Miao, Y., Xu, H., & Wang, S. (2024). PartIES: a disease subtyping framework with Partition-level Integration using diffusion-Enhanced Similarities from multi-omics Data. Briefings in Bioinformatics, 26(1). https://doi.org/10.1093/bib/bbae609

Shen, Y., Domingo-Relloso, A., Kupsco, A., Kioumourtzoglou, M.-A., Tellez-Plaza, M., Umans, J. G., Fretts, A. M., Zhang, Y., Schnatz, P. F., Casanova, R., Martin, L. W., Horvath, S., Manson, J. E., Cole, S. A., Wu, H., Whitsel, E. A., Baccarelli, A. A., Navas-Acien, A., & Gao, F. (2024). AESurv: autoencoder survival analysis for accurate early prediction of coronary heart disease. Briefings in Bioinformatics, 25(6). https://doi.org/10.1093/bib/bbae479

Ruprecht, N. A., Kennedy, J. D., Bansal, B., Singhal, S., Sens, D., Maggio, A., Doe, V., Hawkins, D., Campbel, R., O’Connell, K., Gill, J. S., Schaefer, K., & Singhal, S. K. (2024). Transcriptomics and epigenetic data integration learning module on Google Cloud. Briefings in Bioinformatics, 25(Supplement_1). https://doi.org/10.1093/bib/bbae352

Chuwdhury, G. S., Guo, Y., Chiang, C.-L., Lam, K.-O., Kam, N.-W., Liu, Z., & Dai, W. (2024). ImmuneMirror: A machine learning-based integrative pipeline and web server for neoantigen prediction. Briefings in Bioinformatics, 25(2). https://doi.org/10.1093/bib/bbae024

Ding, R., Zou, X., Qin, Y., Gong, L., Chen, H., Ma, X., Guang, S., Yu, C., Wang, G., & Li, L. (2023). xQTLbiolinks: a comprehensive and scalable tool for integrative analysis of molecular QTLs. Briefings in Bioinformatics, 25(1). https://doi.org/10.1093/bib/bbad440

Yang, Z., Cieza, B., Reyes-Dumeyer, D., Montesinos, R., Soto-Añari, M., Custodio, N., & Tosto, G. (2023). A benchmark study on current GWAS models in admixed populations. Briefings in Bioinformatics, 25(1). https://doi.org/10.1093/bib/bbad437

Li, B., Wang, T., Qian, M., & Wang, S. (2023). MKMR: a multi-kernel machine regression model to predict health outcomes using human microbiome data. Briefings in Bioinformatics, 24(3). https://doi.org/10.1093/bib/bbad158

Fan, X., Pan, H., Tian, A., Chung, W. K., & Shen, Y. (2022). SHINE: protein language model-based pathogenicity prediction for short inframe insertion and deletion variants. Briefings in Bioinformatics, 24(1). https://doi.org/10.1093/bib/bbac584

He, B., Wang, K., Xiang, J., Bing, P., Tang, M., Tian, G., Guo, C., Xu, M., & Yang, J. (2022). DGHNE: network enhancement-based method in identifying disease-causing genes through a heterogeneous biomedical network. Briefings in Bioinformatics, 23(6). https://doi.org/10.1093/bib/bbac405

Zhang, M., Gelfman, S., Martins Moreno, C. A., McCarthy, J. M., Harms, M. B., Goldstein, D. B., & Allen, A. S. (2021). Focused goodness of fit tests for gene set analyses. Briefings in Bioinformatics, 23(1). https://doi.org/10.1093/bib/bbab472