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Showing results 1 to 44 of 44

Issue Date	Title / Author(s) / Citation	File
2013	Cloud Prediction of Protein Structure and Function with PredictProtein for Debian Kajan, Laszlo; Yachdav, Guy; Vicedo, Esmeralda; Steinegger, Martin; Mirdita, Milot; Angermueller, Christof; Boehm, Ariane; Domke, Simon; Ertl, Julia; Mertes, Christian; Reisinger, Eva; Staniewski, Cedric; Rost, Burkhard BIOMED RESEARCH INTERNATIONAL, Vol.2013	DOI
2016-05	MMseqs software suite for fast and deep clustering and searching of large protein sequence sets Hauser, Maria; Steinegger, Martin; Soeding, Johannes Bioinformatics, Vol.32 No.9, pp.1323-1330	DOI
2017-01	Uniclust databases of clustered and deeply annotated protein sequences and alignments Mirdita, Milot; von den Driesch, Lars; Galiez, Clovis; Martin, Maria J.; Soeding, Johannes; Steinegger, Martin Nucleic Acids Research, Vol.45 No.D1, pp.D170-D176	DOI
2017-11	MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets Steinegger, Martin; Soeding, Johannes Nature Biotechnology, Vol.35 No.11, pp.1026-1028	DOI
2018-06	Clustering huge protein sequence sets in linear time Steinegger, Martin; Soeding, Johannes Nature Communications, Vol.9 No.1, p. 2542	DOI
2018-07	HFSP: high speed homology-driven function annotation of proteins Mahlich, Yannick; Steinegger, Martin; Rost, Burkhard; Bromberg, Yana Bioinformatics, Vol.34 No.13, pp.304-312	DOI
2019-07	Protein-level assembly increases protein sequence recovery from metagenomic samples manyfold Steinegger, Martin; Mirdita, Milot; Soeding, Johannes Nature Methods, Vol.16 No.7, pp.603-609	DOI
2019-08	MMseqs2 desktop and local web server app for fast, interactive sequence searches Mirdita, Milot; Steinegger, Martin; Soeding, Johannes Bioinformatics, Vol.35 No.16, pp.2856-2858	DOI
2019-09	HH-suite3 for fast remote homology detection and deep protein annotation Steinegger, Martin; Meier, Markus; Mirdita, Milot; Voehringer, Harald; Haunsberger, Stephan J.; Soeding, Johannes BMC Bioinformatics, Vol.20 No.1, p. 473	DOI
2020-05	Terminating contamination: large-scale search identifies more than 2,000,000 contaminated entries in GenBank Steinegger, Martin; Salzberg, Steven L. Genome Biology, Vol.21 No.1, p. 115	DOI
2020-11	Metagenomic Association Analysis of Gut Symbiont Limosilactobacillus reuteri Without Host-Specific Genome Isolation Park, Sein; Steinegger, Martin; Cho, Ho-Seong; Chun, Jongsik Frontiers in Microbiology, Vol.11, p. 585622	DOI
2020-12	Protein Sequence Analysis Using the MPI Bioinformatics Toolkit Gabler, Felix; Nam, Seung-Zin; Till, Sebastian; Mirdita, Milot; Steinegger, Martin; Söding, Johannes; Lupas, Andrei N.; Alva, Vikram Current Protocols in Bioinformatics, Vol.72 No.1, p. e108	DOI
2021-01	DescribePROT: database of amino acid-level protein structure and function predictions Zhao, Bi; Katuwawala, Akila; Oldfield, Christopher J.; Dunker, A. Keith; Faraggi, Eshel; Gsponer, Jorg; Kloczkowski, Andrzej; Malhis, Nawar; Mirdita, Milot; Obradovic, Zoran; Soding, Johannes; Steinegger, Martin; Zhou, Yaoqi; Kurgan, Lukasz Nucleic Acids Research, Vol.49 No.D1, pp.D298-D308	DOI
2021-06	Going to extremes - a metagenomic journey into the dark matter of life Aevarsson, Arnthor; Kaczorowska, Anna-Karina; Adalsteinsson, Bjorn Thor; Ahlqvist, Josefin; Al-Karadaghi, Salam; Altenbuchner, Joseph; Arsin, Hasan; Atlasson, Ulfur August; Brandt, David; Cichowicz-Cieslak, Magdalena; Cornish, Katy A. S.; Courtin, Jeremy; Dabrowski, Slawomir; Dahle, Hakon; Djeffane, Samia; Dorawa, Sebastian; Dusaucy, Julia; Enault, Francois; Fedoy, Anita-Elin; Freitag-Pohl, Stefanie; Fridjonsson, Olafur H.; Galiez, Clovis; Glomsaker, Eirin; Guerin, Mickael; Gundeso, Sigurd E.; Gudmundsdottir, Elisabet E.; Gudmundsson, Hordur; Hakansson, Maria; Henke, Christian; Helleux, Alexandra; Henriksen, Jorn Remi; Hjorleifdottir, Sigridur; Hreggvidsson, Gudmundur O.; Jasilionis, Andrius; Jochheim, Annika; Jonsdottir, Ilmur; Jonsdottir, Lilja Bjork; Jurczak-Kurek, Agata; Kaczorowski, Tadeusz; Kalinowski, Jorn; Kozlowski, Lukasz P.; Krupovic, Mart; Kwiatkowska-Semrau, Karolina; Lanes, Olav; Lange, Joanna; Lebrat, Julien; Linares-Pasten, Javier; Liu, Ying; Lorentsen, Steffen A.; Lutterman, Tobias; Mas, Thibaud; Merre, William; Mirdita, Milot; Morzywolek, Agnieszka; Ndela, Eric Olo; Karlsson, Eva Nordberg; Olgudottir, Edda; Pedersen, Cathrine; Perler, Francine; Petursdottir, Solveig K.; Plotka, Magdalena; Pohl, Ehmke; Prangishvili, David; Ray, Jessica L.; Reynisson, Birkir; Robertsdottir, Tara; Sandaa, Ruth-Anne; Sczyrba, Alexander; Skirnisdottir, Sigurlaug; Soding, Johannes; Solstad, Terese; Steen, Ida H.; Stefansson, Sigmar Karl; Steinegger, Martin; Overa, Katrine Stange; Striberny, Bernd; Svensson, Anders; Szadkowska, Monika; Tarrant, Emma J.; Terzian, Paul; Tourigny, Mathilde; van den Bergh, Tom; Vanhalst, Justine; Vincent, Jonathan; Vroling, Bas; Walse, Bjorn; Wang, Lei; Watzlawick, Hildegard; Welin, Martin; Werbowy, Olesia; Wons, Ewa; Zhang, Ruoshi FEMS Microbiology Letters, Vol.368 No.12, p. fnab067	DOI
2021-06	Highly multiplexed oligonucleotide probe-ligation testing enables efficient extraction-free SARS-CoV-2 detection and viral genotyping Credle, Joel J.; Robinson, Matthew L.; Gunn, Jonathan; Monaco, Daniel; Sie, Brandon; Tchir, Alexandra; Hardick, Justin; Zheng, Xuwen; Shaw-Saliba, Kathryn; Rothman, Richard E.; Eshleman, Susan H.; Pekosz, Andrew; Hansen, Kasper; Mostafa, Heba; Steinegger, Martin; Larman, H. Benjamin Modern Pathology, Vol.34 No.6, pp.1093-1103	DOI
2021-07	PredictProtein - Predicting Protein Structure and Function for 29 Years Bernhofer, Michael; Dallago, Christian; Karl, Tim; Satagopam, Venkata; Heinzinger, Michael; Littmann, Maria; Olenyi, Tobias; Qiu, Jiajun; Schuetze, Konstantin; Yachdav, Guy; Ashkenazy, Haim; Ben-Tal, Nir; Bromberg, Yana; Goldberg, Tatyana; Kajan, Laszlo; O'Donoghue, Sean; Sander, Chris; Schafferhans, Andrea; Schlessinger, Avner; Vriend, Gerrit; Mirdita, Milot; Gawron, Piotr; Gu, Wei; Jarosz, Yohan; Trefois, Christophe; Steinegger, Martin; Schneider, Reinhard; Rost, Burkhard Nucleic Acids Research, Vol.49 No.W1, pp.W535-W540	DOI
2021-08	Highly accurate protein structure prediction with AlphaFold Jumper, John; Evans, Richard; Pritzel, Alexander; Green, Tim; Figurnov, Michael; Ronneberger, Olaf; Tunyasuvunakool, Kathryn; Bates, Russ; Žídek, Augustin; Potapenko, Anna; Bridgland, Alex; Meyer, Clemens; Kohl, Simon A. A.; Ballard, Andrew J.; Cowie, Andrew; Romera-Paredes, Bernardino; Nikolov, Stanislav; Jain, Rishub; Adler, Jonas; Back, Trevor; Petersen, Stig; Reiman, David; Clancy, Ellen; Zielinski, Michal; Steinegger, Martin; Pacholska, Michalina; Berghammer, Tamas; Bodenstein, Sebastian; Silver, David; Vinyals, Oriol; Senior, Andrew W.; Kavukcuoglu, Koray; Kohli, Pushmeet; Hassabis, Demis Nature, Vol.596 No.7873, pp.583-589	DOI
2021-09	Fast and sensitive taxonomic assignment to metagenomic contigs Mirdita, M.; Steinegger, Martin; Breitwieser, F.; Soeding, J.; Karin, E. Levy Bioinformatics, Vol.37 No.18, pp.3029-3031	DOI
2021-09	Accurate protein structure prediction: what comes next? Seok, Chaok; Baek, Minkyung; Martin, Steinegger; Park, Hahnbeom; Lee, Gyu Rie; Won, Jonghun Biodesign, Vol.9 No.3, pp.47-50	DOI
2021-12	MMseqs2 profile/profile: fast and ultra-sensitive searches beyond the twilight zone Mirdita, Milot; Ji, Hyunjoo; Karin, Eli Levy; Sommer, Hans-Georg; Galiez, Clovis; Soeding, Johannes; Steinegger, Martin BMC BIOINFORMATICS, Vol.22 No.SUPPL 16
2021-12	Applying and improving AlphaFold at CASP14 Jumper, John; Evans, Richard; Pritzel, Alexander; Green, Tim; Figurnov, Michael; Ronneberger, Olaf; Tunyasuvunakool, Kathryn; Bates, Russ; Zidek, Augustin; Potapenko, Anna; Bridgland, Alex; Meyer, Clemens; Kohl, Simon A. A.; Ballard, Andrew J.; Cowie, Andrew; Romera-Paredes, Bernardino; Nikolov, Stanislav; Jain, Rishub; Adler, Jonas; Back, Trevor; Petersen, Stig; Reiman, David; Clancy, Ellen; Zielinski, Michal; Steinegger, Martin; Pacholska, Michalina; Berghammer, Tamas; Silver, David; Vinyals, Oriol; Senior, Andrew W.; Kavukcuoglu, Koray; Kohli, Pushmeet; Hassabis, Demis Proteins: Structure, Function and Genetics, Vol.89 No.12, pp.1711-1721	DOI
2022-01	3D-Beacons: Decreasing the gap between protein sequences and structures through a federated network of protein structure data resources Varadi, Mihaly; Nair, Sreenath; Sillitoe, Ian; Tauriello, Gerardo; Anyango, Stephen; Bienert, Stefan; Borges, Clemente; Deshpande, Mandar; Green, Tim; Hassabis, Demis; Hatos, Andras; Hegedus, Tamas; Hekkelman, Maarten L; Joosten, Robbie; Jumper, John; Laydon, Agata; Molodenskiy, Dmitry; Piovesan, Damiano; Salladini, Edoardo; Salzberg, Steven L; Sommer, Markus J; Steinegger, Martin; Suhajda, Erzsebet; Svergun, Dmitri; Tenorio-Ku, Luiggi; Tosatto, Silvio; Tunyasuvunakool, Kathryn; Waterhouse, Andrew Mark; Zídek, Augustin; Schwede, Torsten; Orengo, Christine; Velankar, Sameer GigaScience, Vol.11, p. giac118	DOI
2022-02	PhyloCSF plus plus : a fast and user-friendly implementation of PhyloCSF with annotation tools Pockrandt, Christopher; Steinegger, Martin; Salzberg, Steven L. Bioinformatics, Vol.38 No.5, pp.1440-1442	DOI
2022-03	Unifying the known and unknown microbial coding sequence space Vanni, Chiara; Schechter, Matthew S.; Acinas, Silvia G.; Barberán, Albert; Buttigieg, Pier Luigi; Casamayor, Emilio O.; Delmont, Tom O.; Duarte, Carlos M.; Eren, A. Murat; Finn, Robert D.; Kottmann, Renzo; Mitchell, Alex; Sanchez, Pablo; Siren, Kimmo; Steinegger, Martin; Glöckner, Frank Oliver; Fernandez-Guerra, Antonio eLife, Vol.11, p. e67667	DOI
2022-06	ColabFold: making protein folding accessible to all Mirdita, Milot; Schutze, Konstantin; Moriwaki, Yoshitaka; Heo, Lim; Ovchinnikov, Sergey; Steinegger, Martin Nature Methods, Vol.19 No.6, pp.679-682	DOI
2022-07	Evolutionary balance between foldability and functionality of a glucose transporter Choi, Hyun-Kyu; Kang, Hyunook; Lee, Chanwoo; Kim, Hyun Gyu; Phillips, Ben P.; Park, Soohyung; Tumescheit, Charlotte; Kim, Sang Ah; Lee, Hansol; Roh, Soung-Hun; Hong, Heedeok; Steinegger, Martin; Im, Wonpil; Miller, Elizabeth A.; Choi, Hee-Jung; Yoon, Tae Young Nature Chemical Biology, Vol.18 No.7, pp.713-723	DOI
2022-10	ProtTrans: Toward Understanding the Language of Life Through Self-Supervised Learning Elnaggar, Ahmed; Heinzinger, Michael; Dallago, Christian; Rehawi, Ghalia; Yu, Wang; Jones, Llion; Gibbs, Tom; Feher, Tamas; Angerer, Christoph; Steinegger, Martin; Bhowmik, Debsindhu; Rost, Burkhard IEEE Transactions on Pattern Analysis and Machine Intelligence, Vol.44 No.10, pp.7112-7127	DOI
2022-11	Nearest neighbor search on embeddings rapidly identifies distant protein relations Schuetze, Konstantin; Heinzinger, Michael; Steinegger, Martin; Rost, Burkhard Frontiers in Bioinformatics, Vol.2, p. 1033775	DOI
2022-12	Metagenome analysis using the Kraken software suite Lu, Jennifer; Rincon, Natalia; Wood, Derrick E.; Breitwieser, Florian P.; Pockrandt, Christopher; Langmead, Ben; Salzberg, Steven L.; Steinegger, Martin Nature Protocols, Vol.17 No.12, pp.2815-2839	DOI
2022-12	Structure-guided isoform identification for the human transcriptome Sommer, Markus J.; Cha, Sooyoung; Varabyou, Ales; Rincon, Natalia; Park, Sukhwan; Minkin, Ilia; Pertea, Mihaela; Steinegger, Martin; Salzberg, Steven L. eLife, Vol.11	DOI
2023-01	UFCG: database of universal fungal core genes and pipeline for genome-wide phylogenetic analysis of fungi Kim, Dongwook; Gilchrist, Cameron L. M.; Chun, Jongsik; Steinegger, Martin Nucleic Acids Research, Vol.51 No.D1, pp.D777-D784	DOI
2023-01	LambdaPP: Fast and accessible protein-specific phenotype predictions Olenyi, Tobias; Marquet, Céline; Heinzinger, Michael; Kröger, Benjamin; Nikolova, Tiha; Bernhofer, Michael; Sändig, Philip; Schütze, Konstantin; Littmann, Maria; Mirdita, Milot; Steinegger, Martin; Dallago, Christian; Rost, Burkhard Protein Science, Vol.32 No.1, p. e4524	DOI
2023-02	AlphaFold2 reveals commonalities and novelties in protein structure space for 21 model organisms Bordin, Nicola; Sillitoe, Ian; Nallapareddy, Vamsi; Rauer, Clemens; Lam, Su Datt; Waman, Vaishali P.; Sen, Neeladri; Heinzinger, Michael; Littmann, Maria; Kim, Stephanie; Velankar, Sameer; Steinegger, Martin; Rost, Burkhard; Orengo, Christine Communications Biology, Vol.6 No.1, p. 160	DOI
2023-04	Foldcomp: a library and format for compressing and indexing large protein structure sets Kim, Hyunbin; Mirdita, Milot; Steinegger, Martin Bioinformatics, Vol.39 No.4	DOI
2023-04	Novel machine learning approaches revolutionize protein knowledge Bordin, Nicola; Dallago, Christian; Heinzinger, Michael; Kim, Stephanie; Littmann, Maria; Rauer, Clemens; Steinegger, Martin; Rost, Burkhard; Orengo, Christine Trends in Biochemical Sciences, Vol.48 No.4, pp.345-359	DOI
2023-05	Cross-phyla protein annotation by structural prediction and alignment Ruperti, Fabian; Papadopoulos, Nikolaos; Musser, Jacob M.; Mirdita, Milot; Steinegger, Martin; Arendt, Detlev Genome Biology, Vol.24 No.1, p. 113	DOI
2023-07	Qualitative metabolomics-based characterization of a phenolic UDP-xylosyltransferase with a broad substrate spectrum from Lentinus brumalis Jeong, Eunah; Kim, Wonyong; Son, Seungju; Yang, Sungyeon; Gwon, Dasom; Hong, Jihee; Cho, Yoonhee; Jang, Chang-Young; Steinegger, Martin; Lim, Young Woon; Kang, Kyo Bin Proceedings of the National Academy of Sciences of the United States of America, Vol.120 No.28, p. e2301007120	DOI
2023-08	Block Aligner: an adaptive SIMD-accelerated aligner for sequences and position-specific scoring matrices Liu, Daniel; Steinegger, Martin Bioinformatics, Vol.39 No.8, p. 487	DOI
2023-10	Clustering predicted structures at the scale of the known protein universe Barrio-Hernandez, Inigo; Yeo, Jingi; Jänes, Jürgen; Mirdita, Milot; Gilchrist, Cameron L. M.; Wein, Tanita; Varadi, Mihaly; Velankar, Sameer; Beltrao, Pedro; Steinegger, Martin Nature, Vol.622 No.7983, pp.637-645	DOI
2023-10	CHESS 3: an improved, comprehensive catalog of human genes and transcripts based on large-scale expression data, phylogenetic analysis, and protein structure Varabyou, Ales; Sommer, Markus J.; Erdogdu, Beril; Shinder, Ida; Minkin, Ilia; Chao, Kuan-Hao; Park, Sukhwan; Heinz, Jakob; Pockrandt, Christopher; Shumate, Alaina; Rincon, Natalia; Puiu, Daniela; Steinegger, Martin; Salzberg, Steven L.; Pertea, Mihaela Genome Biology, Vol.24 No.1, p. 249	DOI
2023-11	DescribePROT in 2023: more, higher-quality and experimental annotations and improved data download options Basu, Sushmita; Zhao, Bi; Biro, Balint; Faraggi, Eshel; Gsponer, Jorg; Hu, Gang; Kloczkowski, Andrzej; Malhis, Nawar; Mirdita, Milot; Soeding, Johannes; Steinegger, Martin; Wang, Duolin; Wang, Kui; Xu, Dong; Zhang, Jian; Kurgan, Lukasz Nucleic Acids Research, Vol.52 No.D1, pp.D426-D433	DOI
2023-11	AlphaFold Protein Structure Database in 2024: providing structure coverage for over 214 million protein sequences Varadi, Mihaly; Bertoni, Damian; Magana, Paulyna; Paramval, Urmila; Pidruchna, Ivanna; Radhakrishnan, Malarvizhi; Tsenkov, Maxim; Nair, Sreenath; Mirdita, Milot; Yeo, Jingi; Kovalevskiy, Oleg; Tunyasuvunakool, Kathryn; Laydon, Agata; Zidek, Augustin; Tomlinson, Hamish; Hariharan, Dhavanthi; Abrahamson, Josh; Green, Tim; Jumper, John; Birney, Ewan; Steinegger, Martin; Hassabis, Demis; Velankar, Sameer Nucleic Acids Research, Vol.52 No.D1, pp.D368-D375	DOI
2024	Petabase-Scale Homology Search for Structure Prediction Lee, Sewon; Kim, Gyuri; Karin, Eli Levy; Mirdita, Milot; Park, Sukhwan; Chikhi, Rayan; Babaian, Artem; Kryshtafovych, Andriy; Steinegger, Martin Cold Spring Harbor perspectives in biology, Vol.16 No.5	DOI
2024-02	Fast and accurate protein structure search with Foldseek van Kempen, Michel; Kim, Stephanie S.; Tumescheit, Charlotte; Mirdita, Milot; Lee, Jeongjae; Gilchrist, Cameron L. M.; Soeding, Johannes; Steinegger, Martin Nature Biotechnology, Vol.42 No.2, pp.243-246	DOI