Prepints/Under Review
- Y. Cao, T. Chen, Z. Wang, and Y. Shen. "Bayesian Learning to Optimize: Quantifying the Optimizer Uncertainty." Under review for International Conference on Learning Representations, 2021
- Y. Cao, P. Das, P. Chen, V. Chen., I. Melnyk, and Y. Shen. "Fold2Seq: A Joint Sequence(1D)-Fold(3D) Embedding-based Generative Model for Protein Design." Under review for International Conference on Learning Representations, 2021
- Y. Cao and Y. Shen. "TALE: Transformer-based protein function Annotation with joint sequence–Label Embedding." Under review for Bioinformatics, 2020
- R. Taftaf and other authors including Y. Cao. "ICAM1 initiates CTC cluster formation and lung metastasis of triple negative breast cancer." Under review for Nature Communications, 2020
Published
- Y. Cao and Y. Shen. "Bayesian Active Learning for Optimization and Uncertainty Quantification in Protein Docking." Journal of Chemical Theory and Computation, 2020
- Y. Cao, T. Chen, Z. Wang, and Y. Shen. "Learning to Optimize in Swarms." Advances in Neural Information Processing Systems, 2019
- Y. Cao and Y. Shen. "Energy-based Graph Convolutional Networks for Scoring Protein Docking Models." Proteins, 2020
- M. Karimi*, S. Zhu*, Y. Cao* and Y. Shen. "De Novo Protein Design for Novel Folds Using GuidedConditional Wasserstein Generative Adversarial Networks." Journal of Chemical Information and Modeling, 2020
- Y. Cao, Y. Sun, M. Karimi, H. Chen, O. Moronfoye, and Y. Shen. "Predicting Pathogenicity of Missense Variants with Weakly Supervised Regression." Human Mutation, 2019
- M. Kawaguchi, N. Dashzeveg, Y. Cao, Y. Jia, X. liu, Y. Shen, and H. Liu. "Extracellular Domains I and II of cell-surface glycoprotein CD44 mediate its trans-homophilic dimerization and tumor cluster aggregation" Journal of Biological Chemistry, 2020
- X. Liu and other authors including Y. Cao. "Homophilic CD44 Interactions Mediate Tumor Cell Aggregation and Polyclonal Metastasis in Patient-derived Breast Cancer Models." Cancer Discovery, 2019
- M. S Cline, G. Babbi, S. Bonache, Y. Cao, et al. "Assessment of blind predictions of the clinical significance of BRCA1 and BRCA2 variants" Human Mutation, 2019
- M. Lensink and other authors including Y. Cao. "Blind prediction of Homo- and Hetero- Protein Complexes: The CASP13-CAPRI Experiment." Proteins: Structure, Function, and Bioinformatics, 2019
- A. Voskanian and other authors including Y. Cao. "Assessing the Performance of in-silico Methods for Predicting the Pathogenicity of Variants in the Gene CHEK2 among Hispanic Females with Breast Cancer." Human Mutation, 2019
