About

Background

I'm a PhD candidate in Quantitative Biomedical Sciences at Dartmouth College. Previously I completed an MS in Computational Biology at Carnegie Mellon University and earned my BSc in Bioinformatics from Xi'an Jiaotong-Liverpool University / University of Liverpool.

I'm actively bridging academic research and product development, with a focus on making ML-driven biological insights accessible through well-designed, reproducible tools.

Research focus

• Machine learning on bulk & single-cell omics for patient stratification and precision medicine
• Interactive, reproducible analysis and visualization tools with R Shiny and Streamlit
• Machine learning DevOps

Skills & tools

Publications & presentations Full list →

• 1.Jarnagin HC, Parvizi R, Gong Z, et al. Multimodal analyses of early, untreated SSc skin identify a proinflammatory vascular niche. JCI Insight. 2025.
• 2.Parvizi R, Gong Z, et al. RUNX1 is associated with disease severity of systemic sclerosis. Annals of the Rheumatic Diseases. 2025.
• 3.Frisby TS, Gong Z, Langmead CJ. Asynchronous parallel Bayesian optimization for AI-driven cloud laboratories. Bioinformatics. 2021.
  doi:10.1093/bioinformatics/btab291 ↗

• 4.Gong Z, et al. Identification and prediction of SSc intrinsic subtypes using semi-supervised and supervised learning on gene expression data of multiple cohorts. [First author · In preparation]
• 5.Jarnagin HC*, Gong Z*, et al. SSc Skin Cell Atlas: a web portal for scRNA-seq analysis underscores immune activation aberrations. [Co-first author · In preparation]
• 6.Gong Z, et al. DeepDerm: hierarchical deconvolution of skin bulk transcriptomes resolves fibroblast subtype composition using an integrated single-cell atlas. [First author · In preparation]

Talks

• "Machine Learning–Based Skin Transcriptome Classifier (v2.0) Links SSc Molecular Subtypes to Disease Severity and Progression." ACR Convergence, Chicago IL · Oct 2025
• "Identification of Systemic Sclerosis Intrinsic Subtypes in the ASSET Clinical Trial Using PBC Gene Expression." ACR Convergence, Washington DC · Nov 2024

Posters

• "Systemic Sclerosis Skin Cell Atlas: Integrating Single-Cell and Spatial Transcriptomics into a Cloud-Based Resource." AMIA Annual Symposium, Atlanta GA · Nov 2025
• "Deconvolution Reveals Differences in Cell Type Composition Among Systemic Sclerosis Intrinsic Subtypes." 8th SSc World Congress, Prague · Mar 2024

Other interests

• AI ethics and humanity
• Mental health, personality psychology, philosophy
• Poetry, pencil drawing, contemporary dance
• Animal welfare — I volunteer at a humane society socializing and walking dogs. It brought me so much joy, especially during a hard time.

CV

My full curriculum vitae is available as a PDF.

Contact