Tianyuan Liu

Transcriptome Universal Single-isoform COntrol: A Framework for Evaluating Transcriptome reconstruction Quality

The paper introduces TUSCO, a framework for evaluating transcriptome reconstruction quality using long-read sequencing by assessing precision and sensitivity with a curated set of single-isoform genes.

Systematic assessment of long-read RNA-seq methods for transcript identification and quantification

Benchmarking six long-read RNA-seq protocol-platform combinations and 14 tools across human, mouse, and manatee shows read length and accuracy drive isoform detection, depth drives quantification.

SQANTI3: curation of long-read transcriptomes for accurate identification of known and novel isoforms

SQANTI3 extends long-read transcriptome quality control with transcript-end subcategories, a short-read TSS ratio, rules or random-forest filters and a rescue module, raising SIRV-benchmarked F-score stepwise.

SQANTI-SIM: a simulator of controlled transcript novelty for lrRNA-seq benchmark

SQANTI-SIM simulates controlled transcript novelty for long-read RNA-seq data to benchmark transcriptome reconstruction pipelines.

Transcriptional differences for COVID-19 Disease Map genes between males and females indicate a different basal immunophenotype relevant to the disease