Publications
Stewart, R., Zhao, C., Liu, T., & Wang, Z. PICNIC: Refinement of AlphaFold2 tertiary structure predictions using deep 3D residual neural networks. In 2024 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). IEEE. (Acceptance rate: 22%)
Zhao, C., Liu, T., & Wang, Z. (2024). PANDA-3D: Protein function prediction based on AlphaFold models. NAR Genomics and Bioinformatics, 6(3), lqae094. 🏅 Editor’s Choice (top 16% of research articles)
Siciliano, A. J., Zhao, C., Liu, T., & Wang, Z. (2024). EGG: Accuracy estimation of individual multimeric protein models using deep energy-based models and graph neural networks. International Journal of Molecular Sciences, 25(11), 6250.
Zhao, C., Liu, T., & Wang, Z. (2022). Predicting residue-specific qualities of individual protein models using residual and graph neural networks. Proteins: Structure, Function, and Bioinformatics, 90(12), 2091–2102. 💡 MASS2 and LAW were the best and second-best single-model methods in the local QA category of CASP14.
Zhao, C., Liu, T., & Wang, Z. (2022). Functional similarities of protein-coding genes in topologically associating domains and spatially proximate genomic regions. Genes, 13(3), 480. 🌟 Selected as the Feature Paper by the journal.
Zhao, C., Liu, T., & Wang, Z. (2022). PANDA2: Protein function prediction using graph neural networks. NAR Genomics and Bioinformatics, 4(1), lqac004.
Zhou, N., Jiang, Y., Bergquist, T. R., Lee, … Zhao, C., … & Salakoski, T. (2019). The CAFA challenge: Reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens. Genome Biology, 20(1), 1–23.
Liu, T., Porter, J., Zhao, C., Zhu, H., Wang, N., Sun, Z., … & Wang, Z. (2019). TADKB: Family classification and a knowledge base of topologically associating domains. BMC Genomics, 20(1), 1–17.
Zhao, C., & Wang, Z. (2018). GOGO: An improved algorithm to measure the semantic similarity between gene ontology terms. Scientific Reports, 8(1), 1–10.
Wang, Z., Zhao, C., Wang, Y., Sun, Z., & Wang, N. (2018). PANDA: Protein function prediction using domain architecture and affinity propagation. Scientific Reports, 8(1), 1–10.