Featured publications
Three Dimensional Multiscalar Neurovascular Nephron Connectivity Map of the Human Kidney Across the Lifespan
Preprint: July 30, 2024
Liam McLaughlin, Bo Zhang, Siddharth Sharma, Amanda L. Knoten, Madhurima Kaushal, Jeffrey M. Purkerson, Heidy Huyck, Gloria S. Pryhuber, Joseph P. Gaut, Sanjay Jain
bioRxiv 2024.07.29.605633; doi: https://www.biorxiv.org/content/10.1101/2024.07.29.605633v1
Related movie collection: https://doi.org/10.5281/zenodo.12802740
This article is a preprint and has not been certified by peer review.
Multi-Molecular Hyperspectral PRM-SRS Imaging
February 21, 2024
Zhang W, Li Y, Fung AA, Li Z, Jang H, Zha H, Chen X, Gao F, Wu JY, Sheng H, Yao J, Skowronska-Krawczyk D, Jain S, Shi L. Multi-molecular hyperspectral PRM-SRS microscopy. Nat Commun. 2024 Feb 21;15(1):1599. doi: 10.1038/s41467-024-45576-6. PMID: 38383552; PMCID: PMC10881988.
An atlas of healthy and injured cell states and niches in the human kidney
July 19, 2023
Lake BB, Menon R, Winfree S, Hu Q, Ferreira RM, Kalhor K, Barwinska D, Otto EA, Ferkowicz M, Diep D, Plongthongkum N, Knoten A, Urata S, Mariani LH, Naik AS, Eddy S, Zhang B, Wu Y, Salamon D, Williams JC, Wang X, Balderrama KS, Hoover PJ, Murray E, Marshall JL, Noel T, Vijayan A, Hartman A, Chen F, Waikar SS, Rosas SE, Wilson FP, Palevsky PM, Kiryluk K, Sedor JR, Toto RD, Parikh CR, Kim EH, Satija R, Greka A, Macosko EZ, Kharchenko PV, Gaut JP, Hodgin JB; KPMP Consortium; Eadon MT, Dagher PC, El-Achkar TM, Zhang K, Kretzler M, Jain S. An atlas of healthy and injured cell states and niches in the human kidney. Nature. 2023 Jul;619(7970):585-594. doi: 10.1038/s41586-023-05769-3. Epub 2023 Jul 19. PMID: 37468583.
A spatially anchored transcriptomic atlas of the human kidney papilla identifies significant immune injury and matrix remodeling in patients with stone disease
July 19, 2023
Canela VH, Bowen WS, Ferreira RM, Syed F, Lingeman JE, Sabo AR, Barwinska D, Winfree S, Lake BB, Cheng YH, Gaut JP, Ferkowicz M, LaFavers KA, Zhang K, Coe FL, Worcester E; Kidney Precision Medicine Project; Jain S, Eadon MT, Williams JC Jr, El-Achkar TM. A spatially anchored transcriptomic atlas of the human kidney papilla identifies significant immune injury in patients with stone disease. Nat Commun. 2023 Jul 19;14(1):4140. doi: 10.1038/s41467-023-38975-8. PMID: 37468493.
Sanjay Jain is co-senior author.
Advances and prospects for the Human BioMolecular Atlas Program (HuBMAP)
July 19, 2023
Jain S, Pei L, Spraggins JM, Angelo M, Carson JP, Gehlenborg N, Ginty F, Gonçalves JP, Hagood JS, Hickey JW, Kelleher NL, Laurent LC, Lin S, Lin Y, Liu H, Naba A, Nakayasu ES, Qian WJ, Radtke A, Robson P, Stockwell BR, Van de Plas R, Vlachos IS, Zhou M; HuBMAP Consortium; Börner K, Snyder MP. Advances and prospects for the Human BioMolecular Atlas Program (HuBMAP). Nat Cell Biol. 2023 Jul 19. doi: 10.1038/s41556-023-01194-w. Epub ahead of print. PMID: 37468756.
The chromatin landscape of healthy and injured cell types in the human kidney
January 10, 2024
Gisch DL, Brennan M, Lake BB, Basta J, Keller MS, Melo Ferreira R, Akilesh S, Ghag R, Lu C, Cheng YH, Collins KS, Parikh SV, Rovin BH, Robbins L, Stout L, Conklin KY, Diep D, Zhang B, Knoten A, Barwinska D, Asghari M, Sabo AR, Ferkowicz MJ, Sutton TA, Kelly KJ, De Boer IH, Rosas SE, Kiryluk K, Hodgin JB, Alakwaa F, Winfree S, Jefferson N, Türkmen A, Gaut JP, Gehlenborg N, Phillips CL, El-Achkar TM, Dagher PC, Hato T, Zhang K, Himmelfarb J, Kretzler M, Mollah S; Kidney Precision Medicine Project (KPMP); Jain S, Rauchman M, Eadon MT. The chromatin landscape of healthy and injured cell types in the human kidney. Nat Commun. 2024 Jan 10;15(1):433. doi: 10.1038/s41467-023-44467-6. PMID: 38199997; PMCID: PMC10781985.
Sanjay Jain, Michael Rauchman, and Michael T. Eadon are co-senior authors
Computational Pathology Fusing Spatial Technologies
March 13, 2023
JBorder S, Lucarelli N, Eadon MT, El-Achkar TM, Jain S, Sarder P. Computational Pathology Fusing Spatial Technologies. Clin J Am Soc Nephrol. 2023 Mar 13. doi: 10.2215/CJN.0000000000000146. Epub ahead of print. PMID: 36913267.
Recent publications
- Mapping human tissues with highly multiplexed RNA in situ hybridizationKalhor, K., Chen, C. J., Lee, H. S., Cai, M., Nafisi, M., Que, R., Palmer, C. R., Yuan, Y., Zhang, Y., Li, X., Song, J., Knoten, A., Lake, B. B., Gaut, J. P., Keene, C. D., Lein, E., Kharchenko, P. V., Chun, J., Jain, S. & Fan, J. B. & 1 others, Zhang, K., Dec 2024, In: Nature communications. 15, 1, 2511.Research output: Contribution to journal › Article › peer-review
- Multi-molecular hyperspectral PRM-SRS microscopyZhang, W., Li, Y., Fung, A. A., Li, Z., Jang, H., Zha, H., Chen, X., Gao, F., Wu, J. Y., Sheng, H., Yao, J., Skowronska-Krawczyk, D., Jain, S. & Shi, L., Dec 2024, In: Nature communications. 15, 1, 1599.Research output: Contribution to journal › Article › peer-review
- The chromatin landscape of healthy and injured cell types in the human kidneyGisch, D. L., Brennan, M., Lake, B. B., Basta, J., Keller, M. S., Melo Ferreira, R., Akilesh, S., Ghag, R., Lu, C., Cheng, Y. H., Collins, K. S., Parikh, S. V., Rovin, B. H., Robbins, L., Stout, L., Conklin, K. Y., Diep, D., Zhang, B., Knoten, A. & Barwinska, D. & 333 others, Asghari, M., Sabo, A. R., Ferkowicz, M. J., Sutton, T. A., Kelly, K. J., De Boer, I. H., Rosas, S. E., Kiryluk, K., Hodgin, J. B., Alakwaa, F., Winfree, S., Jefferson, N., Türkmen, A., Gaut, […]
- Spatial transcriptomics in health and diseaseJain, S. & Eadon, M. T., Oct 2024, In: Nature Reviews Nephrology. 20, 10, p. 659-671 13 p.Research output: Contribution to journal › Review article › peer-review
- Role of Artificial Intelligence in Kidney Pathology: Promises and PitfallsGoodman, K., Sarullo, K., Swamidass, S. J., Gaut, J. P. & Jain, S., Jul 1 2024, In: Kidney360. 5, 7, p. 1044-1046 3 p.Research output: Contribution to journal › Article › peer-review
- Correction to: Advances and prospects for the Human BioMolecular Atlas Program (HuBMAP) (Nature Cell Biology, (2023), 25, 8, (1089-1100), 10.1038/s41556-023-01194-w)HuBMAP Consortium, Jain, S., Pei, L., Spraggins, J. M., Angelo, M., Carson, J. P., Gehlenborg, N., Ginty, F., Gonçalves, J. P., Hagood, J. S., Hickey, J. W., Kelleher, N. L., Laurent, L. C., Lin, S., Lin, Y., Liu, H., Naba, A., Nakayasu, E. S., Qian, W. J. & Radtke, A. & 181 others, Robson, P., Stockwell, B. R., Van de Plas, R., Vlachos, I. S., Zhou, M., Börner, K., Snyder, M. P., Ahn, K. J., Allen, J., Anderson, D. M., Anderton, […]
- Precision Medicine in Nephrology: An Integrative Framework of Multidimensional Data in the Kidney Precision Medicine ProjectKidney Precision Medicine Project, Mar 2024, In: American Journal of Kidney Diseases. 83, 3, p. 402-410 9 p.Research output: Contribution to journal › Article › peer-review
- Molecular Signatures of Glomerular Neovascularization in a Patient with Diabetic Kidney DiseaseKidney Precision Medicine Project, Ferkowicz, M. J., Verma, A., Barwinska, D., Melo Ferreira, R., Henderson, J. M., Kirkpatrick, M., Silva, P. S., Steenkamp, D. W., Phillips, C. L., Waikar, S. S., Sutton, T. A., Lake, B., Zhang, K., Lecker, S., Morales, A., Stillman, I., Bogen, S., Amodu, A. A. & Beck, L. & 181 others, Henderson, J., Ilori, T., Maikhor, S., Onul, I., Schmidt, I., Verma, A., Waikar, S., Yadati, P., Yu, G., Colona, M. R., McMahon, G., Weins, A., Hacohen, N., Greka, A., Hoover, P. J., Marshall, J. […]
- Sensory neurons promote immune homeostasis in the lungTamari, M., Del Bel, K. L., Ver Heul, A. M., Zamidar, L., Orimo, K., Hoshi, M., Trier, A. M., Yano, H., Yang, T. L., Biggs, C. M., Motomura, K., Shibuya, R., Yu, C. D., Xie, Z., Iriki, H., Wang, Z., Auyeung, K., Damle, G., Demircioglu, D. & Gregory, J. K. & 13 others, Hasson, D., Dai, J., Chang, R. B., Morita, H., Matsumoto, K., Jain, S., Van Dyken, S., Milner, J. D., Bogunovic, D., Hu, H., Artis, D., Turvey, S. E. & Kim, B. S., Jan 4 2024, In: Cell. 187, 1, p. […]
- CODEX and H&E Imaging: Cell Type Mapping, Analysis, and Visualization PipelineMaragall, J. A., Lucarelli, N., Naglah, A., Border, S., Winfree, S., Laszik, Z., Eadon, M., El-Achkar, T. M., Jain, S. & Sarder, P., 2024, Medical Imaging 2024: Digital and Computational Pathology. Tomaszewski, J. E. & Ward, A. D. (eds.). SPIE, 129330W. (Progress in Biomedical Optics and Imaging – Proceedings of SPIE; vol. 12933).Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review
Book Chapters
Jain S. (2014) Kidney Development and Related Anomalies. In: Linda M. McManus, Richard N. Mitchell, editors. Pathobiology of Human Disease. San Diego: Elsevier; 2014. p. 2701-2715.
Following 9 chapters in Diagnostic Pathology: Kidney Diseases, 3rd edition, Editor Robert Colvin and Anthony Chang, Publisher- Elsevier Inc. 2019. IISBN 978-0-323-66108-9
*First Prize, British Medical Association book award in the Pathology category (2015 2nd edition)
1.Jain S. Normal Kidney Development, 36-45.
2.Jain S. Overview and Classification of Genetic Diseases of the Glomerulus, 350-351
3.Jain S. Overview of Congenital Anomalies of the Kidney and Urinary Tract, 828-831
4.Jain S. Dysplasia, Hypoplasia and Agenesis, 832-837
5.Jain S. Ectopia, Malrotation, Duplication, Fusion, Supernumerary Kidney, 840-843
6.Jain S. Introduction to Impediments to Urine Flow, 914-917
7.Jain S. Reflux Nephropathy, 918-921
8.Jain S. Obstructive Nephropathy, 922-925
9.Jain S. Diagnostic Genetics of Kidney Diseases, 1098-1101
PhD Thesis (1999): Characterization of a subset of bHLH-PAS superfamily of transcription factors. (Ph.D., Northwestern University).