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- Burkhard Rost
TU Munich, Faculty of Computer Science
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Publication search results
found 109 matches
- 2023
- Vamsi Nallapareddy, Nicola Bordin, Ian Sillitoe, Michael Heinzinger, Maria Littmann, Vaishali P. Waman, Neeladri Sen, Burkhard Rost, Christine A. Orengo:
CATHe: detection of remote homologues for CATH superfamilies using embeddings from protein language models. Bioinform. 39(1) (2023) - Alessio Del Conte, Adel Bouhraoua, Mahta Mehdiabadi, Damiano Clementel, Alexander Miguel Monzon, Alex S. Holehouse, Daniel A. Griffith, Ryan J. Emenecker, Ashwini Patil, Ronesh Sharma, Tatsuhiko Tsunoda, Alok Sharma, Yi Jun Tang, Bin Liu, Claudio Mirabello, Björn Wallner, Burkhard Rost, Dagmar Ilzhöfer, Maria Littmann, Michael Heinzinger, Lea I M. Krautheimer, Michael Bernhofer, Liam J. McGuffin, Isabelle Callebaut, Tristan Bitard Feildel, Jian Liu, Jianlin Cheng, Zhiye Guo, Jinbo Xu, Sheng Wang, Nawar Malhis, Jörg Gsponer, Chol-Song Kim, Kun-Sop Han, Myong-Chol Ma, Lukasz A. Kurgan, Sina Ghadermarzi, Akila Katuwawala, Bi Zhao, Zhenling Peng, Zhonghua Wu, Gang Hu, Kui Wang, Md. Tamjidul Hoque, Md Wasi Ul Kabir, Michele Vendruscolo, Pietro Sormanni, Min Li, Fuhao Zhang, Pengzhen Jia, Yida Wang, Michail Yu. Lobanov, Oxana V. Galzitskaya, Wim F. Vranken, Adrián Díaz, Thomas Litfin, Yaoqi Zhou, Jack Hanson, Kuldip K. Paliwal, Zsuzsanna Dosztányi, Gábor Erdös, Silvio C. E. Tosatto, Damiano Piovesan:
CAID prediction portal: a comprehensive service for predicting intrinsic disorder and binding regions in proteins. Nucleic Acids Res. 51(W1): 62-69 (2023) - Ahmed Elnaggar, Hazem Essam, Wafaa Salah-Eldin, Walid Moustafa, Mohamed Elkerdawy, Charlotte Rochereau, Burkhard Rost:
Ankh: Optimized Protein Language Model Unlocks General-Purpose Modelling. CoRR abs/2301.06568 (2023) - 2022
- Michael Bernhofer, Burkhard Rost:
TMbed: transmembrane proteins predicted through language model embeddings. BMC Bioinform. 23(1): 326 (2022) - Dagmar Ilzhöfer, Michael Heinzinger, Burkhard Rost:
SETH predicts nuances of residue disorder from protein embeddings. Frontiers Bioinform. 2 (2022) - Konstantin Schütze, Michael Heinzinger, Martin Steinegger, Burkhard Rost:
Nearest neighbor search on embeddings rapidly identifies distant protein relations. Frontiers Bioinform. 2 (2022) - Ludwig Lautenbacher, Patroklos Samaras, Julian Muller, Andreas Grafberger, Marwin Shraideh, Johannes Rank, Simon T. Fuchs, Tobias K. Schmidt, Matthew The, Christian Dallago, Holger Wittges, Burkhard Rost, Helmut Krcmar, Bernhard Küster, Mathias Wilhelm:
ProteomicsDB: toward a FAIR open-source resource for life-science research. Nucleic Acids Res. 50(D1): 1541- (2022) - Ahmed Elnaggar, Michael Heinzinger, Christian Dallago, Ghalia Rehawi, Yu Wang, Llion Jones, Tom Gibbs, Tamas Feher, Christoph Angerer, Martin Steinegger, Debsindhu Bhowmik, Burkhard Rost:
ProtTrans: Toward Understanding the Language of Life Through Self-Supervised Learning. IEEE Trans. Pattern Anal. Mach. Intell. 44(10): 7112-7127 (2022) - Gabriel Foley, Ariane Mora, Connie M. Ross, Scott Bottoms, Leander Sützl, Marnie L. Lamprecht, Julian Zaugg, Alexandra Essebier, Brad Balderson, Rhys Newell, Raine E. S. Thomson, Bostjan Kobe, Ross T. Barnard, Luke Guddat, Gerhard Schenk, Jörg Carsten, Yosephine Gumulya, Burkhard Rost, Dietmar Haltrich, Volker Sieber, Elizabeth M. J. Gillam, Mikael Bodén:
Engineering indel and substitution variants of diverse and ancient enzymes using Graphical Representation of Ancestral Sequence Predictions (GRASP). PLoS Comput. Biol. 18(10): 1010633 (2022) - 2021
- Jan Zaucha, Michael Heinzinger, A. Kulandaisamy, Evans Kataka, Óscar Llorian Salvádor, Petr Popov, Burkhard Rost, M. Michael Gromiha, Boris S. Zhorov, Dmitrij Frishman:
Mutations in transmembrane proteins: diseases, evolutionary insights, prediction and comparison with globular proteins. Briefings Bioinform. 22(3) (2021) - Maria Littmann, Nicola Bordin, Michael Heinzinger, Konstantin Schütze, Christian Dallago, Christine A. Orengo, Burkhard Rost:
Clustering FunFams using sequence embeddings improves EC purity. Bioinform. 37(20): 3449-3455 (2021) - 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:
PredictProtein - Predicting Protein Structure and Function for 29 Years. Nucleic Acids Res. 49(Webserver-Issue): 535-540 (2021) - Ahmed Elnaggar, Wei Ding, Llion Jones, Tom Gibbs, Tamas Feher, Christoph Angerer, Silvia Severini, Florian Matthes, Burkhard Rost:
CodeTrans: Towards Cracking the Language of Silicone's Code Through Self-Supervised Deep Learning and High Performance Computing. CoRR abs/2104.02443 (2021) - 2020
- Jiajun Qiu, Dmitrii Nechaev, Burkhard Rost:
Protein-protein and protein-nucleic acid binding residues important for common and rare sequence variants in human. BMC Bioinform. 21(1): 452 (2020) - Jonas Reeb, Theresa Wirth, Burkhard Rost:
Variant effect predictions capture some aspects of deep mutational scanning experiments. BMC Bioinform. 21(1): 107 (2020) - Maria Littmann, Katharina Selig, Liel Cohen-Lavi, Yotam Frank, Peter Hönigschmid, Evans Kataka, Anja Mösch, Kun Qian, Avihai Ron, Sebastian Schmid, Adam Sorbie, Liran Szlak, Ayana Dagan-Wiener, Nir Ben-Tal, Masha Y. Niv, Daniel Razansky, Björn W. Schuller, Donna P. Ankerst, Tomer Hertz, Burkhard Rost:
Validity of machine learning in biology and medicine increased through collaborations across fields of expertise. Nat. Mach. Intell. 2(1): 18-24 (2020) - Ahmed Elnaggar, Michael Heinzinger, Christian Dallago, Ghalia Rehawi, Yu Wang, Llion Jones, Tom Gibbs, Tamas Feher, Christoph Angerer, Martin Steinegger, Debsindhu Bhowmik, Burkhard Rost:
ProtTrans: Towards Cracking the Language of Life's Code Through Self-Supervised Deep Learning and High Performance Computing. CoRR abs/2007.06225 (2020) - 2019
- Michael Heinzinger, Ahmed Elnaggar, Yu Wang, Christian Dallago, Dmitrii Nechaev, Florian Matthes, Burkhard Rost:
Modeling aspects of the language of life through transfer-learning protein sequences. BMC Bioinform. 20(1): 723 (2019) - Maria Littmann, Tatyana Goldberg, Sebastian Seitz, Mikael Bodén, Burkhard Rost:
Detailed prediction of protein sub-nuclear localization. BMC Bioinform. 20(1): 205:1-205:15 (2019) - Maria Littmann, Tatyana Goldberg, Sebastian Seitz, Mikael Bodén, Burkhard Rost:
Correction to: Detailed prediction of protein sub-nuclear localization. BMC Bioinform. 20(1): 727 (2019) - Linus Scheibenreif, Maria Littmann, Christine A. Orengo, Burkhard Rost:
FunFam protein families improve residue level molecular function prediction. BMC Bioinform. 20(1): 400:1-400:9 (2019) - Jonas Reeb, Burkhard Rost:
Secondary Structure Prediction. Encyclopedia of Bioinformatics and Computational Biology (2) 2019: 488-496 - 2018
- Yannick Mahlich, Martin Steinegger, Burkhard Rost, Yana Bromberg:
HFSP: high speed homology-driven function annotation of proteins. Bioinform. 34(13): i304-i312 (2018) - Valérie Marot-Lassauzaie, Michael Bernhofer, Burkhard Rost:
Correcting mistakes in predicting distributions. Bioinform. 34(19): 3385-3386 (2018) - Juan Miguel Cejuela, Shrikant Vinchurkar, Tatyana Goldberg, Madhukar Sollepura Prabhu Shankar, Ashish Baghudana, Aleksandar Bojchevski, Carsten Uhlig, André Ofner, Pandu Raharja-Liu, Lars Juhl Jensen, Burkhard Rost:
LocText: relation extraction of protein localizations to assist database curation. BMC Bioinform. 19(1): 15:1-15:11 (2018) - Michael Bernhofer, Tatyana Goldberg, Silvana Wolf, Mohamed Ahmed, Julian Zaugg, Mikael Bodén, Burkhard Rost:
NLSdb - major update for database of nuclear localization signals and nuclear export signals. Nucleic Acids Res. 46(Database-Issue): D503-D508 (2018) - 2017
- Juan Miguel Cejuela, Aleksandar Bojchevski, Carsten Uhlig, Rustem Bekmukhametov, Sanjeev Kumar Karn, Shpend Mahmuti, Ashish Baghudana, Ankit Dubey, Venkata P. Satagopam, Burkhard Rost:
nala: text mining natural language mutation mentions. Bioinform. 33(12): 1852-1858 (2017) - Julien Gagneur, Caroline C. Friedel, Volker Heun, Ralf Zimmer, Burkhard Rost:
Bioinformatics advances biology and medicine by turning big data troves into knowledge. Inform. Spektrum 40(2): 153-160 (2017) - Julien Gagneur, Caroline C. Friedel, Volker Heun, Ralf Zimmer, Burkhard Rost:
Bioinformatics Advances Biology and Medicine by Turning Big Data Troves into Knowledge. 50 Jahre Universitäts-Informatik in München 2017: 33-45 - 2016
- Guy Yachdav, Sebastian Wilzbach, Benedikt Rauscher, Robert Sheridan, Ian Sillitoe, James B. Procter, Suzanna E. Lewis, Burkhard Rost, Tatyana Goldberg:
MSAViewer: interactive JavaScript visualization of multiple sequence alignments. Bioinform. 32(22): 3501-3503 (2016)
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