Zoe Rudnick

Bramble improves transcript quantification by projecting spliced genomic alignments into transcriptomic coordinates, enhancing accuracy across simulated datasets.

StringTie3 improves total RNA-seq assembly by resolving nascent and mature transcripts, reducing errors and enhancing precision and sensitivity in both short- and long-read data.

SpaTRACE jointly infers gene regulatory networks and cell-cell signaling from spatial transcriptomics data, outperforming existing methods in synthetic benchmarks and revealing novel interactions in development and regeneration.

The paper identifies isoswitching, a phenomenon of isoform usage changes in human brain development and aging, and shows it can predict age across the lifespan using RNA-seq data.