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Publications/Citing CTD

Contents

  1. Citing CTD
  2. Publications
  3. Presentations
  4. Related Publications from the MDIBL Center for Comparative Toxicology

Top Top of page Citing CTD

Please use the following citation for the Comparative Toxicogenomics Database site in your publications and presentations:

Davis AP, Murphy CG, Saraceni-Richards CA, Rosenstein MC, Wiegers TC, Mattingly CJ. Comparative Toxicogenomics Database: a knowledgebase and discovery tool for chemical–gene–disease networks. Nucleic Acids Res. 2009 Jan;37(Database issue):D786-92.

To cite specific data, use the following citation:

Curated [chemical–gene interactions|chemical–disease|gene–disease] data were retrieved from the Comparative Toxicogenomics Database (CTD), Mount Desert Island Biological Laboratory, Salisbury Cove, Maine. World Wide Web (URL: http://ctd.mdibl.org/). [Month, year (when you retrieved the data)].

Top Top of page Publications

  1. Davis AP, Murphy CG, Saraceni-Richards CA, Rosenstein MC, Wiegers TC, Hampton TH, Mattingly CJ. GeneComps and ChemComps: a new CTD metric to identify genes and chemicals with shared toxicogenomic profiles. Bioinformation. 2009 Oct 15;4(4):173-4. [PubMed:20198196]
  2. Wiegers TC, Davis AP, Cohen KB, Hirschman L, Mattingly CJ. Text mining and manual curation of chemical–gene–disease networks for the Comparative Toxicogenomics Database (CTD). BMC Bioinformatics. 2009 Oct 8;10(1):326. [PubMed:19814812]
  3. Gohlke JM, Thomas R, Zhang Y, Rosenstein MC, Davis AP, Murphy C, Becker KG, Mattingly CJ, Portier CJ. Genetic and environmental pathways to complex diseases. BMC Syst Biol. 2009 May 5;3(1):46. [PubMed:19416532]
  4. Mattingly CJ, Hampton T, Brothers K, Griffin NE, Planchart AJ. Perturbation of defense pathways by low-dose arsenic exposure in zebrafish embryos. Environ Health Perspect. 2009 Jun;117(6):981-7. [PubMed:19590694]
  5. Davis AP, Murphy CG, Saraceni-Richards CA, Rosenstein MC, Wiegers TC, Mattingly CJ. Comparative Toxicogenomics Database: a knowledgebase and discovery tool for chemical–gene–disease networks. Nucleic Acids Res. 2009 Jan;37(Database issue):D786-92. [PubMed:18782832]
  6. Mattingly CJ. Chemical databases for environmental health and clinical research. Toxicol Lett. 2009 Apr 10;186(1):62-5. [PubMed:18996453]
  7. Davis AP, Murphy CG, Rosenstein MC, Wiegers TC, Mattingly CJ. The Comparative Toxicogenomics Database facilitates identification and understanding of chemical–gene–disease associations: arsenic as a case study. BMC Med Genomics. 2008 Oct 9;1(1):48. [PubMed:18845002]
  8. Mattingly CJ, Colby GT, Rosenstein MC, Forrest JN, Boyer JL. The Comparative Toxicogenomics Database (CTD): a resource for comparative toxicological studies. J Exp Zoolog A Comp Exp Biol. 2006 Sep 1;305(9):689-92. [PubMed:16902965]
  9. Mattingly CJ, Rosenstein MC, Davis AP, Colby GT, Forrest JN, Boyer JL. The Comparative Toxicogenomics Database: a cross-species resource for building chemical–gene interaction networks. Toxicol Sci. 2006 Aug;92(2):587-95. [PubMed:16675512]
  10. Mattingly CJ, Colby GT, Rosenstein MC, Forrest JN, Boyer JL. Promoting comparative molecular studies in environmental health research: an overview of the comparative toxicogenomics database (CTD). Pharmacogenomics J. 2004;4(1):5-8. [PubMed:14735110]
  11. Mattingly CJ, Colby GT, Forrest JN, Boyer JL. The Comparative Toxicogenomics Database (CTD). Environ Health Perspect. 2003 May;111(6):793-5. [PubMed:12760826]

Top Top of page Presentations

  1. Wiegers TC, Murphy C, Saraceni-Richards CA, Rosenstein MC, Davis AP, Mattingly CJ. The Comparative Toxicogenomics Database (CTD) Text Mining Study. 3rd International Biocuration Conference. Berlin, Germany. Apr 2009.
  2. Mattingly CJ, Murphy C, Saraceni-Richards CA, Rosenstein MC, Wiegers TC, Davis AP. The Comparative Toxicogenomics Database (CTD): A discovery tool for identifying chemical–gene–disease networks. 48th Annual Society of Toxicology. Baltimore, MD, USA. Mar 2009.
  3. Mattingly CJ, Murphy C, Saraceni-Richards CA, Rosenstein MC, Wiegers TC, Davis AP. Using the Comparative Toxicogenomics Database (CTD) to identify chemical–gene–disease associations. Society of Experimental Toxicology and Chemistry. Tampa, FL, USA. Nov 2008.
  4. Mattingly, CJ. The Comparative Toxicogenomics Database. Annual environmental health sciences core centers meeting. Philadelphia, PA. Oct 2008.
  5. CJ Mattingly, Using the Comparative Toxicogenomics Database (CTD) to Explore Chemical–Gene–Disease Connections. University of Maine Graduate School of Biomedical Sciences Symposium. Orono, ME, USA. May 2008.
  6. Mattingly CJ, Davis AP, Rosenstein MC, Wiegers T, Forrest JN, Boyer JL. Using the Comparative Toxicogenomics Database to identify chemical–gene–disease associations: arsenic as a case study. 47th Annual Society of Toxicology Meeting. Seattle, WA, USA. Mar 2008.
  7. CJ Mattingly. The Comparative Toxicogenomics Database (CTD): Promoting understanding of chemical–gene–disease associations. NERC International Collaboration Initiative: Bioinformatics Workshop. Birmingham, UK. Mar 2008.
  8. Davis AP, Murphy C, Rosenstein MC, Wiegers T, Forrest JN, Boyer JL, Mattingly CJ. Curating the Comparative Toxicogenomics Database: a knowledge and discovery environment for chemical–gene–disease associations. Second International Biocuration Meeting. San Jose, CA, USA. Oct 2007. [Abstract] [Presentation]
  9. Mattingly, CJ. The Comparative Toxicogenomics Database: Promoting Understanding About the Mechanisms of Chemical Actions. Toxicology Division of the American Society for Pharmacology and Experimental Therapeutics (ASPET) “Toxicogenomics Approaches for Evaluating Drug and Chemical Toxicity” Symposium at the Experimental Biology Annual Meeting. Washington, DC, USA. Apr 2007.
  10. Davis AP, Mattingly CJ, Rosenstein MC, Wiegers T, Forrest JN, Boyer JL. The Comparative Toxicogenomics Database: connecting chemicals, genes, and diseases. Society of Toxicology. Charlotte, NC, USA. Mar 2007. [Abstract] [Poster]
  11. Davis AP, Mattingly CJ, Rosenstein MC, Forrest JN, Boyer JL. The Comparative Toxicogenomics Database: A Public Resource for Chemical–Gene and Chemical–Protein Interactions. EPA Science Forum 2006, U.S Environmental Protection Agency, Washington, DC, USA. May 2006.
  12. Mattingly CJ, Rosenstein MC, Davis AP, Colby GC, Forrest JN, Boyer JL. Comparative Toxicogenomics Database (CTD): Promoting Understanding of Chemical–Gene Interactions Keystone: The Molecular and Integrative Basis for Toxic Responses. Victoria, BC. May 2006.
  13. Mattingly CJ, Rosenstein MC, Davis AP, Forrest JN, Boyer JL. The Comparative Toxicogenomics Database (CTD). Society of Toxicology. San Diego, CA, USA. Mar 2006.
  14. Colby GT, Mattingly CJ, Rosenstein, MC, Forrest JN, Boyer JL. Data Integration in the Comparative Toxicogenomics Database (CTD). Annual meeting of the International Society for Computational Biology. Detroit, MI, USA. Jun 2005.
  15. Mattingly, CJ. Cross-Species Comparative Approaches to Understanding Chemical–Gene Interactions. 15th International Conference of Comparative Endocrinology. Boston, MA, USA. May 2005.
  16. Mattingly, CJ. Comparative Approaches to Understanding Gene–Chemical Interactions. Northland Chapter of the Society of Toxicology Meeting. Minneapolis, MN, USA. Apr 2005.
  17. Mattingly CJ, Colby GT, Rosenstein MC, Forrest JN, Boyer JL. The Comparative Toxicogenomics Database (CTD). Society of Toxicology. New Orleans, LA, USA. Mar 2005.
  18. Mattingly, CJ. The Comparative Toxicogenomics Database (CTD): Comparative Molecular Approaches to Environmental Health Research. American Chemical Society National Meeting. Philadelphia, PA, USA. Aug 2004.
  19. Mattingly, CJ. Comparative Approaches to Understanding Mechanisms of Toxicity: CTD. 2004 World Congress on In Vitro Biology. San Francisco, CA, USA. May 2004.
  20. Mattingly CJ, Colby GT, Rosenstein MC, Forrest JN, Boyer JL. The Comparative Toxicogenomics Database (CTD). Society of Toxicology. Salt Lake City, UT, USA. Mar 2004.

Top Top of page Related Publications from the MDIBL Center for Comparative Toxicology

  1. Ballatori N, Madejczyk MS. Transport of nonessential metals across mammalian cell membranes. Topics in Current Genetics. 2006;14:455-483.
  2. Ballatori N, et al. Retention of structural and functional polarity in cultured skate hepatocytes undergoing in vitro morphogenesis. Comp Biochem Physiol B Biochem Mol Biol. 2006 Jun;144(2):167-79. [PubMed:16567119]
  3. Boyer JL, et al. Upregulation of a basolateral FXR-dependent bile acid efflux transporter OSTalpha-OSTbeta in cholestasis in humans and rodents. Am J Physiol Gastrointest Liver Physiol. 2006 Jun;290(6):G1124-30. [PubMed:16423920]
  4. Cai SY, et al. The farnesoid X receptor FXRalpha/NR1H4 acquired ligand specificity for bile salts late in vertebrate evolution. Am J Physiol Regul Integr Comp Physiol. 2007 Sep;293(3):R1400-9. [PubMed:17567710]
  5. Congdon CB, et al. An evaluation of information content as a metric for the inference of putative conserved noncoding regions in DNA sequences using a genetic algorithms approach. IEEE/ACM Trans Comput Biol Bioinform. 2008 Jan-Mar;5(1):1-14. [PubMed:18245871]
  6. Congdon CB, et al. Preliminary Results for GAMI: A Genetic Algorithms Approach to Motif Inference. CIBCB. 2006:97-104.
  7. Congdon CB, et al. Towards Interactive Visualization for Exploring Conserved Motifs in Noncoding DNA Sequence. Proceedings of Frontiers in the Convergence of Bioscience and Information Technologies 2007. FBIT 2007 (IEEE Press).
  8. Duncan DE. Experimental Man: What One Man's Body Reveals about His Future, Your Health, and Our Toxic World. Wiley, John and Sons, March 2009.
  9. Forest D, et al. RNA expression in a cartilaginous fish cell line reveals ancient 3' noncoding regions highly conserved in vertebrates. Proc Natl Acad Sci USA. 2007 Jan 23;104(4):1224-9. [PubMed:17227856]
  10. Mattingly CJ, Calhoun JD, Planchart AJ. Preliminary investigations indicate that Crot and Abcb genes from the spiny dogfish (Squalus acanthias) are syntenic. Bull Mt Desert Isl Biol Lab Salisb Cove Maine. 2007;46.
  11. Parton A, et al. Cell and molecular biology of SAE, a cell line from the spiny dogfish shark, Squalus acanthias. Comp Biochem Physiol C Toxicol Pharmacol. 2007 Feb;145(1):111-9. [PubMed:16949345]
  12. Shaw JR, et al. Role of glucocorticoid receptor in acclimation of killifish (Fundulus heteroclitus) to seawater and effects of arsenic. Am J Physiol Regul Integr Comp Physiol. 2007 Feb;292(2):R1052-60. [PubMed:17038445]
  13. Stanton CR, et al. Arsenic inhibits CFTR-mediated chloride secretion by killifish (Fundulus heteroclitus) opercular membrane. Cell Physiol Biochem. 2006;17(5-6):269-78. [PubMed:16791002]
  14. Villalobos AR, Renfro JL. Trimethylamine oxide suppresses stress-induced alteration of organic anion transport in choroid plexus. J Exp Biol. 2007 Feb;210(Pt 3):541-52. [PubMed:17234624]
  15. Weber GJ, et al. Mercury and zinc differentially inhibit shark and human CFTR orthologues: involvement of shark cysteine 102. Am J Physiol Cell Physiol. 2006 Mar;290(3):C793-801. [PubMed:16236827]