Jing Li

The paper identifies thousands of human orphan genes from RNA-Seq data, validates them with single-cell RNA-seq, and provides a compendium for future research.

The paper evaluates gene annotation pipelines for predicting orphan genes in genomes, finding that combining methods improves prediction accuracy, especially for Arabidopsis.

The paper re-mines RNA-Seq data to identify unannotated ORFs in yeast, revealing many likely protein-coding genes and providing a resource for further study.

The paper introduces phylostratr, an R package for phylostratigraphy, enabling automated and customizable analysis of gene evolutionary origins across species.

synder infers genomic orthologs by using synteny maps to trace features between genomes, demonstrated with Arabidopsis thaliana transcription factors.