy Karin
2021 J jnl
PredictProtein - Predicting Protein Structure and Function for 29 Years.
Nucleic Acids Res.
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, Yana Bromberg, Tatyana Goldberg, László Kaján, Seán I. O'Donoghue, Chris Sander, Andrea Schafferhans, Avner Schlessinger, Gerrit Vriend, Milot Mirdita, Piotr Gawron, Wei Gu, Yohan Jarosz, Christophe Trefois, Martin Steinegger, Reinhard Schneider, Burkhard Rost
2020 J jnl
ProtTrans: Towards Cracking the Language of Life's Code Through Self-Supervised Deep Learning and High Performance Computing.
CoRR
Ahmed Elnaggar, Michael Heinzinger, Christian Dallago, Ghalia Rehawi, Yu Wang, Llion Jones, Tom Gibbs, Tamas Feher, Christoph Angerer, Martin Steinegger, Debsindhu Bhowmik, Burkhard Rost
2019 J jnl
HH-suite3 for fast remote homology detection and deep protein annotation.
BMC Bioinform.
Martin Steinegger, Markus Meier, Milot Mirdita, Harald Vöhringer, Stephan J. Haunsberger, Johannes Söding
2019 J jnl
MMseqs2 desktop and local web server app for fast, interactive sequence searches.
Bioinform.
Milot Mirdita, Martin Steinegger, Johannes Söding
2018 J jnl
HFSP: high speed homology-driven function annotation of proteins.
Bioinform.
Yannick Mahlich, Martin Steinegger, Burkhard Rost, Yana Bromberg
2017 J jnl
Uniclust databases of clustered and deeply annotated protein sequences and alignments.
Nucleic Acids Res.
Milot Mirdita, Lars von den Driesch, Clovis Galiez, Maria Jesus Martin, Johannes Söding, Martin Steinegger
2017 C conf
Updating lidar-derived crown cover density products with sentinel-2.
IGARSS
Janik Deutscher, Klaus Granica, Martin Steinegger, Manuela Hirschmugl, Roland Perko, Mathias Schardt
2016 J jnl
MMseqs software suite for fast and deep clustering and searching of large protein sequence sets.
Bioinform.
Maria Hauser, Martin Steinegger, Johannes Söding
2015 J jnl
Remote Sensing Based Two-Stage Sampling for Accuracy Assessment and Area Estimation of Land Cover Changes.
Remote. Sens.
Heinz Gallaun, Martin Steinegger, Roland Wack, Mathias Schardt, Birgit Kornberger, Ursula Schmitt
2014 J jnl
Mapping Forest Degradation due to Selective Logging by Means of Time Series Analysis: Case Studies in Central Africa.
Remote. Sens.
Manuela Hirschmugl, Martin Steinegger, Heinz Gallaun, Mathias Schardt