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2020 – today
- 2023
[j10]Maxim Zvyagin, Alexander Brace, Kyle Hippe, Yuntian Deng, Bin Zhang, Cindy Orozco Bohorquez, Austin Clyde, Bharat Kale, Danilo Perez-Rivera, Heng Ma, Carla M. Mann
, Michael W. Irvin, Defne G. Ozgulbas, Natalia Vassilieva, J. Gregory Pauloski, Logan T. Ward, Valérie Hayot-Sasson, Murali Emani, Sam Foreman, Zhen Xie, Diangen Lin, Maulik Shukla, Weili Nie, Josh Romero, Christian Dallago, Arash Vahdat, Chaowei Xiao, Thomas Gibbs, Ian T. Foster, James J. Davis, Michael E. Papka, Thomas S. Brettin, Rick Stevens, Anima Anandkumar, Venkatram Vishwanath, Arvind Ramanathan:
GenSLMs: Genome-scale language models reveal SARS-CoV-2 evolutionary dynamics. Int. J. High Perform. Comput. Appl. 37(6): 683-705 (2023)- [i4]Shuaiwen Leon Song, Bonnie Kruft, Minjia Zhang, Conglong Li, Shiyang Chen, Chengming Zhang, Masahiro Tanaka, Xiaoxia Wu, Jeff Rasley, Ammar Ahmad Awan, Connor Holmes, Martin Cai, Adam Ghanem, Zhongzhu Zhou, Yuxiong He, Pete Luferenko, Divya Kumar, Jonathan A. Weyn, Ruixiong Zhang, Sylwester Klocek, Volodymyr Vragov, Mohammed AlQuraishi, Gustaf Ahdritz, Christina Floristean, Cristina Negri, Rao Kotamarthi, Venkatram Vishwanath, Arvind Ramanathan, Sam Foreman, Kyle Hippe, Troy Arcomano, Romit Maulik, Maxim Zvyagin, Alexander Brace, Bin Zhang, Cindy Orozco Bohorquez, Austin Clyde, Bharat Kale, Danilo Perez-Rivera, Heng Ma, Carla M. Mann, Michael W. Irvin, J. Gregory Pauloski, Logan T. Ward, Valérie Hayot-Sasson, Murali Emani, Zhen Xie, Diangen Lin, Maulik Shukla, Ian T. Foster, James J. Davis, Michael E. Papka, Thomas S. Brettin, Prasanna Balaprakash, Gina Tourassi, John Gounley, Heidi A. Hanson, Thomas E. Potok, Massimiliano Lupo Pasini, Kate Evans, Dan Lu, Dalton D. Lunga, Junqi Yin, Sajal Dash, Feiyi Wang, Mallikarjun Shankar, Isaac Lyngaas, Xiao Wang, Guojing Cong, Pei Zhang, Ming Fan, Siyan Liu, Adolfy Hoisie, Shinjae Yoo, Yihui Ren, William Tang, Kyle Felker, Alexey Svyatkovskiy, Hang Liu, Ashwin M. Aji, Angela Dalton, Michael J. Schulte, Karl Schulz, Yuntian Deng, Weili Nie, Josh Romero, Christian Dallago, Arash Vahdat, Chaowei Xiao, Thomas Gibbs, Anima Anandkumar, Rick Stevens:
DeepSpeed4Science Initiative: Enabling Large-Scale Scientific Discovery through Sophisticated AI System Technologies. CoRR abs/2310.04610 (2023) - 2022
- [j9]Valérie de Crécy-Lagard, Rocio Amorin de Hegedus, Cecilia N. Arighi, Jill Babor, Alex Bateman, Ian Blaby, Crysten Blaby-Haas, Alan J. Bridge, Stephen K. Burley, Stacey Cleveland, Lucy J. Colwell, Ana Conesa, Christian Dallago, Antoine Danchin, Anita de Waard, Adam Deutschbauer, Raquel Dias, Yousong Ding, Gang Fang, Iddo Friedberg, John Gerlt, Joshua Goldford, Mark Gorelik, Benjamin M. Gyori, Christopher S. Henry, Geoffrey Hutinet, Marshall Jaroch, Peter D. Karp, Liudmyla Kondratova, Zhiyong Lu, Aron Marchler-Bauer, Maria Jesus Martin, Claire D. McWhite, Gaurav D. Moghe, Paul Monaghan, Anne Morgat, Christopher J. Mungall, Darren A. Natale, William C. Nelson, Seán I. O'Donoghue, Christine A. Orengo, Katherine H. O'Toole, Predrag Radivojac, Colbie Reed, Richard J. Roberts, Dmitri Rodionov, Irina A. Rodionova, Jeffrey DePons, Lana Saleh, Gloria M. Sheynkman, Françoise Thibaud-Nissen, Paul D. Thomas, Peter Uetz, David Vallenet, Erica Watson Carter, Peter Weigele, Valerie Wood, Elisha M. Wood-Charlson, Jin Xu:
A roadmap for the functional annotation of protein families: a community perspective. Database J. Biol. Databases Curation 2022(2022) (2022) - [j8]Ludwig Lautenbacher, Patroklos Samaras, Julian Müller, 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) - [j7]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) - [c2]Hannes Stärk, Dominique Beaini, Gabriele Corso, Prudencio Tossou, Christian Dallago, Stephan Günnemann, Pietro Lió:
3D Infomax improves GNNs for Molecular Property Prediction. ICML 2022: 20479-20502 - 2021
- [j6]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) - [j5]Max Franz, Jeffrey V. Wong, Metin Can Siper, Christian Dallago, John M. Giorgi, Emek Demir, Chris Sander, Gary D. Bader:
A flexible search system for high-accuracy identification of biological entities and molecules. J. Open Source Softw. 6(67): 3756 (2021) - [j4]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) - [c1]Christian Dallago, Jody Mou, Kadina E. Johnston, Bruce J. Wittmann, Nicholas Bhattacharya, Samuel Goldman, Ali Madani, Kevin K. Yang:
FLIP: Benchmark tasks in fitness landscape inference for proteins. NeurIPS Datasets and Benchmarks 2021 - [i3]Hannes Stärk, Dominique Beaini, Gabriele Corso, Prudencio Tossou, Christian Dallago, Stephan Günnemann, Pietro Liò:
3D Infomax improves GNNs for Molecular Property Prediction. CoRR abs/2110.04126 (2021) - 2020
- [j3]Igor V. Rodchenkov, Ozgun Babur, Augustin Luna, Bülent Arman Aksoy, Jeffrey V. Wong, Dylan Fong, Max Franz, Metin Can Siper, Manfred Cheung, Michael Wrana, Harsh Mistry, Logan Mosier, Jonah Dlin, Qizhi Wen, Caitlin O'Callaghan, Wanxin Li, Geoffrey Elder, Peter T. Smith, Christian Dallago, Ethan Cerami, Benjamin Gross, Ugur Dogrusoz, Emek Demir, Gary D. Bader, Chris Sander:
Pathway Commons 2019 Update: integration, analysis and exploration of pathway data. Nucleic Acids Res. 48(Database-Issue): D489-D497 (2020) - [i2]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) - [i1]Roc Reguant, Yevgeniy Antipin, Robert P. Sheridan, Christian Dallago, Drew Diamantoukos, Augustin Luna, Chris Sander, Nicholas Paul Gauthier:
AlignmentViewer: Sequence Analysis of Large Protein Families. F1000Research 9: 213 (2020)
2010 – 2019
- 2019
- [j2]Thomas A. Hopf, Anna G. Green, Benjamin Schubert, Sophia Mersmann, Charlotta Schärfe, John Ingraham, Ágnes Tóth-Petróczy, Kelly Brock, Adam J. Riesselman, Perry Palmedo, Chan Kang, Robert P. Sheridan, Eli J. Draizen, Christian Dallago, Chris Sander, Debora S. Marks:
The EVcouplings Python framework for coevolutionary sequence analysis. Bioinform. 35(9): 1582-1584 (2019) - [j1]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)
Coauthor Index
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