Yi Xing

The paper presents scMOCHA, a tool to analyze mtDNA heteroplasmy from scRNA-seq data, revealing cell type-specific mtDNA variants and disease mechanisms in hematopoietic cells.

Amaranth improves single-cell transcript assembly by discriminatively modeling UMI and internal reads, outperforming existing assemblers on Smart-seq3 datasets.

The paper identifies intron retention quantitative trait loci (irQTLs) in human tissues and shows their association with GWAS traits and eQTLs, revealing shared genetic regulation and potential NMD effects.

This paper introduces Patho-DBiT, a method for spatial transcriptomics in FFPE tissues, enabling RNA biology analysis including splicing, variants, and regulatory networks in clinical samples.

The paper functionally tests ESRP1/2 variants and CTNND1 isoforms in orofacial cleft models, finding some variants are benign and showing CTNND1's role in palatogenesis.

The paper identifies hnRNP H and F as regulators of Myc-dependent HRAS exon splicing in prostate cancer, showing their roles in splicing activation and correlation with Myc hallmarks.

IRIS identifies cancer immunotherapy targets from alternative splicing using transcriptomics data and validates them with patient T cells.

abPOA is a fast partial order alignment library using SIMD acceleration, achieving 15x speed improvement over SPOA with similar accuracy.

The paper identifies key RNA-binding proteins regulating alternative splicing during osteogenic differentiation using time-course RNA-seq and a computational approach.

The paper investigates the role of Esrp1 in cleft lip and palate development in mice, identifying altered Wnt signaling and epithelial-mesenchymal interactions as key factors.

ASPRIN identifies genetic variants altering RBP-RNA interactions by comparing CLIP-seq and RNA-seq allelic preferences in human cell lines.

The paper identifies and characterizes m6A methylated circular RNAs, showing cell-type specificity and cross-talk with m6A-mRNAs through YTHDF2.