Publications

# denote co-first author; * denote the corresponding author.

[2024+]

Cao, X.#, Zhu, L.#, Liang, X., Zhang, S. & Sha, Q.* (2024+). Constructing genotype and phenotype network helps reveal disease heritability and phenome-wide association studies. Submitted in October 2023. medRxiv software
Zhao, C.#, Su, K.#, Wu, C., Cao, X., Sha, Q., Li, W., Luo, Z., Qin, T., Qiu, C., Liu, A., Jiang, L., Zhang, X., Shen, H., Deng, H.W.* & Zhou, W.* (2024+). Multi-View Variational Autoencoder for Missing Value Imputation in Untargeted Metabolomics. Submitted in October 2023. arXiv
Qi, Z., Pelletier, A., Willwerscheid, J. Cao, X., Wen, X., Cruchaga, C., De Jager, P.L., TCW, J.* & Wang, G.* (2024+). Novel Missing Data Imputation Approaches Enhance Quantitative Trait Loci Discovery in Multi-Omics Analysis. Preprinted in November 2023. medRxiv

Cao, X., Zhang, S., & Sha, Q.* (2024). A novel method for multiple phenotype association studies based on genotype and phenotype network. PLoS Genetics. Accepted. bioRxiv software
Cao, X.#, Keyak, J.H.#, Sigurdsson, S., Zhao, C., Zhou, W., Liu, A., Lang, T.F., Deng, H.W., Guðnason, V.* & Sha, Q.* (2024). A New Hip Fracture Risk Index Derived from FEA-Computed Proximal Femur Fracture Loads and Energies-to-Failure. Osteoporosis International. 35, 785–794. doi
Zhu, L., Yan, S., Cao, X., Sha, Q. & Zhang, S.* (2024). Integrating external controls by regression calibration for genome-wide association study. Genes. 15(1), 67. doi
Zhao, C., Liu, A., Zhang, X., Cao, X., Ding, Z., Sha, Q., Shen, H., Deng, H.W.* & Zhou, W.* CLCLSA: Cross-omics Linked embedding with Contrastive Learning and Self Attention for multi-omics integration with incomplete multi-omics data. (2024). Computers in Biology and Medicine. doi

Cao, X.#, Zhang, L.#, Islam, M.K., Zhao, M., He, C., Zhang, K., Liu, S., Sha, Q.* & Wei, H.*, (2023). TGPred: efficient methods for predicting target genes of a transcription factor by integrating statistics, machine learning and optimization. NAR Genomics and Bioinformatics, 5(3), p.lqad083. doi
Xie, H., Cao, X., Zhang, S. & Sha, Q. (2023+). Joint analysis of multiple phenotypes for extremely unbalanced case-control association studies using multi-layer network. Bioinformatics. 39(12), btad707. doi
Wang, M., Cao, X., Zhang, S. & Sha, Q.* (2023). A clustering linear combination method for multiple phenotype association studies based on GWAS summary statistics. Scientific Reports. 13(1), p.3389. doi
Xie, H., Cao, X., Zhang, S. & Sha, Q.* (2023). Joint analysis of multiple phenotypes for extremely unbalanced case-control association studies. Genetic Epidemiology. 47(2), pp.185-197. doi
Zhao, C.#, Keyak, J.H.#, Cao, X., Sha, Q., Wu, L., Luo, Z., Zhao, L., Tian, Q., Qiu, C., Su, R., Shen, H., Deng, H.W.* & Zhou, W.* (2023). Multi-view information fusion using multi-view variational autoencoders to predict proximal femoral strength. Frontiers in Endocrinology, section Bone Research. doi

Cao, X., Liang, X., Zhang, S. & Sha, Q.* (2022). Gene selection by incorporating genetic networks into case-control association studies. European Journal of Human Genetics. doi
Cao, X., Wang, X., Zhang, S. & Sha, Q.* (2022). Gene-based association tests using GWAS summary statistics and incorporating eQTL. Scientific Reports. 12(1):3553. doi
Boby, N.#, Cao, X.#, Williams, K., Gadila, S.K.G., Shroyer, M.N., Didier, P.J., Srivastav, S.K., Das, A., Baker, K., Sha, Q. & Pahar, B.* (2022). Simian Immunodeficiency Virus Infection Mediated Changes in Jejunum and Peripheral SARS-CoV-2 Receptor ACE2 and Associated Proteins or Genes in Rhesus Macaques. Frontiers in Immunology. 13, p.835686. doi
Liang, X., Cao, X., Sha, Q. & Zhang, S.* (2022). HCLC-FC: a Novel Statistical Method for Phenome-Wide Association Studies. PLOS ONE. 17(11): e0276646. doi

Boby, N.#, Cao, X.#, Ransom, A., Pace, B.T., Mabee, C., Shroyer, M.N., Das, A., Didier, P.J., Srivastav, S.K., Porter, E., Sha, Q. & Pahar, B.* (2021) Identification, Characterization, and Transcriptional Reprogramming of Epithelial Stem Cells and Intestinal Enteroids in Simian Immunodeficiency Virus Infected Rhesus Macaques. Frontiers in Immunology. 12, p.769990. doi