Publications

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# Co-first authors; * Co-corresponding authors

Members of the zhoulab indicated in boldface

2025

Lin, Y.^#, Lin, F.^#, Zhang, Y.^#, Wen, J., Li, G., Zeng, X., … & Zhou, J. (2025). PathoEye: a deep learning framework for the whole-slide image analysis of skin tissue. bioRxiv, 2025-06.

Lin, Y.^#, Zhang, Y.^#, Sun, H., Jiang, H., Zhao, X., Teng, X., Lin, J., Shu, B., Sun, H., Liao, Y. and Zhou, J., 2024. NanoDeep: a deep learning framework for nanopore adaptive sampling on microbial sequencing. Briefings in Bioinformatics, 25(1), p.bbad499.
Yan, T., Sun, H., Liao, Y. and Zhou, J., 2024. Helicobacter pylori mediated niche environment aberrations promote the progression of gastric cancer. Genes & Diseases, 11(5), p.101207.
Yao, M., Zhang, L., Teng, X., Lei, Y., Xing, X., Ren, T., Pan, Y., Zhang, L., Li, Z., Lin, J., Zheng, Y., Xing, L., Zhou, J., Wu, C., 2024. Transcriptomic profiling of Dip2a in the neural differentiation of mouse embryonic stem cells. Computational and Structural Biotechnology Journal, 23, pp.700-710.
Li, Z., Li, X., Lin, J., Wang, Y., Cao, H. and Zhou, J., 2024. Reevaluation by the CRISPR/Cas9 knockout approach revealed that multiple pluripotency-associated lncRNAs are dispensable for pluripotency maintenance while Snora73a/b is essential for pluripotency exit. Science China Life Sciences, 67(10), pp.2198-2212.

Wang, X., Liu, J., Chen, J., Xu, X., Zhong, Y., Xu, Y., Lu P., Zhou J., Lin Z., Yang B.& Yang, C. (2023). Loss‐of‐function mutations in CST6 cause dry skin, desquamation and abnormal keratosis without hypotrichosis. Clinical Genetics, 103(3), 301-309.

Wan, P., Huang, S., Luo, Y., Deng, C., Zhou, J.^*, Long, E.^*, & Zhuo, Y.^* (2022). Reciprocal regulation between lncRNA ANRIL and p15 in steroid-induced glaucoma. Cells, 11(9), 1468.

Zhang, Y.^#, Shi, Y.^#, Lin, J., Li, X., Bin, Y.^*, & Zhou, J^*. (2021). Immune cell infiltration analysis demonstrates excessive mast cell activation in psoriasis. Frontiers in Immunology, 4941.
Huang, H.^#, Hu, Y.^#, Huang, G., Ma, S., Feng, J., Wang, D., Lin, Y.^*, Zhou, J.^* and Rong, Z.^*, 2021. Tag-seq: a convenient and scalable method for genome-wide specificity assessment of CRISPR/Cas nucleases. Communications biology, 4(1), pp.1-8.

Li, X.^#, Lin, J., Hu, Y. and Zhou, J.^*, 2020. PARMAP: A Pan-Genome-Based Computational Framework for Predicting Antimicrobial Resistance. Frontiers in microbiology, 11.

Zhao, Y.^#, Zhou, J.^#, He, L., Li, Y., Yuan, J., Sun, K., Chen, X., Bao, X., Esteban, M.A., Sun, H.^* and Wang, H.^*, 2019. MyoD induced enhancer RNA interacts with hnRNPL to activate target gene transcription during myogenic differentiation. Nature communications, 10(1), pp.1-17.
Zhou, J.^#, So, K.K.^#, Li, Y.^#, Li, Y., Yuan, J., Ding, Y., Chen, F., Huang, Y., Liu, J., Lee, W., Li, G., Ju, Z., Sun, H.^*, Wang, H.^*, 2019. Elevated H3K27ac in aged skeletal muscle leads to increase in extracellular matrix and fibrogenic conversion of muscle satellite cells. Aging cell, 18(5), p.e12996.

Chen, F., Zhou, J., Li, Y., Zhao, Y., Yuan, J., Cao, Y., Wang, L., Zhang, Z., Zhang, B., Wang, C.C.,Cheung, T.H., Sun, H.^* and Wang H.^*, 2019. YY 1 regulates skeletal muscle regeneration through controlling metabolic reprogramming of satellite cells. The EMBO journal, 38(10), p.e99727.
Zhou, J.^#, Huang, Y., Ding, Y., Yuan, J., Wang, H. and Sun, H.^*, 2018. lncFunTK: a toolkit for functional annotation of long noncoding RNAs. Bioinformatics, 34(19), pp.3415-3416.
Zhou, J.^#, Zhang, S.^#, Wang, H.^* and Sun, H.^*, 2017. LncFunNet: an integrated computational framework for identification of functional long noncoding RNAs in mouse skeletal muscle cells. Nucleic acids research, 45(12), pp.e108-e108.
Nygaard, S., Zhang, G., Schiøtt, M., Li, C., Wurm, Y., Hu, H., Zhou, J., Ji, L., Qiu, F., Rasmussen, M. and Pan, H., 2011. The genome of the leaf-cutting ant Acromyrmex echinatior suggests key adaptations to advanced social life and fungus farming. Genome research, 21(8), pp.1339-1348.