My main projects

RNAdecayCafe

Summary

• Presents a first-of-its-kind database of high quality RNA stability estimates from pulse-label NR-seq experiments. Data can be accessed here.
• Paper presents a meta-analysis that shows how pulse-label NR-seq data is often highly consistent across labs, cell lines, method variations, etc. In contrast, we found pulse-chase NR-seq data to be batch effect-ridden and difficult to consistently interpret.
• We used this data to highlight the sometimes underappreciated role of RNA stability in tuning gene expression levels within a given cell line and in establishing differences across cell lines.

Link to preprint

Isoform stability quantification

Summary

• Developed method to quantify the stabilities of individual transcript isoforms from full-length (as opposed to 3’-end) NR-seq data.
• Used this method to rigorously identify and study the properties of NMD-sensitive transcript isoforms.
• Developed and interpreted a simple classification model that identified features which appeared to be major drivers of NMD sensitivity.
• Identified a unique class of alternative splicing coupled NMD that did not involve premature termination codons.

Link to preprint

The EZbakR-suite

Summary

• Introduced Snakemake pipeline (fastq2EZbakR) and R package (EZbakR)
• Generalizes feature assignment: the set of annotated genomic features that you can perform analyses on.
• Generalizes mixture modeling: how the fraction of reads from labeled RNA are estimated.
• Generalizes dynamical systems modeling: how kinetic parameters are estimated from NR-seq data.
• Generalizes comparative analyses: how kinetic parameters are compared across biological conditions.

Link to paper

bakR

Summary

• Introduced an R package (bakR) designed to compare RNA synthesis and degradation rate constants across biological conditions.
• Also introduced a hierarchical modeling strategy to increase statistical power of these comparisons.

Link to paper