Jarny Choi

This paper establishes that FRDA autonomic neurons are hyperexcitable and exhibit mitochondrial dysfunction using iPSC-derived models.

This study uses iPSCs from FRDA patients to model cardiac dysfunction, finding transcriptional dysregulation and phenotypes like increased cell size and mitochondrial stress.

Phi-Space ST identifies continuous cell states in spatial transcriptomics data using scRNA-seq references, revealing niche-specific cell types and patterns in cancer tissues.

The paper introduces quasar, a software for eQTL mapping that offers faster performance and better statistical models compared to existing methods.

NeighbourNet constructs cell-specific co-expression networks to uncover regulatory patterns in single-cell data, improving efficiency and enabling downstream analysis.

StableMate identifies stable predictors across omics datasets to improve reproducibility and interpretability of biological associations.

The paper describes the Stemformatics data portal, which curates and integrates gene expression datasets for stem cell research, enabling cross-dataset comparisons and benchmarking of cell types.

Sincast projects single cell RNA-seq data onto bulk reference atlases to predict cell identities without batch correction, highlighting new cell states.

constclust identifies robust cell clusters in scRNA-seq data by reconciling clustering results across parameter variations, improving accuracy and reproducibility with lower computational cost.

The paper integrates hundreds of transcriptome datasets from multiple platforms to create a cross-platform blood cell atlas, enabling robust cell type clustering without batch correction.

The paper analyzes myeloid cells from various sources to identify gaps in in vitro models compared to in vivo biology.

BioPyramid provides a python package to streamline the development of online genomics applications with built-in tools for gene annotation, dataset management, and visualization.