James Alexander Thomson

The paper develops CRSP, a pipeline for RNA-seq analysis in species without a sequenced genome or reference transcripts, and applies it to generate a comprehensive Nile grass rat transcriptomic atlas.

This paper presents a haplotype-resolved genome assembly of the Nile rat, revealing unique genomic features relevant to type 2 diabetes and metabolic dysfunctions.

This study shows that equalizing cDNA library concentrations before pooling improves gene detection rates and reduces technical artifacts in single-cell RNA-seq data.

This study shows that co-differentiating human and mouse pluripotent stem cells accelerates human neural differentiation, with gene expression changes correlating with in utero development.

This study evaluates the reproducibility of spatial ordering analysis across different single-cell RNA-seq protocols, finding high reproducibility despite differences in sequencing depth and computational methods.

Trendy uses segmented regression to analyze gene expression dynamics in ordered experiments, identifying gene-specific patterns and overall transcriptome changes.

SCnorm provides a quantile-regression based normalization method for scRNA-seq data to reduce artifacts and improve downstream analysis accuracy.