Lingyun Song

This study quantifies intrinsic dCas9-DNA recognition using TANGO, identifying key factors affecting gRNA performance and revealing new aspects of dCas9 specificity.

The paper identifies transcription factors for reprogramming human astrocytes to neurons using CRISPRa screens and scRNA-seq, showing INSM1's broad neurogenic activity and cofactor interactions.

The paper identifies mechanoenhancers that regulate transcription in response to matrix stiffness and shows their potential for reprogramming cellular responses to mechanical cues.

The paper introduces TOP, a Bayesian framework that quantifies TF occupancy across many conditions using a single DNase-seq experiment, showing changes in 1500 TF motifs across cell types, hormone exposure, and genetic backgrounds.

The paper identifies enhancer elements that regulate epicardial gene expression during zebrafish heart regeneration by analyzing transcriptomes and chromatin accessibility.

The paper identifies sex-dependent glial-specific chromatin accessibility changes in late-onset Alzheimer's disease brains using ATAC-seq and links them to LOAD-GWAS regions.

This paper performs a large-scale eQTL meta-analysis across cerebral cortical and cerebellar brain regions, identifying distinct eQTL patterns and demonstrating improved power over existing studies.

The paper functionally annotates rare structural variants in the human brain by integrating SV calling with RNA-seq data to assess their regulatory effects and prioritize pathogenic deletions.

This study connects schizophrenia GWAS findings to specific genes, tissues, and regulatory mechanisms through transcriptome-wide and chromatin activity analyses.

The paper quantifies incomplete gene expression and chromatin accessibility changes during MyoD-induced transdifferentiation of human fibroblasts into myoblasts, linking chromatin remodeling deficiencies to incomplete reprogramming.

This study identifies Hnf4a as a mediator of microbial control of intestinal gene expression and inflammation across species.

The paper evaluates chromatin accessibility in prefrontal cortex samples from schizophrenia cases and controls, finding high heritability enrichment in open chromatin regions but no differential accessibility between groups.