Conrad G. Oakes

The paper analyzes RNA-seq data from rats to show gene expression predicts exercise training levels, reveals isoform-level changes, and identifies a potential novel virus affecting physiological measurements.

The paper shows that gene syntax influences supercoiling-mediated transcriptional feedback, affecting adjacent gene expression in human cells.

The paper adapts kallisto-bustools for bacterial scRNA-seq to enable uniform preprocessing and analysis of microbial single-cell transcriptomics.

The paper introduces accumap, a statistical inference method that improves spatial transcriptomics array reconstruction compared to UMAP.

The paper develops lr-kallisto, a tool for accurate long-read transcriptome quantification using ONT data, showing improved results with exome capture.

The paper measures mRNA and protein levels in single cells for synthetic promoters, finding that promoter strength affects both transcription and translation, and introduces a framework for comparing gene regulation.

The paper identifies a quiescent-like state with reduced nuclear size and transcriptional activity that enables efficient TF-mediated conversion of fibroblasts to neurons.