Fibroblast hierarchy dynamics during mammary gland morphogenesis and tumorigenesis
Pascual, R., Cheng, J. et al (2025). "Fibroblast hierarchy dynamics during mammary gland morphogenesis and tumorigenesis." The EMBO Journal. 1-35.
CV
Education
- PhD in Bioinformatics, WEHI, The University of Melbourne, 2020-2024
- M.Sc. in Bioinformatics, Shanghai Jiao Tong University, 2015-2018
- B.Eng. in Bioinformatics, Huazhong University of Science and Technology, 2011-2015
Work Experience
- 2019.07-2020.05: Intern
- CAS-MPG Partner Institute for Computational Biology, Shanghai, China
- Duties includes: Analyzing WGS and RNA-seq data of pancreatic cancer
- Supervisor and collaborators: Dr Liyun Yuan, Prof Guoqing Zhang and Prof Wu Wei.
- 2018.08-2019.05: Scientific Visitor
- European Molecular Biology Laboratory, Heidelberg, Germany
- Duties includes: Exploring factors influencing editing efficiency of CRISPR-Cas9 sgRNA
- Supervisor and collaborators: Prof Lars Steinmetz, Dr Shengdi Li, Dr Sibylle Vonesch
Skills
- Bioinformatics
- Gene Expression
- Single Cell Sequencing
- Spatial transcriptomics
- DNA Methylation
- Shell, R and Rmarkdown
Selected Publications
MCL‑1 safeguards activated hair follicle stem cells to enable adult hair regeneration
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.
Benchmarking cell type annotation methods for 10x Xenium spatial transcriptomics data
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.
Self-maintenance of zonal hepatocytes during adult homeostasis and their complex plasticity upon distinct liver injuries
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)
Unraveling the timeline of gene expression: A pseudotemporal trajectory analysis of single-cell RNA sequencing data
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.
Integrative analysis of DNA methylation and gene expression reveals hepatocellular carcinoma-specific diagnostic biomarkers
Cheng, J. et al. (2018). "Integrative analysis of DNA methylation and gene expression reveals hepatocellular carcinoma-specific diagnostic biomarkers." Genome Medicine. 10, 1-11.
Talks
Exploring mammary gland developmental stages and breast cancer heterogeneity using single-cell technologies
Talk at The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Cell type annotation for imaging-based spatial transcriptomics data
Talk at The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Time course analysis of pseudo-bulk samples from single cell RNA sequencing data
Talk at RMIT University, Melbourne, Australia
Understanding cell lineage commitment and breast cancer development by single cell RNA-seq
Talk at The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia