You can also find my articles on my Google Scholar profile. († indicates equal contribution.)

Preprints

PRETZEL: A Benchmark for Cyclic Peptide Structure Prediction
Hong, Y.†, Fang, Z.†, Ubale, M.†, Chen, X., Liu, Y., & Katritch, V.
Preprint (2026).

Scaling Graph Neural Bandits to Million-Molecule Virtual Screening
Siam, Z. S.†, Hong, Y.†, Katritch, V., Liu, Y., Kang, J., & Liu, C.
Preprint (2026).

When DL-Based Prescreening Meets Synthon-Based Docking: Target-Adapting PharmacoNet via MEL-Steered Correction
Liu, W.†, Hong, Y.†, Ku, T.†, Lee, W.†, Nguyen, E., Xu, A., & Katritch, V.
bioRxiv (2026). [Preprint]

Peer-Reviewed Publications

Trustworthy Protein–Ligand Binding Affinity Prediction via Reliability-Aware Multi-Engine Fusion
Hong, Y., Cao, D., Liu, W., Ku, T., Lam, J. H., Nguyen, E., Neiswanger, W., Katritch, V., & Liu, Y.
Proceedings of the 32nd ACM SIGKDD Conference on Knowledge Discovery and Data Mining (KDD 2026). Accepted.

GLACIER: A Multimodal Student-Teacher Foundation Model for Molecular Property Prediction
Nguyen, E., Hong, Y., Toshniwal, H., Liu, Y., & Luttens, A.
Proceedings of the 32nd ACM SIGKDD Conference on Knowledge Discovery and Data Mining (KDD 2026). Accepted.

PLATE-VS: a web server for protein–ligand assay curation and cross-target virtual screening datasets
Xu, A.†, Hong, Y.†, Lam, J. H.†, & Katritch, V.
Nucleic Acids Research (2025). [Paper]

RNAproDB: a webserver and interactive database for analyzing protein–RNA interactions
Mitra, R., Cohen, A. S., Tang, W. Y., Hosseini, H., Hong, Y., Berman, H. M., & Rohs, R.
Journal of Molecular Biology, 169012 (2025).

XenoGI 3: Using the DTLOR model to reconstruct the evolution of gene families in clades of microbes
Liu, N., Gonzalez, T. A., Fischer, J., Hong, C., Johnson, M., Mawhorter, R., Mugnatto, F., Soh, R., Somji, S., Wirth, J. S., Libeskind-Hadas, R., & Bush, E. C.
BMC Bioinformatics, 24(1) (2023). [Paper]

Proteasome β5 subunit overexpression improves proteostasis during aging and extends lifespan in Drosophila melanogaster
Nguyen, N. N., Rana, A., Goldman, C., Moore, R., Tai, J., Hong, Y., Shen, J., Walker, D. W., & Hur, J. H.
Scientific Reports, 9(1) (2019). [Paper]