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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 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, […]
  • 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
  • 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, May 2024, In: Nature Cell Biology. 26, 5, p. 839 1 p.Research output: Contribution to journal › Comment/debate
  • 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, Feb 2024, In: Clinical Journal of the American Society of Nephrology. 19, 2, p. 266-275 10 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 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
  • Spatial transcriptomics in health and diseaseJain, S. & Eadon, M. T., 2024, (Accepted/In press) In: Nature Reviews Nephrology.Research output: Contribution to journal › Review article › peer-review
  • Computational Integration of CODEX and Brightfield Histology for Cell Annotation using Deep LearningLucarelli, N., Laszik, Z., Winfree, S., El-Achkar, T. M., Eadon, M., Jain, S. & Sarder, P., 2024, Medical Imaging 2024: Digital and Computational Pathology. Tomaszewski, J. E. & Ward, A. D. (eds.). SPIE, 129331F. (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).