Jilin Zhang

Cross-species analysis identifies APOBEC3-associated spliceosomal snRNA hypermutability

The paper identifies APOBEC3-associated hypermutability in spliceosomal snRNA genes across species, showing lineage-specific activity rather than R-loop formation alone.

Unmasking genetic load: Genomic inbreeding drives growth depression in captive critically endangered Chinese Bahaba (Bahaba taipingensis)

The paper investigates genomic inbreeding effects on growth depression in captive Chinese bahaba, identifying genetic factors linked to skeletal and immune pathways.

Modtector: Ultra-Fast Modification Signal Mining on Mapped Sequencing Reads

Modtector efficiently extracts RNA modification signals from sequencing data, outperforming existing tools on large datasets.

Augmented prediction of multi-species protein--RNA interactions using evolutionary conservation of RNA-binding proteins

MuSIC predicts cross-species RBP-RNA interactions using evolutionary conservation and label smoothing, outperforming existing methods and quantifying variant effects on binding.

Dysregulated RNA G-quadruplex binding proteins reveal shifted stress responses in Alzheimer's Disease

The paper identifies dysregulated RNA G-quadruplex binding proteins (RG4BPs) in Alzheimer's Disease, linking their altered expression to glial cell dysfunction and stress state shifts.

Modification of RNAs in natural rG4 (MoRNiNG), A Database of RNA Modification Sites Associated with the Dynamics of RNA Secondary Structures

The paper introduces MoRNiNG, a database of RNA modification sites associated with RNA secondary structure dynamics, and validates the impact of modifications on G-quadruplex formation.

Multi-layered dosage compensation of the avian Z chromosome

The paper examines dosage compensation mechanisms on the avian Z chromosome in female, male, and intersex chickens, revealing transcriptional and translational strategies similar to mammalian X-chromosome compensation.

Single-nuclei histone modification profiling of the adult human central nervous system unveils epigenetic memory of developmental programs

The paper profiles histone modifications in adult human CNS cells, revealing epigenetic memory of developmental programs in oligodendroglia.

DNA methylation patterns of transcription factor binding regions characterize their functional and evolutionary contexts

The paper identifies DNA methylation patterns at TF binding sites across species, linking them to functional roles and evolutionary changes.

The highly conserved RNA-binding specificity of nucleocapsid protein facilitates the identification of drugs with broad anti-coronavirus activity

This study identifies conserved RNA-binding motifs in coronavirus nucleocapsid proteins that enable broad-spectrum antiviral drug development.

A new duck genome reveals conserved and convergently evolved chromosome architectures of birds and mammals

This study presents a nearly complete duck genome assembly, revealing conserved and convergent chromosome architectures between birds and mammals, including TAD organization and W chromosome evolution.

Binding specificities of human RNA binding proteins towards structured and linear RNA sequences

The paper identifies binding specificities of human RNA-binding proteins using HTR-SELEX, revealing that 70% bind linear sequences and 30% bind structured motifs, with novel roles for ZC3H12A/B/C in viral transcript degradation.

CRISPR/Cas9 screening using unique molecular identifiers

This paper introduces RSLs as UMIs to improve CRISPR/Cas9 screening reproducibility by enhancing precision and reducing required cells and sequencing reads.