John F. Ouyang

PathPinpointR predicts scRNA-seq sample positions along reference trajectories using switching-gene events to assign pseudo-time values.

This study shows that mitochondrial DNA mutations are linked to better responses to kinase inhibitor therapy and reduced oxidative phosphorylation in CML patients.

ShinyCell2 provides an interactive R package for visualizing spatial, peak-based, and multi-omic single-cell data with advanced features and ease of use.

The paper introduces BrainSTEM, a multi-resolution mapping framework to evaluate midbrain differentiation protocols by comparing them to a fetal brain atlas, revealing off-target cell types in most published models.

scPanel identifies a minimal gene panel for patient classification from scRNA-seq data, achieving high accuracy with fewer than 20 genes across multiple datasets.

cellstruct quantifies biological similarity between 2D and higher-dimensional embeddings in scRNA-seq data to identify poorly preserved cell populations.

The paper identifies a matrisome-associated macrophage polarization state in fibrotic tissues across multiple organs using single-cell RNA sequencing.

ShinyCell converts single-cell RNA sequencing data into interactive, shareable visualizations for easier exploration and sharing.

The paper functionally annotates human long non-coding RNAs by systematically knocking down 285 lncRNAs and analyzing molecular phenotypes using CAGE sequencing.

GeneSwitches identifies the order of gene-expression and functional events along pseudo-time trajectories in single-cell experiments.

The paper introduces Xtail, a method to identify differentially translated genes by analyzing Ribo-seq data while accounting for mRNA abundance variations.

This study identifies that amyloid plaque phagocytosis through Hif1α controls microglial phenotypes in Alzheimer’s disease in both mice and humans.

This paper creates a single-cell brain atlas of Alzheimer’s disease, identifying cell-type specific gene expression patterns and regulatory networks associated with disease.