∗ Joint first authors

Xie, J., Jeon, H., Chang, W., Jeon, Y., Li, Z., Ma, Q., & Chung, D. (2024). spaDesign: A statistical framework to improve the design of sequencing-based spatial transcriptomics experiments. Submitted to PLOS Computational Biology

Xie, J.∗, Jung, K. J.∗, Allen, C.∗, Chang, Y., Paul, S., Li, Z., ... & Chung, D. (2024). Analysis of community connectivity in spatial transcriptomics data. Frontiers in Applied Mathematics and Statistics, 10, 1403901.

Xie, J., Jeon, H., Xin, G., Ma, Q., & Chung, D. (2023). LRT: Integrative analysis of scRNA-seq and scTCR-seq data to investigate clonal differentiation heterogeneity. PLOS Computational Biology, 19(7), e1011300.

Jeon, H.∗, Xie, J.∗, Jeon, Y.∗, Jung, K. J., Gupta, A., Chang, W., & Chung, D. (2023). Statistical power analysis for designing bulk, single-cell, and spatial transcriptomics experiments: review, tutorial, and perspectives. Biomolecules, 13(2), 221.

Xie, J., Ma, A., Zhang, Y., Liu, B., Cao, S., Wang, C., ... & Ma, Q. (2020). QUBIC2: a novel and robust biclustering algorithm for analyses and interpretation of large-scale RNA-Seq data. Bioinformatics, 36(4), 1143-1149.

Xie, J., Ma, A., Fennell, A., Ma, Q., & Zhao, J. (2019). It is time to apply biclustering: a comprehensive review of biclustering applications in biological and biomedical data. Briefings in bioinformatics, 20(4), 1450-1465.

McDermaid, A., Chen, X., Zhang, Y., Wang, C., Gu, S., Xie, J., & Ma, Q. (2018). A new machine learning-based framework for mapping uncertainty analysis in RNA-Seq read alignment and gene expression estimation. Frontiers in genetics, 9, 313.

Zhang, Y.∗, Xie, J.∗, Yang, J., Fennell, A., Zhang, C., & Ma, Q. (2017). QUBIC: a bioconductor package for qualitative biclustering analysis of gene co-expression data. Bioinformatics, 33(3), 450-452.

Song, N.J., Xie, J., Jung, K. J., Wang, Y., Pozniak, J., Roda, N,..., & Li, Z. (2025). Tumor-associated NK cells regulate distinct CD8+ T cell differentiation program in cancer and contribute to resistance against immune checkpoint blocker. Cancer Discovery, 15(9), 1835-1857

George, V. K., Wong, H. C., Felices, M., Rubinstein, M. P., Shrestha, N., Valderrama, N., ... Xie, J., ... & Geller, M. A. (2025). TGF-βRII/IL-15 immunotherapeutic complex targets exhausted CD8+ T-cell subsets in lymph nodes and tumors. Journal for Immunotherapy of Cancer, 13(12), e013533.

Khadka, V. S., Vaughn, K., Xie, J., Swaminathan, P., Ma, Q., Cramer, G. R., & Fennell, A. Y. (2019). Transcriptomic response is more sensitive to water deficit in shoots than roots of Vitis riparia (Michx.). BMC plant biology, 19, 1-20.

Damodaran, S., Dubois, A., Xie, J., Ma, Q., Hindi, V., & Subramanian, S. (2019). GmZPR3d interacts with GmHD-ZIP III proteins and regulates soybean root and nodule vascular development. International journal of molecular sciences, 20(4), 827.

Xu, Z., Zhang, X., Xie, J., Yuan, G., Tang, X., Sun, X., & Yu, G. (2014). Total nitrogen concentrations in surface water of typical agro-and forest ecosystems in China, 2004-2009. PloS one, 9(3), e92850. 

Xie, J., Zhang, X., Xu, Z., Yuan, G., Tang, X., Sun, X., & Ballantine, D. J. (2014). Total phosphorus concentrations in surface water of typical agro-and forest ecosystems in China, 2004–2010. Frontiers of Environmental Science & Engineering, 8, 561-569. 

Zhang, X., Juan, X. I. E., Fengting, Y. A. N. G., Wenyi, D. O. N. G., Xiaoqin, D. A. I., Yang, Y. A. N. G., & Xiaomin, S. U. N. (2018). Specific responses of soil microbial residue carbon to long-term mineral fertilizer applications to reddish paddy soils. Pedosphere, 28(3), 488-496.