Mapping Forest Degradation due to Selective Logging by Means of Time Series Analysis: Case Studies in Central Africa. - Manuela Hirschmugl; Martin Steinegger; Heinz Gallaun; Mathias Schardt (Remote. Sens., 2014)

Remote Sensing Based Two-Stage Sampling for Accuracy Assessment and Area Estimation of Land Cover Changes. - Heinz Gallaun; Martin Steinegger; Roland Wack; Mathias Schardt; Birgit Kornberger; Ursula Schmitt (Remote. Sens., 2015)

MMseqs software suite for fast and deep clustering and searching of large protein sequence sets. - Maria Hauser; Martin Steinegger; Johannes Söding (Bioinform., 2016)

Updating lidar-derived crown cover density products with sentinel-2. - Janik Deutscher; Klaus Granica; Martin Steinegger; Manuela Hirschmugl; Roland Perko; Mathias Schardt (IGARSS, 2017)

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)

HFSP: high speed homology-driven function annotation of proteins. - Yannick Mahlich; Martin Steinegger; Burkhard Rost; Yana Bromberg (Bioinform., 2018)

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)

ProtTrans: Towards Cracking the Language of Life's Code Through Self-Supervised Deep Learning and High Performance Computing. - Ahmed Elnaggar; Michael Heinzinger; Christian Dallago; Ghalia Rehawi; Yu Wang; Llion Jones; Tom Gibbs; Tamas Feher; Christoph Angerer; Martin Steinegger; Debsindhu Bhowmik; Burkhard Rost (CoRR, 2020)

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

PhyloCSF++: a fast and user-friendly implementation of PhyloCSF with annotation tools. - Christopher Pockrandt; Martin Steinegger; Steven L. Salzberg (Bioinform., 2022)

Nearest neighbor search on embeddings rapidly identifies distant protein relations. - Konstantin Schütze; Michael Heinzinger; Martin Steinegger; Burkhard Rost (Frontiers Bioinform., 2022)

ProtTrans: Toward Understanding the Language of Life Through Self-Supervised Learning. - Ahmed Elnaggar; Michael Heinzinger; Christian Dallago; Ghalia Rehawi; Yu Wang; Llion Jones; Tom Gibbs; Tamas Feher; Christoph Angerer; Martin Steinegger; Debsindhu Bhowmik; Burkhard Rost (IEEE Trans. Pattern Anal. Mach. Intell., 2022)

UFCG: database of universal fungal core genes and pipeline for genome-wide phylogenetic analysis of fungi. - Dongwook Kim; Cameron L. M. Gilchrist; Jongsik Chun; Martin Steinegger (Nucleic Acids Res., 2023)

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

Block Aligner: an adaptive SIMD-accelerated aligner for sequences and position-specific scoring matrices. - Daniel Liu; Martin Steinegger (Bioinform., 2023)

BioNeMo Framework: a modular, high-performance library for AI model development in drug discovery. - 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; et al. (CoRR, 2024)