Published in The EMBO Journal, 2025
This paper reveals the fibroblast subpopulations in mouse mammary gland and fibroblast changes during mammary tumor development.
Recommended citation: Pascual, R., Cheng, J. et al (2025). "Fibroblast hierarchy dynamics during mammary gland morphogenesis and tumorigenesis." The EMBO Journal. 1-35.
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Published in Nature Communications, 2025
This paper reveals that MCL-1 is essential for the survival of activated HFSCs during hair regeneration but dispensable for quiescent HFSCs.
Recommended citation: Chin, H. S., Cheng, J. et al (2025). "MCL‑1 safeguards activated hair follicle stem cells to enable adult hair regeneration." Nature Communications. 16(1), 2829.
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Published in BMC Bioinformatics, 2025
This paper is about benchmarking five different reference-based cell type annotation methods for 10x Xenium data.
Recommended citation: Cheng, J., Jin, X., Smyth, G. K., and Chen, Y. (2025). "Benchmarking cell type annotation methods for 10x Xenium spatial transcriptomics data." BMC Bioinformatics. 26(1), 22.
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Published in Cell Reports, 2024
This paper reveals for the first time that there are only two major hepatocyte populations in normal mouse liver: Cyp2e1+ (pericentral) and Gls2+ (periportal), which suggests liver has 2 zones rather than traditionally thought 3 zones.
Recommended citation: Ang, C. H., Arandjelovic, P., Cheng, J. et al. (2025). "Self-maintenance of zonal hepatocytes during adult homeostasis and their complex plasticity upon distinct liver injuries." Cell Reports. 44(1)
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Published in F1000 Research, 2023
This paper demonstrates a workflow of pseudotime course analysis for single-cell RNA data.
Recommended citation: Cheng, J., Smyth, G. K., and Chen, Y. (2023). "Unraveling the timeline of gene expression: A pseudotemporal trajectory analysis of single-cell RNA sequencing data." F1000 Research. 12.
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Published in Genome Medicine, 2018
This paper is about liver cancer-specific diagnostic biomarkers.
Recommended citation: Cheng, J. et al. (2018). "Integrative analysis of DNA methylation and gene expression reveals hepatocellular carcinoma-specific diagnostic biomarkers." Genome Medicine. 10, 1-11.
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