Gene Expression Analysis Genomic Database Development Cancer Genomics - particularly aCGH analysis Next Generation Sequencing Analysis

Publications

• Deep sequencing the circadian and diurnal transcriptome of Drosophila brain Hughes ME, Grant GR, Paquin C, Qian J, Nitabach MN. Genome Research (2012) In press.

• Comparative Analysis of RNA-Seq Alignment Algorithms and the RNA-Seq Unified Mapper (RUM) Gregory R. Grant, Michael H. Farkas, Angel Pizarro, Nicholas Lahens, Jonathan Schug, Brian Brunk, Christian J. Stoeckert Jr, John B. Hogenesch and Eric A. Pierce. Bioinformatics (2011) 2011 Sep 15;27(18):2518-28.

• Side-Specific Expression of Activated Leukocyte Adhesion Molecule (ALCAM; CD166) in Pathosusceptible Regions of Swine Aortic Valve Endothelium Marie A. Guerraty, Gregory R. Grant, John W. Karanian, Oscar A. Chiesa, William F. Pritchard, Peter F. Davies. The Journal of Heart Valve Disease (2011);20:165-167

• Microsomal Prostaglandin E₂Synthase-1 Modulates the Response to Vascular Injury. Miao Wang, Kaori Ihida-Stansbury, Devashish Kothapalli, Mathieu C. Tamby, Zhou Yu, Lihong Chen, Gregory Grant, Yan Cheng, John A. Lawson, Richard K. Assoian, Peter L. Jones, PhD; Garret A. FitzGerald, MD Cicrulation (2011) (123:631-639)

• Epigenetic Propagation of Adipogenic Signals by Glucocorticoid Receptor and CEBPbeta. David J. Steger, Gregory R. Grant, Michael Schupp, Takuya Tomaru, Martina I. Lefterova, Jonathan Schug, Elisabetta Manduchi, Christian J. Stoeckert Jr., and Mitchell A. Lazar Genes & Dev (2010) 24(10)

• Cell-Specific Determinants of PPARgamma Function in Adipocytes and Macrophages. Martina I. Lefterova, David J. Steger, David Zhuo, Mohammed Qatanani, Shannon E. Mullican, Geetu Tuteja, Elisabetta Manduchi, Gregory R. Grant, and Mitchell A. Lazar Molecular and Cellular Biology (2010) 30(9):2078-89

• Hypercholesterolemia induces side-specific phenotype changes and PPARgamma pathway activation in swine aortic valve endothelium. Marie A. Guerraty, Gregory R. Grant, John W. Karanian, Oscar A. Chiesa, William F. Pritchard, and Peter F. Davies. Arteriosclerosis, Thrombosis, and Vascular Biology (2010) Feb;30(2):225-31

• Pre-lesional arterial endothelial phenotypes in hypercholesterolemia: Universal ABCA1 upregulation contrasts with region-specific gene expression in vivo. Civelek Mete, Gregory R Grant, Irolla CR, Shi C, Riley RJ, Chiesa OA, Stoeckert CJ Jr, Karanian JW, Pritchard WF, Peter F Davies. Am J Physiol Heart Circ Physiol. (2009) Nov 6

• TriTrypDB: A Functional Genomic Resource for the Trypanosomatidae. Mark Aslett, Critina Aurrecoechea, Mathew Berriman, et al. Nucleic Acids Research (2009) Jan;38 (Database issue) :D457-62.

• A Flexible Two Stage Procedure for Identifying Gene Sets that are Differentially Expressed. Ruth Heller, Elisabetta Manduchi, Gregory R. Grant, Warren J. Ewens. Bioinformatics (2009), 25(8): 1019-1025.

• Molecular Karyotype of Sporadic Unilateral Retinoblastoma Tumors. Arupa Ganguly, Kim Nichols, Gregory R. Grant, Eric Rappaport, Carol Shields. RETINA (2009) 29(7): 1002-1012.

• PlasmoDB: a functional genomic database for malaria parasites. Aurrecoechea C, Brestelli J, Brunk BP, Dommer J, Fischer S, Gajria B, Gao X, Gingle A, Grant G, Harb OS, Heiges M, Innamorato F, Iodice J, Kissinger JC, Kraemer E, Li W, Miller JA, Nayak V, Pennington C, Pinney DF, Roos DS, Ross C, Stoeckert CJ Jr, Treatman C, Wang H. Nucleic Acids Res. (2009) Jan;37(Database issue):D539-43

• GiardiaDB and TrichDB: integrated genomic resources for the eukaryotic protist pathogens Giardia lamblia and Trichomonas vaginalis. Aurrecoechea C, Brestelli J, Brunk BP, Carlton JM, Dommer J, Fischer S, Gajria B, Gao X, Gingle A, Grant G, Harb OS, Heiges M, Innamorato F, Iodice J, Kissinger JC, Kraemer E, Li W, Miller JA, Morrison HG, Nayak V, Pennington C, Pinney DF, Roos DS, Ross C, Stoeckert CJ Jr, Sullivan S, Treatman C, Wang H. Nucleic Acids Res. (2009) Jan;37(Database issue):D526-30.

• Assessing the Significance of Conserved Genomic Aberrations Using High Resolution Genomic Microarrays. Mitchell Guttman, Carolyn Mies, Katarzyna Dudycz-Sulicz, Sharon J. Diskin, Don A. Baldwin, Christian J. Stoeckert Jr., Gregory R. Grant. PLoS Genetics Vol. 3, No. 8, e143 doi:10.1371 (2007).

• Human miR-155 on chromosome 21 differentially interacts with its polymorphic target in the AGTR1 3'UTR -- a mechanism for functional SNPs related to phenotypes. Praveen Sethupathy, Christelle Borel, Maryline Gagnebin, Gregory R. Grant, Samuel Deutsch, Terry S. Elton, Artemis G. Hatzigeorgiou, Stylianos E. Antonarakis. The American Journal of Human Genetics Am J Hum Genet. (2007) August; 81(2): 405-413.

• Analysis and management of microarray gene expression data, Unit 19.6 in Current Protocols in Molecular Biology. Grant G.R., Manduchi E., Stoeckert C.J. Jr. (2007) John Wiley & Sons.

• Biochemical, molecular and behavioral phenotypes of Rab3A mutations in the mouse. Shuzhang Yang, Michael Farias, David Kapfhamer, John Tobias, Gregory Grant, Ted Abel, Maja Bucan. Genes Brain Behav 6: 77-96 (2007).

• STAC: A method for testing the significance of DNA copy-number aberrations across multiple array-CGH experiments. Sharon J. Diskin, Thomas Eck, Joel Greshock, Yael P. Mosse, Tara Naylor, Christian J. Stoeckert, Jr., Barbara L. Weber, John M. Maris and Gregory R. Grant. Genome Research (2006). 16: 1149-1158.

• Integrative genomics identifies distinct molecular classes of neuroblastoma and demonstrates that multiple genes are targeted by regional alterations in DNA copy number. Qun Wang, Sharon Diskin, Eric Rappaport, Edward Attiyeh, Yael Mosse, Daniel Shue, Eric Seiser, Jayanti Jagannathan, Suzanne Shusterman, Manisha Bansal, Deepa Khazi, Cynthia Winter, Erin Okowa, Gregory Grant, Avital Cnbaan, Huaqing Zhao, Nai-Kong Cheung, William Gerald, Wendy London, Katherine K. Matthay, Garrett M. Brodeur and John M. Maris. Cancer Research (2006). Cancer Research 66, 6050-6062.

• Regional determinants of arterial endothelial phenotype dominate the impact of gender or short-term exposure to a high-fat diet Anthony G. Passerini , Congzhu Shi, Nadeene M. Francesco, Peiying Chuan, Elisabetta Manduchi, Gregory R. Grant, Christian J. Stoeckert Jr., John W. Karanian, Diane Wray-Cahen , William F. Pritchard and Peter F. Davies (2005). Biochemical and Biophysical Research Communications, Vol 21 no 11, 2684-2690.

• A practical false discovery rate approach to identifying patterns of differential expression in microarray data. Grant, G.R, Junmin Liu, Stoeckert, C.J.Jr. (2005). Bioinformatics - 2005 21(11):2684-2690

• Spatial heterogeneity of endothelial phenotypes correlates with side-specific vulnerability to calcification in normal porcine aortic valves. (2005). Simmons C.A., Grant G.R., Manduchi E., Davies P.F., Circulation Research, 96(7):792-799

• Textbook: Statistical Methods in Bioinformatics: An Introduction EDITION 2.  W. Ewens, G. Grant, Textbook, Springer-Verlag (2005).

• Coexisting proinflammatory and antioxidative endothelial transcription profiles in a disturbed flow region of the adult porcine aorta (2004). Anthony G. Passerini, Denise C. Polacek, Congzhu Shi, Nadeene M. Francesco, Elisabetta Manduchi, Gregory R. Grant, William F. Pritchard, Steven Powell, Gary Y. Chang, Christian J. Stoeckert, Jr. and Peter F. Davies. (2004) PNAS vol. 101, no. 8 2482-2487

• RAD and the RAD Study-Annotator: an approach to collection, organization, and exchange of all relevant information for high-throughput gene expression studies. (2004) Manduchi M., Grant G.R., He H., Liu J., Mailman M.D., Pizarro A.D., Whetzel P.L., Stoeckert C.J. Jr. Bioinformatics, 20(4): 452-459

• Maintaining data integrity in microarray data management. Grant G.R., Manduchi M., Pizzaro, A., Stoeckert C.J. Jr. (2003), Biotechnology and Bioengineering,

• Comment on 'Resampling-based multiple testing for DNA microarray data analysis' by Ge, Dudoit, and Speed (2003). Test, 12: 1-77.

• Fidelity and enhanced sensitivity of differential transcription profiles following linear amplification of nanogram amounts of endothelial mRNA. 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), Physiological Genomics 13: 147-156.

• The Plasmodium genome database. Kissinger, J.C., Brunk, B.P., Crabtree, J., Fraunholz, M.J., Gajria, B., Milgram, A.J., Pearson, D.S., Schug, J., Bahl, A., Diskin, S.J., Ginsburg, H., Grant, G.R., Gupta, D., Labo, P., Li, L., Mailman, M.D., McWeeney, S.K., Whetzel, P., Stoeckert, C.J. Jr., Roos, D.S. Nature. (2002) Oct 3;419(6906):490-2.

• Comparison of different labeling methods for two-channel high-density microarray experiments. Manduchi, E., Scearce$*, Carolyn Mies2, Katarzyna Dudycz-Sulicz2, Sharon J. Diskin3, Don A. Baldwin4, Christian J. Stoeckert Jr.1,5, Gregory R. Grant1,5 , L.M., Brestelli, J.E., Grant, G.R., Kaestner, K.H., Stoeckert, C.J. Jr. Physiol Genomics. (2002) Sep 3;10(3):169-179.

• PlasmoDB: The Plasmodium Genome Resource. An integrated database providing tools for accessing and analyzing mapping, expression and sequence data (both finished and unfinished). Bahl, A., Brunk, B., Coppel, R.L., Crabtree, J., Diskin, S.J., Fraunholz, M.J., Grant, G.R., Gupta, D., Huestis, R.L., Kissinger, J.C., Labo, P., Li, L., McWeeney, S.K., Milgram, A.J., Roos, D.S., Schug, J., Stoeckert, C.J. Nucleic Acids Res. 30: 87-90 (2002)

• Using Non-Parametric Methods in the Context of Multiple Testing to Identify Differentially Expressed Genes. G. Grant, E. Manduchi and C. Stoeckert, Critical Assessment of Microarray Data Analysis (CAMDA00) 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.)

• Textbook: Statistical Methods in Bioinformatics: An Introduction.  W. Ewens, G. Grant, Textbook, Springer-Verlag (2001).

• Generation of Patterns from Gene Expression Data by Assigning Confidence to Differentially Expressed Genes. E. Manduchi, G. Grant, C. Stoeckert, S. McKenzie, S. Surry, C. Overton, C. Stoeckert, Bioinformatics (2000) 16, 685-698.

• Significance Testing for Direct Identity-by-descent Mapping. G. Grant, E. Manduchi, V. Cheung, W. Ewens, Annals of Human Genetics (1999) 63, 441-454.

 
Pure Math

Arithmetic Geometry Number Theory

Publications

• Root Numbers and Algebraic Points on Elliptic Surfaces with Base an Elliptic Curve. G. Grant, E. Manduchi, Duke Mathematical Journal (1998) Vol. 93, No.3, 479-486
  
• Root Numbers and Algebraic Points on Elliptic Surfaces with Base P¹, G. Grant, E. Manduchi, Duke Mathematical Journal (1997) Vol. 89, No.3, 413-422.
  
• Thesis: Galois PSL₂(F_q) extensions, Root Numbers and Elliptic Curves. (1995).