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A user-friendly tool for cloud-based whole slide image segmentation with examples from renal histopathology.
Lutnick B, Manthey D, Becker JU, Ginley B, Moos K, Zuckerman JE, Rodrigues L, Gallan AJ, Barisoni L, Alpers CE, Wang XX, Myakala K, Jones BA, Levi M, Kopp JB, Yoshida T, Zee J, Han SS, Jain S, Rosenberg AZ, Jen KY, Sarder P; Kidney Precision Medicine Project. Lutnick B, et al. Among authors: jain s. Commun Med (Lond). 2022 Aug 19;2:105. doi: 10.1038/s43856-022-00138-z. eCollection 2022. Commun Med (Lond). 2022. PMID: 35996627 Free PMC article.
The chromatin landscape of healthy and injured cell types in the human kidney.
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. Gisch DL, et al. Among authors: jain s. bioRxiv [Preprint]. 2023 Jun 8:2023.06.07.543965. doi: 10.1101/2023.06.07.543965. bioRxiv. 2023. PMID: 37333123 Free PMC article. Updated. Preprint.
Single Nucleus RNA Sequencing of Remnant Kidney Biopsies and Urine Cell RNA Sequencing Reveal Cell Specific Markers of Covid-19 Acute Kidney Injury.
Ghag R, Kaushal M, Nwanne G, Knoten A, Kiryluk K, Rosenberg A, Menez S, Bagnasco SM, Sperati CJ, Atta MG, Gaut JP, Williams JC, El-Achkar TM, Arend LJ, Parikh CR, Jain S. Ghag R, et al. Among authors: jain s. bioRxiv [Preprint]. 2023 Nov 12:2023.11.10.566497. doi: 10.1101/2023.11.10.566497. bioRxiv. 2023. PMID: 37986991 Free PMC article. Preprint.
The chromatin landscape of healthy and injured cell types in the human kidney.
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. Gisch DL, et al. Among authors: jain s. Nat Commun. 2024 Jan 10;15(1):433. doi: 10.1038/s41467-023-44467-6. Nat Commun. 2024. PMID: 38199997 Free PMC article.
Ontology-based modeling, integration, and analysis of heterogeneous clinical, pathological, and molecular kidney data for precision medicine.
He YO, Barisoni L, Rosenberg AZ, Robinson P, Diehl AD, Chen Y, Phuong JP, Hansen J, Herr BW, Börner K, Schaub J, Bonevich N, Arnous G, Boddapati S, Zheng J, Alakwaa F, Sarder P, Duncan WD, Liang C, Valerius MT, Jain S, Iyengar R, Himmelfarb J, Kretzler M; Kidney Precision Medicine Project. He YO, et al. Among authors: jain s. bioRxiv [Preprint]. 2024 Apr 2:2024.04.01.587658. doi: 10.1101/2024.04.01.587658. bioRxiv. 2024. PMID: 38617362 Free PMC article. Preprint.
Spatial transcriptomics in health and disease.
Jain S, Eadon MT. Jain S, et al. Nat Rev Nephrol. 2024 May 8. doi: 10.1038/s41581-024-00841-1. Online ahead of print. Nat Rev Nephrol. 2024. PMID: 38719971 Review.
Large-scale, three-dimensional tissue cytometry of the human kidney: a complete and accessible pipeline.
Ferkowicz MJ, Winfree S, Sabo AR, Kamocka MM, Khochare S, Barwinska D, Eadon MT, Cheng YH, Phillips CL, Sutton TA, Kelly KJ, Dagher PC, El-Achkar TM, Dunn KW; Kidney Precision Medicine Project. Ferkowicz MJ, et al. Lab Invest. 2021 May;101(5):661-676. doi: 10.1038/s41374-020-00518-w. Epub 2021 Jan 6. Lab Invest. 2021. PMID: 33408350 Free PMC article.
Rationale and design of the Kidney Precision Medicine Project.
de Boer IH, Alpers CE, Azeloglu EU, Balis UGJ, Barasch JM, Barisoni L, Blank KN, Bomback AS, Brown K, Dagher PC, Dighe AL, Eadon MT, El-Achkar TM, Gaut JP, Hacohen N, He Y, Hodgin JB, Jain S, Kellum JA, Kiryluk K, Knight R, Laszik ZG, Lienczewski C, Mariani LH, McClelland RL, Menez S, Moledina DG, Mooney SD, O'Toole JF, Palevsky PM, Parikh CR, Poggio ED, Rosas SE, Rosengart MR, Sarwal MM, Schaub JA, Sedor JR, Sharma K, Steck B, Toto RD, Troyanskaya OG, Tuttle KR, Vazquez MA, Waikar SS, Williams K, Wilson FP, Zhang K, Iyengar R, Kretzler M, Himmelfarb J; Kidney Precision Medicine Project. de Boer IH, et al. Among authors: jain s. Kidney Int. 2021 Mar;99(3):498-510. doi: 10.1016/j.kint.2020.08.039. Kidney Int. 2021. PMID: 33637194 Free PMC article.
Cadherin-11, Sparc-related modular calcium binding protein-2, and Pigment epithelium-derived factor are promising non-invasive biomarkers of kidney fibrosis.
Schmidt IM, Colona MR, Kestenbaum BR, Alexopoulos LG, Palsson R, Srivastava A, Liu J, Stillman IE, Rennke HG, Vaidya VS, Wu H, Humphreys BD, Waikar SS; Kidney Precision Medicine Project (KPMP). Schmidt IM, et al. Kidney Int. 2021 Sep;100(3):672-683. doi: 10.1016/j.kint.2021.04.037. Epub 2021 May 27. Kidney Int. 2021. PMID: 34051265 Free PMC article.
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