Hui Shen

This study shows that using graph-based pangenomes and inferred donor-specific assemblies improves somatic variant detection compared to GRCh38.

This study shows dietary restriction enhances CD8+ T cell ketolysis, improving mitochondrial function and anti-tumor immunity by reducing exhaustion.

The paper develops a framework to detect and trace somatic retrotransposition events in human tissues, identifying rare L1 insertions and improving detection accuracy.

The paper develops a pangenomic method to create a benchmark resource for somatic variant detection using HapMap mixtures, identifying millions of variants across different genomic regions.

Tranquillyzer is a deep learning framework for processing long-read single-cell RNA-seq data, enabling accurate identification of structural elements and demultiplexing despite sequencing errors and library variability.

The paper introduces scDEEP-mC, a single-cell DNA methylation profiling method, and shows it can identify cell types, X-inactivation states, and replication dynamics with high coverage.

Synthbar adds synthetic cell barcodes to sequencing reads to enable compatibility with computational tools that require them.

This study identifies high-risk mesenchymal stem cells (hrMSCs) that drive DNA damage and promote high-grade serous ovarian cancer initiation in fallopian tube epithelium.

The paper develops M2AE, a multi-task multi-view model to impute blood SCFA levels using gut metagenomic data, dietary features, and host characteristics, showing improved performance over existing methods.

omicsMIC benchmarks 28 imputation methods for mass spectrometry-based omics data, enabling researchers to evaluate and select methods based on real-time visualizations.

The paper shows that DNA methylation loss in late-replicating domains is driven by cell division and replication, and introduces a model to estimate replicative history.

This paper develops a high-throughput DNA methylation array and atlas for mice, revealing tissue-specific methylation patterns and their associations with aging, differentiation, and disease.

STORM-seq improves single-cell RNA sequencing by enhancing detection of non-coding transcripts and transcript-level complexity, revealing new cell states in human fallopian tube epithelium.

Compartmap infers higher-order chromatin structure from scRNA-seq and scATAC-seq data, matching specialized chromatin capture methods and identifying clinically relevant structural alterations in single cells.