Rui Chen

The paper identifies biallelic DDX41 variants in LCA/EOSRD patients and shows they disrupt retinal homeostasis through loss-of-function mechanisms in mouse models.

A combinatorial gene therapy targeting inflammation and chondrocyte health slows OA progression and reduces pain in murine and equine models.

The paper constructs a multi-omics single-cell atlas of human RPE and choroid, identifying cell types, aging patterns, and genetic risk factors for AMD.

The paper creates a multi-omics atlas of human trabecular meshwork and ciliary body cells, identifying cell types and regulatory programs linked to glaucoma.

The paper identifies systemic epigenetic variants linked to periconceptional environments in human fetal development, finding more variants in Black Americans and associations with cancer and neurodevelopment.

This study evaluates somatic variant calling in normal tissues using single-cell RNA and ATAC sequencing, showing Monopogen outperforms other tools in accuracy and sensitivity.

This paper identifies genetic variants and genes associated with foveal hypoplasia using GWAS and multi-omics data, and establishes a zebrafish model to study the condition.

This study uses synthetic serum markers (RMAs) to monitor retinal gene expression and cell survival through blood tests, showing high sensitivity and non-destructiveness.

The paper introduces a standardized, open-source protocol for noninvasive joint injury in mice, resulting in post-traumatic osteoarthritis, and provides tools for reproducibility and analysis.

The paper identifies conserved and species-specific aging mechanisms in retinal cells across zebrafish, mice, and humans using single-cell multi-omics analyses.

This study identifies sensory fiber types in mouse TMJ tissues using immunohistochemistry, finding peptidergic fibers dominate with minimal non-peptidergic nociceptors.

This paper introduces DeepSAS, a deep graph framework to identify senescent cells and their associated genes, revealing cell-type-specific senescence features in aging and disease.

This study identifies 123 genome-wide significant loci associated with foveal pit depth, revealing new biological pathways and genes involved in human foveal development.

This study develops a mouse model of rhodopsin sector RP and shows that dim red light and S1PR agonist treatment can prevent light-induced photoreceptor degeneration.

The paper compares short-read and long-read single-cell RNA sequencing in mouse retina, identifying 44,325 transcript isoforms, 38% previously uncharacterized.

This study performs single-cell RNA sequencing on primary human trabecular meshwork cells in vitro to compare gene expression with in situ tissue, providing a public resource for studying cellular identity and translatability.

The paper introduces a sample multiplexing method for scRNA-seq to improve resolution of sample origin and phenotypic data in mouse retinal ganglion cells.

The paper generates a large-scale single-cell RNA-seq dataset of the mouse retina and integrates it with public data to create a comprehensive cell atlas.

This study generates a single cell RNA sequence atlas of the early Drosophila larval eye covering six developmental stages, identifying cell types and specific genes involved in eye development.

The paper creates a comprehensive human retina cell atlas using single-cell multi-omics data, revealing over 110 cell types and their gene regulatory networks, and enables fine-mapping of GWAS and eQTL variants.

DeMixSC improves deconvolution accuracy by using single-cell RNA-seq and a benchmark dataset to account for technological discrepancies in complex tissue samples.

STAREG identifies replicable spatially variable genes across spatial transcriptomic studies using an empirical Bayesian approach with improved power and false discovery rate control.

This paper presents a comprehensive single-cell multi-omics atlas of the human retina, integrating RNA-seq and ATAC-seq data to identify cell-type-specific cis-element-gene relationships and transcription factor regulons.

The paper shows SOX7 deficiency causes ventricular septal defects by impairing endocardial-to-mesenchymal transition through reduced Wnt4 and Bmp2 expression in developing atrioventricular canals.

This study identifies 16 pathogenic structural variants in 16 IRD families using whole-genome sequencing, finding SVs contribute 2.1% to unresolved IRD cases but less than SNVs and indels.

The paper identifies CoRSIVs with strong genetic control of methylation and links them to transposable elements and disease.

The paper performs spatial transcriptomic profiling of the mouse retina to uncover its laminar organization and generates a comprehensive spatial single cell reference atlas.

Monopogen calls single nucleotide variants from single-cell sequencing data, achieving high accuracy in germline variant detection and enabling ancestry inference and variant association analysis.