Wei Li

This study identifies epigenetic biomarkers in cell-free DNA for ALS diagnosis and progression prediction using methylation analysis.

The paper compares the clinical impact of missense variants in CALM1, CALM2, and CALM3 genes by analyzing expression levels and translation efficiency in cardiac tissue.

This study shows that COPS5 is essential for Sertoli cell function and male fertility in mice, as its loss causes infertility through disrupted cell polarity, blood-testis barrier integrity, and gap junction communication.

The paper identifies a nuclear RNA degradation code (NRDC) that recognizes transcripts with both a 5' splice site and a poly(A) junction, leading to their degradation and contributing to disease.

The paper maps liver chromatin architecture using ATAC-seq and shows sex is the main factor driving diet-induced nucleosome dynamics in mice.

This study identifies 413 APA-linked cancer susceptibility genes by integrating GWAS data with APA quantification, showing genetic variants associated with APA explain a large portion of cancer heritability.

The paper identifies TDP-43 dysregulation of polyadenylation site selection as a key feature of RNA misprocessing in ALS/FTD and related disorders, linking it to increased tau phosphorylation.

The paper identifies sequence-specific sensitivity to JTE-607 in mRNA 3' processing by analyzing over 260,000 sequence variants and developing a predictive model.

The paper identifies FEDORA, a lncRNA with sex- and cell-type-specific effects on depression in females.

The paper constructs a gene regulatory network (GRN) for alveologenesis in a mouse model of BPD, revealing how IGF1 signaling regulates lung development and identifies potential therapeutic targets.

The paper re-evaluates differential expression methods on semi-synthetic RNA-seq data without normalization, finding the Wilcoxon rank-sum test still outperforms dearseq in FDR control and power.

The paper shows that popular differential expression methods like DESeq2 and edgeR have high false discovery rates in population-level RNA-seq data, recommending the Wilcoxon rank-sum test instead.

The paper benchmarks PCA against hidden variable inference methods for QTL mapping, finding PCA to be faster, better-performing, and more interpretable.

Clipper provides a p-value-free FDR control method for high-throughput data from two conditions, outperforming existing approaches without relying on p-values or distributional assumptions.

scDaPars analyzes alternative polyadenylation in scRNA-seq data to identify cell subpopulations missed by gene expression analysis.

The paper identifies an atlas of 3QTLs associated with alternative polyadenylation across 46 tissues, showing they explain 16.1% of trait-associated variants and contribute to disease independently of gene expression.

DORGE identifies cancer driver genes by integrating genetic and epigenetic data, finding histone modifications predict TSGs and missense mutations predict OGs.

The paper identifies cell type-specific chromatin loops anchored at large DNA methylation nadirs, revealing their role in stem and progenitor cell function.

The paper introduces CHALM, a methylation quantification method that accounts for cellular heterogeneity, improving the correlation between methylation and gene expression.

The paper presents a chromosome-scale reference genome of tea tree using SMRT sequencing and Hi-C, enabling annotation of gene families and retrotransposon diversity.

This study de novo assembles and annotates the chloroplast and mitochondrial genomes of Camellia sinensis var. assamica, revealing structural and functional features of these genomes.

This study uses whole exome sequencing to identify genetic causes of short stature in 20 patients, finding molecular diagnoses in 45% with discrepancies between clinical and genetic diagnoses.

Poly(A)-ClickSeq enables high-quality RNA-seq libraries of poly(A) site junctions without RNA enrichment or fragmentation, revealing new poly(A) sites and APA regulation.

The paper identifies alternative splicing transitions during postnatal skeletal muscle development and shows their role in calcium handling through calcineurin A isoform regulation.

MACS calls ChIP-Seq peaks by estimating tag shift from Watson/Crick strand offsets and testing enrichment against a locally adaptive Poisson background, improving specificity and binding-site resolution.