100 Washtenaw Ave.
Ann Arbor, Michigan 48109
Available to mentor
• With my extensive bioinformatics and molecular biology background, I have developed several bioinformatics analysis pipelines for analyzing and integrating different types of high-throughput data. I also collaborate actively with other University of Michigan researchers on kidney related research topics. Since December 2020, I have the role as the director of the single cell gene expression core of Michigan Kidney Translational Center.
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Center MemberPrecision Health Initiative
• With my computational and molecular biology background, I have been analyzing and integrating different types of high-throughput data generated from human disease samples. From the findings of these analyses, I have multiple first author and corresponding author papers in top ranking journals.
• One of my research interests focuses on alternative splice isoforms that are involved in different types of human diseases., The functional roles of splice isoforms are still not well understood. By integrating different computational tools, I predict the potential functions and interactions of these isoforms. My work on splice isoforms in human cancers are published in Cancer Research.
• Since 2017, I started working closely with Dr. Matthias Kretzler and my research is now focused on kidney-diseases using single cell transcriptomics. I was one of the early investigators, who was able to identify distinct cell types including rare ones in fetal, organoid, and adult kidney samples. I have identified both known and novel markers for distinct cell types and have published multiple papers on this topic. I am currently working with researchers from Broad Institute to successfully implement spatial Image technologies including MerFish and Xenium.in kidney tissue. I also collaborate actively with other University of Michigan researchers on kidney related research topics.
• As an active member of Kidney Precision Medicine Project (KPMP) (NIH funded consortium), I analyze kidney single cell data and interact/collaborate with researchers from multiple institutions across the country. I had a lead role in the integration and annotation of kidney single cell atlas (version1) (accepted in Nature 2023). This dataset is hosted at the KPMP site and is being interrogated by researchers from all over the world. My current project is to study the disease cell states in the different renal cell types in detail.
• I also plan to extend my experience in alternative splice isoform research to kidney cell types. Towards that I will be working with long reads generated from kidney reference and disease biopsies at single cell level.
• In addition, I am also actively involved in the data integration projects across international research institutions (Sanger/Helmholtz Munich and Human Cell Atlas).
Since December 2022, I have the role as the director of the single cell gene expression core in the Michigan Kidney Translational Research Centre directed by Dr. Matthias Kretzler.
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Lay AC, Tran VDT, Nair V, Betin V, Hurcombe JA, Barrington AF, Pope RJ, Burdet F, Mehl F, Kryvokhyzha D, Ahmad A, Sinton MC, Lewis P, Wilson MC, Menon R, Otto E, Heesom KJ, Ibberson M, Looker HC, Nelson RG, Ju W, Kretzler M, Satchell SC, Gomez MF, Coward RJM, BEAt-DKD consortium . Nat Commun, 2024 Nov 19; 15 (1): 10018Journal ArticleProfiling of insulin-resistant kidney models and human biopsies reveals common and cell-type-specific mechanisms underpinning Diabetic Kidney Disease.
DOI:10.1038/s41467-024-54089-1 PMID: 39562547 -
Keller F, Denicolò S, Leierer J, Kruus M, Heinzel A, Kammer M, Ju W, Nair V, Burdet F, Ibberson M, Menon R, Otto E, Choi YJ, Pyle L, Ladd P, Bjornstad PM, Eder S, Rosivall L, Mark PB, Wiecek A, Heerspink HJL, Kretzler M, Oberbauer R, Mayer G, Perco P. Kidney Blood Press Res, 2024 Nov 7; 1 - 21.Journal ArticleAssociation of urinary EGF, FABP3, and VCAM1 levels with the progression of early diabetic kidney disease.
DOI:10.1159/000542267 PMID: 39510044 -
Schaub JA, Castro AMV, Menez S, Wen Y, Menon R, Bhatraju PK, Wilson FP, Coca SG, Eadon MT, Bomback AS, Moledina DG, Cantley LG, Palevsky PM, D'Agati VD, Randhawa PS, Murugan R, Alpers CE, Kretzler M, Himmelfarb J, Parikh CR. Journal of the American Society of Nephrology, 2024 Oct; 35 (10S): 10.1681/asn.2024cxh8wvkyJournal ArticleAKI in the Kidney Precision Medicine Project: Acute Tubular Injury vs. Acute Interstitial Nephritis
DOI:10.1681/asn.2024cxh8wvky -
Limonte CP, Eddy S, Gharib S, Alpers CE, Barisoni L, Menon R, Nair V, Rosas SE, Poggio ED, De Boer I. Journal of the American Society of Nephrology, 2024 Oct; 35 (10S): 10.1681/asn.2024kvvct9pnJournal ArticleAutophagy-Related Gene Expression in Diabetes and CKD
DOI:10.1681/asn.2024kvvct9pn -
Madapoosi SS, Tisch A, Blough SA, Rosa JS, Eddy S, Naik AS, Limonte CP, McCown PJ, Menon R, Rosas SE, Parikh CR, Mariani LH, Kretzler M, Mahfouz A, Alakwaa F. Journal of the American Society of Nephrology, 2024 Oct; 35 (10S): 10.1681/asn.2024qx0f9jkh - 10.1681/asn.2024qx0f9jkh.Journal ArticleIdentification of Kidney Cell Types in Single-Cell RNA Sequencing and Single-Nucleus RNA Sequencing Data Using Machine-Learning Algorithms
DOI:10.1681/asn.2024qx0f9jkh -
Lake B, Menon R, Ferreira RM, Chen X, Hansen J, Sealfon RS, Schaub JA, Rosas SE, Gaut J, Barisoni L, Kretzler M, Zhang K, Hodgin JB, Eadon MT, Jain S. Journal of the American Society of Nephrology, 2024 Oct; 35 (10S): 10.1681/asn.2024vgp4tabyJournal ArticleMultimodal Single-Cell and Spatial Atlas of Interstitial and Vascular Niches in Reference and Diseased Kidneys
DOI:10.1681/asn.2024vgp4taby -
Kim T, Surapaneni AL, Schmidt IM, Eadon MT, Kalim S, Srivastava A, Palsson R, Stillman IE, Hodgin JB, Menon R, Otto EA, Coresh J, Grams ME, Waikar SS, Rhee EP, Kidney Precision Medicine Project . J Am Soc Nephrol, 2024 Jul 1; 35 (7): 910 - 922.Journal ArticlePlasma Proteins Associated with Chronic Histopathologic Lesions on Kidney Biopsy.
DOI:10.1681/ASN.0000000000000358 PMID: 38656806 -
Tisch A, Madapoosi S, Blough S, Rosa J, Eddy S, Mariani L, Naik A, Limonte C, Mccown P, Menon R, Rosas S, Parikh C, Kretzler M, Mahfouz A, Alakwaa F. 2024Additional ScholarshipIdentification of Kidney Cell Types in scRNA-seq and snRNA-seq Data Using Machine Learning Algorithms
DOI:10.21203/rs.3.rs-3814951/v1