∗ 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. (2024). Natural killer cells regulate distinct CD8+ T cell differentiation program in cancer and contribute to resistance against immune checkpoint blocker. Submitted to Cancer Discovery

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.