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Manduchi E, Romano JD, Moore JH. The promise of automated machine learning for the genetic analysis of complex traits. Hum Genet. 2022 Sep;141(9):1529-1544. doi: 10.1007/s00439-021-02393-x. Epub 2021 Oct 28. Review. PubMed PMID: 34713318; PubMed Central PMCID: PMC9360157.
Mota PC, Soares ML, Vasconcelos CD, Ferreira AC, Lima BA, Manduchi E, Moore JH, Melo N, Novais-Bastos H, Pereira JM, Guimarães S, Moura CS, Marques JA, Morais A. Predictive value of common genetic variants in idiopathic pulmonary fibrosis survival. J Mol Med (Berl). 2022 Sep;100(9):1341-1353. doi: 10.1007/s00109-022-02242-y. Epub 2022 Aug 19. PubMed PMID: 35986225.
Lasconi C, Pahl MC, Pippin JA, Su C, Johnson ME, Chesi A, Boehm K, Manduchi E, Ou K, Golson ML, Wells AD, Kaestner KH, Grant SFA. Variant-to-gene-mapping analyses reveal a role for pancreatic islet cells in conferring genetic susceptibility to sleep-related traits. Sleep. 2022 Aug 11;45(8). doi: 10.1093/sleep/zsac109. PubMed PMID: 35537191; PubMed Central PMCID: PMC9366645.
A Romero RA, Y Deypalan MN, Mehrotra S, Jungao JT, Sheils NE, Manduchi E, Moore JH. Benchmarking AutoML frameworks for disease prediction using medical claims. BioData Min. 2022 Jul 26;15(1):15. doi: 10.1186/s13040-022-00300-2. PubMed PMID: 35883154; PubMed Central PMCID: PMC9327416.
Manduchi E, Le TT, Fu W, Moore JH. Genetic Analysis of Coronary Artery Disease Using Tree-Based Automated Machine Learning Informed By Biology-Based Feature Selection. IEEE/ACM Trans Comput Biol Bioinform. 2022 May-Jun;19(3):1379-1386. doi: 10.1109/TCBB.2021.3099068. Epub 2022 Jun 3. PubMed PMID: 34310318; PubMed Central PMCID: PMC9291719.
Vujkovic M, Ramdas S, Lorenz KM, Guo X, Darlay R, Cordell HJ, He J, Gindin Y, Chung C, Myers RP, Schneider CV, Park J, Lee KM, Serper M, Carr RM, Kaplan DE, Haas ME, MacLean MT, Witschey WR, Zhu X, Tcheandjieu C, Kember RL, Kranzler HR, Verma A, Giri A, Klarin DM, Sun YV, Huang J, Huffman JE, Creasy KT, Hand NJ, Liu CT, Long MT, Yao J, Budoff M, Tan J, Li X, Lin HJ, Chen YI, Taylor KD, Chang RK, Krauss RM, Vilarinho S, Brancale J, Nielsen JB, Locke AE, Jones MB, Verweij N, Baras A, Reddy KR, Neuschwander-Tetri BA, Schwimmer JB, Sanyal AJ, Chalasani N, Ryan KA, Mitchell BD, Gill D, Wells AD, Manduchi E, Saiman Y, Mahmud N, Miller DR, Reaven PD, Phillips LS, Muralidhar S, DuVall SL, Lee JS, Assimes TL, Pyarajan S, Cho K, Edwards TL, Damrauer SM, Wilson PW, Gaziano JM, O'Donnell CJ, Khera AV, Grant SFA, Brown CD, Tsao PS, Saleheen D, Lotta LA, Bastarache L, Anstee QM, Daly AK, Meigs JB, Rotter JI, Lynch JA, Rader DJ, Voight BF, Chang KM. A multiancestry genome-wide association study of unexplained chronic ALT elevation as a proxy for nonalcoholic fatty liver disease with histological and radiological validation. Nat Genet. 2022 Jun;54(6):761-771. doi: 10.1038/s41588-022-01078-z. Epub 2022 Jun 2. PubMed PMID: 35654975; NIHMSID:NIHMS1826339.
Doliba NM, Rozo AV, Roman J, Qin W, Traum D, Gao L, Liu J, Manduchi E, Liu C, Golson ML, Vahedi G, Naji A, Matschinsky FM, Atkinson MA, Powers AC, Brissova M, Kaestner KH, Stoffers DA. α Cell dysfunction in islets from nondiabetic, glutamic acid decarboxylase autoantibody-positive individuals. J Clin Invest. 2022 Jun 1;132(11). doi: 10.1172/JCI156243. PubMed PMID: 35642629; PubMed Central PMCID: PMC9151702.
Sanavia T, Huang C, Manduchi E, Xu Y, Dadi PK, Potter LA, Jacobson DA, Di Camillo B, Magnuson MA, Stoeckert CJ Jr, Gu G. Temporal Transcriptome Analysis Reveals Dynamic Gene Expression Patterns Driving β-Cell Maturation. Front Cell Dev Biol. 2021;9:648791. doi: 10.3389/fcell.2021.648791. eCollection 2021. PubMed PMID: 34017831; PubMed Central PMCID: PMC8129579.
Manduchi E, Moore JH. Leveraging Automated Machine Learning for the Analysis of Global Public Health Data: A Case Study in Malaria. Int J Public Health. 2021;66:614296. doi: 10.3389/ijph.2021.614296. eCollection 2021. PubMed PMID: 34744577; PubMed Central PMCID: PMC8565284.
Osipovich AB, Dudek KD, Greenfest-Allen E, Cartailler JP, Manduchi E, Potter Case L, Choi E, Chapman AG, Clayton HW, Gu G, Stoeckert CJ Jr, Magnuson MA. A developmental lineage-based gene co-expression network for mouse pancreatic β-cells reveals a role for Zfp800 in pancreas development. Development. 2021 Mar 21;148(6). doi: 10.1242/dev.196964. PubMed PMID: 33653874; PubMed Central PMCID: PMC8015253.
Manduchi E, Fu W, Romano JD, Ruberto S, Moore JH. Embedding covariate adjustments in tree-based automated machine learning for biomedical big data analyses. BMC Bioinformatics. 2020 Oct 1;21(1):430. doi: 10.1186/s12859-020-03755-4. PubMed PMID: 32998684; PubMed Central PMCID: PMC7528347.
Reizel Y, Morgan A, Gao L, Lan Y, Manduchi E, Waite EL, Wang AW, Wells A, Kaestner KH. Collapse of the hepatic gene regulatory network in the absence of FoxA factors. Genes Dev. 2020 Aug 1;34(15-16):1039-1050. doi: 10.1101/gad.337691.120. Epub 2020 Jun 19. PubMed PMID: 32561546; PubMed Central PMCID: PMC7397852.
Su C, Johnson ME, Torres A, Thomas RM, Manduchi E, Sharma P, Mehra P, Le Coz C, Leonard ME, Lu S, Hodge KM, Chesi A, Pippin J, Romberg N, Grant SFA, Wells AD. Mapping effector genes at lupus GWAS loci using promoter Capture-C in follicular helper T cells. Nat Commun. 2020 Jul 3;11(1):3294. doi: 10.1038/s41467-020-17089-5. PubMed PMID: 32620744; PubMed Central PMCID: PMC7335045.
Moore JH, Olson RS, Schmitt P, Chen Y, Manduchi E. How Computational Experiments Can Improve Our Understanding of the Genetic Architecture of Common Human Diseases. Artif Life. 2020 Winter;26(1):23-37. doi: 10.1162/artl_a_00308. Epub 2020 Feb 6. PubMed PMID: 32027528.
Liu Y, Huang J, Urbanowicz RJ, Chen K, Manduchi E, Greene CS, Moore JH, Scheet P, Chen Y. Embracing study heterogeneity for finding genetic interactions in large-scale research consortia. Genet Epidemiol. 2020 Jan;44(1):52-66. doi: 10.1002/gepi.22262. Epub 2019 Oct 4. PubMed PMID: 31583758; PubMed Central PMCID: PMC6980207.
Le T, Gong H, Orzechowski P, Manduchi E, Moore JH. Expanding Polygenic Risk Scores to Include Automatic Genotype Encodings and Gene-gene Interactions. Proceedings of the 13th International Joint Conference on Biomedical Engineering Systems and Technologies. 2020; 3:79-84.
Manduchi E, Hemerich D, van Setten J, Tragante V, Harakalova M, Pei J, Williams SM, van der Harst P, Asselbergs FW, Moore JH. A comparison of two workflows for regulome and transcriptome-based prioritization of genetic variants associated with myocardial mass. Genet Epidemiol. 2019 Sep;43(6):717-726. doi: 10.1002/gepi.22215. Epub 2019 May 30. PubMed PMID: 31145509; PubMed Central PMCID: PMC6687530.
Fernández-Santiago R, Martín-Flores N, Antonelli F, Cerquera C, Moreno V, Bandres-Ciga S, Manduchi E, Tolosa E, Singleton AB, Moore JH, Martí MJ, Ezquerra M, Malagelada C. SNCA and mTOR Pathway Single Nucleotide Polymorphisms Interact to Modulate the Age at Onset of Parkinson's Disease. Mov Disord. 2019 Sep;34(9):1333-1344. doi: 10.1002/mds.27770. Epub 2019 Jun 24. PubMed PMID: 31234232; PubMed Central PMCID: PMC7322732.
Manduchi E, Orzechowski PR, Ritchie MD, Moore JH. Exploration of a diversity of computational and statistical measures of association for genome-wide genetic studies. BioData Min. 2019;12:14. doi: 10.1186/s13040-019-0201-4. eCollection 2019. PubMed PMID: 31320928; PubMed Central PMCID: PMC6617598.
Çalışkan M, Manduchi E, Rao HS, Segert JA, Beltrame MH, Trizzino M, Park Y, Baker SW, Chesi A, Johnson ME, Hodge KM, Leonard ME, Loza B, Xin D, Berrido AM, Hand NJ, Bauer RC, Wells AD, Olthoff KM, Shaked A, Rader DJ, Grant SFA, Brown CD. Genetic and Epigenetic Fine Mapping of Complex Trait Associated Loci in the Human Liver. Am J Hum Genet. 2019 Jul 3;105(1):89-107. doi: 10.1016/j.ajhg.2019.05.010. Epub 2019 Jun 13. PubMed PMID: 31204013; PubMed Central PMCID: PMC6612522.
Chesi A, Wagley Y, Johnson ME, Manduchi E, Su C, Lu S, Leonard ME, Hodge KM, Pippin JA, Hankenson KD, Wells AD, Grant SFA. Genome-scale Capture C promoter interactions implicate effector genes at GWAS loci for bone mineral density. Nat Commun. 2019 Mar 19;10(1):1260. doi: 10.1038/s41467-019-09302-x. PubMed PMID: 30890710; PubMed Central PMCID: PMC6425012.
Manduchi E, Williams SM, Chesi A, Johnson ME, Wells AD, Grant SFA, Moore JH. Leveraging epigenomics and contactomics data to investigate SNP pairs in GWAS. Hum Genet. 2018 May;137(5):413-425. doi: 10.1007/s00439-018-1893-0. Epub 2018 May 24. PubMed PMID: 29797095; PubMed Central PMCID: PMC5996751.
Manduchi E, Chesi A, Hall MA, Grant SFA, Moore JH. Leveraging putative enhancer-promoter interactions to investigate two-way epistasis in Type 2 Diabetes GWAS. Pac Symp Biocomput. 2018;23:548-558. PubMed PMID: 29218913; PubMed Central PMCID: PMC5728670.
Gallagher MD, Posavi M, Huang P, Unger TL, Berlyand Y, Gruenewald AL, Chesi A, Manduchi E, Wells AD, Grant SFA, Blobel GA, Brown CD, Chen-Plotkin AS. A Dementia-Associated Risk Variant near TMEM106B Alters Chromatin Architecture and Gene Expression. Am J Hum Genet. 2017 Nov 2;101(5):643-663. doi: 10.1016/j.ajhg.2017.09.004. Epub 2017 Oct 19. PubMed PMID: 29056226; PubMed Central PMCID: PMC5673619.
McCormick ME, Manduchi E, Witschey WRT, Gorman RC, Gorman JH 3rd, Jiang YZ, Stoeckert CJ Jr, Barker AJ, Yoon S, Markl M, Davies PF. Spatial phenotyping of the endocardial endothelium as a function of intracardiac hemodynamic shear stress. J Biomech. 2017 Jan 4;50:11-19. doi: 10.1016/j.jbiomech.2016.11.018. Epub 2016 Nov 16. PubMed PMID: 27916240; PubMed Central PMCID: PMC5513694.
Davies PF, Manduchi E, Jiménez JM, Jiang YZ. Biofluids, cell mechanics and epigenetics: Flow-induced epigenetic mechanisms of endothelial gene expression. J Biomech. 2017 Jan 4;50:3-10. doi: 10.1016/j.jbiomech.2016.11.017. Epub 2016 Nov 11. PubMed PMID: 27865480; PubMed Central PMCID: PMC5191929.
Clayton HW, Osipovich AB, Stancill JS, Schneider JD, Vianna PG, Shanks CM, Yuan W, Gu G, Manduchi E, Stoeckert CJ Jr, Magnuson MA. Pancreatic Inflammation Redirects Acinar to β Cell Reprogramming. Cell Rep. 2016 Nov 15;17(8):2028-2041. doi: 10.1016/j.celrep.2016.10.068. PubMed PMID: 27851966; PubMed Central PMCID: PMC5131369.
Xia Q, Chesi A, Manduchi E, Johnston BT, Lu S, Leonard ME, Parlin UW, Rappaport EF, Huang P, Wells AD, Blobel GA, Johnson ME, Grant SFA. The type 2 diabetes presumed causal variant within TCF7L2 resides in an element that controls the expression of ACSL5. Diabetologia. 2016 Nov;59(11):2360-2368. doi: 10.1007/s00125-016-4077-2. Epub 2016 Aug 18. PubMed PMID: 27539148.
Bandrowski A, Brinkman R, Brochhausen M, Brush MH, Bug B, Chibucos MC, Clancy K, Courtot M, Derom D, Dumontier M, Fan L, Fostel J, Fragoso G, Gibson F, Gonzalez-Beltran A, Haendel MA, He Y, Heiskanen M, Hernandez-Boussard T, Jensen M, Lin Y, Lister AL, Lord P, Malone J, Manduchi E, McGee M, Morrison N, Overton JA, Parkinson H, Peters B, Rocca-Serra P, Ruttenberg A, Sansone SA, Scheuermann RH, Schober D, Smith B, Soldatova LN, Stoeckert CJ Jr, Taylor CF, Torniai C, Turner JA, Vita R, Whetzel PL, Zheng J. The Ontology for Biomedical Investigations. PLoS One. 2016;11(4):e0154556. doi: 10.1371/journal.pone.0154556. eCollection 2016. PubMed PMID: 27128319; PubMed Central PMCID: PMC4851331.
McCormick ME, Manduchi E, Witschey WR, Gorman RC, Gorman JH 3rd, Jiang YZ, Stoeckert CJ Jr, Barker AJ, Markl M, Davies PF. Integrated Regional Cardiac Hemodynamic Imaging and RNA Sequencing Reveal Corresponding Heterogeneity of Ventricular Wall Shear Stress and Endocardial Transcriptome. J Am Heart Assoc. 2016 Apr 18;5(4):e003170. doi: 10.1161/JAHA.115.003170. PubMed PMID: 27091183; PubMed Central PMCID: PMC4859290.
Jiang YZ, Manduchi E, Stoeckert CJ Jr, Davies PF. Arterial endothelial methylome: differential DNA methylation in athero-susceptible disturbed flow regions in vivo. BMC Genomics. 2015 Jul 7;16:506. doi: 10.1186/s12864-015-1656-4. PubMed PMID: 26148682; PubMed Central PMCID: PMC4492093.
Jiang YZ, Manduchi E, Jiménez JM, Davies PF. Endothelial epigenetics in biomechanical stress: disturbed flow-mediated epigenomic plasticity in vivo and in vitro. Arterioscler Thromb Vasc Biol. 2015 Jun;35(6):1317-26. doi: 10.1161/ATVBAHA.115.303427. Epub 2015 Apr 2. Review. PubMed PMID: 25838424; PubMed Central PMCID: PMC4441576.
Davies PF, Manduchi E, Stoeckert CJ, Jiménez JM, Jiang YZ. Emerging topic: flow-related epigenetic regulation of endothelial phenotype through DNA methylation. Vascul Pharmacol. 2014 Aug;62(2):88-93. doi: 10.1016/j.vph.2014.05.007. Epub 2014 May 27. Review. PubMed PMID: 24874278; PubMed Central PMCID: PMC4116435.
Osipovich AB, Long Q, Manduchi E, Gangula R, Hipkens SB, Schneider J, Okubo T, Stoeckert CJ Jr, Takada S, Magnuson MA. Insm1 promotes endocrine cell differentiation by modulating the expression of a network of genes that includes Neurog3 and Ripply3. Development. 2014 Aug;141(15):2939-49. doi: 10.1242/dev.104810. PubMed PMID: 25053427; PubMed Central PMCID: PMC4197673.
Choi E, Kraus MR, Lemaire LA, Yoshimoto M, Vemula S, Potter LA, Manduchi E, Stoeckert CJ Jr, Grapin-Botton A, Magnuson MA. Dual lineage-specific expression of Sox17 during mouse embryogenesis. Stem Cells. 2012 Oct;30(10):2297-308. doi: 10.1002/stem.1192. PubMed PMID: 22865702; PubMed Central PMCID: PMC3448801.
Zheng J, Stoyanovich J, Manduchi E, Liu J, Stoeckert CJ Jr. AnnotCompute: annotation-based exploration and meta-analysis of genomics experiments. Database (Oxford). 2011;2011:bar045. doi: 10.1093/database/bar045. Print 2011. PubMed PMID: 22190598; PubMed Central PMCID: PMC3244265.
Civelek M, Manduchi E, Riley RJ, Stoeckert CJ Jr, Davies PF. Coronary artery endothelial transcriptome in vivo: identification of endoplasmic reticulum stress and enhanced reactive oxygen species by gene connectivity network analysis. Circ Cardiovasc Genet. 2011 Jun;4(3):243-52. doi: 10.1161/CIRCGENETICS.110.958926. Epub 2011 Apr 14. PubMed PMID: 21493819; PubMed Central PMCID: PMC3116084.
Civelek M, Manduchi E, Grant GR, Stoeckert CJ Jr, Davies PF. Discovery approaches to UPR in athero-susceptible endothelium in vivo. Methods Enzymol. 2011;489:109-26. doi: 10.1016/B978-0-12-385116-1.00007-8. PubMed PMID: 21266227; PubMed Central PMCID: PMC3833809.
Fang Y, Shi C, Manduchi E, Civelek M, Davies PF. MicroRNA-10a regulation of proinflammatory phenotype in athero-susceptible endothelium in vivo and in vitro. Proc Natl Acad Sci U S A. 2010 Jul 27;107(30):13450-5. doi: 10.1073/pnas.1002120107. Epub 2010 Jul 12. PubMed PMID: 20624982; PubMed Central PMCID: PMC2922125.
Steger DJ, Grant GR, Schupp M, Tomaru T, Lefterova MI, Schug J, Manduchi E, Stoeckert CJ Jr, Lazar MA. Propagation of adipogenic signals through an epigenomic transition state. Genes Dev. 2010 May 15;24(10):1035-44. doi: 10.1101/gad.1907110. PubMed PMID: 20478996; PubMed Central PMCID: PMC2867208.
Lefterova MI, Steger DJ, Zhuo D, Qatanani M, Mullican SE, Tuteja G, Manduchi E, Grant GR, Lazar MA. Cell-specific determinants of peroxisome proliferator-activated receptor gamma function in adipocytes and macrophages. Mol Cell Biol. 2010 May;30(9):2078-89. doi: 10.1128/MCB.01651-09. Epub 2010 Feb 22. PubMed PMID: 20176806; PubMed Central PMCID: PMC2863586.
Granot Z, Swisa A, Magenheim J, Stolovich-Rain M, Fujimoto W, Manduchi E, Miki T, Lennerz JK, Stoeckert CJ Jr, Meyuhas O, Seino S, Permutt MA, Piwnica-Worms H, Bardeesy N, Dor Y. LKB1 regulates pancreatic beta cell size, polarity, and function. Cell Metab. 2009 Oct;10(4):296-308. doi: 10.1016/j.cmet.2009.08.010. PubMed PMID: 19808022; PubMed Central PMCID: PMC2790403.
Civelek M, Manduchi E, Riley RJ, Stoeckert CJ Jr, Davies PF. Chronic endoplasmic reticulum stress activates unfolded protein response in arterial endothelium in regions of susceptibility to atherosclerosis. Circ Res. 2009 Aug 28;105(5):453-61. doi: 10.1161/CIRCRESAHA.109.203711. Epub 2009 Aug 6. PubMed PMID: 19661457; PubMed Central PMCID: PMC2746924.
Heller R, Manduchi E, Grant GR, Ewens WJ. A flexible two-stage procedure for identifying gene sets that are differentially expressed. Bioinformatics. 2009 Apr 15;25(8):1019-25. doi: 10.1093/bioinformatics/btp076. Epub 2009 Feb 11. PubMed PMID: 19213738.
Heller R, Manduchi E, Small DS. Matching methods for observational microarray studies. Bioinformatics. 2009 Apr 1;25(7):904-9. doi: 10.1093/bioinformatics/btn650. Epub 2008 Dec 19. PubMed PMID: 19098026.
Hardy OT, Hohmeier HE, Becker TC, Manduchi E, Doliba NM, Gupta RK, White P, Stoeckert CJ Jr, Matschinsky FM, Newgard CB, Kaestner KH. Functional genomics of the beta-cell: short-chain 3-hydroxyacyl-coenzyme A dehydrogenase regulates insulin secretion independent of K+ currents. Mol Endocrinol. 2007 Mar;21(3):765-73. doi: 10.1210/me.2006-0411. Epub 2006 Dec 21. PubMed PMID: 17185391.
Mazzarelli JM, Brestelli J, Gorski RK, Liu J, Manduchi E, Pinney DF, Schug J, White P, Kaestner KH, Stoeckert CJ Jr. EPConDB: a web resource for gene expression related to pancreatic development, beta-cell function and diabetes. Nucleic Acids Res. 2007 Jan;35(Database issue):D751-5. doi: 10.1093/nar/gkl748. Epub 2006 Oct 27. PubMed PMID: 17071715; PubMed Central PMCID: PMC1781120.
Grant GR, Manduchi E, Stoeckert CJ Jr. Analysis and management of microarray gene expression data. Curr Protoc Mol Biol. 2007 Jan;Chapter 19:Unit 19.6. doi: 10.1002/0471142727.mb1906s77. Review. PubMed PMID: 18265395.
Passerini AG, Shi C, Francesco NM, Chuan P, Manduchi E, Grant GR, Stoeckert CJ Jr, Karanian JW, Wray-Cahen D, Pritchard WF, Davies PF. Regional determinants of arterial endothelial phenotype dominate the impact of gender or short-term exposure to a high-fat diet. Biochem Biophys Res Commun. 2005 Jun 24;332(1):142-8. doi: 10.1016/j.bbrc.2005.04.103. PubMed PMID: 15896310.
Simmons CA, Grant GR, Manduchi E, Davies PF. Spatial heterogeneity of endothelial phenotypes correlates with side-specific vulnerability to calcification in normal porcine aortic valves. Circ Res. 2005 Apr 15;96(7):792-9. doi: 10.1161/01.RES.0000161998.92009.64. Epub 2005 Mar 10. PubMed PMID: 15761200; PubMed Central PMCID: PMC3057118.
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