Yin Shen

The paper develops a computational method to predict structural variant impacts on genome folding and identifies ASD-associated variants disrupting neuronal regulatory interactions.

This paper introduces ccMPRA, a method that combines Capture-C and MPRA to study promoter interactions and regulatory activity, identifying enhancers and silencers.

Benchmarking six long-read RNA-seq protocol-platform combinations and 14 tools across human, mouse, and manatee shows read length and accuracy drive isoform detection, depth drives quantification.

The paper identifies PRC2.1's role in opposing G1 progression by regulating CCND1 and CCND2, showing its importance in cell proliferation across multiple cancer types.

This paper introduces PRIME, a high-throughput prime editing screen that identifies functional DNA variants in the human genome with base-pair resolution.

The paper identifies functional CREs in iPSCs and neurons and links them to neuropsychiatric disease risk variants.

The paper reports 109 non-coding CRISPR screens analyzing 13.3Mb of the genome, identifies CRE-gene links, and provides guidelines and tools for screening non-coding regulatory elements.

This study introduces S-BEAM, a semi-supervised ensemble method to prioritize non-coding variants and their target genes in microglia for Alzheimer's disease, identifying 11 risk variants and proposing 37 for further study.

THUNDER is a deconvolution method that infers cell type proportions from bulk Hi-C data, outperforming existing methods in accuracy.

The paper identifies a transcription factor network and enhancers involved in cortical regional patterning using mouse embryonic data.

The paper identifies 491,818 candidate cis regulatory elements in adult mouse brain sub-types and links them to target genes and transcriptional regulators involved in various pathways.

HPRep quantifies reproducibility in HiChIP and PLAC-seq data by using a stratified and weighted correlation metric, outperforming existing Hi-C-based measures.

CRISPRpath enables parallel characterization of cis-regulatory elements for multiple genes in a pathway, identifying functional enhancers and distinguishing their impact on gene expression.

The study identifies TMEM132D's role in neuronal morphogenesis through interaction with NAP1 and the WAVE regulatory complex in C. elegans.

This study characterizes 3D epigenomic landscapes during human corticogenesis, revealing chromatin looping and super interactive promoters involved in lineage-specific gene regulation.

SMNN improves batch effect correction in scRNA-seq by using supervised mutual nearest neighbor detection within cell types, leading to better merging and retention of cell-type specific features.

SAME-clustering improves single-cell RNA-seq clustering by combining multiple methods to produce a more accurate and diverse ensemble solution.

The paper identifies cis-regulatory chromatin contacts in neural cells and links them to genetic variants associated with complex neurological disorders.

This study shows that adult microglia self-renew to restore homeostasis after ablation, with specific maturation programs and spatial organization.