Minyi Shi

This paper investigates the effects of Hippo pathway inhibition through pharmacological and genetic approaches, identifying kidney, pancreas, and thymus as target organs with dose-dependent toxicities.

The paper maps 3D genome organization and DNA methylation across 86,689 single nuclei from 16 human tissues, revealing cell-type-specific variations and discrepancies between methylation and chromatin structure.

The paper identifies synthetic lethality between POLE exonuclease deficiency and high aneuploidy in cancer cells, suggesting POLE inhibition as a therapeutic strategy for aneuploid tumors.

TumorLens detects genetic and epigenetic alterations in cancer using long reads, revealing key somatic events and methylation patterns across tumor samples.

This study identifies a SWI/SNF-targeting therapy effective against a double-negative prostate cancer subtype, showing it reduces viability in both AR-dependent and WNT-dependent models.

Epiregulon infers single-cell TF activity using ATAC-seq and RNA-seq to predict drug response and identify drivers of cell state.

This study shows that mesothelioma cells develop drug resistance by reverting to a promoter-centric gene regulation mechanism when treated with a TEAD inhibitor.

The paper identifies cell type-specific and shared chromatin-associated protein co-association modules using ChIP-Seq and machine learning in K562 and HepG2 cells.

OAK enables ultra-high throughput single-cell multiomic profiling with high sensitivity and reduced labor, demonstrating its utility in detecting rare resistant cell populations.

This study introduces scTaILoR-seq, a long-read targeted RNA sequencing method, to enhance single-cell transcriptome analysis and identify isoform variation and SNV associations in ovarian cancer.

This study compares ten commercial scRNA-seq technologies using PBMCs, finding the 10x Genomics kit offers superior performance and the Becton Dickinson kit provides cost-effective performance per cell.

The paper identifies regulatory programs in postnatal mouse development using single-nucleus data, revealing cell-type-specific and common regulatory topics across multiple tissues.

The paper evaluates 23 imputation models for cross-cell type epigenomic data, finding quality assessment challenging due to distributional shifts, data availability, and redundant metrics.

The paper introduces the EN-TEx resource, which provides personal epigenomes and variant-impact models across multiple tissues, revealing allele-specific loci and their associations with GWAS loci.

The paper shows how KLF4 interacts with SWI/SNF to increase chromatin accessibility at enhancers under laminar shear stress, promoting endothelial homeostasis and suppressing inflammation.

This study identifies 690 candidate ALS genes using a hierarchical Bayesian model, highlighting genetic convergence on the distal axon and functional significance in motor neurons.

The paper identifies dynamic cis-regulatory elements in epidermal differentiation using multi-omic data and deep learning, revealing combinatorial motif rules linked to gene expression and polygenic skin disease.

This study identifies NF90/ILF3 as a transcription factor that promotes proliferation over differentiation in K562 cells by hierarchically regulating key transcription factors.