Ence Yang

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.

Comprehensive benchmarking with guidelines for analyzing transposable element-derived RNA expression

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.

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.

Common Signatures of Neutrophils in Diverse Disease Conditions

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

The Genomes of Nematode-Trapping Fungi Provide Insights into the Origin and Diversification of Fungal Carnivorism

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.

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.

MTM: a multi-task learning framework to predict individualized tissue gene expression profiles

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

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.

DEBKS: A Tool to Detect Differentially Expressed Circular RNA

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