Serena Y. Tan

Benchmarking Cell Type and Gene Set Annotation by Large Language Models with AnnDictionary

The paper benchmarks large language models for cell-type and gene set annotation using AnnDictionary, finding high accuracy in cell-type annotation and strong functional gene set recovery.

Dissecting regulatory syntax in human development with scalable multiomics and deep learning

The paper presents a single-cell multi-omics atlas of human development and uses deep learning to analyze regulatory DNA motifs and their impact on chromatin accessibility and gene expression.

sc-SPLASH provides ultra-efficient reference-free discovery in barcoded single-cell sequencing

sc-SPLASH enables reference-free discovery in scRNA-seq and spatial transcriptomics, uncovering novel transcriptomic features like V(D)J recombination and secreted repeat proteins.

IFNγ-Expressing Myeloid Cells Localize within Lipoproteinosis during Drug-Associated Pulmonary Alveolar Proteinosis occurring in Systemic Juvenile Idiopathic Arthritis

This study identifies IFNγ-expressing myeloid cells in lipoproteinosis regions of sJIA-daPAP patients, suggesting their role in immune pathology.

The Tabula Sapiens: a multiple organ single cell transcriptomic atlas of humans

Nearly 500,000 cells from 24 human tissues, many from one donor, characterize over 400 cell types and enable within-donor study of T-cell clones, B-cell mutation rates and splicing.

RNA splicing programs define tissue compartments and cell types at single cell resolution

The paper introduces SpliZ, a statistical method to detect cell-type-specific splicing regulation in single-cell RNA-seq data, finding 9.1% of genes show such regulation in human tissues.

Single-cell transcriptomic characterization of 20 organs and tissues from individual mice creates a Tabula Muris

The paper creates a single-cell transcriptomic atlas of 20 mouse organs and tissues, providing a resource for studying gene expression across cell types.