Publications

An explainable deep learning platform for molecular discovery

Felix Wong, Satotaka Omori, Alicia Li, Aarti Krishnan, Ryan S. Lach, Joseph Rufo, Maxwell Z. Wilson & James J. Collins (2024)

Accurate RNA 3D structure prediction using a language model-based deep learning approach

Tao Shen, Zhihang Hu, Siqi Sun, Di Liu, Felix Wong, Jiuming Wang, Jiayang Chen, Yixuan Wang, Liang Hong, Jin Xiao, Liangzhen Zheng, Tejas Krishnamoorthi, Irwin King, Sheng Wang, Peng Yin, James J. Collins & Yu Li (2024)

Deep generative design of RNA aptamers using structural predictions

Felix Wong, Dongchen He, Aarti Krishnan, Liang Hong, Alexander Z. Wang, Jiuming Wang, Zhihang Hu, Satotaka Omori, Alicia Li, Jiahua Rao, Qinze Yu, Wengong Jin, Tianqing Zhang, Katherine Ilia, Jack X. Chen, Shuangjia Zheng, Irwin King, Yu Li & James J. Collins (2024)

Discovery of a structural class of antibiotics with explainable deep learning

Felix Wong, Erica J. Zheng, Jacqueline A. Valeri, Nina M. Donghia, Melis N. Anahtar, Satotaka Omori, Alicia Li, Andres Cubillos-Ruiz, Aarti Krishnan, Wengong Jin, Abigail L. Manson, Jens Friedrichs, Ralf Helbig, Behnoush Hajian, Dawid K. Fiejtek, Florence F. Wagner, Holly H. Soutter, Ashlee M. Earl, Jonathan M. Stokes, Lars D. Renner & James J. Collins (2024)

Optogenetic control of the integrated stress response reveals proportional encoding and the stress memory landscape

Taivan Batjargal, Francesca Zappa, Ryan J. Grant, Robert A. Piscopio, Alex Chialastri, Siddharth S. Dey, Diego Acosta-Alvear & Maxwell Z. Wilson (2023)

Discovering small-molecule senolytics with deep neural networks

Felix Wong, Satotaka Omori, Nina M. Donghia, Erica J. Zheng & James J. Collins (2023)