G R Grant

Summary

Affiliation: University of Pennsylvania
Country: USA

Publications

  1. ncbi request reprint A practical false discovery rate approach to identifying patterns of differential expression in microarray data
    Gregory R Grant
    Center for Bioinformatics, University of Pennsylvania, 1429 Blockley Hall, 423 Guardian Drive, Philadelphia, PA 19104 6021, USA
    Bioinformatics 21:2684-90. 2005
  2. ncbi request reprint Significance testing for direct identity-by-descent mapping
    G R Grant
    Center for Bioinformatics, University of Pennsylvania, Philadelphia 19104 6021, USA
    Ann Hum Genet 63:441-54. 1999
  3. pmc Comparative analysis of RNA-Seq alignment algorithms and the RNA-Seq unified mapper (RUM)
    Gregory R Grant
    Penn Center for Bioinformatics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
    Bioinformatics 27:2518-28. 2011
  4. ncbi request reprint RAD and the RAD Study-Annotator: an approach to collection, organization and exchange of all relevant information for high-throughput gene expression studies
    E Manduchi
    Center for Bioinformatics, University of Pennsylvania, 14th Floor Blockley Hall, 423 Guardian Drive, Philadelphia, PA 19104 6021, USA
    Bioinformatics 20:452-9. 2004
  5. ncbi request reprint Maintaining data integrity in microarray data management
    G R Grant
    Penn Center for Bioinformatics PCBI, University of Pennsylvania, 1429 Blockley Hall, 423 Guardian Drive, Philadelphia, Pennsylvania 19104 6021, USA
    Biotechnol Bioeng 84:795-800. 2003
  6. ncbi request reprint Generation of patterns from gene expression data by assigning confidence to differentially expressed genes
    E Manduchi
    Center for Bioinformatics, University of Pennsylvania, Philadelphia, PA 19104, USA
    Bioinformatics 16:685-98. 2000
  7. pmc Prelesional arterial endothelial phenotypes in hypercholesterolemia: universal ABCA1 upregulation contrasts with region-specific gene expression in vivo
    Mete Civelek
    Institute for Medicine and Engineering, University of Pennsylvania, Philadelphia, PA 19104, USA
    Am J Physiol Heart Circ Physiol 298:H163-70. 2010
  8. doi request reprint A flexible two-stage procedure for identifying gene sets that are differentially expressed
    Ruth Heller
    Department of Statistics, Wharton School, University of Pennsylvania, Philadelphia, PA 19104 6340, USA
    Bioinformatics 25:1019-25. 2009
  9. ncbi request reprint Regional determinants of arterial endothelial phenotype dominate the impact of gender or short-term exposure to a high-fat diet
    Anthony G Passerini
    Institute for Medicine and Engineering, University of Pennsylvania, Philadelphia, PA, USA
    Biochem Biophys Res Commun 332:142-8. 2005
  10. ncbi request reprint Comparison of different labeling methods for two-channel high-density microarray experiments
    Elisabetta Manduchi
    Center for Bioinformatics, Univ of Pennsylvania, Philadelphia, Pennsylvania 19104 6021, USA
    Physiol Genomics 10:169-79. 2002

Research Grants

Collaborators

Detail Information

Publications20

  1. ncbi request reprint A practical false discovery rate approach to identifying patterns of differential expression in microarray data
    Gregory R Grant
    Center for Bioinformatics, University of Pennsylvania, 1429 Blockley Hall, 423 Guardian Drive, Philadelphia, PA 19104 6021, USA
    Bioinformatics 21:2684-90. 2005
    ..For example, the log transform can both help and hurt at the same time, depending on the gene. We examine issues surrounding the SAM 'fudge factor' parameter, and how to handle these issues by optimizing with respect to power...
  2. ncbi request reprint Significance testing for direct identity-by-descent mapping
    G R Grant
    Center for Bioinformatics, University of Pennsylvania, Philadelphia 19104 6021, USA
    Ann Hum Genet 63:441-54. 1999
    ..We give examples that we have calculated by implementing this method, including an application to real data...
  3. pmc Comparative analysis of RNA-Seq alignment algorithms and the RNA-Seq unified mapper (RUM)
    Gregory R Grant
    Penn Center for Bioinformatics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
    Bioinformatics 27:2518-28. 2011
    ..The exercise to rigorously compare all viable published RNA-Seq algorithms has not been performed previously...
  4. ncbi request reprint RAD and the RAD Study-Annotator: an approach to collection, organization and exchange of all relevant information for high-throughput gene expression studies
    E Manduchi
    Center for Bioinformatics, University of Pennsylvania, 14th Floor Blockley Hall, 423 Guardian Drive, Philadelphia, PA 19104 6021, USA
    Bioinformatics 20:452-9. 2004
    ..This infrastructure enables a large variety of queries that incorporate visualization and analysis tools and have been tailored to serve the specific needs of projects focusing on particular organisms or biological systems...
  5. ncbi request reprint Maintaining data integrity in microarray data management
    G R Grant
    Penn Center for Bioinformatics PCBI, University of Pennsylvania, 1429 Blockley Hall, 423 Guardian Drive, Philadelphia, Pennsylvania 19104 6021, USA
    Biotechnol Bioeng 84:795-800. 2003
    ..Finally, we present some preliminary guidelines and some specific approaches that we believe should be the focus of future research...
  6. ncbi request reprint Generation of patterns from gene expression data by assigning confidence to differentially expressed genes
    E Manduchi
    Center for Bioinformatics, University of Pennsylvania, Philadelphia, PA 19104, USA
    Bioinformatics 16:685-98. 2000
    ..Satisfactory results can be obtained using this method with as few as two replicates...
  7. pmc Prelesional arterial endothelial phenotypes in hypercholesterolemia: universal ABCA1 upregulation contrasts with region-specific gene expression in vivo
    Mete Civelek
    Institute for Medicine and Engineering, University of Pennsylvania, Philadelphia, PA 19104, USA
    Am J Physiol Heart Circ Physiol 298:H163-70. 2010
    ..Both region-specific and ubiquitous (ABCA1) phenotype changes were identified as early prelesional responses of the endothelium to hypercholesterolemia...
  8. doi request reprint A flexible two-stage procedure for identifying gene sets that are differentially expressed
    Ruth Heller
    Department of Statistics, Wharton School, University of Pennsylvania, Philadelphia, PA 19104 6340, USA
    Bioinformatics 25:1019-25. 2009
    ..These tests may be powerful at detecting subtle changes in expression, but findings at the gene set level need to be examined further to understand whether they are informative and if so how...
  9. ncbi request reprint Regional determinants of arterial endothelial phenotype dominate the impact of gender or short-term exposure to a high-fat diet
    Anthony G Passerini
    Institute for Medicine and Engineering, University of Pennsylvania, Philadelphia, PA, USA
    Biochem Biophys Res Commun 332:142-8. 2005
    ..The results implicate regional hemodynamics as a predominant epigenetic determinant of endothelial phenotypic heterogeneity underlying atherosusceptibility in vivo...
  10. ncbi request reprint Comparison of different labeling methods for two-channel high-density microarray experiments
    Elisabetta Manduchi
    Center for Bioinformatics, Univ of Pennsylvania, Philadelphia, Pennsylvania 19104 6021, USA
    Physiol Genomics 10:169-79. 2002
    ..These findings are helping to guide our decisions on what labeling method to use for subsequent studies, based on the purpose of a specific study and its limitations in terms of available material...
  11. pmc Spatial heterogeneity of endothelial phenotypes correlates with side-specific vulnerability to calcification in normal porcine aortic valves
    Craig A Simmons
    Institute for Medicine and Engineering, University of Pennsylvania, Philadelphia PA 19104, USA
    Circ Res 96:792-9. 2005
    ..These data implicate the endothelium in regulating valvular calcification and suggest that spatial heterogeneity of valvular endothelial phenotypes may contribute to the focal susceptibility for lesion development...
  12. pmc Assessing the significance of conserved genomic aberrations using high resolution genomic microarrays
    Mitchell Guttman
    Penn Center for Bioinformatics, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
    PLoS Genet 3:e143. 2007
    ..The algorithm has been fully implemented and tested and is freely available as a Java application at http://www.cbil.upenn.edu/MSA...
  13. ncbi request reprint Analysis and management of microarray gene expression data
    Gregory R Grant
    University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, USA
    Curr Protoc Mol Biol . 2007
    ....
  14. pmc Coexisting proinflammatory and antioxidative endothelial transcription profiles in a disturbed flow region of the adult porcine aorta
    Anthony G Passerini
    Institute for Medicine and Engineering, Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
    Proc Natl Acad Sci U S A 101:2482-7. 2004
    ..The introduction of additional risk factors may shift this balance to favor lesion development...
  15. pmc Hypercholesterolemia induces side-specific phenotypic changes and peroxisome proliferator-activated receptor-gamma pathway activation in swine aortic valve endothelium
    MARIE A GUERRATY
    Institute for Medicine and Engineering, University of Pennsylvania, Philadelphia 19104, USA
    Arterioscler Thromb Vasc Biol 30:225-31. 2010
    ..Side-specific global gene expression can address endothelial phenotype balance in early aortic valve sclerosis...
  16. pmc Human microRNA-155 on chromosome 21 differentially interacts with its polymorphic target in the AGTR1 3' untranslated region: a mechanism for functional single-nucleotide polymorphisms related to phenotypes
    Praveen Sethupathy
    Department of Genetics, School of Medicine, University of Pennsylvania, PA, USA, and University Hospitals of Geneva, Switzerland
    Am J Hum Genet 81:405-13. 2007
    ..Indeed, we have shown in fibroblasts from monozygotic twins discordant for trisomy 21 that levels of AGTR1 protein are lower in trisomy 21...
  17. pmc PlasmoDB: the Plasmodium genome resource. A database integrating experimental and computational data
    Amit Bahl
    Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
    Nucleic Acids Res 31:212-5. 2003
    ..The software used to develop PlasmoDB has been used to create a second Apicomplexan parasite genome database, ToxoDB (http://ToxoDB.org)...
  18. pmc PlasmoDB: the Plasmodium genome resource. An integrated database providing tools for accessing, analyzing and mapping expression and sequence data (both finished and unfinished)
    Amit Bahl
    Department of Biology, University of Pennsylvania, 415 South University Avenue, Philadelphia, PA 19104 6018, USA
    Nucleic Acids Res 30:87-90. 2002
    ..g. by malaria researchers working in the field). The goal of PlasmoDB is to enhance utilization of the vast quantities of data emerging from genome-scale projects by the global malaria research community...
  19. ncbi request reprint Fidelity and enhanced sensitivity of differential transcription profiles following linear amplification of nanogram amounts of endothelial mRNA
    Denise C Polacek
    Institute for Medicine and Engineering, University of Pennsylvania, Philadelphia 19104, USA
    Physiol Genomics 13:147-56. 2003
    ....
  20. pmc STAC: A method for testing the significance of DNA copy number aberrations across multiple array-CGH experiments
    Sharon J Diskin
    Division of Oncology, Children s Hospital of Philadelphia, Pennsylvania 19104, USA
    Genome Res 16:1149-58. 2006
    ..We conclude that STAC is a powerful tool for identifying nonrandom genomic amplifications and deletions across multiple experiments. A Java version of STAC is freely available for download at http://cbil.upenn.edu/STAC...

Research Grants1

  1. MENTORED QUANTITATIVE RESEARCH CAREER DEVELOPMENT AWARD
    Gregory Grant; Fiscal Year: 2005
    ..4) To complete a six-month lab rotation, the exact details of which are still to be worked out. This has been informally arranged with Dr. Vivian Cheung (Children's Hospital of Philadelphia). ..