Zhao H, Velez C, Navarene A, Saha A, Feldman J, Skolnick J, Murray D, Honig B. (2026) Combining Structural Modeling and Deep Learning to Calculate the E. coli Protein Interactome and Functional Networks. Nature Communications. [PDF]

Wang Y, Hu Y, Ku Z, Yeung J, Zou J, Prokhorov M, Knyazhanskaya E, Zhao H, Sherman M, An Z, Carroll S, Shi P, Leiman P, Xie X. (2026) Neutralization of SARS-CoV-2 by IgM-14 via Engagement of Two Distinct Spike Epitopes. PLOS Pathogens. [PDF]

Hou C, Zhao H, Shen Y. (2026) Protein Language Models Trained on Biophysical Dynamics Inform Mutation Effects. Proceedings of the National Academy of Sciences. [PDF]

Wong R, Song Z, Zheng Y, Zhao H^[+], Bai D^[+]. (2025) Electrostatic Interaction Determines the Docking Specificity and the Formation of Functional Cx36 Gap Junction Channels. BioRxiv. [PDF]

Yang Q, Fan X, Zhao H, Ma Z, Stanifer M, Bian J, Salemi M, Yin R. (2025) SEHI-PPI: An End-to-End Sampling-Enhanced Human-Influenza Protein-Protein Interaction Prediction Framework with Double-View Learning. BioRxiv. [PDF]

Farmer S, Solbach A, Xu S, Rios B, Ye X, Gao A, Covarrubias D, Yu Y, Ye L, Chuong V, Stimming E, Zhao H, Zhang S. (2025) Structural-functional analyses of the Huntingtin/HAP40 complex in Drosophila and Humans. Journal of Biomolecular Structure and Dynamics. [PDF]

Zhao H, Petrey D, Murray D, Honig B. (2024) ZEPPI: Proteome-scale sequence-based evaluation of protein–protein interaction models. Proceedings of the National Academy of Sciences. [PDF]

Zhao H, Wu H, Guseman A, Abeykoon D, Camara C, Dalal Y, Fushman D, Papoian G. (2024) The role of cryptic ancestral symmetry in histone folding mechanisms across Eukarya and Archaea. PLOS Computational Biology. [PDF]

Petrey D*, Zhao H*, Trudeau S*, Murray D, Honig B. (2023) PrePPI: A Structure Informed Proteome-wide Database of Protein–Protein Interactions. Journal of Molecular Biology. [PDF]

Su Z, Kon N, Yi J, Zhao H, Zhang W, Tang Q, Li H, Kobayashi5 H, Li Z, Duan S, Liu Y, Olive K, Zhang Z, Honig B, Manfredi J, Rustgi A, Gu W. (2023) Specific Regulation of BACH1 by the Hotspot Mutant p53(R175H) Reveals A Distinct Gain-of-function Mechanism. Nature Cancer. [PDF]

Sheng Z, Bimela J, Katsamba P, Patel S, Guo Y, Zhao H, Guo Y, Kwong P, Shapiro L. (2022) Structural Basis of Antibody Conformation and Stability Modulation by Framework Somatic Hypermutation. Frontiers in Immunology. [PDF]

Zhao H. (2021) Self-assembled Nucleoid Proteins Scaffold Bacterial DNA. Biophysical Journal. [PDF]

Zhao H, Winogradoff D, Dalal Y, Papoian G. (2019) The Oligomerization Landscape of Histones. Biophysical Journal. [PDF]

Zhao H, Winogradoff D, Bui M, Dalal Y, Papoian G. (2016) Promiscuous Histone Mis-Assembly Is Actively Prevented by Chaperones. Journal of the American Chemical Society. [PDF]

Winogradoff D, Zhao H, Dalal Y, Papoian G. (2015) Shearing of the CENP-A Dimerization Interface Mediates Plasticity in the octameric Centromeric Nucleosome. Scientific Reports. [PDF]

Melters D, Nye J, Zhao H, Dalal a. (2015) Chromatin Dynamics in Vivo: A Game of Musical Chairs. Genes. [PDF]

Zhao H, Shi R, Wang Y. (2011) Nanoscale Tail Aggregation in Ionic Liquids: Roles of Electrostatic and van der Waals Interactions. Communications in Theoretical Physics. [PDF]