Xinshu Grace Xiao

Allele-specific splicing modulates protein isoforms and Alzheimer's risk

The paper identifies allele-specific splicing events in brain tissues linked to Alzheimer's disease risk and functional genetic variation.

Allele-specific alternative polyadenylation links noncoding genetic variation to Alzheimer's disease risk

The paper identifies allele-specific alternative polyadenylation events in Alzheimer's disease brains and links them to genetic risk loci for neurodevelopmental and neurodegenerative disorders.

Genetic variation shapes human mRNA translation and disease risk

The paper develops a deep learning method to map SNV effects on translation efficiency, finding that variants influence disease risk through translation regulation.

Cell-Type-Resolved Isoform Atlas of Human Tissues Reveals Age and Alzheimer's Disease-Associated Splicing Changes

The paper introduces Sciege, a method to estimate cell type-specific isoform distributions using bulk and single-cell RNA-seq data, revealing age and Alzheimer's disease-related splicing changes.

Long-read RNA-seq demarcates cis- and trans-directed alternative RNA splicing

The paper uses long-read RNA-seq and isoLASER to distinguish cis- and trans-directed splicing events in human and mouse data, identifying thousands of cis-regulated events in disease-relevant genes.

Meta-analysis of genetic regulation of RNA editing in the human brain identifies new genes underlying neurological disease

The paper identifies 38,731 edQTLs in 3,554 genes through a meta-analysis of A-to-I RNA editing in the human brain and links 24 GWAS loci for neurological disorders to edQTLs.

Differing genetics of saline and cocaine self administration in the hybrid mouse diversity panel

The paper identifies genetic loci associated with saline self-administration in mice, finding distinct genetic bases compared to cocaine self-administration.

Cytosine-to-uracil RNA editing is upregulated by pro-inflammatory stimulation of myeloid cells

The paper analyzes RNA editing in myeloid cells under inflammatory stimulation, finding that C-to-U editing has a larger effect on proteome recoding compared to A-to-I editing.

L-GIREMI uncovers RNA editing sites in long-read RNA-seq

L-GIREMI detects RNA editing sites in long-read RNA-seq with high accuracy by addressing sequencing errors and biases.

dsRID: Editing-free in silico identification of dsRNA region using long-read RNA-seq data

dsRID predicts dsRNA regions using long-read RNA-seq data, showing high accuracy in Alzheimer's disease datasets and identifying distinct dsRNA expression patterns between AD and controls.

LINE-associated cryptic splicing induces dsRNA-mediated interferon response and tumor immunity

This study identifies hnRNPM as a suppressor of cryptic splicing and shows its role in preventing dsRNA-mediated interferon responses and tumor immunity.

Genetic pathways regulating the longitudinal acquisition of cocaine self-administration in inbred and recombinant inbred mice

The paper identifies genetic loci and pathways associated with cocaine self-administration in mice using GWAS and TWAS, highlighting Trpv2 as a key gene.

scAllele: a versatile tool for the detection and analysis of variants in scRNA-seq

scAllele detects and analyzes nucleotide variants and their allelic linkage to splicing in scRNA-seq data, outperforming existing tools and enabling allele-specific splicing analysis.

Genetics of white color and iridophoroma in "Lemon Frost" leopard geckos

The paper identifies a mutation in leopard geckos causing white coloration and tumors, linking it to a tumor suppressor gene.

Allele-specific alternative splicing in human tissues

The paper identifies allele-specific alternative splicing events across human tissues and develops a method to predict functional splicing-altering variants, finding many are linked to GWAS SNPs.

Extracellular microRNA 3' end modification across diverse body fluids

The paper develops a method to identify 3' end modifications of miRNAs in extracellular biofluids and finds that uridylation levels distinguish biofluid types better than overall miRNA expression.

Fe(III) heme sets an activation threshold for processing distinct groups of pri-miRNAs in mammalian cells

The paper investigates how Fe(III) heme availability affects pri-miRNA processing by DGCR8 and identifies a heme affinity threshold for Microprocessor activity.

Allele-specific binding of RNA-binding proteins reveals functional genetic variants in the RNA

The paper introduces BEAPR, a computational method to detect allele-specific binding of RNA-binding proteins, showing it outperforms existing methods and identifies disease-relevant variants.

Widespread RNA editing dysregulation in Autism Spectrum Disorders

This study identifies widespread hypo-editing in ASD brains and links RNA editing dysregulation to Fragile X syndrome through FMRP/FXR1P-ADAR interactions.

Co-regulation of alternative splicing by hnRNPM and ESRP1 during EMT

This study identifies co-regulated alternative splicing events by hnRNPM and ESRP1 during EMT, revealing their antagonistic roles and links to cancer survival.

Loss of MECP2 leads to induction of p53 and cell senescence

This study shows that loss of MECP2 in neurons leads to p53 induction and cell senescence, causing dendritic defects.