Houlin Yu

Scalable single-cell isoform profiling with sequencing-by-expansion

This paper introduces a high-throughput single-cell RNA isoform sequencing method using sequencing-by-expansion (SBX) and the CUDLL algorithm, achieving high accuracy and enabling isoform-level analysis across cell types.

The Ancient Origin and Dynamic Diversification of the Fungal Poly(ADP)-ribose Polymerase Protein Family

This study analyzes the evolution of fungal PARP proteins across 534 species, identifying dynamic diversification and lineage-specific gains and losses.

Accurate strand-specific long-read transcript isoform discovery and quantification at bulk, single-cell, and single-nucleus resolution

The paper introduces LRAA, a framework for accurate isoform discovery and quantification in long-read RNA-seq data, outperforming existing methods across multiple benchmarks.

SpaceSequest: A unified pipeline for spatial transcriptomics data analysis

SpaceSequest provides a unified pipeline for analyzing spatial transcriptomics data from multiple platforms, enabling standardized processing, analysis, and visualization.

RNA splicing dynamics in CD8 T cells uncovers isoforms that impact T cell-mediated cancer immunotherapy

The paper constructs a single-cell splicing atlas of human CD8 T cells and identifies isoform-specific immune checkpoints that enhance effector function and tumor control.

Multi-platform evaluation and optimization of single-cell RNA isoform sequencing

The paper evaluates and optimizes single-cell RNA isoform sequencing by analyzing artifacts from three platforms and introducing methods to reduce their impact.

CTAT-LR-fusion: accurate fusion transcript identification from long and short read isoform sequencing at bulk or single cell resolution

CTAT-LR-fusion detects fusion transcripts from long and short read RNA-seq data, improving accuracy in bulk and single cell transcriptomes.

The Origin and Evolution of Orphan Genes: A Case Study in Tea Plant Family

The study decodes the genome of Stewartia gemmata and identifies orphan genes and transcription factors in Theaceae, revealing their evolutionary origins and functional roles.

Conservation and Expansion of Transcriptional Factor Repertoire in the Fusarium oxysporum Species Complex

This study examines transcription factor repertoires in the Fusarium oxysporum species complex, finding expanded families linked to host-specific adaptation and pathogenicity.

Chromosome-scale genome assembly of Fusarium oxysporum strain Fo47, a fungal endophyte and biocontrol agent

The paper presents a chromosome-level genome assembly of Fusarium oxysporum strain Fo47, highlighting its unique genomic features and potential for studying plant interactions.