My Bibliography

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Evangelista JE, Ali-Nasser T, Malek LE, Xie Z, Marino GB, Bester AC, Ma'ayan A. lncRNAlyzr: Enrichment Analysis for lncRNA Sets. J Mol Biol. 2025 Aug 1;437(15):168938. doi: 10.1016/j.jmb.2025.168938. Epub 2025 Jan 11. PubMed PMID: 40133794; PubMed Central PMCID: PMC12145269.

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Weins A, Wong JS, Basgen J, Gupta R, Daehn I, Casagrande LC, Lessman D, Schwartzman L, Meliambro K, Patrakka J, Shaw A, Tryggvason K, He JC, Kriz W, Nicholas S, Mundel P, Campbell KN. Dendrin ablation prolongs life span by delaying renal failure. The American journal of pathology. Forthcoming.

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Min L, Chen Y, Liu R, Li Z, Gu L, Mallipattu S, Das B, Lee K, He JC, Zhong F. Targeting Krüppel-Like Factor 2 as a Novel Therapy for Glomerular Endothelial Cell Injury in Diabetic Kidney Disease. J Am Soc Nephrol. 2025 Feb 1;36(2):193-204. doi: 10.1681/ASN.0000000000000498. Epub 2024 Oct 9. PubMed PMID: 39382984; PubMed Central PMCID: PMC11801754.

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Estrada CC, Wilson C, Gujarati N, Ahmed S, Bronstein R, Daehn IS, Revelo MP, Guo Y, Mallipattu SK. Induction of plasmalemmal vesicle-associated protein exacerbates glomerular endothelial injury in thrombotic microangiopathy. Am J Physiol Renal Physiol. 2025 Feb 1;328(2):F190-F203. doi: 10.1152/ajprenal.00283.2024. Epub 2024 Dec 20. PubMed PMID: 39706169; NIHMSID:NIHMS2085893.

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DiMartino S, Revelo MP, Mallipattu SK, Piret SE. Activation of branched chain amino acid catabolism protects against nephrotoxic acute kidney injury. Am J Physiol Renal Physiol. 2025 Jan 1;328(1):F152-F163. doi: 10.1152/ajprenal.00260.2024. Epub 2024 Dec 9. PubMed PMID: 39653371; PubMed Central PMCID: PMC11918290.

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Marino GB, Clarke DJB, Lachmann A, Deng EZ, Ma'ayan A. RummaGEO: Automatic mining of human and mouse gene sets from GEO. Patterns (N Y). 2024 Oct 11;5(10):101072. doi: 10.1016/j.patter.2024.101072. eCollection 2024 Oct 11. PubMed PMID: 39569206; PubMed Central PMCID: PMC11573963.

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Deng EZ, Marino GB, Clarke DJB, Diamant I, Resnick AC, Ma W, Wang P, Ma'ayan A. Multiomics2Targets identifies targets from cancer cohorts profiled with transcriptomics, proteomics, and phosphoproteomics. Cell Rep Methods. 2024 Aug 19;4(8):100839. doi: 10.1016/j.crmeth.2024.100839. Epub 2024 Aug 9. PubMed PMID: 39127042; PubMed Central PMCID: PMC11384097.

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Min L, Zhong F, Gu L, Lee K, He JC. Krüppel-like factor 2 is an endoprotective transcription factor in diabetic kidney disease. Am J Physiol Cell Physiol. 2024 Aug 1;327(2):C477-C486. doi: 10.1152/ajpcell.00222.2024. Epub 2024 Jul 9. Review. PubMed PMID: 38981608; PubMed Central PMCID: PMC11901337.

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Feng Y, Sun Z, Fu J, Zhong F, Zhang W, Wei C, Chen A, Liu BC, He JC, Lee K. Podocyte-derived soluble RARRES1 drives kidney disease progression through direct podocyte and proximal tubular injury. Kidney Int. 2024 Jul;106(1):50-66. doi: 10.1016/j.kint.2024.04.011. Epub 2024 Apr 30. PubMed PMID: 38697478; PubMed Central PMCID: PMC11193616.

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Rein JL, Mackie K, Kleyman TR, Satlin LM. Cannabinoid receptor type 1 activation causes a water diuresis by inducing an acute central diabetes insipidus in mice. Am J Physiol Renal Physiol. 2024 Jun 1;326(6):F917-F930. doi: 10.1152/ajprenal.00320.2022. Epub 2024 Apr 18. PubMed PMID: 38634131; PubMed Central PMCID: PMC12040313.

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Li X, Bhattacharya D, Yuan Y, Wei C, Zhong F, Ding F, D'Agati VD, Lee K, Friedman SL, He JC. Chronic kidney disease in a murine model of non-alcoholic steatohepatitis (NASH). Kidney Int. 2024 Mar;105(3):540-561. doi: 10.1016/j.kint.2023.12.009. Epub 2023 Dec 28. PubMed PMID: 38159678; PubMed Central PMCID: PMC10922588.

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Gujarati NA, Chow AK, Mallipattu SK. Central role of podocytes in mediating cellular cross talk in glomerular health and disease. Am J Physiol Renal Physiol. 2024 Mar 1;326(3):F313-F325. doi: 10.1152/ajprenal.00328.2023. Epub 2024 Jan 11. Review. PubMed PMID: 38205544; PubMed Central PMCID: PMC11207540.

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Oh W, Jayaraman P, Tandon P, Chaddha US, Kovatch P, Charney AW, Glicksberg BS, Nadkarni GN. A novel method leveraging time series data to improve subphenotyping and application in critically ill patients with COVID-19. Artif Intell Med. 2024 Feb;148:102750. doi: 10.1016/j.artmed.2023.102750. Epub 2023 Dec 20. PubMed PMID: 38325922; PubMed Central PMCID: PMC10864255.

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Fang Z, Lee K, He JC. Injury in nonaged podocytes as an accelerator of glomerular aging. Am J Physiol Renal Physiol. 2024 Jan 1;326(1):F118-F119. doi: 10.1152/ajprenal.00344.2023. Epub 2023 Nov 30. PubMed PMID: 38031730.

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Mallipattu SK. The loss of profilin1 is catastrophic to podocytes. J Clin Invest. 2023 Dec 15;133(24). doi: 10.1172/JCI175594. PubMed PMID: 38099501; PubMed Central PMCID: PMC10721137.

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Latt KZ, Yoshida T, Shrivastav S, Abedini A, Reece JM, Sun Z, Lee H, Okamoto K, Dagur P, Heymann J, Zhao Y, Chung JY, Hewitt S, Jose PA, Lee K, He JC, Winkler CA, Knepper MA, Kino T, Rosenberg AZ, Susztak K, Kopp JB. HIV viral protein R induces loss of DCT1-type renal tubules. bioRxiv. 2023 Nov 13;. doi: 10.1101/2023.02.02.526686. PubMed PMID: 36945458; PubMed Central PMCID: PMC10028744.

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Bronstein R, Pace J, Gowthaman Y, Salant DJ, Mallipattu SK. Podocyte-Parietal Epithelial Cell Interdependence in Glomerular Development and Disease. J Am Soc Nephrol. 2023 May 1;34(5):737-750. doi: 10.1681/ASN.0000000000000104. Epub 2023 Feb 16. Review. PubMed PMID: 36800545; PubMed Central PMCID: PMC10125654.

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Piret SE, Mallipattu SK. Transcriptional regulation of proximal tubular metabolism in acute kidney injury. Pediatr Nephrol. 2023 Apr;38(4):975-986. doi: 10.1007/s00467-022-05748-2. Epub 2022 Oct 1. Review. PubMed PMID: 36181578.

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Blasi M, Klotman M. HIV-1 infection of renal epithelial cells: 30 years of evidence from transgenic animal models, human studies and in vitro experiments. Retrovirology. 2023 Mar 16;20(1):2. doi: 10.1186/s12977-023-00617-8. Review. PubMed PMID: 36927552; PubMed Central PMCID: PMC10018895.

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Marino GB, Wojciechowicz ML, Clarke DJB, Kuleshov MV, Xie Z, Jeon M, Lachmann A, Ma'ayan A. lncHUB2: aggregated and inferred knowledge about human and mouse lncRNAs. Database (Oxford). 2023 Mar 4;2023. doi: 10.1093/database/baad009. PubMed PMID: 36869839; PubMed Central PMCID: PMC9985331.

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Chen Y, Chen Y, Fu J, Sun Z, Li H, Xiao W, E J, Lo BY, Wang N, Zhang W, Klotman ME, Klotman PE, Kopp JB, D'Agati VD, He JC, Lee K. Tubular-specific expression of HIV protein Vpr leads to severe tubulointerstitial damage accompanied by progressive fibrosis and cystic development. Kidney Int. 2023 Mar;103(3):529-543. doi: 10.1016/j.kint.2022.12.012. Epub 2022 Dec 22. PubMed PMID: 36565808; PubMed Central PMCID: PMC9974916.

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Cai H, Chen Y, Feng Y, Asadi M, Kaufman L, Lee K, Kehrer T, Miorin L, Garcia-Sastre A, Gusella GL, Gu L, Ni Z, Mou S, He JC, Zhou W. SARS-CoV-2 viral protein ORF3A injures renal tubules by interacting with TRIM59 to induce STAT3 activation. Mol Ther. 2023 Mar 1;31(3):774-787. doi: 10.1016/j.ymthe.2022.12.008. Epub 2022 Dec 15. PubMed PMID: 36523164; PubMed Central PMCID: PMC9750503.

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Lachmann A, Rizzo KA, Bartal A, Jeon M, Clarke DJB, Ma'ayan A. PrismEXP: gene annotation prediction from stratified gene-gene co-expression matrices. PeerJ. 2023;11:e14927. doi: 10.7717/peerj.14927. eCollection 2023. PubMed PMID: 36874981; PubMed Central PMCID: PMC9979837.

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Zhong F, Cai H, Fu J, Sun Z, Li Z, Bauman D, Wang L, Das B, Lee K, He JC. TYRO3 agonist as therapy for glomerular disease. JCI Insight. 2023 Jan 10;8(1). doi: 10.1172/jci.insight.165207. PubMed PMID: 36454644; PubMed Central PMCID: PMC9870075.

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Oh W, Nadkarni GN. Federated Learning in Health care Using Structured Medical Data. Adv Kidney Dis Health. 2023 Jan;30(1):4-16. doi: 10.1053/j.akdh.2022.11.007. Review. PubMed PMID: 36723280; PubMed Central PMCID: PMC10208416.

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Fu J, Sun Z, Wang X, Zhang T, Yuan W, Salem F, Yu SM, Zhang W, Lee K, He JC. The single-cell landscape of kidney immune cells reveals transcriptional heterogeneity in early diabetic kidney disease. Kidney Int. 2022 Dec;102(6):1291-1304. doi: 10.1016/j.kint.2022.08.026. Epub 2022 Sep 13. PubMed PMID: 36108806; PubMed Central PMCID: PMC9691617.

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Lucas A, Wyatt CM. HIV at 40: kidney disease in HIV treatment, prevention, and cure. Kidney Int. 2022 Oct;102(4):740-749. doi: 10.1016/j.kint.2022.06.021. Epub 2022 Jul 16. Review. PubMed PMID: 35850290; PubMed Central PMCID: PMC9509437.

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Jang HS, Noh MR, Plumb T, Lee K, He JC, Ferrer FA, Padanilam BJ. Hepatic and proximal tubule angiotensinogen play distinct roles in kidney dysfunction, glomerular and tubular injury, and fibrosis progression. Am J Physiol Renal Physiol. 2022 Oct 1;323(4):F435-F446. doi: 10.1152/ajprenal.00029.2022. Epub 2022 Aug 4. PubMed PMID: 35924445; PubMed Central PMCID: PMC9485008.

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Jeon M, Xie Z, Evangelista JE, Wojciechowicz ML, Clarke DJB, Ma'ayan A. Transforming L1000 profiles to RNA-seq-like profiles with deep learning. BMC Bioinformatics. 2022 Sep 13;23(1):374. doi: 10.1186/s12859-022-04895-5. PubMed PMID: 36100892; PubMed Central PMCID: PMC9472394.

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Xie Y, E J, Cai H, Zhong F, Xiao W, Gordon RE, Wang L, Zheng YL, Zhang A, Lee K, He JC. Reticulon-1A mediates diabetic kidney disease progression through endoplasmic reticulum-mitochondrial contacts in tubular epithelial cells. Kidney Int. 2022 Aug;102(2):293-306. doi: 10.1016/j.kint.2022.02.038. Epub 2022 Apr 22. PubMed PMID: 35469894; PubMed Central PMCID: PMC9329239.

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Evangelista JE, Clarke DJB, Xie Z, Lachmann A, Jeon M, Chen K, Jagodnik KM, Jenkins SL, Kuleshov MV, Wojciechowicz ML, Schürer SC, Medvedovic M, Ma'ayan A. SigCom LINCS: data and metadata search engine for a million gene expression signatures. Nucleic Acids Res. 2022 Jul 5;50(W1):W697-W709. doi: 10.1093/nar/gkac328. PubMed PMID: 35524556; PubMed Central PMCID: PMC9252724.

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Estrada CC, Cardona S, Guo Y, Revelo MP, D'Agati VD, Koganti S, Devaraj J, He JC, Heeger PS, Mallipattu SK. Endothelial-specific loss of Krüppel-Like Factor 4 triggers complement-mediated endothelial injury. Kidney Int. 2022 Jul;102(1):58-77. doi: 10.1016/j.kint.2022.03.025. Epub 2022 Apr 26. PubMed PMID: 35483525.

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Wu J, Sun Z, Yang S, Fu J, Fan Y, Wang N, Hu J, Ma L, Peng C, Wang Z, Lee K, He JC, Li Q. Kidney single-cell transcriptome profile reveals distinct response of proximal tubule cells to SGLT2i and ARB treatment in diabetic mice. Mol Ther. 2022 Apr 6;30(4):1741-1753. doi: 10.1016/j.ymthe.2021.10.013. Epub 2021 Oct 19. PubMed PMID: 34678510; PubMed Central PMCID: PMC9077318.

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Salem F, Li XZ, Hindi J, Casablanca NM, Zhong F, El Jamal SM, Haroon Al Rasheed MR, Li L, Lee K, Chan L, He JC. Activation of STAT3 signaling pathway in the kidney of COVID-19 patients. J Nephrol. 2022 Apr;35(3):735-743. doi: 10.1007/s40620-021-01173-0. Epub 2021 Oct 9. PubMed PMID: 34626364; PubMed Central PMCID: PMC8501346.

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Ye L, Liu Y, Zhu X, Duan T, Wang C, Fu X, Song P, Yuan S, Liu H, Sun L, Liu F, Lee K, He JC, Chen A. Digital Spatial Profiling of Individual Glomeruli From Patients With Anti-Neutrophil Cytoplasmic Autoantibody-Associated Glomerulonephritis. Front Immunol. 2022;13:831253. doi: 10.3389/fimmu.2022.831253. eCollection 2022. PubMed PMID: 35309370; PubMed Central PMCID: PMC8924137.

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Clarke DJB, Kuleshov MV, Xie Z, Evangelista JE, Meyers MR, Kropiwnicki E, Jenkins SL, Ma'ayan A. Gene and drug landing page aggregator. Bioinform Adv. 2022;2(1):vbac013. doi: 10.1093/bioadv/vbac013. eCollection 2022. PubMed PMID: 35368424; PubMed Central PMCID: PMC8969666.

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Kropiwnicki E, Lachmann A, Clarke DJB, Xie Z, Jagodnik KM, Ma'ayan A. DrugShot: querying biomedical search terms to retrieve prioritized lists of small molecules. BMC Bioinformatics. 2022 Feb 19;23(1):76. doi: 10.1186/s12859-022-04590-5. PubMed PMID: 35183110; PubMed Central PMCID: PMC8858480.

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Khan S, Bolotova O, Sahib H, Foster D, Mallipattu SK. Endotoxemia in Critically Ill Patients with COVID-19. Blood Purif. 2022;51(6):513-519. doi: 10.1159/000518230. Epub 2021 Aug 20. PubMed PMID: 34515062; PubMed Central PMCID: PMC8450835.

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Chen A, Yin L, Lee K, He JC. Similarities and Differences between COVID-19-Associated Nephropathy and HIV-Associated Nephropathy. Kidney Dis (Basel). 2022 Jan;8(1):1-12. doi: 10.1159/000520235. eCollection 2022 Jan. Review. PubMed PMID: 35127839; PubMed Central PMCID: PMC8805054.

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Piret SE, Attallah AA, Gu X, Guo Y, Gujarati NA, Henein J, Zollman A, Hato T, Ma'ayan A, Revelo MP, Dickman KG, Chen CH, Shun CT, Rosenquist TA, He JC, Mallipattu SK. Loss of proximal tubular transcription factor Krüppel-like factor 15 exacerbates kidney injury through loss of fatty acid oxidation. Kidney Int. 2021 Dec;100(6):1250-1267. doi: 10.1016/j.kint.2021.08.031. Epub 2021 Oct 9. PubMed PMID: 34634362; PubMed Central PMCID: PMC8608748.

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Cintron Pregosin N, Bronstein R, Mallipattu SK. Recent Advances in Kidney Bioengineering. Front Pediatr. 2021;9:743301. doi: 10.3389/fped.2021.743301. eCollection 2021. Review. PubMed PMID: 34900859; PubMed Central PMCID: PMC8655860.

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Gujarati NA, Leonardo AR, Vasquez JM, Guo Y, Frimpong BO, Fozilov E, Revelo MP, Daehn IS, He JC, Bogenhagen D, Mallipattu SK. Loss of Functional SCO2 Attenuates Oxidative Stress in Diabetic Kidney Disease. Diabetes. 2021 Oct 26;71(1):142-56. doi: 10.2337/db21-0316. [Epub ahead of print] PubMed PMID: 34702781; PubMed Central PMCID: PMC8763871.

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Gujarati NA, Leonardo AR, Vasquez JM, Guo Y, Frimpong BO, Fozilov E, Revelo MP, Daehn IS, He JC, Bogenhagen D, Mallipattu SK. Loss of Functional SCO2 Attenuates Oxidative Stress in Diabetic Kidney Disease. Diabetes. 2021 Oct 21;. doi: 10.2337/db21-0316. [Epub ahead of print] PubMed PMID: 34957485.

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Yu SM, He JC. Happy gut, happy kidneys? Restoration of gut microbiome ameliorates acute and chronic kidney disease. Cell Metab. 2021 Oct 5;33(10):1901-1903. doi: 10.1016/j.cmet.2021.08.019. PubMed PMID: 34614404; PubMed Central PMCID: PMC8994854.

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Chen A, Lee K, He JC. Autocrine and paracrine effects of a novel podocyte gene, RARRES1. Kidney Int. 2021 Oct;100(4):745-747. doi: 10.1016/j.kint.2021.07.008. PubMed PMID: 34556297; PubMed Central PMCID: PMC9037532.

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Pace JA, Bronstein R, Guo Y, Yang Y, Estrada CC, Gujarati N, Salant DJ, Haley J, Bialkowska AB, Yang VW, He JC, Mallipattu SK. Podocyte-specific KLF4 is required to maintain parietal epithelial cell quiescence in the kidney. Sci Adv. 2021 Sep 3;7(36):eabg6600. doi: 10.1126/sciadv.abg6600. Epub 2021 Sep 3. PubMed PMID: 34516901; PubMed Central PMCID: PMC8442927.

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Abramson M, Mon-Wei Yu S, Campbell KN, Chung M, Salem F. IgA Nephropathy After SARS-CoV-2 Vaccination. Kidney Med. 2021 Sep-Oct;3(5):860-863. doi: 10.1016/j.xkme.2021.05.002. Epub 2021 Jul 14. PubMed PMID: 34278290; PubMed Central PMCID: PMC8277542.

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Salem F, Rein JL, Yu SM, Abramson M, Cravedi P, Chung M. Report of Three Cases of Minimal Change Disease Following the Second Dose of mRNA SARS-CoV-2 COVID-19 Vaccine. Kidney Int Rep. 2021 Sep;6(9):2523-2524. doi: 10.1016/j.ekir.2021.07.017. Epub 2021 Jul 27. PubMed PMID: 34337193; PubMed Central PMCID: PMC8313814.

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Fu J, Yi Z, Cai M, Yuan W, Zhang W, Lee K, He JC. Global transcriptomic changes in glomerular endothelial cells in mice with podocyte depletion and glomerulosclerosis. Cell Death Dis. 2021 Jul 9;12(7):687. doi: 10.1038/s41419-021-03951-x. PubMed PMID: 34244474; PubMed Central PMCID: PMC8270962.

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Lee K, Gusella GL, He JC. Epithelial proliferation and cell cycle dysregulation in kidney injury and disease. Kidney Int. 2021 Jul;100(1):67-78. doi: 10.1016/j.kint.2021.03.024. Epub 2021 Apr 6. Review. PubMed PMID: 33831367; PubMed Central PMCID: PMC8855879.