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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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.Additional ScholarshipIdentification of Kidney Cell Types in scRNA-seq and snRNA-seq Data Using Machine Learning Algorithms
DOI:10.21203/rs.3.rs-3814951/v1 -
Lassé M, El Saghir J, Berthier CC, Eddy S, Fischer M, Laufer SD, Kylies D, Hutzfeldt A, Bonin LL, Dumoulin B, Menon R, Vega-Warner V, Eichinger F, Alakwaa F, Fermin D, Billing AM, Minakawa A, McCown PJ, Rose MP, Godfrey B, Meister E, Wiech T, Noriega M, Chrysopoulou M, Brandts P, Ju W, Reinhard L, Hoxha E, Grahammer F, Lindenmeyer MT, Huber TB, Schlüter H, Thiel S, Mariani LH, Puelles VG, Braun F, Kretzler M, Demir F, Harder JL, Rinschen MM. Nat Commun, 2023 Aug 14; 14 (1): 4903Journal ArticleAn integrated organoid omics map extends modeling potential of kidney disease.
DOI:10.1038/s41467-023-39740-7 PMID: 37580326 -
Beamish JA, Telang AC, McElliott MC, Al-Suraimi A, Chowdhury M, Ference-Salo JT, Otto EA, Menon R, Soofi A, Weinberg JM, Patel SR, Dressler GR. Kidney Int, 2024 Feb; 105 (2): 312 - 327.Journal ArticlePax protein depletion in proximal tubules triggers conserved mechanisms of resistance to acute ischemic kidney injury preventing transition to chronic kidney disease.
DOI:10.1016/j.kint.2023.10.022 PMID: 37977366 -
Sharma K, Zhang G, Hansen J, Bjornstad P, Lee HJ, Menon R, Hejazi L, Liu J-J, Franzone A, Looker HC, Choi BY, Fernandez R, Venkatachalam MA, Kugathasan L, Sridhar VS, Natarajan L, Zhang J, Sharma VS, Kwan B, Waikar SS, Himmelfarb J, Tuttle KR, Kestenbaum B, Fuhrer T, Feldman HI, de Boer IH, Tucci FC, Sedor J, Heerspink HL, Schaub J, Otto EA, Hodgin JB, Kretzler M, Anderton CR, Alexandrov T, Cherney D, Lim SC, Nelson RG, Gelfond J, Iyengar R, Kidney Precision Medicine Project . J Clin Invest, 2023 Oct 16; 133 (20):Journal ArticleEndogenous adenine mediates kidney injury in diabetic models and predicts diabetic kidney disease in patients.
DOI:10.1172/JCI170341 PMID: 37616058 -
Beamish JA, Telang AC, McElliott MC, Al-Suraimi A, Chowdhury M, Ference-Salo JT, Otto EA, Menon R, Soofi A, Weinberg JM, Patel SR, Dressler GR. 2023 Oct 5;PreprintPax Protein Depletion in Proximal Tubules Triggers Conserved Mechanisms of Resistance to Acute Ischemic Kidney Injury and Prevents Transition to Chronic Kidney Disease.
DOI:10.1101/2023.10.03.559511 PMID: 37873377 -
Sen T, Ju W, Nair V, Ladd P, Menon R, Otto EA, Pyle L, Vigers T, Nelson RG, Arnott C, Neal B, Hansen MK, Kretzler M, Bjornstad P, Heerspink HJL. Kidney Int, 2023 Oct; 104 (4): 828 - 839.Journal ArticleSodium glucose co-transporter 2 inhibition increases epidermal growth factor expression and improves outcomes in patients with type 2 diabetes.
DOI:10.1016/j.kint.2023.07.007 PMID: 37543256 -
Menon R, Otto EA, Barisoni L, Melo Ferreira R, Limonte CP, Godfrey B, Eichinger F, Nair V, Naik AS, Subramanian L, D'Agati V, Henderson JM, Herlitz L, Kiryluk K, Moledina DG, Moeckel GW, Palevsky PM, Parikh CR, Randhawa P, Rosas SE, Rosenberg AZ, Stillman I, Toto R, Torrealba J, Vazquez MA, Waikar SS, Alpers CE, Nelson RG, Eadon MT, Kretzler M, Hodgin JB, Kidney Precision Medicine Project (KPMP) , Nephrotic Syndrome Study Network (NEPTUNE) . medRxiv, 2023 Aug 23;Additional ScholarshipDefining the molecular correlate of arteriolar hyalinosis in kidney disease progression by integration of single cell transcriptomic analysis and pathology scoring.
DOI:10.1101/2023.06.14.23291150 PMID: 37398386 -
Lake BB, Menon R, Winfree S, Hu Q, Melo Ferreira R, 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. Nature, 2023 Jul; 619 (7970): 585 - 594.Journal ArticleAn atlas of healthy and injured cell states and niches in the human kidney.
DOI:10.1038/s41586-023-05769-3 PMID: 37468583