Published in Nature Communications, 2024
Generative diffusion model for protein structures; trigonometry is all you need!
Recommended citation: Wu, K. E., Yang, K. K., van den Berg, R., Alamdari, S., Zou, J. Y., Lu, A. X., & Amini, A. P. (2024). Protein structure generation via folding diffusion. Nature Communications, 15(1), 1059. https://www.nature.com/articles/s41467-024-45051-2
Published in bioRxiv, 2021
Large language modeling of T-cell receptor sequences
Recommended citation: Wu, K., Yost, K.E., Daniel, B., Belk, J.A., Xia, Y., Egawa, T., Satpathy, A., Chang, H.Y. and Zou, J., 2021. TCR-BERT: learning the grammar of T-cell receptors for flexible antigen-xbinding analyses. bioRxiv. https://www.biorxiv.org/content/10.1101/2021.11.18.469186v1.full.pdf
Published in Proceedings of the National Academy of Sciences, 2021
BABEL enables computational imputation of single-cell multi-omic profiles with only a single modality as input
Recommended citation: Wu, K.E., Yost, K.E., Chang, H.Y. and Zou, J., 2021. BABEL enables cross-modality translation between multiomic profiles at single-cell resolution. Proceedings of the National Academy of Sciences, 118(15), p.e2023070118. https://www.pnas.org/doi/abs/10.1073/pnas.2023070118
Published in Cell systems, 2020
Machine learning model for RNA localization allows hypothesis generation regarding behavior of SARS-CoV-2 transcriptome
Recommended citation: Wu, K.E., Fazal, F.M., Parker, K.R., Zou, J. and Chang, H.Y., 2020. RNA-GPS predicts SARS-CoV-2 RNA residency to host mitochondria and nucleolus. Cell systems, 11(1), pp.102-108. https://www.sciencedirect.com/science/article/pii/S2405471220302374
Published in RNA, 2020
Biologically-inspired featurization of RNA transcripts enables state-of-the-art modeling of RNA subcellular localization
Recommended citation: Wu, K.E., Parker, K.R., Fazal, F.M., Chang, H.Y. and Zou, J., 2020. RNA-GPS predicts high-resolution RNA subcellular localization and highlights the role of splicing. RNA, 26(7), pp.851-865. Vancouver https://rnajournal.cshlp.org/content/26/7/851.short