| Categorical dimensions of human odor descriptor space revealed by non-negative matrix factorization JB Castro, A Ramanathan, CS Chennubhotla PloS one 8 (9), e73289, 2013 | 199 | 2013 |
| Supercomputer-based ensemble docking drug discovery pipeline with application to COVID-19 A Acharya, R Agarwal, MB Baker, J Baudry, D Bhowmik, S Boehm, ... Journal of chemical information and modeling 60 (12), 5832-5852, 2020 | 183 | 2020 |
| 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 | 179 | 2021 |
| Hierarchical attention networks for information extraction from cancer pathology reports S Gao, MT Young, JX Qiu, HJ Yoon, JB Christian, PA Fearn, GD Tourassi, ... Journal of the American Medical Informatics Association 25 (3), 321-330, 2018 | 165 | 2018 |
| Evolutionarily Conserved Linkage between Enzyme Fold, Flexibility, and Catalysis A Ramanathan, PK Agarwal PLoS Biology 9 (11), e1001193, 2011 | 131 | 2011 |
| Protein conformational populations and functionally relevant substates A Ramanathan, A Savol, V Burger, CS Chennubhotla, PK Agarwal Accounts of chemical research 47 (1), 149-156, 2014 | 118 | 2014 |
| 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 | 113 | 2021 |
| 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 | 102 | 2023 |
| Discovery of Small Molecules that Inhibit the Disordered Protein, p27Kip1 LI Iconaru, D Ban, K Bharatham, A Ramanathan, W Zhang, AA Shelat, ... Scientific reports 5 (1), 15686, 2015 | 88 | 2015 |
| Deepdrivemd: Deep-learning driven adaptive molecular simulations for protein folding H Lee, M Turilli, S Jha, D Bhowmik, H Ma, A Ramanathan 2019 IEEE/ACM Third Workshop on Deep Learning on Supercomputers (DLS), 12-19, 2019 | 86 | 2019 |
| Discovering conformational sub-states relevant to protein function A Ramanathan, AJ Savol, CJ Langmead, PK Agarwal, CS Chennubhotla PLoS ONE 6 (1), e15827, 2011 | 84 | 2011 |
| Deep clustering of protein folding simulations D Bhowmik, S Gao, MT Young, A Ramanathan BMC bioinformatics 19, 47-58, 2018 | 83 | 2018 |
| # 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 | 80 | 2023 |
| Machine learning–driven multiscale modeling reveals lipid-dependent dynamics of RAS signaling proteins HI Ingólfsson, C Neale, TS Carpenter, R Shrestha, CA López, TH Tran, ... Proceedings of the National Academy of Sciences 119 (1), e2113297119, 2022 | 79 | 2022 |
| Hierarchical convolutional attention networks for text classification S Gao, A Ramanathan, G Tourassi Proceedings of The Third Workshop on Representation Learning for NLP, 11-23, 2018 | 75 | 2018 |
| Mechanism of glucocerebrosidase activation and dysfunction in Gaucher disease unraveled by molecular dynamics and deep learning R Romero, A Ramanathan, T Yuen, D Bhowmik, M Mathew, LB Munshi, ... Proceedings of the National Academy of Sciences 116 (11), 5086-5095, 2019 | 72 | 2019 |
| Accounting for conformational entropy in predicting binding free energies of protein‐protein interactions H Kamisetty, A Ramanathan, C Bailey‐Kellogg, CJ Langmead Proteins: Structure, Function, and Bioinformatics 79 (2), 444-462, 2011 | 68 | 2011 |
| Classifying cancer pathology reports with hierarchical self-attention networks S Gao, JX Qiu, M Alawad, JD Hinkle, N Schaefferkoetter, HJ Yoon, ... Artificial intelligence in medicine 101, 101726, 2019 | 65 | 2019 |
| A text-guided protein design framework S Liu, Y Li, Z Li, A Gitter, Y Zhu, J Lu, Z Xu, W Nie, A Ramanathan, C Xiao, ... arXiv preprint arXiv:2302.04611, 2023 | 64 | 2023 |
| Computational identification of slow conformational fluctuations in proteins A Ramanathan, PK Agarwal Journal of Physical Chemistry B 113 (52), 16669–16680, 2009 | 62 | 2009 |