S. Z. Li

TxNova: recovery of recurrent unannotated intergenic splice loci from existing bulk RNA-seq alignments

TxNova identifies recurrent unannotated intergenic splice junctions from bulk RNA-seq alignments, providing candidate leads for experimental validation.

scFair: Geometry-Aware Gene Budgets and Same-Rank Extension for Highly Variable Gene Selection

scFair improves highly variable gene selection by automatically setting list length and adding a tail to reduce bias from fixed cutoffs.

scATrans: annotating single-cell differential expression as transcription- or stabilization-weighted using unspliced RNA

scATrans annotates single-cell differential expression as transcription- or stabilization-weighted using unspliced RNA, without additional experiments, and recovers mechanism-specific biology from standard scRNA-seq data.