Seth Winfree

DigitAb: Domain-Adaptive Cell Type Prediction Method from Light Microscopy Images

DigitAb predicts cell types from H&E-stained slides using deep learning, achieving high accuracy without specialized assays or immunostains.

A MEF2C transcription factor network regulates proliferation of glomerular endothelial cells in diabetic kidney disease

This study identifies a MEF2C transcription factor network that regulates endothelial cell proliferation in diabetic kidney disease and shows that SGLT2i treatment can reverse its dysregulation.

Uromodulin promotes immune zonation and inhibits alternative inflammasome-mediated activation of immune-to-collecting duct inflammatory signaling in early acute kidney injury

This study investigates how Uromodulin affects immune zonation and inflammasome activity in kidney injury, showing it reduces inflammation and immune cell interactions in specific kidney regions.

The immunometabolic topography of tuberculosis granulomas governs cellular organization and bacterial control

This study identifies hypoxia as a key driver of immune dysfunction in TB granulomas, correlating with bacterial persistence.

Integration of spatial multiplexed protein imaging and transcriptomics in the human kidney tracks the regenerative potential timeline of proximal tubules

A Quantitative Metric of Confidence For Segmentation of Nuclei in Large Spatially Variable Image Volumes

The paper introduces a confidence metric for nuclei segmentation in large spatially variable image volumes, showing it correlates with segmentation quality and F1 scores.

The chromatin landscape of healthy and injured cell types in the human kidney

The paper defines the chromatin landscape of healthy and injured kidney cells using multi-omics data, identifying regulatory elements and transcription factor networks involved in injury response.

An atlas of healthy and injured cell states and niches in the human kidney

The paper creates a high-resolution cellular atlas of healthy and injured kidney cell states and niches using single-cell and spatial technologies, identifying molecular signatures and pathways related to kidney injury.

A spatially anchored transcriptomic atlas of the human kidney papilla identifies significant immune injury and matrix remodeling in patients with stone disease

This study maps the spatial transcriptomic landscape of the human kidney papilla in stone disease, identifying immune injury and matrix remodeling as key features.

A reference tissue atlas for the human kidney

The paper constructs a reference tissue atlas of the human kidney using multi-omics data to identify cell types, pathways, and genes across nephron segments and interstitium.

Integration of spatial transcriptomic and single cell sequencing identifies expression patterns underlying immune and epithelial cell cross-talk in acute kidney injury

The paper integrates spatial transcriptomics and single cell sequencing to identify immune and epithelial cell cross-talk patterns in acute kidney injury models.

The orchestrated cellular and molecular responses of the kidney to endotoxin define the sepsis timeline

This study uses single-cell RNA sequencing to define the temporal cellular and molecular changes in the kidney during sepsis, identifying key gene expression shifts and communication failures that mark critical points in the sepsis timeline.