Ruqian Lyu

This study identifies dysregulated epithelial cell death signaling in inflammatory bowel disease, showing it persists during remission despite therapy.

The paper introduces SpatialRNA, a Python package enabling the application of Graph Neural Networks to spatial transcriptomics data for domain detection.

This paper creates a spatial transcriptomic atlas of acute neonatal lung injury across development and disease severity using 1.2 million cells from 17 human infant lungs.

Xenium profiling of 343 genes in 1,126,820 nuclei from 19 human lungs maps fibrosis niches and orders alveolar remodeling from alveolar-capillary disruption to SPP1+ macrophage accumulation.

This paper introduces sgcocaller and comapr, tools for haplotype assembly and crossover map analysis from single-gamete sequencing data, showing improved accuracy and efficiency over existing methods.

This study shows Fancm deficiency increases crossover frequencies and disrupts gametogenesis in mice, with potential implications for human genomic instability disorders.

This study compares proliferation and tolerance in tissue-resident and recruited macrophages using single-cell RNA sequencing, finding that proliferative capacity differs between cell types.

The paper introduces a single-sample scoring method for gene set analysis that is stable across varying sample compositions and demonstrates improved computational efficiency compared to existing methods.