* co-first authors ___ corresponding authors + advisees
Published
Xi, M.N., Ji, H.L., and Wang, L. (2024). Understanding Sarcoidosis Using Large Language Models and Social Media Data. Journal of Healthcare Informatics Research, 1-26. [PDF]
Jain, K.G., Liu, Y., Zhao, R., Muire, P.J., Xi, M.N., Ji, H.L. (2024). Surfactant Protein-C Regulates Alveolar Type 2 Epithelial Cell Lineages via the CD74 Receptor. Journal of Respiratory Biology and Translational Medicine, 1 (4), 10017. [PDF]
Zhao, R., Hadisurya, M., Ndetan, H., Xi, M.N., Adduri, R., Konduru, N.V., Samten, B., Tao, W.A., Singh, K.P., and Ji, H.L. (2024). Regenerative Signatures in Bronchioalveolar Lavage of Acute Respiratory Distress Syndrome. American Journal of Respiratory Cell and Molecular Biology, 71 (6), 740-742. [PDF]
Xi, M.N. and Huang, D. (2024). Drug Safety Assessment by Machine Learning Models. Journal of Biopharmaceutical Statistics, 1-12. [PDF]
Ji, H.L., Xi N.M., Mohan, C., Yan, X., Jain, K.G., Zang, Q., Zhao, R. (2024). Biomarkers and Molecular Endotypes of Sarcoidosis: Lessons from Omics and Non-Omics Studies. Frontiers in Immunology, Volume 14. [PDF]
Jain, K.G., Xi, N.M., Zhao, R., Ahmad, W., Ali, G., and Ji, H.L. (2023). Alveolar Type 2 Epithelial Cell Organoids: Focus on Culture Methods. Biomedicines, 11(11), 3034. [PDF]
Xi, N.M. and Li, J.J. (2023). Exploring the Optimization of Autoencoder Design for Imputing Single-Cell RNA Sequencing Data. Computational and Structural Biotechnology Journal. Volume 21, P4079-4095. [PDF]
Xi, M.N. and Vasilopoulos, A.+ (2023). Tuning Hyperparameters of Doublet-Detection Methods for Single-Cell RNA Sequencing Data. Quantitative Biology. In press. [PDF]
Vasilopoulos, A.+ and Xi, M.N. (2023). Predicting Survival of Tongue Cancer Patients by Machine Learning Models. Advances in Artificial Intelligence and Machine Learning, 3(1):53. [PDF]
Xi, M.N., Wang, L., and Yang, C. (2022). Improving the Diagnosis of Thyroid Cancer by Machine Learning and Clinical Data. Scientific Report 12, 1143. [PDF] [Code] [Data]
Xi, M.N., Hsu, Y., Dang, Q., and Huang, D. (2022). Statistical Learning in Preclinical Drug Proarrhythmic Assessment. Journal of Biopharmaceutical Statistics, 32 (3):450-473. [PDF] [Code]
Song, D.*, Xi, M.N.*, Li, J.J., and Wang, L. (2022). scSampler: fast diversity-preserving subsampling of large-scale single-cell transcriptomic data. Bioinformatics 38 (11): 3126-3127. [PDF] [Software]
Foster-Burns, J.+ and Xi, M.N. (2022). Prediction of Drug-Induced TdP Risks Using Machine Learning and Rabbit Ventricular Wedge Assay. International Journal of Multidisciplinary Research and Analysis Volume 05, Issue 10. [PDF]
Xi, M.N. and Li, J.J. (2021). Protocol for Executing and Benchmarking Eight Computational Doublet-Detection Methods in Single-Cell RNA Sequencing Data Analysis. STAR Protocols 2(3):100699. [PDF] [Software]
Xi, M.N. and Li, J.J. (2021). Benchmarking computational doublet-detection methods for single-cell RNA sequencing data. Cell Systems 12: 1-19. [PDF] [Code] [Data]Â
Xi, N., Ma, D., Liou, M., Steinert-Threlkeld, Z., Anastasopoulos, J., and Joo, J. (2020). Understanding the Political Ideology of Legislators from Social Media Images. The International AAAI Conference on Web and Social Media (ICWSM). [PDF]
Xi, N. and Joo, J. (2019). Face Attribute Dataset for Balanced Race. The Conference on Computer Vision and Pattern Recognition (CVPR) Workshop. [PDF]
Xi, N. (2011). The Duopoly Analysis of Graphics Card Market. China Urban Economy 8: 64-65. [PDF]
Submitted
1. Xi, M.N., Jin, M.M., Wang, L., and Huang, X. (2025). Synergy-Informed Design of Platform Trials for Combination Therapies. [PDF]
2. Xi, M.N., Deng, Y., and Wang, L. (2025). Leveraging Large Language Models for Rare Disease Named Entity Recognition.
Software
DoubletCollection
An R package integrating the installation, execution, and benchmark of eight cutting-edge computational doublet-detection methods in single-cell RNA sequencing data analysis.
GitHub: https://github.com/xnnba1984/DoubletCollection
scSampler
Python library and R Package for fast diversity-preserving subsampling of large-scale single-cell transcriptomic data. Joint work with Dongyuan Song.
GitHub: https://github.com/SONGDONGYUAN1994/scsampler
combodesign
An R package implementing generalized Dunnett-based false positive control, optimal allocation, and power-calibrated sample size calculation for early-phase platform trials evaluating combination therapies.
GitHub: https://github.com/xnnba1984/combodesign