Publications

  1. Davis AP, Wiegers TC, King BL, Wiegers J, Grondin CJ, Sciaky D, Johnson RJ, Mattingly CJ. 2016. Generating Gene Ontology-Disease Inferences to Explore Mechanisms of Human Disease at the Comparative Toxicogenomics Database. PLoS One 11:e0155530.10.1371/journal.pone.0155530 PMC:4865041.
  2. Grondin CJ, Davis AP, Wiegers TC, King BL, Wiegers JA, Reif DM, Hoppin JA, Mattingly CJ. 2016. Advancing Exposure Science through Chemical Data Curation and Integration in the Comparative Toxicogenomics Database. Environ Health Perspect.10.1289/EHP174
  3. Li J, Sun Y, Johnson RJ, Sciaky D, Wei CH, Leaman R, Davis AP, Mattingly CJ, Wiegers TC, Lu Z. 2016. BioCreative V CDR task corpus: a resource for chemical disease relation extraction. Database (Oxford) 2016.10.1093/database/baw068 PMC:4860626.
  4. Manrai AK, Cui Y, Bushel PR, Hall M, Karakitsios S, Mattingly CJ, Ritchie M, Schmitt C, Sarigiannis DA, Thomas DC, Wishart D, Balshaw DM, Patel CJ. 2016. Informatics and Data Analytics to Support Exposome-Based Discovery for Public Health. Annual review of public health.10.1146/annurev-publhealth-082516-012737
  5. Mattingly CJ, Boyles R, Lawler CP, Haugen AC, Dearry A, Haendel M. 2016. Laying a Community-Based Foundation for Data-Driven Semantic Standards in Environmental Health Sciences. Environ Health Perspect.10.1289/ehp.1510438
  6. Pelletier D, Wiegers TC, Enayetallah A, Kibbey C, Gosink M, Koza-Taylor P, Mattingly CJ, Lawton M. 2016. ToxEvaluator: an integrated computational platform to aid the interpretation of toxicology study-related findings. Database (Oxford) 2016.10.1093/database/baw062 PMC:4860628.
  7. Planchart A, Mattingly CJ, Allen D, Ceger P, Casey W, Hinton D, Kanungo J, Kullman SW, Tal T, Bondesson M, Burgess SM, Sullivan C, Kim C, Behl M, Padilla S, Reif DM, Tanguay RL, Hamm J. 2016. Advancing toxicology research using in vivo high throughput toxicology with small fish models. ALTEX 33:435-452.10.14573/altex.1601281
  8. Watson AT, Planchart A, Mattingly CJ, Winkler C, Reif DM, Kullman SW. 2016. Embryonic Exposure to TCDD Impacts Osteogenesis of the Axial Skeleton in Japanese medaka, Oryzias latipes. Toxicol Sci.10.1093/toxsci/kfw229
  9. Wei CH, Peng Y, Leaman R, Davis AP, Mattingly CJ, Li J, Wiegers TC, Lu Z. 2016. Assessing the state of the art in biomedical relation extraction: overview of the BioCreative V chemical-disease relation (CDR) task. Database (Oxford) 2016.10.1093/database/baw032 PMC:4799720.
  10. Davis AP, Grondin CJ, Lennon-Hopkins K, Saraceni-Richards C, Sciaky D, King BL, Wiegers TC, Mattingly CJ. 2015. The Comparative Toxicogenomics Database’s 10th year anniversary: update 2015. Nucleic Acids Res 43:D914-920.10.1093/nar/gku935 PMC:4384013.
  11. Mattingly CJ. 2015. Integrating literature-based curated data to predict mechanisms of toxicity. In: OpenTox. Baltimore, MD.
  12. Comeau DC, Batista-Navarro RT, Dai HJ, Dogan RI, Yepes AJ, Khare R, Lu Z, Marques H, Mattingly CJ, Neves M, Peng Y, Rak R, Rinaldi F, Tsai RT, Verspoor K, Wiegers TC, Wu CH, Wilbur WJ. 2014. BioC interoperability track overview. Database (Oxford) 2014.10.1093/database/bau053 PMC:4074764.
  13. Wiegers TC, Davis AP, Mattingly CJ. 2014. Web services-based text-mining demonstrates broad impacts for interoperability and process simplification. Database (Oxford) 2014.10.1093/database/bau050
  14. Davis AP, Murphy CG, Johnson R, Lay JM, Lennon-Hopkins K, Saraceni-Richards C, Sciaky D, King BL, Rosenstein MC, Wiegers TC, Mattingly CJ. 2013a. The Comparative Toxicogenomics Database: update 2013. Nucleic Acids Res 41:D1104-1114.10.1093/nar/gks994 PMC:3531134.
  15. Davis AP, Wiegers TC, Johnson RJ, Lay JM, Lennon-Hopkins K, Saraceni-Richards C, Sciaky D, Murphy CG, Mattingly CJ. 2013b. Text mining effectively scores and ranks the literature for improving chemical-gene-disease curation at the comparative toxicogenomics database. PLoS One 8:e58201.10.1371/journal.pone.0058201 PMC:3629079.
  16. Davis AP, Wiegers TC, Roberts PM, King BL, Lay JM, Lennon-Hopkins K, Sciaky D, Johnson R, Keating H, Greene N, Hernandez R, McConnell KJ, Enayetallah AE, Mattingly CJ. 2013c. A CTD-Pfizer collaboration: manual curation of 88,000 scientific articles text mined for drug-disease and drug-phenotype interactions. Database (Oxford) 2013:bat080.10.1093/database/bat080 PMC:3842776.
  17. Bello SM, Richardson JE, Davis AP, Wiegers TC, Mattingly CJ, Dolan ME, Smith CL, Blake JA, Eppig JT. 2012. Disease model curation improvements at Mouse Genome Informatics. Database (Oxford) 2012:bar063.10.1093/database/bar063 PMC:3308153.
  18. Cheng KC, Hinton DE, Mattingly CJ, Planchart A. 2012. Aquatic models, genomics and chemical risk management. Comparative biochemistry and physiology Toxicology & pharmacology : CBP 155:169-173.10.1016/j.cbpc.2011.06.009
  19. Davis AP, Johnson RJ, Lennon-Hopkins K, Sciaky D, Rosenstein MC, Wiegers TC, Mattingly CJ. 2012a. Targeted journal curation as a method to improve data currency at the Comparative Toxicogenomics Database. Database (Oxford) 2012:bas051.10.1093/database/bas051 PMC:3515863.
  20. Davis AP, Wiegers TC, Rosenstein MC, Mattingly CJ. 2012b. MEDIC: a practical disease vocabulary used at the Comparative Toxicogenomics Database. Database (Oxford) 2012:bar065.10.1093/database/bar065 PMC:3308155.
  21. King BL, Davis AP, Rosenstein MC, Wiegers TC, Mattingly CJ. 2012. Ranking transitive chemical-disease inferences using local network topology in the comparative toxicogenomics database. PLoS One 7:e46524.10.1371/journal.pone.0046524 PMC:3492369.
  22. Mattingly CJ, McKone TE, Callahan MA, Blake JA, Hubal EA. 2012. Providing the missing link: the exposure science ontology ExO. Environ Sci Technol 46:3046-3053.10.1021/es2033857 PMC:3314380.
  23. Wiegers TC, Davis AP, Mattingly CJ. 2012. Collaborative biocuration–text-mining development task for document prioritization for curation. Database (Oxford) 2012:bas037.10.1093/database/bas037 PMC:3504477.
  24. Wu CH, Arighi CN, Cohen KB, Hirschman L, Krallinger M, Lu Z, Mattingly C, Valencia A, Wiegers TC, John Wilbur W. 2012. BioCreative-2012 virtual issue. Database (Oxford) 2012:bas049.10.1093/database/bas049 PMC:3514749.
  25. Davis AP, King BL, Mockus S, Murphy CG, Saraceni-Richards C, Rosenstein M, Wiegers T, Mattingly CJ. 2011a. The Comparative Toxicogenomics Database: update 2011. Nucleic Acids Res 39:D1067-1072.10.1093/nar/gkq813 PMC:3013756.
  26. Davis AP, Rosenstein MC, Wiegers TC, Mattingly CJ. 2011b. DiseaseComps: a metric that discovers similar diseases based upon common toxicogenomic profiles at CTD. Bioinformation 7:154-156 PMC:3220301.
  27. Davis AP, Wiegers TC, Murphy CG, Mattingly CJ. 2011c. The curation paradigm and application tool used for manual curation of the scientific literature at the Comparative Toxicogenomics Database. Database (Oxford) 2011:bar034.bar034 [pii] 1093/database/bar034 PMC:3176677.
  28. Mattingly CJ. 2010. Understanding environment-disease connections: An introduction to the Comparative Toxicogenomics Database (CTD). Nature Pathway Interaction Database doi:10.1038/pid.2011.2
  29. Planchart A, Mattingly CJ. 2010. 2,3,7,8-TCDD Upregulates FoxQ1b in Zebrafish Jaw Primordium Chemical research in toxicology 23:480-487
  30. Davis AP, Murphy CG, Saraceni-Richards CA, Rosenstein MC, Wiegers TC, Hampton TH, Mattingly CJ. 2009a. GeneComps and ChemComps: a new CTD metric to identify genes and chemicals with shared toxicogenomic profiles. Bioinformation 4:173-174 PMC:2825594.
  31. Davis AP, Murphy CG, Saraceni-Richards CA, Rosenstein MC, Wiegers TC, Mattingly CJ. 2009b. Comparative Toxicogenomics Database: a knowledgebase and discovery tool for chemical-gene-disease networks. Nucleic Acids Res 37:D786-792.gkn580 [pii] 1093/nar/gkn580 PMC:2686584.
  32. Gohlke JM, Thomas R, Zhang Y, Rosenstein MC, Davis AP, Murphy C, Becker KG, Mattingly CJ, Portier CJ. 2009. Genetic and environmental pathways to complex diseases. BMC Syst Biol 3:46.1752-0509-3-46 [pii] 1186/1752-0509-3-46 PMC:2680807.
  33. Mattingly CJ. 2009. Chemical databases for environmental health and clinical research. Toxicology letters 186:62-65
  34. Mattingly CJ, Hampton TH, Brothers KM, Griffin NE, Planchart A. 2009. Perturbation of defense pathways by low-dose arsenic exposure in zebrafish embryos. Environ Health Perspect 117:981-987.10.1289/ehp.0900555 PMC:2702417.
  35. Wiegers TC, Davis AP, Cohen KB, Hirschman L, Mattingly CJ. 2009. Text mining and manual curation of chemical-gene-disease networks for the comparative toxicogenomics database (CTD). BMC Bioinformatics 10:326.1471-2105-10-326 [pii] 1186/1471-2105-10-326 PMC:2768719.
  36. Davis AP, Murphy CG, Rosenstein MC, Wiegers TC, Mattingly CJ. 2008. The Comparative Toxicogenomics Database facilitates identification and understanding of chemical-gene-disease associations: arsenic as a case study. BMC Med Genomics 1:48.1755-8794-1-48 [pii] 1186/1755-8794-1-48 PMC:2576347.
  37. Congdon CB, Aman J, Nava GM, Gaskins HR, Mattingly CM. 2007a. An evaluation of information content as a metric for the inference of   putative conserved non-coding regions in DNA sequence using a genetic algorithms approach. IEEE/ACM TCBB, 13 June
  38. Congdon CB, Gaskins HR, Nava GM, Mattingly CM. 2007b. Towards Interactive Visualization for Exploring Conserved Motifs in Noncoding DNA Sequence. . Proceedings of Frontiers in the Convergence of Bioscience and Information Technologies FBIT 2007
  39. Congdon CB, FIzer C, Smith NW, Gaskins HR, Aman J, Nava GM, Mattingly C. 2006. Preliminary Results for GAMI: A Genetic Algorithms Approach to Motif Inference. CIBCB:97-104
  40. Mattingly CJ, Rosenstein MC, Colby GT, Forrest JN, Jr., Boyer JL. 2006a. The Comparative Toxicogenomics Database (CTD): a resource for comparative toxicological studies. J Exp Zoolog A Comp Exp Biol 305:689-692
  41. Mattingly CJ, Rosenstein MC, Davis AP, Colby GT, Forrest JN, Jr., Boyer JL. 2006b. The comparative toxicogenomics database: a cross-species resource for building chemical-gene interaction networks. Toxicol Sci 92:587-595
  42. Barnes D, Mattingly C, Parton A, Dowell L, Bayne C, Forrest JN. 2005. Marine organism cell biology and regulatory sequence discovery in comparative functional genomics. Cytotechnology 43:123-137
  43. Mattingly C, Parton A, Dowell L, Rafferty J, Barnes D. 2004. Cell and Molecular Biology of Marine Elasmobranchs: Squalus acanthias and Raja erinacea. Zebrafish 1
  44. Mattingly CJ, Colby GT, Rosenstein MC, Forrest JN, Jr., Boyer JL. 2004. Promoting comparative molecular studies in environmental health research: an overview of the comparative toxicogenomics database (CTD). The pharmacogenomics journal 4:5-8
  45. Mattingly CJ, Colby GT, Forrest JN, Boyer JL. 2003. The Comparative Toxicogenomics Database (CTD). Environ Health Perspect 111:793-795
  46. Mattingly CJ, McLachlan JA, Toscano WA, Jr. 2001. Green fluorescent protein (GFP) as a marker of aryl hydrocarbon receptor (AhR) function in developing zebrafish (Danio rerio). Environ Health Perspect 109:845-849
  47. Mattingly CJ, Toscano WA. 2001. Posttranscriptional silencing of cytochrome P4501A1 (CYP1A1) during zebrafish (Danio rerio) development. Developmental dynamics : an official publication of the American Association of Anatomists 222:645-654
  48. Ricci MS, Toscano DG, Mattingly CJ, Toscano WA, Jr. 1999. Estrogen receptor reduces CYP1A1 induction in cultured human endometrial cells. The Journal of biological chemistry 274:3430-3438.