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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.
Marciano PG, Brettschneider J, Manduchi E, Davis JE, Eastman S, Raghupathi R, Saatman KE, Speed TP, Stoeckert CJ Jr, Eberwine JH, McIntosh TK. Neuron-specific mRNA complexity responses during hippocampal apoptosis after traumatic brain injury. J Neurosci. 2004 Mar 24;24(12):2866-76. doi: 10.1523/JNEUROSCI.5051-03.2004. PubMed PMID: 15044525; PubMed Central PMCID: PMC6729833.
Manduchi E, Grant GR, He H, Liu J, Mailman MD, Pizarro AD, Whetzel PL, Stoeckert CJ Jr. RAD and the RAD Study-Annotator: an approach to collection, organization and exchange of all relevant information for high-throughput gene expression studies. Bioinformatics. 2004 Mar 1;20(4):452-9. doi: 10.1093/bioinformatics/btg428. Epub 2004 Jan 22. PubMed PMID: 14990441.
Passerini AG, Polacek DC, Shi C, Francesco NM, Manduchi E, Grant GR, Pritchard WF, Powell S, Chang GY, Stoeckert CJ Jr, Davies PF. Coexisting proinflammatory and antioxidative endothelial transcription profiles in a disturbed flow region of the adult porcine aorta. Proc Natl Acad Sci U S A. 2004 Feb 24;101(8):2482-7. doi: 10.1073/pnas.0305938101. PubMed PMID: 14983035; PubMed Central PMCID: PMC356976.
Grant GR, Manduchi E, Pizarro A, Stoeckert CJ Jr. Maintaining data integrity in microarray data management. Biotechnol Bioeng. 2003 Dec 30;84(7):795-800. doi: 10.1002/bit.10847. Review. PubMed PMID: 14708120.
Kaestner KH, Lee CS, Scearce LM, Brestelli JE, Arsenlis A, Le PP, Lantz KA, Crabtree J, Pizarro A, Mazzarelli J, Pinney D, Fischer S, Manduchi E, Stoeckert CJ Jr, Gradwohl G, Clifton SW, Brown JR, Inoue H, Cras-Méneur C, Permutt MA. Transcriptional program of the endocrine pancreas in mice and humans. Diabetes. 2003 Jul;52(7):1604-10. doi: 10.2337/diabetes.52.7.1604. PubMed PMID: 12829622.
Polacek DC, Passerini AG, Shi C, Francesco NM, Manduchi E, Grant GR, Powell S, Bischof H, Winkler H, Stoeckert CJ Jr, Davies PF. Fidelity and enhanced sensitivity of differential transcription profiles following linear amplification of nanogram amounts of endothelial mRNA. Physiol Genomics. 2003 Apr 16;13(2):147-56. doi: 10.1152/physiolgenomics.00173.2002. PubMed PMID: 12700361.
Manduchi E, Scearce LM, Brestelli JE, Grant GR, Kaestner KH, Stoeckert CJ Jr. Comparison of different labeling methods for two-channel high-density microarray experiments. Physiol Genomics. 2002 Sep 3;10(3):169-79. doi: 10.1152/physiolgenomics.00120.2001. PubMed PMID: 12209019.
Stoeckert C, Pizarro A, Manduchi E, Gibson M, Brunk B, Crabtree J, Schug J, Shen-Orr S, Overton GC. A relational schema for both array-based and SAGE gene expression experiments. Bioinformatics. 2001 Apr;17(4):300-8. doi: 10.1093/bioinformatics/17.4.300. PubMed PMID: 11301298.
Manduchi E, Grant GR, McKenzie SE, Overton GC, Surrey S, Stoeckert CJ Jr. Generation of patterns from gene expression data by assigning confidence to differentially expressed genes. Bioinformatics. 2000 Aug;16(8):685-98. doi: 10.1093/bioinformatics/16.8.685. PubMed PMID: 11099255.
Grant GR, Manduchi E, Cheung VG, Ewens WJ. Significance testing for direct identity-by-descent mapping. Ann Hum Genet. 1999 Sep;63(Pt 5):441-54. doi: 10.1046/j.1469-1809.1999.6350441.x. PubMed PMID: 10735585.
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