Benjamin D. Humphreys

The paper uses spatial transcriptomics to identify hypoxia-adapted VSMC remodeling in human aortic dissection, linking it to interlamellar separation.

This study shows that SOX9 upregulation in injured proximal tubular cells is driven by androgens in males but blunted in females, revealing sex-specific repair mechanisms in AKI.

The paper identifies thin descending limb cells in developing mouse kidneys using scRNA-seq and shows they originate from proximal tubule cells, with Hnf4a playing a role in their development.

The paper identifies a unique pericystic endothelium in ADPKD that contributes to microvascular remodelling and impaired perfusion, suggesting vascular targets for early intervention.

The paper identifies cell type-specific lncRNAs in human kidneys and finds TARID, a podocyte-specific lncRNA, is upregulated in diabetic kidney disease and critical for actin cytoskeleton reorganization.

This study uses single-nucleus multi-omics to analyze mouse PKD progression, identifying cell-type-specific gene and epigenetic changes and conserved regulatory pathways between mouse and human.

This study maps epigenetic changes during AKI repair in mice and humans, identifying CREB5 as a regulator of both successful and failed tubular repair.

The paper identifies high-resolution eQTLs in kidney tissues using Bayesian fine mapping with integrative priors, improving resolution and functional relevance.

The paper develops RENIN, a regularized regression method, to predict gene regulatory networks from single nucleus multiomic data and applies it to identify regulators of failed kidney injury response.

The paper introduces gkmQC, a sequence-based model to assess and refine chromatin accessibility data quality, improving peak calling and regulatory element alignment.

This study uses single-cell multiomic analysis to define cellular complexity in ADPKD, identifying novel transcriptomic and epigenomic features in cystic kidney cells.

This study uses multimodal single-cell sequencing to show that chromatin accessibility and genetic background influence diabetic kidney disease progression through cell-specific mechanisms.

This study integrates snATAC-seq and snRNA-seq data to redefine cellular heterogeneity in the adult human kidney by identifying functional differences in chromatin accessibility and gene expression.

This study compares single nucleus RNASeq (snRNASeq) and single cell RNASeq (scRNASeq) in mouse lung, finding snRNASeq reduces dissociation bias and better detects rare cell types.

The paper uses exome sequencing and scRNA-seq to identify donor and recipient immune cells in kidney transplants and finds distinct transcriptional profiles in donor macrophages and T cells.

The paper uses single nucleus RNA sequencing to identify a proinflammatory and profibrotic proximal tubule cell state in mouse AKI that fails to repair, suggesting it as a therapeutic target.

This study uses snRNAseq to analyze early diabetic nephropathy in human kidneys, identifying gene expression changes in potassium secretion and angiogenic signaling across multiple cell types.

This study identifies 93 genetic loci associated with kidney function across four ancestry groups and highlights causal effects on kidney-related diseases.

The paper compares kidney organoid and adult human kidney single-cell and single-nucleus transcriptomes to assess differentiation maturity and identify transcription factor networks.