Rafael A Irizarry

The paper introduces derfinder, a tool for RNA-seq analysis that identifies differentially expressed regions at single base resolution without relying on gene annotations, showing it works well with incomplete annotations and large datasets.

The paper introduces a method to correct RNA-seq transcript abundance estimates by modeling fragment sequence bias, reducing false positives related to alternative isoform usage.

IVT-seq identifies significant technical biases in RNA-seq library preparation and sequencing, revealing coverage inconsistencies and rRNA depletion as major contributors.