Publications

See below the selected publications from my work. You can also find my articles on my Google Scholar profile.

Journal Articles

SpNeigh: spatial neighborhood and differential expression analysis for high-resolution spatial transcriptomics

Published in NAR Genomics and Bioinformatics, 2026

This software paper shows utility of SpNeigh in spatial neighborhood and differential expression analysis.

Recommended citation: Cheng, J., Chow, P., and Liu, N. (2026). "SpNeigh: spatial neighborhood and differential expression analysis for high-resolution spatial transcriptomics." NAR Genomics and Bioinformatics. 8(2), lqag039.
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Fibroblast hierarchy dynamics during mammary gland morphogenesis and tumorigenesis

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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MCL‑1 safeguards activated hair follicle stem cells to enable adult hair regeneration

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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Benchmarking cell type annotation methods for 10x Xenium spatial transcriptomics data

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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Self-maintenance of zonal hepatocytes during adult homeostasis and their complex plasticity upon distinct liver injuries

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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Unraveling the timeline of gene expression: A pseudotemporal trajectory analysis of single-cell RNA sequencing data

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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Integrative analysis of DNA methylation and gene expression reveals hepatocellular carcinoma-specific diagnostic biomarkers

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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Jinming Cheng