Available to mentor
Dr. Fadhl Alakwaa is a faculty member at the University of Michigan, Ann Arbor. His research focuses is on the extraction of biological insight from big data and the development of a data-driven approach for personalized medicine using multi-omics data and modern machine learning algorithms. He developed many bioinformatics pipelines for analyzing multi-omics data such as transcriptomics, metabolomics, microbiome, proteomics, and single-cell omics data. He leads multi-disciplinary projects and has more than 8 federal and non-federal grants as co-I. Dr. Alakwaa has more than 10 years of experience teaching and mentoring undergraduate and graduate students and he got nominated as an outstanding UROP mentor for the 2020-2021 academic year.
The main purpose of my research is to either apply established or innovative novel computational,
bioinformatics, or statistical algorithm to find meaningful patterns in complex multiscalar omics-based data
(metabolomic, microbiome, methylation, etc) in complex diseases like chronic kidney disease. Keywords:
Bioinformatics, Big data integration, drug repurposing.
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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 . bioRxiv, 2024 Apr 2;Journal ArticleOntology-based modeling, integration, and analysis of heterogeneous clinical, pathological, and molecular kidney data for precision medicine.
DOI:10.1101/2024.04.01.587658 PMID: 38617362 -
Schuchman M, Brady TM, Glenn DA, Tuttle KR, Cara-Fuentes G, Levy RV, Gonzalez-Vicente A, Alakwaa FM, Srivastava T, Sethna CB. J Nephrol, 2024 Apr; 37 (3): 647 - 660.Journal ArticleAssociation of mental health-related patient reported outcomes with blood pressure in adults and children with primary proteinuric glomerulopathies.
DOI:10.1007/s40620-024-01919-6 PMID: 38512380 -
Alakwaa F, Naik A, Menon R, Otto E, Pyle L, Choi Y, Kretzler M, Bjornstad P. Kidney International Reports, 2024 Apr; 9 (4): s615 - s616.Journal ArticleWCN24-1387 Integration of Single Cell Data from Human and RNA-Seq Analysis from Rat to Identify Surrogate Drugs Mimicking the Effects of Metabolic Bariatric Surgery
DOI:10.1016/j.ekir.2024.02.1296 -
Kugathasan L, Sridhar VS, Lovblom LE, Matta S, Saliba A, Debnath S, AlAkwaa FM, Nair V, Bjornstad P, Kretzler M, Perkins BA, Sharma K, Cherney DZI. Diabetes, 2024 Mar 1; 73 (3): 401 - 411.Journal ArticleInteractive Effects of Empagliflozin and Hyperglycemia on Urinary Amino Acids in Individuals With Type 1 Diabetes.
DOI:10.2337/db23-0694 PMID: 38015810 -
El-Achkar TM, Eadon MT, Kretzler M, Himmelfarb J, Kidney Precision Medicine Project . Am J Kidney Dis, 2024 Mar; 83 (3): 402 - 410.Journal ArticlePrecision Medicine in Nephrology: An Integrative Framework of Multidimensional Data in the Kidney Precision Medicine Project.
DOI:10.1053/j.ajkd.2023.08.015 PMID: 37839688 -
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 -
Gisch DL, Brennan M, Lake BB, Basta J, Keller MS, Melo Ferreira R, Akilesh S, Ghag R, Lu C, Cheng Y-H, 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. Nat Commun, 2024 Jan 10; 15 (1): 433Journal ArticleThe chromatin landscape of healthy and injured cell types in the human kidney.
DOI:10.1038/s41467-023-44467-6 PMID: 38199997 -
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
