Ence Yang

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

The paper benchmarks 16 teRNA analysis tools using simulated and real datasets, identifies performance trade-offs at different levels, and provides guidelines and a pipeline for best practices.

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.

The paper identifies two distinct neutrophil clusters with unique immune features across diverse disease conditions in mouse models.

This study compares the genomes of nematode-trapping fungi and non-NTF to identify genomic changes linked to carnivorism and adaptation to post-Permian-Triassic extinction environments.

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

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.

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.

MTM predicts individualized tissue gene expression profiles from peripheral samples using a multi-task learning framework, improving prediction accuracy and preserving biological variation.

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.

DEBKS detects differentially expressed circular RNAs by analyzing back-splicing events in RNA-seq data, showing efficiency and accuracy through real and simulated data.