Elisabetta Manduchi's page

Elisabetta Manduchi

Address
Computational Biology and Informatics Laboratory
Center for Bioinformatics
University of Pennsylvania
1428 Blockley Hall
423 Guardian Drive
Philadelphia, PA 19104-6021
Contact
phone: (215) 573-4408
fax: (215) 573-3111
email: manduchi@pcbi.upenn.edu

Background
Current research interests
Publications and Preprints

Background

I got my undergraduate degree in Mathematics in Italy at the University of Rome I and my PhD in Mathematics in 1994 at the University of Maryland in College Park. My dissertation, directed by Prof. David Rohrlich, was in the field of Algebraic Number Theory and Algebraic Geometry (here is a link to my "math genealogy"). From 1994 to 1996 I held a postdoctoral position as Lecturer in Mathematics in the Department of Mathematics at the University of Pennsylvania and from 1996 to 1998 I was Visiting Assistant Professor in the Department of Mathematics at Haverford College. I have been at the Computational Biology and Informatics Laboratory (CBIL) within the Penn Center for Bioinformatics (PCBI) since July 1998, first as a post-doc and, as of January 2001, as Research Project Manager.

Current research interests

I work on the analysis and management of high-throughput biological data, including development of algorithms, computational tools, and web resources at CBIL. The projects which I have been involved with include: Beta Cell Genomics (Project Manager), RAD and its Study-Annotator (Project Manager), PaGE, and Significance Testing for Direct Identity-by-descent mapping (STeDI).

Publications and Preprints

Mathematics

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.

Computational Biology/Bioinformatics

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/bar049.