Selected publications are listed. Please see Google Scholar for more.

2024 and after

Combining Structural Modeling and Deep Learning to Calculate the E. coli Protein Interactome and Functional Networks

Haiqing Zhao, Caroline Velez, Anekit Navarene, Aakash Saha, Jonathan Feldman, Jeffrey Skolnick, Diana Murray, Barry Honig, 2025, bioRxiv

Learning Biophysical Dynamics with Protein Language Models

Chao Hou, Haiqing Zhao, Yufeng Shen, 2025, bioRxiv

SEHI-PPI: An End-to-End Sampling-Enhanced Human-Influenza Protein-Protein Interaction Prediction Framework with Double-View Learning

Qiang Yang, Xiao Fan, Haiqing Zhao, Zhe Ma, Megan Stanifer, Jiang Bian, Marco Salemi, Rui Yin, 2025, BioRxiv

Structural-functional analyses of the Huntingtin/HAP40 complex in Drosophila and Humans

Stephen Farmer, Amanda Solbach, Shiyu Xu, Beatriz Rios, Xin Ye, Amy Gao, Daniela Covarrubias, Yue Yu, Lili Ye, Vicky Chuong, Erin Furr Stimming, Haiqing Zhao, Sheng Zhang, 2025, Journal of Biomolecular Structure and Dynamics

ZEPPI: Proteome-scale sequence-based evaluation of protein–protein interaction models

Haiqing Zhao, Donald Petrey, Diana Murraya, Barry Honig, 2024, Proceedings of the National Academy of Sciences

The role of cryptic ancestral symmetry in histone folding mechanisms across Eukarya and Archaea

Haiqing Zhao, Hao Wu, Alex Guseman, Dulith Abeykoon, Christina M. Camara, Yamini Dalal, David Fushman, Garegin A. Papoian, 2024, PLOS Computational Biology

2023 and before

PrePPI: A Structure Informed Proteome-wide Database of Protein–Protein Interactions

Donald Petrey, Haiqing Zhao, Stephen J Trudeau, Diana Murray, Barry Honig, 2023, Journal of Molecular Biology

Specific Regulation of BACH1 by the Hotspot Mutant p53(R175H) Reveals A Distinct Gain-of-function Mechanism

Zhenyi Su, Ning Kon, Jingjie Yi, Haiqing Zhao, Wanwei Zhang, Qiaosi Tang, Huan Li, Hiroki Kobayashi5, Zhiming Li, Shoufu Duan, Yanqing Liu, Kenneth P. Olive, Zhiguo Zhang, Barry Honig, James J. Manfredi, Anil K. Rustgi, Wei Gu, 2023, Nature Cancer

Structural Basis of Antibody Conformation and Stability Modulation by Framework Somatic Hypermutation

Zizhang Sheng, Jude S. Bimela, Phinikoula S. Katsamba, Saurabh D. Patel, Yicheng Guo, Haiqing Zhao, Youzhong Guo, Peter D. Kwong, Lawrence Shapiro, 2022, Frontiers in Immunology

Self-assembled Nucleoid Proteins Scaffold Bacterial DNA

Haiqing Zhao, 2021, Biophysical Journal

The Oligomerization Landscape of Histones

Haiqing Zhao, David Winogradoff, Yamini Dalal, Garegin A. Papoian, 2019, Biophysical Journal

Promiscuous Histone Mis-Assembly Is Actively Prevented by Chaperones

Haiqing Zhao, David Winogradoff, Minh Bui, Yamini Dalal, Garegin A. Papoian, 2016, Journal of the American Chemical Society

Shearing of the CENP-A Dimerization Interface Mediates Plasticity in the octameric Centromeric Nucleosome

David Winogradoff, Haiqing Zhao, Yamini Dalal, Garegin A. Papoian, 2015, Scientific Reports

Chromatin Dynamics in Vivo: A Game of Musical Chairs

Daniël P. Melters, Jonathan Nye, Haiqing Zhao, and Yamini Dalal, 2015, Genes

Nanoscale Tail Aggregation in Ionic Liquids: Roles of Electrostatic and van der Waals Interactions

Haiqing Zhao, Rui Shi, Yanting Wang, 2011, Communications in Theoretical Physics