Jeffrey A. Farrell

This study identifies the developmental origin and regulation of best4+ intestinal cells in zebrafish and demonstrates their functional roles and limitations.

This study identifies and characterizes specialized endothelial cells in zebrafish gills that resemble mammalian lung aerocytes, using single-cell RNA sequencing and advanced imaging techniques.

This study characterizes the nervous system of Hydra vulgaris using scRNA-seq, identifying 15 neuron subtypes, mapping their spatial distribution, and exploring regulatory mechanisms through ATAC-seq and trajectory inference.

This study shows prdm1a drives a fate switch between zebrafish lateral line and ear hair cells, altering morphology and transcriptome.

This paper characterizes the zebrafish meninges using single-cell transcriptomics, identifying a novel cell type essential for brain development.

The paper reconstructs gene modules during cellular differentiation in zebrafish secretory tissues, identifying key transcription factors that regulate general and specialized secretion programs.

A 489,686-cell scRNA-seq atlas of 62 zebrafish stages (3.3–120 hpf) identifies 90 multi-tissue gene programs and markers for pericyte subtypes, intestinal smooth muscle layers, and best4+ enterocytes.

This study uses single-cell RNA sequencing to analyze zebrafish testis development, finding that infertile testes lack mature germ cells and show increased immune cell presence.

The paper quantifies transcription and degradation rates of mRNA in zebrafish embryos to understand their roles in cell-type specific gene expression.

This study provides the first single-cell RNA-seq time course of zebrafish brain development, revealing the emergence of neuronal diversity and distinct neurogenic regulatory patterns across developmental stages.

This study maps stem cell differentiation trajectories in Hydra using single-cell transcriptomics, revealing shared progenitor states for neurons and gland cells and creating a gene expression map of the nervous system.