Xueyan Hu

Non-coding RNAs drive transcriptional network rewiring underlying thermal dimorphism in a human pathogenic fungus

MycoCirc: A Pan-Fungal Multi-Modal Pretrained Model for Fungal circRNA Prediction from Genome Sequence

The paper introduces mycoCirc, a pan-fungal model for circRNA prediction from genome sequences, achieving better performance than existing methods across multiple fungal groups.

TEITbase: a database for transposable element (TE)-initiated transcripts in human cancers

The paper develops TEITbase, a database of TE-initiated transcripts in 33 cancer types, identifying 38,995 transcripts and 6,203 tumor-specific ones, with tools for downstream analysis.

Functional diversification of the MADS-box gene family in fine-tuning the dimorphic transition of Talaromyces marneffei

The paper identifies functional diversification of MADS-box genes in Talaromyces marneffei, showing mads9 inhibits hyphal-to-yeast transition while mads10 does not.

Transposable elements drive species-specific and tissue-specific transcriptomes in human development

The paper identifies TE-initiated transcripts across human tissues and embryonic stem cells, showing tissue-specific activation and primate-specific TSSs contributing to gene regulation.

Species-specific circular RNA circDS-1 enhances adaptive evolution in Talaromyces marneffei through regulation of dimorphic transition and virulence

This study identifies circDS-1, a circular RNA in Talaromyces marneffei, that promotes dimorphic transition and virulence, revealing a novel mechanism for fungal thermal adaptation.

circFL-seq reveals full-length circular RNAs with rolling circular reverse transcription and nanopore sequencing

The paper introduces circFL-seq, a method for full-length circRNA sequencing using RCRT and nanopore sequencing, identifying 77,606 high-quality circRNAs from human cell lines and tissues.