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Modelling kidney disease using ontology: insights from the Kidney Precision Medicine Project.
Ong E, Wang LL, Schaub J, O'Toole JF, Steck B, Rosenberg AZ, Dowd F, Hansen J, Barisoni L, Jain S, de Boer IH, Valerius MT, Waikar SS, Park C, Crawford DC, Alexandrov T, Anderton CR, Stoeckert C, Weng C, Diehl AD, Mungall CJ, Haendel M, Robinson PN, Himmelfarb J, Iyengar R, Kretzler M, Mooney S, He Y; Kidney Precision Medicine Project. Ong E, et al. Among authors: valerius mt. Nat Rev Nephrol. 2020 Nov;16(11):686-696. doi: 10.1038/s41581-020-00335-w. Epub 2020 Sep 16. Nat Rev Nephrol. 2020. PMID: 32939051 Free PMC article. Review.
(Re)Building a Kidney.
Oxburgh L, Carroll TJ, Cleaver O, Gossett DR, Hoshizaki DK, Hubbell JA, Humphreys BD, Jain S, Jensen J, Kaplan DL, Kesselman C, Ketchum CJ, Little MH, McMahon AP, Shankland SJ, Spence JR, Valerius MT, Wertheim JA, Wessely O, Zheng Y, Drummond IA. Oxburgh L, et al. Among authors: valerius mt. J Am Soc Nephrol. 2017 May;28(5):1370-1378. doi: 10.1681/ASN.2016101077. Epub 2017 Jan 17. J Am Soc Nephrol. 2017. PMID: 28096308 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.
Anatomical structures, cell types and biomarkers of the Human Reference Atlas.
Börner K, Teichmann SA, Quardokus EM, Gee JC, Browne K, Osumi-Sutherland D, Herr BW 2nd, Bueckle A, Paul H, Haniffa M, Jardine L, Bernard A, Ding SL, Miller JA, Lin S, Halushka MK, Boppana A, Longacre TA, Hickey J, Lin Y, Valerius MT, He Y, Pryhuber G, Sun X, Jorgensen M, Radtke AJ, Wasserfall C, Ginty F, Ho J, Sunshine J, Beuschel RT, Brusko M, Lee S, Malhotra R, Jain S, Weber G. Börner K, et al. Among authors: valerius mt. Nat Cell Biol. 2021 Nov;23(11):1117-1128. doi: 10.1038/s41556-021-00788-6. Epub 2021 Nov 8. Nat Cell Biol. 2021. PMID: 34750582 Free PMC article. Review.
A reference tissue atlas for the human kidney.
Hansen J, Sealfon R, Menon R, Eadon MT, Lake BB, Steck B, Anjani K, Parikh S, Sigdel TK, Zhang G, Velickovic D, Barwinska D, Alexandrov T, Dobi D, Rashmi P, Otto EA, Rivera M, Rose MP, Anderton CR, Shapiro JP, Pamreddy A, Winfree S, Xiong Y, He Y, de Boer IH, Hodgin JB, Barisoni L, Naik AS, Sharma K, Sarwal MM, Zhang K, Himmelfarb J, Rovin B, El-Achkar TM, Laszik Z, He JC, Dagher PC, Valerius MT, Jain S, Satlin LM, Troyanskaya OG, Kretzler M, Iyengar R, Azeloglu EU; Kidney Precision Medicine Project. Hansen J, et al. Among authors: valerius mt. Sci Adv. 2022 Jun 10;8(23):eabn4965. doi: 10.1126/sciadv.abn4965. Epub 2022 Jun 8. Sci Adv. 2022. PMID: 35675394 Free PMC article.
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. 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.
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: valerius mt. bioRxiv [Preprint]. 2024 Apr 2:2024.04.01.587658. doi: 10.1101/2024.04.01.587658. bioRxiv. 2024. PMID: 38617362 Free PMC article. Preprint.
Modelling kidney disease with CRISPR-mutant kidney organoids derived from human pluripotent epiblast spheroids.
Freedman BS, Brooks CR, Lam AQ, Fu H, Morizane R, Agrawal V, Saad AF, Li MK, Hughes MR, Werff RV, Peters DT, Lu J, Baccei A, Siedlecki AM, Valerius MT, Musunuru K, McNagny KM, Steinman TI, Zhou J, Lerou PH, Bonventre JV. Freedman BS, et al. Among authors: valerius mt. Nat Commun. 2015 Oct 23;6:8715. doi: 10.1038/ncomms9715. Nat Commun. 2015. PMID: 26493500 Free PMC article.
Flow-enhanced vascularization and maturation of kidney organoids in vitro.
Homan KA, Gupta N, Kroll KT, Kolesky DB, Skylar-Scott M, Miyoshi T, Mau D, Valerius MT, Ferrante T, Bonventre JV, Lewis JA, Morizane R. Homan KA, et al. Among authors: valerius mt. Nat Methods. 2019 Mar;16(3):255-262. doi: 10.1038/s41592-019-0325-y. Epub 2019 Feb 11. Nat Methods. 2019. PMID: 30742039 Free PMC article.
55 results