Hyun Joo Ji

T2T-HG002v1.1, a complete diploid HG002 assembly lacking detectable errors over 99.4% of its length, enables genome-based benchmarking of assemblies, sequencing reads, and phased variant calls.

The paper identifies off-target probe binding in 10x Genomics Xenium gene panels and develops a tool to assess its impact on spatial transcriptomic accuracy.

TranSigner improves transcript abundance estimation by accurately assigning long reads to transcripts, outperforming existing tools in simulated and experimental data.

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.

TD2 is a new tool for ab initio annotation of protein-coding ORFs in transcripts, showing sensitivity and precision across diverse eukaryotic transcriptomes.

The paper analyzes 2,199 upstream ORFs to determine if they can be novel exons added to existing genes, finding 582 with strong evidence for new protein isoforms.

EASTR corrects systematic alignment errors in multi-exon genes by detecting and removing falsely spliced transcripts, improving alignment accuracy across species.