Russell G. Snell

Protocol for designing and interpreting minigene assays to validate candidate splice altering variants

This paper presents a protocol for minigene assays to validate splice-altering variants using locus-specific design, gene synthesis, and long-read sequencing.

ICARUS v3, a massively scalable web server for single cell RNA-seq analysis of millions of cells.

ICARUS v3 efficiently analyzes large-scale single cell RNA-seq datasets with over 1 million cells using geometric cell sketching and downstream analysis tools.

Evidence for glutamate excitotoxicity that occurs before the onset of striatal cell loss and motor symptoms in an ovine Huntington's Disease model.

The paper identifies transcriptional upregulation of glutamate receptors and downregulation of oxidative phosphorylation in an ovine HD model before neuronal loss and motor symptoms.

Isolated nuclei from frozen tissue are the superior source for single cell RNA-seq compared with whole cells.

This study compares single cell RNA-seq data from frozen tissue cells and nuclei, finding nuclei provide higher quality data with more gene and UMI counts and better clustering resolution.

Delineation of complex gene expression patterns in single cell RNA-seq data with ICARUS v2.0

ICARUS v2.0 provides a web-based tool for analyzing single cell RNA-seq data with features for gene network analysis, trajectory inference, cell communication, and GWAS integration.

Optimised multiplex amplicon sequencing for mutation identification using the MinION nanopore sequencer

The paper develops a multiplexing assay for MinION sequencing to identify genetic variants in small genomic regions, achieving accurate results for most targets despite sequencing biases.

Castration delays epigenetic aging and feminises DNA methylation at androgen-regulated loci

This study develops an epigenetic clock for sheep and finds that castration slows aging and feminizes DNA methylation at androgen-regulated loci.

The genomes of precision edited cloned calves show no evidence for off-target events or increased de novo mutagenesis

The study examines gene-edited cloned calves and finds no off-target events or increased de novo mutagenesis compared to unedited controls.

Testes of DAZL null sheep lack spermatogonia and maintain normal somatic cells

The paper generates DAZL-null sheep that lack germ cells but have normal somatic cells, demonstrating the feasibility of using absolute donor germline transmitters in livestock breeding.

A new mechanism for a familiar mutation - bovine DGAT1 K232A modulates gene expression through multi-junction exon splice enhancement

The paper re-examines the mechanism of the DGAT1 K232A mutation in bovine milk production, showing it modulates gene expression through splicing enhancement.

Natural cryptic variation in epigenetic modulation of an embryonic gene regulatory network

The paper investigates how heritable epigenetic factors contribute to cryptic variation in the requirement for SKN-1 in endoderm development in C. elegans.

RBV: Read balance validator, a tool for prioritising copy number variations in germline conditions

RBV prioritises and validates copy number variations using read balance from genome or exome sequencing data.

Extensive intraspecies cryptic variation in an ancient embryonic gene regulatory network

The paper identifies cryptic variation in the C. elegans endoderm gene regulatory network, showing that some embryos can develop endoderm without key regulators, while others require them.

Evaluation of the performance of copy number variant prediction tools for the detection of deletions from whole genome sequencing data

This study evaluates CNV detection tools for deletions in WGS data, finding Breakdancer and Delly perform best with high sensitivity and moderate FDR.

Multiple QTL underlie milk phenotypes at the CSF2RB locus

The paper identifies multiple QTL at the CSF2RB locus associated with milk yield and composition traits in dairy cattle and explores their genetic and molecular mechanisms.

Widespread cis-regulation of RNA-editing in a large mammal

The paper identifies cis-regulated RNA editing quantitative trait loci (edQTL) in cattle, linking them to gene expression and lactation traits.