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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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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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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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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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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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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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Understanding cell lineage commitment and breast cancer development by single cell RNA-seq

Published: August 25, 2021

This is a single-cell RNA-seq lecture presented at 2021 WEHI Bioinformatics and Computational Biology Virtual Masterclass.

Time course analysis of pseudo-bulk samples from single cell RNA sequencing data

Published: December 01, 2022

This is a talk presented at BioC Asia Conference in 2022. I also presented a poster of this study at Oz Single Cell 2022 (15 Sep 2022), ABACBS 2022 (29 Nov 2022) and Lorne Cancer 2023 (09 Feb 2023).

Cell type annotation for imaging-based spatial transcriptomics data

Published: November 27, 2023

This is a talk presented at WEHI Student Symposium in 2023. I also presented a poster of this study at Lorne Genome 2024 (12 Feb 2024).

Exploring mammary gland developmental stages and breast cancer heterogeneity using single-cell technologies

Published: June 18, 2024

This is my PhD Completion Seminar presented at WEHI Bioinformatics Division on 18 June 2024. The abstract of this talk can be found here.

WEHI 2022 tidyverse R course tutor

Workshop, The Walter and Eliza Hall Institute of Medical Research, 2022

I was a tutor for the WEHI 2022 tidyverse R course on 09, 16, 23 November 2022.

WEHI 2023 base R course tutor

Workshop, The Walter and Eliza Hall Institute of Medical Research, 2023

I was a tutor for the WEHI 2022 tidyverse R course on 08, 15, 22, 29 March 2023.

WEHI 2023 tidyverse R course tutor

Workshop, The Walter and Eliza Hall Institute of Medical Research, 2023

I was a tutor for the WEHI 2023 tidyverse R course on 20, 27 September and 04, 11 October 2023.