Xiaoying Fan

This paper introduces RB-dRNAseq, a multiplexed direct RNA sequencing method that improves demultiplexing accuracy and read recovery compared to conventional DNA barcoding methods.

SpliCOOL-seq enables high-throughput co-profiling of DNA methylation and chromatin accessibility in single cells, revealing epigenetic heterogeneity in lung cancer subclones and drug response patterns.

This paper introduces MethylAI, a deep learning framework that predicts DNA methylation states from genomic sequence and identifies sequence determinants of methylation through in silico perturbation.

The paper uses single-cell full-length transcriptome sequencing to study isoform regulation in developing mouse cortices, identifying dysregulated isoforms in Autism Spectrum Disorder.

This study identifies a CNV involving three enhancers that drive bilateral constricted ear malformations by coordinating HMX1 expression through distinct regulatory mechanisms.

This study investigates NEUROD1-induced astrocyte-to-neuron conversion using single-cell multiomics, revealing transcriptional and epigenetic changes and comparing it to ASCL1-induced conversion.

This study uses single-cell RNA sequencing to analyze immune responses in COVID-19 patients, identifying key immune cell changes and molecular pathways linked to disease severity.

This study uses single-cell RNA sequencing on multi-sector glioma biopsies to analyze tumor heterogeneity, revealing spatial patterns of invasion, progression branches, and cell-cell communication.

The paper identifies HSC-primed hemogenic endothelial cells in mouse embryos using single-cell transcriptomics and functional validation, revealing their developmental trajectory and bi-potential.

This study identifies Hand2as as a key lncRNA regulating HAND2 expression in heart development through single-cell RNA sequencing and knockout models, leading to congenital defects and perinatal lethality.

The paper shows that a TALE-based repressor targeting Xist intron 1 enhances iPSC generation and SCNT embryo development in mice, without affecting Xist expression.

This paper introduces a vector-independent method for multiplexed sgRNA expression, enabling efficient and scalable single non-repetitive DNA labeling and gene regulation in live cells.