Publications & Presentations

Peer-reviewed publications

Published

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, Vol. 37, Supplement 1, July 2021, pp. i451–i459

[TODO: Zhiyun to add additional publications here]

In preparation

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

[TODO: Zhiyun to add additional presentations and posters here]

[TODO: Zhiyun to add preprints here]