Xin Dong

Xin Dong

PhD in Bioinformatics.

Publications

[Google Scholar] [ORCID] [PubMed Bibliography]

Asterisk (*) denotes the Co-first Authors and Hashtag (#) denotes the Corresponding Authors.

  • Chang, Z.*, Xu, Y.*, Dong, X.*, Gao, Y. & Wang, C.# Single-cell and spatial multiomic inference of gene regulatory networks using SCRIPro. Bioinformatics 40, btae466 (2024). [Web]

  • Sun, F.*, Li, H.*, Sun, D.*, Fu, S.*, Gu, L.*, Shao, X.*, Wang, Q.*, Dong, X.*, Duan, B.*, Xing, F.*, Wu, J.*, Xiao, M.#, Zhao, F.#, Han, J.-D. J.#, Liu, Q.#, Fan, X.#, Li, C.#, Wang, C.# & Shi, T.# Single-cell omics: experimental workflow, data analyses and applications. SCIENCE CHINA Life Sciences (2024). [Web]

  • Ren, P.*, Shi, X.*, Yu, Z., Dong, X., Ding, X., Wang, J., Sun, L., Yan, Y., Hu, J., Zhang, P., Chen, Q., Zhang, J., Li, T. & Wang, C.# Single-cell assignment using multiple-adversarial domain adaptation network with large-scale references. Cell Reports Methods, 3, 100577 (2023). [Web] [Abstract]

  • Han, Y.*, Wang, Y.*, Dong, X.*, Sun, D., Liu, Z., Yue, J., Wang, H., Li, T.# & Wang, C.# TISCH2: expanded datasets and new tools for single-cell transcriptome analyses of the tumor microenvironment. Nucleic Acids Research, 51, D1029-D1037 (2022). [Web] [Abstract] [PDF]

  • Shi, X.*, Yu, Z.*, Ren, P., Dong, X., Ding, X., Song, J., Zhang, J., Li, T.# & Wang, C.# HUSCH: an integrated single-cell transcriptome atlas for human tissue gene expression visualization and analyses. Nucleic Acids Research, 51, D1425-D1431 (2022). [Web] [Abstract] [PDF]

  • Dong, X.*, Tang, K.*, Xu, Y., Wei, H., Han, T. & Wang, C. # Single-cell gene regulation network inference by large-scale data integration. Nucleic Acids Research, 50, e126 (2022). [Web] [Abstract] [PDF]

  • Xu, R.*, Li, S.*, Wu, Q.*, Li, C.*, Jiang, M.*, Guo, L., Chen, M., Yang, L., Dong, X., Wang, H., Wang, C.#, Liu, X.#, Ou, X.# & Gao, S.# Stage-specific H3K9me3 occupancy ensures retrotransposon silencing in human pre-implantation embryos. Cell Stem Cell, 29, 1051-1066.e8 (2022). [Web] [Abstract]

  • Sun, D.*, Wang, J.*, Han, Y.*, Dong, X., Ge, J., Zheng, R., Shi, X., Wang, B., Li, Z., Ren, P., Sun, L., Yan, Y., Zhang, P., Zhang, F.#, Li, T.# & Wang, C.# TISCH: a comprehensive web resource enabling interactive single-cell transcriptome visualization of tumor microenvironment. Nucleic Acids Research, 49, D1420-D1430 (2021). [Web] [Abstract] [PDF]

  • Zheng, R.*, Dong, X.*, Wan, C., Shi, X., Zhang, X.# & Meyer, C.A.# Cistrome Data Browser and Toolkit: analyzing human and mouse genomic data using compendia of ChIP-seq and chromatin accessibility data. Quantitative Biology, 8, 267-276 (2020). [Web][PDF]

  • Chen, C.-H., Zheng, R., Tokheim, C., Dong, X., Fan, J., Wan, C., Tang, Q., Brown, M., Liu, J.S., Meyer, C.A. # & Liu, X.S.# Determinants of transcription factor regulatory range. Nature Communications, 11, 2472 (2020). [Web] [Abstract] [PDF]

  • Li, S.*, Wan, C.*, Zheng, R., Fan, J., Dong, X., Meyer, C.A.# & Liu, X.S.# Cistrome-GO: a web server for functional enrichment analysis of transcription factor ChIP-seq peaks. Nucleic Acids Research, 47, W206–W211 (2019). [Web][Abstract][PDF]