Featured publications
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.
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
June 8, 2023
Gisch DL, Brennan M, Lake BB, Basta J, Keller M, Ferreira RM, Akilesh S, Ghag R, Lu C, Cheng YH, Collins KS, Parikh SV, Rovin BH, Robbins L, Conklin KY, Diep D, Zhang B, Knoten A, Barwinska D, Asghari M, Sabo AR, Ferkowicz MJ, Sutton TA, Kelly KJ, Boer IH, Rosas SE, Kiryluk K, Hodgin JB, Alakwaa F, Jefferson N, 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. bioRxiv [Preprint]. 2023 Jun 8:2023.06.07.543965. doi: 10.1101/2023.06.07.543965. PMID: 37333123; PMCID: PMC10274789.
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.
Multi-Molecular Hyperspectral PRM-SRS Imaging
July 25, 2022
Wenxu Zhang, Yajuan Li, Anthony A. Fung, Zhi Li, Hongje Jang, Honghao Zha, Xiaoping Chen, Fangyuan Gao, Jane Y. Wu, Huaxin Sheng, Junjie Yao, Dorota Skowronska-Krawczyk, Sanjay Jain, Lingyan Shi, Multi-Molecular Hyperspectral PRM-SRS Imaging. bioRxiv 2022.07.25.501472
Recent publications
- 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 othersAsghari, 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, J. P., […]
- 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 othersZhang, K., Dec 2024, In: Nature communications. 15, 1, 2511.Research output: Contribution to journal › Article › peer-review
- 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
- 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 othersHasson, 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. 44-61.e17Research output: […]
- Shank2 identifies a subset of glycinergic neurons involved in altered nociception in an autism modelShank2 identifies a subset of glycinergic neurons involved in altered nociception in an autism modelOlde Heuvel, F., Ouali Alami, N., Aousji, O., Pogatzki-Zahn, E., Zahn, P. K., Wilhelm, H., Deshpande, D., Khatamsaz, E., Catanese, A., Woelfle, S., Schön, M., Jain, S., Grabrucker, S., Ludolph, A. C., Verpelli, C., Michaelis, J., Boeckers, T. M. & Roselli, F., Dec 2023, In: Molecular Autism. 14, 1, 21.Research output: Contribution to journal › Article › peer-review
- Aberrant centrosome biogenesis disrupts nephron and collecting duct progenitor growth and fate resulting in fibrocystic kidney diseaseCheng, T., Agwu, C., Shim, K., Wang, B., Jain, S. & Mahjoub, M. R., Dec 2023, In: Development (Cambridge). 150, 24Research output: Contribution to journal › Article › peer-review
- Navigating the kidney organoid: insights into assessment and enhancement of nephron functionTabibzadeh, N., Satlin, L. M., Jain, S. & Morizane, R., Dec 2023, In: American Journal of Physiology – Renal Physiology. 325, 6, p. F695-F706Research output: Contribution to journal › Article › peer-review
- Correlating Deep Learning-Based Automated Reference Kidney Histomorphometry with Patient Demographics and CreatinineLucarelli, N., Ginley, B., Zee, J., Mimar, S., Paul, A. S., Jain, S., Han, S. S., Rodrigues, L., Ozrazgat-Baslanti, T., Wong, M. L., Nadkarni, G., Clapp, W. L., Jen, K. Y. & Sarder, P., Dec 1 2023, In: Kidney360. 4, 12, p. 1726-1737 12 p.Research output: Contribution to journal › Article › peer-review
- A spatially anchored transcriptomic atlas of the human kidney papilla identifies significant immune injury in patients with stone diseasethe Kidney Precision Medicine Project, Dec 2023, In: Nature communications. 14, 1, 4140.Research output: Contribution to journal › Article › peer-review
- Evaluation of Plasma Biomarkers to Predict Major Adverse Kidney Events in Hospitalized Patients With COVID-19TRIKIC Consortium, Sep 2023, In: American Journal of Kidney Diseases. 82, 3, p. 322-332.e1Research output: Contribution to journal › Article › 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).