Qian Shi

Amaranth: Enhanced Single-Cell Transcript Assembly via Discriminative Modeling of UMI Reads and Internal Reads

Amaranth improves single-cell transcript assembly by discriminatively modeling UMI and internal reads, outperforming existing assemblers on Smart-seq3 datasets.

Transcriptome Assembly at Single-Cell Resolution with Beaver

Beaver improves transcriptome assembly at single-cell resolution by combining a fragment graph with random forest models, outperforming existing assemblers in precision.

Accurate Assembly of Circular RNAs with TERRACE

TERRACE improves circRNA assembly accuracy by using a splice graph and dynamic programming, outperforming existing methods in sensitivity and precision.

Scallop2 enables accurate assembly of multiple-end RNA-seq data

Scallop2 improves transcript assembly accuracy for multiple-end RNA-seq data by efficiently bridging gaps and reducing false positives.

On bridging paired-end RNA-seq data

This paper introduces algorithms to reconstruct full RNA-seq fragments from paired-end reads, improving transcriptome assembly and expression quantification.

Coral accurately bridges paired-end RNA-seq reads alignment

Coral improves transcript assembly by accurately bridging paired-end RNA-seq reads, achieving 7.5% and 11.2% adjusted precision improvements on GTEx data.