Integration of human organoids single‐cell transcriptomic profiles and human genetics repurposes critical cell type‐specific drug targets for severe COVID‐19

Y Ma, Y Zhou, D Jiang, W Dai, J Li, C Deng… - Cell …, 2024 - Wiley Online Library
Human organoids recapitulate the cell type diversity and function of their primary organs
holding tremendous potentials for basic and translational research. Advances in single‐cell …

[HTML][HTML] Alterations in gut microbiota and host transcriptome of patients with coronary artery disease

L Chen, X Mou, J Li, M Li, C Ye, X Gao, X Liu, Y Ma… - BMC microbiology, 2023 - Springer
Background Coronary artery disease (CAD) is a widespread heart condition caused by
atherosclerosis and influences millions of people worldwide. Early detection of CAD is …

[HTML][HTML] Integrating genetic regulation and single-cell expression with GWAS prioritizes causal genes and cell types for glaucoma

AR Hamel, W Yan, JM Rouhana… - Nature …, 2024 - nature.com
Primary open-angle glaucoma (POAG), characterized by retinal ganglion cell death, is a
leading cause of irreversible blindness worldwide. However, its molecular and cellular …

Linking regulatory variants to target genes by integrating single-cell multiome methods and genomic distance

ER Dorans, K Jagadeesh, K Dey, AL Price - medRxiv, 2024 - medrxiv.org
Methods that analyze single-cell paired RNA-seq and ATAC-seq multiome data have shown
great promise in linking regulatory elements to genes. However, existing methods differ in …

[HTML][HTML] Inferring causal cell types of human diseases and risk variants from candidate regulatory elements

A Kim, Z Zhang, C Legros, Z Lu, A de Smith, JE Moore… - medRxiv, 2024 - ncbi.nlm.nih.gov
The heritability of human diseases is extremely enriched in candidate regulatory elements
(cRE) from disease-relevant cell types. Critical next steps are to infer which and how many …

[HTML][HTML] Deconvolution of polygenic risk score in single cells unravels cellular and molecular heterogeneity of complex human diseases

S Zhang, H Shu, J Zhou, J Rubin-Sigler, X Yang, Y Liu… - bioRxiv, 2024 - ncbi.nlm.nih.gov
Polygenic risk scores (PRSs) are commonly used for predicting an individual's genetic risk of
complex diseases. Yet, their implication for disease pathogenesis remains largely limited …

Mendelian randomization analysis identifies a causal effect of Streptococcus salivarius on DR mediating via the level of host fasting glucose

J Li, G Zheng, D Jiang, C Deng, Y Zhang, Y Ma, J Su - medRxiv, 2023 - medrxiv.org
Background: Diabetic retinopathy (DR) is one of leading causes of vision loss in adults with
increasing prevalence worldwide. Increasing evidence has emphasized the importance of …

Uncovering disease-related multicellular pathway modules on large-scale single-cell transcriptomes with scPAFA

Z Huang, Y Zheng, W Wang, W Zhou, C Wei, X Zhang… - bioRxiv, 2024 - biorxiv.org
Pathway analysis is a crucial analytical phase in disease research on single-cell RNA
sequencing (scRNA-seq) data, offering biological interpretations based on prior knowledge …

Systematic dissection of pleiotropic loci and critical regulons in exhibitory neurons and microglia relevant to neuropsychiatric and ocular diseases

D Jiang, Y Ma, J Su, J Li, G Zheng, Y Deng, X Gou… - 2024 - researchsquare.com
Background: Single-cell multimodal techniques have advanced the functional elucidation of
disease-relevant loci identified in genome-wide association studies (GWASs). However, the …

Microbial Antioxidants and Their Interactions with Gastrointestinal Tract Epithelial Cells in the Cattle

HZ Sun, S Zhu, M Jia, HC Li, B Han, T Shi, Q Zhang… - 2024 - researchsquare.com
Oxidative stress is a pivotal trigger of immune responses and cellular dysfunction. The
ruminant gastrointestinal tract (GIT) with complex microbial community demonstrated strong …