The paper presents a multi-modal atlas of human kidney disease, identifying cellular and spatial mechanisms of injury resolution or failure and linking them to clinical outcomes.

bioRxiv · Sep 26, 2025 · PreprintMolecular Biology

Three Dimensional Multiscalar Neurovascular Nephron Connectivity Map of the Human Kidney Across the Lifespan

Liam McLaughlin, Zhang Bo, Siddharth Sharma, Amanda L. Knoten, Madhurima Kaushal, Jeffrey M. Purkerson, Heidie L. Huyck, Gloria Pryhuber, Joseph P. Gaut, Sanjay R. Jain

This paper constructs a 3D map of neurovascular nephron connectivity in the human kidney across the lifespan and identifies structural changes in development and disease.

Nature Communications · Jun 3, 2025Peer-reviewedNeuroscience

Mapping Human Tissues with Highly Multiplexed RNA in situ Hybridization

Kian Kalhor, Chien-Ju Chen, Ho Suk Lee, Matthew Cai, Mahsa Nafisi, Richard A. Que, Carter R. Palmer, Yixu Yuan, Yida Zhang, Xuwen Li, Jinghui Song, Amanda L. Knoten, Blue B. Lake, Joseph P. Gaut, Christopher Dirk Keene, , Kun Zhang

The paper introduces DART-FISH, a multiplexed RNA in situ hybridization technique for high-resolution profiling of human tissues, demonstrating its application on brain and kidney samples.

Nature Communications · Mar 20, 2024Peer-reviewedGenomics

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

Debora L. Gisch, Michelle Brennan, Blue B. Lake, Jeannine M. Basta, Mark S. Keller, Ricardo Melo Ferreira, Shreeram Akilesh, Reetika R. Ghag, Charles Lu, Ying‐Hua Cheng, Kimberly S. Collins, Samir V. Parikh, Brad H. Rovin, Lynn Robbins, Lisa Stout, , Joana P. Gonçalves

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.

Nature Communications · Jan 10, 2024Peer-reviewedMolecular Biology

Single Nucleus RNA Sequencing of Remnant Kidney Biopsies and Urine Cell RNA Sequencing Reveal Cell Specific Markers of Covid-19 Acute Kidney Injury

Reetika R. Ghag, Madhurima Kaushal, Gerald Nwanne, Amanda L. Knoten, Krzysztof Kiryluk, Avi Z. Rosenberg, Steven P. Menez, Serena Maria Bagnasco, Christopher John Sperati, Mohamed G. Atta, Joseph P. Gaut, James C. Williams, Tarek M. El‐Achkar, Lois Johanna Arend, Chirag R. Parikh, Sanjay R. Jain

bioRxiv · Nov 10, 2023 · PreprintGenetics

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

Blue B. Lake, Rajasree Menon, Seth Winfree, Qiwen Hu, Ricardo Melo Ferreira, Kian Kalhor, Daria Barwinska, Edgar A. Otto, Michael J. Ferkowicz, Dinh H. Diep, Nongluk Plongthongkum, Amanda L. Knoten, Sarah M. Urata, Laura H. Mariani, Abhijit S. Naik, , Ljiljana Paša‐Tolić

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.

Nature · Jul 19, 2023Peer-reviewedGenomics