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Martin Steinegger - Publications

Affiliations: 
2018- Biomedical Engineering Johns Hopkins University, Baltimore, MD 
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34 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Hamamsy T, Barot M, Morton JT, Steinegger M, Bonneau R, Cho K. Learning sequence, structure, and function representations of proteins with language models. Biorxiv : the Preprint Server For Biology. PMID 38045331 DOI: 10.1101/2023.11.26.568742  0.403
2023 Basu S, Zhao B, Biró B, Faraggi E, Gsponer J, Hu G, Kloczkowski A, Malhis N, Mirdita M, Söding J, Steinegger M, Wang D, Wang K, Xu D, Zhang J, et al. DescribePROT in 2023: more, higher-quality and experimental annotations and improved data download options. Nucleic Acids Research. PMID 37933852 DOI: 10.1093/nar/gkad985  0.304
2023 Varabyou A, Sommer MJ, Erdogdu B, Shinder I, Minkin I, Chao KH, Park S, Heinz J, Pockrandt C, Shumate A, Rincon N, Puiu D, Steinegger M, Salzberg SL, Pertea M. CHESS 3: an improved, comprehensive catalog of human genes and transcripts based on large-scale expression data, phylogenetic analysis, and protein structure. Genome Biology. 24: 249. PMID 37904256 DOI: 10.1186/s13059-023-03088-4  0.64
2023 Liu D, Steinegger M. Block Aligner: an adaptive SIMD-accelerated aligner for sequences and position-specific scoring matrices. Bioinformatics (Oxford, England). 39. PMID 37535681 DOI: 10.1093/bioinformatics/btad487  0.357
2023 Ruperti F, Papadopoulos N, Musser JM, Mirdita M, Steinegger M, Arendt D. Cross-phyla protein annotation by structural prediction and alignment. Genome Biology. 24: 113. PMID 37173746 DOI: 10.1186/s13059-023-02942-9  0.366
2023 van Kempen M, Kim SS, Tumescheit C, Mirdita M, Lee J, Gilchrist CLM, Söding J, Steinegger M. Fast and accurate protein structure search with Foldseek. Nature Biotechnology. PMID 37156916 DOI: 10.1038/s41587-023-01773-0  0.312
2022 Sommer MJ, Cha S, Varabyou A, Rincon N, Park S, Minkin I, Pertea M, Steinegger M, Salzberg SL. Structure-guided isoform identification for the human transcriptome. Elife. 11. PMID 36519529 DOI: 10.7554/eLife.82556  0.661
2022 Schütze K, Heinzinger M, Steinegger M, Rost B. Nearest neighbor search on embeddings rapidly identifies distant protein relations. Frontiers in Bioinformatics. 2: 1033775. PMID 36466147 DOI: 10.3389/fbinf.2022.1033775  0.417
2022 Olenyi T, Marquet C, Heinzinger M, Kröger B, Nikolova T, Bernhofer M, Sändig P, Schütze K, Littmann M, Mirdita M, Steinegger M, Dallago C, Rost B. LambdaPP: Fast and accessible protein-specific phenotype predictions. Protein Science : a Publication of the Protein Society. e4524. PMID 36454227 DOI: 10.1002/pro.4524  0.32
2022 Varadi M, Nair S, Sillitoe I, Tauriello G, Anyango S, Bienert S, Borges C, Deshpande M, Green T, Hassabis D, Hatos A, Hegedus T, Hekkelman ML, Joosten R, Jumper J, ... ... Steinegger M, et al. 3D-Beacons: decreasing the gap between protein sequences and structures through a federated network of protein structure data resources. Gigascience. 11. PMID 36448847 DOI: 10.1093/gigascience/giac118  0.528
2022 Kim D, Gilchrist CLM, Chun J, Steinegger M. UFCG: database of universal fungal core genes and pipeline for genome-wide phylogenetic analysis of fungi. Nucleic Acids Research. PMID 36271795 DOI: 10.1093/nar/gkac894  0.347
2022 Lu J, Rincon N, Wood DE, Breitwieser FP, Pockrandt C, Langmead B, Salzberg SL, Steinegger M. Metagenome analysis using the Kraken software suite. Nature Protocols. PMID 36171387 DOI: 10.1038/s41596-022-00738-y  0.445
2022 Vanni C, Schechter MS, Acinas SG, Barberán A, Buttigieg PL, Casamayor EO, Delmont TO, Duarte CM, Eren AM, Finn RD, Kottmann R, Mitchell A, Sánchez P, Siren K, Steinegger M, et al. Unifying the known and unknown microbial coding sequence space. Elife. 11. PMID 35356891 DOI: 10.7554/eLife.67667  0.381
2021 Pockrandt C, Steinegger M, Salzberg SL. PhyloCSF ++: A fast and user-friendly implementation of PhyloCSF with annotation tools. Bioinformatics (Oxford, England). PMID 34734986 DOI: 10.1093/bioinformatics/btab756  0.605
2021 Jumper J, Evans R, Pritzel A, Green T, Figurnov M, Ronneberger O, Tunyasuvunakool K, Bates R, Žídek A, Potapenko A, Bridgland A, Meyer C, Kohl SAA, Ballard AJ, Cowie A, ... ... Steinegger M, et al. Applying and improving AlphaFold at CASP14. Proteins. PMID 34599769 DOI: 10.1002/prot.26257  0.314
2021 Jumper J, Evans R, Pritzel A, Green T, Figurnov M, Ronneberger O, Tunyasuvunakool K, Bates R, Žídek A, Potapenko A, Bridgland A, Meyer C, Kohl SAA, Ballard AJ, Cowie A, ... ... Steinegger M, et al. Highly accurate protein structure prediction with AlphaFold. Nature. PMID 34265844 DOI: 10.1038/s41586-021-03819-2  0.318
2021 Bernhofer M, Dallago C, Karl T, Satagopam V, Heinzinger M, Littmann M, Olenyi T, Qiu J, Schütze K, Yachdav G, Ashkenazy H, Ben-Tal N, Bromberg Y, Goldberg T, Kajan L, ... ... Steinegger M, et al. PredictProtein - Predicting Protein Structure and Function for 29 Years. Nucleic Acids Research. PMID 33999203 DOI: 10.1093/nar/gkab354  0.364
2021 Credle JJ, Robinson ML, Gunn J, Monaco D, Sie B, Tchir A, Hardick J, Zheng X, Shaw-Saliba K, Rothman RE, Eshleman SH, Pekosz A, Hansen K, Mostafa H, Steinegger M, et al. Highly multiplexed oligonucleotide probe-ligation testing enables efficient extraction-free SARS-CoV-2 detection and viral genotyping. Modern Pathology : An Official Journal of the United States and Canadian Academy of Pathology, Inc. PMID 33536572 DOI: 10.1038/s41379-020-00730-5  0.344
2020 Park S, Steinegger M, Cho HS, Chun J. Metagenomic Association Analysis of Gut Symbiont Without Host-Specific Genome Isolation. Frontiers in Microbiology. 11: 585622. PMID 33329454 DOI: 10.3389/fmicb.2020.585622  0.314
2020 Gabler F, Nam SZ, Till S, Mirdita M, Steinegger M, Söding J, Lupas AN, Alva V. Protein Sequence Analysis Using the MPI Bioinformatics Toolkit. Current Protocols in Bioinformatics. 72: e108. PMID 33315308 DOI: 10.1002/cpbi.108  0.51
2020 Zhao B, Katuwawala A, Oldfield CJ, Dunker AK, Faraggi E, Gsponer J, Kloczkowski A, Malhis N, Mirdita M, Obradovic Z, Söding J, Steinegger M, Zhou Y, Kurgan L. DescribePROT: database of amino acid-level protein structure and function predictions. Nucleic Acids Research. PMID 33119734 DOI: 10.1093/nar/gkaa931  0.348
2020 Credle JJ, Robinson ML, Gunn J, Monaco D, Sie B, Tchir A, Hardick J, Zheng X, Shaw-Saliba K, Rothman RE, Eshleman SH, Pekosz A, Hansen K, Mostafa H, Steinegger M, et al. Highly multiplexed oligonucleotide probe-ligation testing enables efficient extraction-free SARS-CoV-2 detection and viral genotyping. Biorxiv : the Preprint Server For Biology. PMID 32577648 DOI: 10.1101/2020.06.03.130591  0.324
2020 Steinegger M, Salzberg SL. Terminating contamination: large-scale search identifies more than 2,000,000 contaminated entries in GenBank. Genome Biology. 21: 115. PMID 32398145 DOI: 10.1186/S13059-020-02023-1  0.646
2020 Steinegger M, Seidel A, Söding J. Protein-guided nucleotide viral genome assembly for huge metagenomic datasets F1000research. 9. DOI: 10.7490/F1000Research.1118321.1  0.425
2019 Steinegger M, Meier M, Mirdita M, Vöhringer H, Haunsberger SJ, Söding J. HH-suite3 for fast remote homology detection and deep protein annotation. Bmc Bioinformatics. 20: 473. PMID 31521110 DOI: 10.1186/S12859-019-3019-7  0.51
2019 Steinegger M, Mirdita M, Söding J. Protein-level assembly increases protein sequence recovery from metagenomic samples manyfold. Nature Methods. 16: 603-606. PMID 31235882 DOI: 10.1038/S41592-019-0437-4  0.496
2019 Mirdita M, Steinegger M, Söding J. MMseqs2 desktop and local web server app for fast, interactive sequence searches. Bioinformatics (Oxford, England). PMID 30615063 DOI: 10.1093/Bioinformatics/Bty1057  0.454
2019 Steinegger M, Mirdita M, Söding J. New algorithms and tools for large-scale sequence analysis of metagenomic data F1000research. 8. DOI: 10.7490/F1000Research.1117602.1  0.423
2018 Steinegger M, Söding J. Clustering huge protein sequence sets in linear time. Nature Communications. 9: 2542. PMID 29959318 DOI: 10.1038/S41467-018-04964-5  0.414
2018 Mahlich Y, Steinegger M, Rost B, Bromberg Y. HFSP: high speed homology-driven function annotation of proteins. Bioinformatics (Oxford, England). 34: i304-i312. PMID 29950013 DOI: 10.1093/bioinformatics/bty262  0.426
2017 Steinegger M, Söding J. MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets. Nature Biotechnology. 35: 1026-1028. PMID 29035372 DOI: 10.1038/Nbt.3988  0.502
2016 Mirdita M, von den Driesch L, Galiez C, Martin MJ, Söding J, Steinegger M. Uniclust databases of clustered and deeply annotated protein sequences and alignments. Nucleic Acids Research. PMID 27899574 DOI: 10.1093/Nar/Gkw1081  0.489
2016 Hauser M, Steinegger M, Söding J. MMseqs software suite for fast and deep clustering and searching of large protein sequence sets. Bioinformatics (Oxford, England). 32: 1323-30. PMID 26743509 DOI: 10.1093/Bioinformatics/Btw006  0.495
2013 Kaján L, Yachdav G, Vicedo E, Steinegger M, Mirdita M, Angermüller C, Böhm A, Domke S, Ertl J, Mertes C, Reisinger E, Staniewski C, Rost B. Cloud prediction of protein structure and function with PredictProtein for Debian. Biomed Research International. 2013: 398968. PMID 23971032 DOI: 10.1155/2013/398968  0.446
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