John S. Tsang

Regulon-based clustering of islet scRNA-seq finds an IRF1-high, cytokine-driven beta cell state with reduced identity and autoantigen genes, enriched in type 1 diabetes donors.

MEA-LINK identifies CCL4-CCR5 signaling as a mechanism by which human microglia regulate neuronal hyperactivity through secreted factors and network activity.

The paper examines immune cell composition and function in placental villi, finding that excessive T cells and cytokines in preterm cases impair trophoblast health.

This study develops mathematical models and simulations to show that antigen-agnostic memory durability is constrained by immune cell turnover, cytokine dependence, and epigenetic state transmission, and can be tuned via cytokine-mediated feedback.

The paper introduces the Immune Signatures Data Resource, a compendium of standardized systems vaccinology datasets for comparative vaccine response analysis.

The paper identifies noise sources in CITE-seq data and provides an R package to denoise and normalize it.

This paper develops a framework combining stochastic simulations and machine learning to create predictive models of gene network phenotypes, showing improved accuracy over analytical methods in complex systems.

eNetXplorer is an R package that evaluates elastic net models for generalized linear models using cross-validation and provides tools for feature selection and significance testing.

This paper introduces a methanol fixation method for preserving PBMCs for scRNA-seq, showing it maintains RNA integrity and transcriptional profiles comparable to live cells.