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Staff Bio profile for manduchi

Elisabetta Manduchi
Manager, Research Project B
  • Bioinformatics Scientist / 2015 - present
    University of Pennsylvania, Institute for Biomedical Informatics, CGL
  • Manager, Research Project B / 2001 - 2015
    University of Pennsylvania, Center for Bioinformatics, CBIL
  • Postdoc (transition from Math to Bioinformatics) / 1998 - 2001
    University of Pennsylvania, Center for Bioinformatics
  • Visiting Assistant Professor / 1996 - 1998
    Haverford College, Department of Mathematics
  • Postdoctoral Lecturer / 1994 - 1996
    University of Pennsylvania, Department of Mathematics
  • Ph.D. / Mathematics - 1994 - University of Maryland, College Park
  • Laurea / Mathematics - 1987 - University of Rome I "La Sapienza"
Research Interests:
  • I am a Bioinformatics Scientist, with extensive experience in analysis and management of high-throughput biological data, including development of methods, algorithms, computational tools, functional genomics databases and web resources. I am a former member of CBIL (UPenn), where I have been involved in several projects including: Beta Cell Genomics (Project Manager), RAD and GUS, PaGE, and Significance Testing for Direct  Identity-by-descent mapping (STeDI). As part of CBIL, I have collaborated with many investigators both within and outside of the University of Pennylvania, including a long-term collaboration with Professor Peter Davies' group at UPenn on analyses of high-throughput datasets relative to Cardiovascular Biology. I have also collaborated with Dr. Greg Grant's bioinformatics group at ITMAT (UPenn) on methods and code to pre-process and analyze RNA-Seq data. In 2015 I have joined the Computational Genetics Laboratory in the Institute for Biomedical Informatics at UPenn where I work on approaches for identifying genetic and genomic biomarkers associated with human health and disease, embracing the complexity of the genotype-to-phenotype mapping relationship due to phenomena such as epistasis. In addition, I spend part of my time working within the Spatial and Functional Genomics Initiative (SFGI) at The Children's Hospital of Philadelphia (CHOP), led by Professors Struan Grant, Gerd Blobel and Andrew Wells. As part of this initiative I work on analysis of Chromosome Conformation Capture high-throuput data.
Recent Publications:
    • Manduchi  E. (1991) Steiner Heptagon Systems. Ars Combinatoria, 31: 105-115.
    • Manduchi  E. (1995) Root numbers of fibers of elliptic surfaces. Compos. Math., 99: 33-58.
    • Manduchi E. (1995) Elliptic surfaces and a conjecture of Mazur. Rendiconti del Seminario Matematico, Universita' e Politecnico di Torino, 53: 339-345.
    • Grant G.R. and Manduchi E. (1997) Root numbers and algebraic points on elliptic surfaces with base P1. Duke Math. Jour., 89(3): 413-422.
    • Grant G.R. and Manduchi E. (1998) Root numbers and algebraic points on elliptic surfaces with elliptic base. Duke Math. Jour., 93(3): 479-486.
    • Grant G.R., Manduchi  E., Cheung V.G., Ewens W.J. (1999) Significance testing for direct identity-by-descent mapping. Ann. Hum. Genet., 63: 441-454.
    • Manduchi E., Grant G.R., McKenzie S.E., Overton G.C., Surrey S., Stoeckert C.J. Jr. (2000) Generation of patterns from gene expression data by assigning confidence to differentially expressed genes. Bioinformatics, 16(8): 685-698.
    • Stoeckert C., Pizarro A., Manduchi E., Gibson M., Brunk B., Crabtree J., Schug J., Shen-Orr S., Overton G.C. (2001) A relational schema for both array-based and SAGE gene expression experiments. Bioinformatics 17(4): 300-308.
    • Grant G., Manduchi E., Stoeckert C. Using non-parametric methods in the context of multiple testing to identify differentially expressed genes.Methods of microarray data analysis, editors S.M. Lin and K.F. Johnson, Kluwer Academic Publishers (Boston, 2002): 37-55. (Winner of the best presentation award CAMDA'00.
    • Manduchi E., Pizarro A., Stoeckert C. (2001) RAD (RNA Abundance Database): an infrastructure for array data analysis. Proc. SPIE, 4266: 68-78.
    • Manduchi E., Scearce L.M., Brestelli J.E., Grant G.R., Kaestner K.H., Stoeckert C.J. Jr. (2002) Comparison of different labeling methods for 2-channel high-density microarray experiments. Physiological Genomics, 10(3): 169-179.
    • Stoeckert, C.J.Jr., Pizarro, A., Crabtree, J., Manduchi, E., Le, P.P., McWeeney, S.K., Grant, G.R. (2003) The RNA Abundance Database RAD, in Lorkowski, S. and Cullen, P. (eds), Analysing Gene Expression, Wiley-VCH, Weinheim.
    • Polacek D.C., Passerini A.G., Shi C., Francesco N.M., Manduchi E., Grant G.R., Powell S., Bischof H., Winkler H., Stoeckert C.J. Jr., Davies P.F. (2003) Fidelity and enhanced sensitivity of differential transcription profiles following linear amplification of nanogram amounts of endothelial mRNA, Physiological Genomics, 13: 147-156
    • Kaestner K.H., Lee C.S., Scearce L.M., Brestelli J.E., Arsenlis A., Le P.P., Lantz K.A., Crahtree J., Pizarro A., Mazzarelli J., Pinney D., Fischer S., Manduchi E., Stoeckert C.J. Jr., Gradwohl G., Clifton S.W., Brown J., Melton D.A., Inoue H., Permutt M.A. (2003) The transcriptional program of the endocrine pancreas in mice and human, Diabetes, 52(7): 1604-1610.
    • Grant G.R., Manduchi E., Pizarro A., Stoeckert C.J. Jr. (2003) Maintaining data integrity in microarray data management, Biotechnology and Bioengineering, 84(7): 795-800.
    • Manduchi E. (2003) Gene expression array studies: challenges, standards, and infrastructures, Minerva Biotecnologica, 15(4): 201-206.
    • Passerini A.G., Polacek D.C., Shi C., Francesco N.M., Manduchi E., Grant G.R., Pritchard W.F., Powell S., Chang G.Y., Stoeckert C.J. Jr., Davies P. (2004) Coexisting pro-inflammatory and anti-oxidative endothelial transcription profiles in a disturbed flow region of the adult porcine aorta, PNAS, 101(8): 2482-2487.
    • Manduchi E., Grant G.R., He H., Liu J., Mailman M.D., Pizarro A.D., Whetzel P.L., Stoeckert C.J. Jr. (2004) RAD and the RAD Study-Annotator: an approach to collection, organization and exchange of all relevant information for high-throughput gene expression studies, Bioinformatics, 20(4): 452-459.
    • Marciano P.G., Brettschneider J., Manduchi E., Davies J.E., Eastman S., Raghupathi R., Saatman K.E., Speed T.P., Stoeckert C.J. Jr., Eberwine J.H., McIntosh T.K. (2004) Neuron-specific mRNA complexity responses during hippocampal apoptosis following traumatic brain injury, The Journal of Neuroscience, 24(12): 2866-2876.
    • Simmons C.A., Grant G.R., Manduchi E., Davies P.F. (2005) Spatial heterogeneity of endothelial phenotypes correlates with side-specific vulnerability to calcification in normal porcine aortic valves, Circulation Research, 96(7): 792-799.
    • Passerini A.G., Shi C., Francesco N.M., Chuan P., Manduchi E., Grant G.R., Stoeckert C.J. Jr., Karanian J.W., Wray-Cahen D., Pritchard W.F., Davies P.F. (2004-2005) Regional determinants of arterial endothelial phenotype dominate the impact of gender or short-term exposure to high-fat diet, Biochemical and Biophysical Research Communications, 332: 142-148.
    • Mazzarelli J., Brestelli J., Gorski R., Liu J., Manduchi E., Pinney D., Schug J., White P., Kaestner K., Stoeckert C. (2006) EPConDB: a web resource for gene expression related to pancreatic development, beta cell function and diabetes, Nucleic Acid Research, doi: 10.1093/nar/gkl748.
    • Hardy O.T., Hohmeier H.E., Becker T.C., Manduchi E., Doliba N.M., Gupta R.K., White P., Stoeckert C.J. Jr., Matschinsky F.M., Newgard C.B., Kaestner K.H. (2006) Functional genomics of the beta-cell: SCHAD regulates insulin secretion independent of K+ currents, Molecular Endocrinology, 21(3): 765-773.
    • Grant G.R., Manduchi E., Stoeckert C.J. Jr. (2007) Analysis and management of microarray gene expression data, Unit 19.6 in Current Protocols in Molecular Biology, John Wiley & Sons.
    • Manduchi E. (2007) Infrastrutture per l'analisi di dati di genomica funzionale: gestione dati, integrazione, standard, in Genomica e Proteomica Computazionale, Patron editore.
    • Heller R., Manduchi E., Small D. (2009) Matching methods for observational microarray studies, Bioinformatics, 25(7): 904-909.
    • Heller R., Manduchi E., Grant G.R., Ewens W.J. (2009) A flexible two-stage procedure for identifying gene sets that are differentially expressed, Bioinformatics, 25(8): 1019-1025.
    • Granot Z., Swisa A., Magenheim J., Stolovich-Rain M., Fujimoto W., Manduchi E., Miki T., Lennerz J.K., Stoeckert C.J. Jr, Meyuhas O., Seino S., Permutt M.A., Piwnica-Worms H., Bardeesy N., Dor Y. (2009) LKB1 Regulates Pancreatic Beta Cell Size, Polarity, and Function, Cell Metabolism, 10(4): 296-308.
    • Civelek M., Manduchi E., Riley R.J., Stoeckert C.J. Jr., Davies P.F. (2009) Chronic endoplasmic reticulum stress activates unfolded protein response in arterial endothelium in regions of susceptibility to atherosclerosis, Circulation Research, 105(5): 453-461.
    • Lefterova M.I., Steger D.J., Zhuo D., Qatanani M., Mullican S.E., Tuteja G., Manduchi E., Grant G.R., Lazar M.A. (2010) Cell-specific determinants of PPARgamma function in adipocytes and macrophages, Molecular and Cellular Biology, 30: 2078-2089.
    • Steger D.J., Grant G.R., Schupp M., Tomaru T., Lefterova M.I., Schug J., Manduchi E., Stoeckert C.J. Jr., Lazar M.A. (2010) Propagation of adipogenic signals through an epigenomic transition state, Genes Dev, 24: 1035-1044.
    • Fang Y., Shi C., Manduchi E., Civelek M., Davies P.F. (2010) MicroRNA-10a regulation of proinflammatory phenotype in athero-susceptible endothelium in vivo and in vitro, PNAS, 107(30): 13450-13455.
    • Civelek M., Manduchi E., Grant G.R., Stoeckert C.J. Jr., Davies P.F. (2011) Discovery approaches to UPR in athero-susceptible endothelium in vivo Methods Enzymol., 489: 109-126.
    • Civelek M., Manduchi E., Riley R.J., Stoeckert C.J. Jr., Davies P.F. (2011) Coronary artery endothelial transcriptome in vivo: identification of endoplasmin reticulum stress and enhanced ROS by gene connectivity network analysis, Circulation Cardiovascular Genetics, 4(3): 243-252.
    • Zheng J., Stoyanovich J., Manduchi E., Liu J., Stoeckert C.J. Jr. (2011) AnnotCompute: annotation-based exploration and meta-analysis of genomics experiments, Database: doi: 10.1093/database/bar045.
    • Choi E., Kraus M.R., Lemaire L.A., Yoshimoto M., Vemula S., Potter L.A., Manduchi E., Stoeckert C.J. Jr. , Grapin-Botton A., Magnuson M.A. (2012) Dual lineage-specific expression of Sox17 during mouse embryogenesis, Stem Cells, 30(10): 2297-308.
    • Davies P.F., Manduchi E., Stoeckert C.J., Jimenez J.M., Jiang Y.Z. (2014) Emerging topic: flow-related epigenetic regulation of endothelial phenotype through DNA methylation, Vascular Pharmacology, doi: 10.1016/j.vph.2014.05.007
    • Osipovich A.B., Long Q., Manduchi E., Gangula R., Hipkens S.B., Schneider J., Okubo T., Stoeckert C.J., Takada S., Magnuson M.A. (2014) Insm1 promotes endocrine cell differentiation by modulating the expression of a network of genes that includes Neurog3 and Ripply3, Development, 141(15): 2939-49.
    • Jiang Y.Z., Manduchi E., JimĂ©nez J.M., Davies P.F. (2015) , Endothelial epigenetics in biomechanical stress: Disturbed flow-mediated epigenomic plasticity in vivo and in vitro, Arteriosclerosis, Thrombosis, and Vascular Biology, in press.
    • Jiang Y.Z., Manduchi E., Stoeckert C.J., Davies P.F. (2015), Arterial endothelial methylome: Differential DNA methylation in athero-susceptible disturbed flow regions in vivo, BMC Genomics, 16: 506.

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