SARS-CoV-2 infects the human kidney and drives fibrosis in kidney organoids J Jansen, KC Reimer, JS Nagai, FS Varghese, GJ Overheul, M de Beer, ... Cell stem cell 29 (2), 217-231. e8, 2022 | 187 | 2022 |
AI-driven multiscale simulations illuminate mechanisms of SARS-CoV-2 spike dynamics L Casalino, AC Dommer, Z Gaieb, EP Barros, T Sztain, SH Ahn, A Trifan, ... The International Journal of High Performance Computing Applications 35 (5 …, 2021 | 162 | 2021 |
High-throughput virtual screening and validation of a SARS-CoV-2 main protease noncovalent inhibitor A Clyde, S Galanie, DW Kneller, H Ma, Y Babuji, B Blaiszik, A Brace, ... Journal of chemical information and modeling 62 (1), 116-128, 2021 | 98 | 2021 |
# COVIDisAirborne: AI-enabled multiscale computational microscopy of delta SARS-CoV-2 in a respiratory aerosol A Dommer, L Casalino, F Kearns, M Rosenfeld, N Wauer, SH Ahn, ... The international journal of high performance computing applications 37 (1 …, 2023 | 70 | 2023 |
GenSLMs: Genome-scale language models reveal SARS-CoV-2 evolutionary dynamics M Zvyagin, A Brace, K Hippe, Y Deng, B Zhang, CO Bohorquez, A Clyde, ... The International Journal of High Performance Computing Applications 37 (6 …, 2023 | 59 | 2023 |
A cross-study analysis of drug response prediction in cancer cell lines F Xia, J Allen, P Balaprakash, T Brettin, C Garcia-Cardona, A Clyde, ... Briefings in bioinformatics 23 (1), bbab356, 2022 | 56 | 2022 |
COVID moonshot: open science discovery of SARS-CoV-2 main protease inhibitors by combining crowdsourcing, high-throughput experiments, computational simulations, and machine … H Achdout, A Aimon, E Bar-David, GM Morris BioRxiv, 2020 | 51 | 2020 |
Deep learning methods for drug response prediction in cancer: predominant and emerging trends A Partin, TS Brettin, Y Zhu, O Narykov, A Clyde, J Overbeek, RL Stevens Frontiers in medicine 10, 1086097, 2023 | 48 | 2023 |
Structural, electronic, and electrostatic determinants for inhibitor binding to subsites S1 and S2 in SARS-CoV-2 main protease DW Kneller, H Li, S Galanie, G Phillips, A Labbé, KL Weiss, Q Zhang, ... Journal of medicinal chemistry 64 (23), 17366-17383, 2021 | 44 | 2021 |
Open science discovery of potent noncovalent SARS-CoV-2 main protease inhibitors ML Boby, D Fearon, M Ferla, M Filep, L Koekemoer, MC Robinson, ... Science 382 (6671), eabo7201, 2023 | 41 | 2023 |
Open Science Discovery of Potent Non-Covalent SARS-CoV-2 Main Protease Inhibitors COVID Moonshot Consortium, H Achdout, A Aimon, DS Alonzi, R Arbon, ... BioRxiv, 2020.10. 29.339317, 2020 | 39 | 2020 |
Pandemic drugs at pandemic speed: infrastructure for accelerating COVID-19 drug discovery with hybrid machine learning-and physics-based simulations on high-performance computers AP Bhati, S Wan, D Alfè, AR Clyde, M Bode, L Tan, M Titov, A Merzky, ... Interface focus 11 (6), 20210018, 2021 | 37 | 2021 |
Impeccable: Integrated modeling pipeline for covid cure by assessing better leads AA Saadi, D Alfe, Y Babuji, A Bhati, B Blaiszik, A Brace, T Brettin, K Chard, ... Proceedings of the 50th International Conference on Parallel Processing, 1-12, 2021 | 37 | 2021 |
Targeting sars-cov-2 with ai-and hpc-enabled lead generation: A first data release Y Babuji, B Blaiszik, T Brettin, K Chard, R Chard, A Clyde, I Foster, Z Hong, ... arXiv preprint arXiv:2006.02431, 2020 | 28 | 2020 |
Scalable HPC & AI infrastructure for COVID-19 therapeutics H Lee, A Merzky, L Tan, M Titov, M Turilli, D Alfe, A Bhati, A Brace, ... Proceedings of the Platform for Advanced Scientific Computing Conference, 1-13, 2021 | 22 | 2021 |
Learning curves for drug response prediction in cancer cell lines A Partin, T Brettin, YA Evrard, Y Zhu, H Yoo, F Xia, S Jiang, A Clyde, ... BMC bioinformatics 22, 1-18, 2021 | 21 | 2021 |
AI-accelerated protein-ligand docking for SARS-CoV-2 is 100-fold faster with no significant change in detection A Clyde, X Liu, T Brettin, H Yoo, A Partin, Y Babuji, B Blaiszik, ... Scientific reports 13 (1), 2105, 2023 | 18 | 2023 |
Intelligent resolution: Integrating cryo-em with ai-driven multi-resolution simulations to observe the sars-cov-2 replication-transcription machinery in action A Trifan, D Gorgun, Z Li, A Brace, M Zvyagin, H Ma, A Clyde, D Clark, ... bioRxiv, 2021.10. 09.463779, 2021 | 12 | 2021 |
Spatial graph attention and curiosity-driven policy for antiviral drug discovery Y Wu, M Cashman, N Choma, ET Prates, VGM Vergara, M Shah, A Chen, ... arXiv preprint arXiv:2106.02190, 2021 | 11 | 2021 |
Regression enrichment surfaces: a simple analysis technique for virtual drug screening models A Clyde, X Duan, R Stevens arXiv preprint arXiv:2006.01171, 2020 | 11 | 2020 |