Davis AP, Wiegers TC, Johnson RJ, Sciaky D, Wiegers J, Mattingly CJ.
Comparative Toxicogenomics Database (CTD): update 2023. Nucleic Acids Res. 2023
Jan 6;51(D1):D1257-D1262. doi: 10.1093/nar/gkac833. PMID: 36169237; PMCID:
PMC9825590.
Grondin CJ, Davis AP, Wiegers JA, Wiegers TC, Sciaky D, Johnson RJ, Mattingly
CJ. Predicting molecular mechanisms, pathways, and health outcomes induced by
Juul e-cigarette aerosol chemicals using the Comparative Toxicogenomics
Database. Curr Res Toxicol. 2021 Aug 5;2:272-281. doi:
10.1016/j.crtox.2021.08.001. PMID: 34458863; PMCID: PMC8379377.
Pinkhasova DV, Jameson LE, Conrow KD, Simeone MP, Davis AP, Wiegers TC,
Mattingly CJ, Leung MCK. Regulatory Status of Pesticide Residues in Cannabis:
Implications to Medical Use in Neurological Diseases. Curr Res Toxicol.
2021;2:140-148. doi: 10.1016/j.crtox.2021.02.007. Epub 2021 Mar 1. PMID:
34308371; PMCID: PMC8296824.
Davis AP, Wiegers TC, Wiegers J, Grondin CJ, Johnson RJ, Sciaky D, Mattingly
CJ. CTD Anatomy: analyzing chemical-induced phenotypes and exposures from an
anatomical perspective, with implications for environmental health studies. Curr
Res Toxicol. 2021;2:128-139. doi: 10.1016/j.crtox.2021.03.001. Epub 2021 Mar 5.
PMID: 33768211; PMCID: PMC7990325.
Davis AP, Wiegers TC, Grondin CJ, Johnson RJ, Sciaky D, Wiegers J, Mattingly
CJ. Leveraging the Comparative Toxicogenomics Database to Fill in Knowledge Gaps for Environmental Health: A Test Case for Air Pollution-induced Cardiovascular
Disease. Toxicol Sci. 2020 Oct 1;177(2):392-404. doi: 10.1093/toxsci/kfaa113.
PMID: 32663284; PMCID: PMC7548289.
Hollander JA, Cory-Slechta DA, Jacka FN, Szabo ST, Guilarte TR, Bilbo SD,
Mattingly CJ, Moy SS, Haroon E, Hornig M, Levin ED, Pletnikov MV, Zehr JL,
McAllister KA, Dzierlenga AL, Garton AE, Lawler CP, Ladd-Acosta C. Beyond the
looking glass: recent advances in understanding the impact of environmental
exposures on neuropsychiatric disease. Neuropsychopharmacology. 2020
Jun;45(7):1086-1096. doi: 10.1038/s41386-020-0648-5. Epub 2020 Feb 28. PMID:
32109936; PMCID: PMC7234981.
House JS, Hall J, Park SS, Planchart A, Money E, Maguire RL, Huang Z,
Mattingly CJ, Skaar D, Tzeng JY, Darrah TH, Vengosh A, Murphy SK, Jirtle RL,
Hoyo C. Cadmium exposure and MEG3 methylation differences between Whites and African Americans in the NEST Cohort. Environ Epigenet. 2019 Aug
29;5(3):dvz014. doi: 10.1093/eep/dvz014. PMID: 31528362; PMCID: PMC6736358.
Kosnik MB, Planchart A, Marvel SW, Reif DM, Mattingly CJ. Integration of
curated and high-throughput screening data to elucidate environmental influences
on disease pathways. Comput Toxicol. 2019 Nov;12:100094. doi:
10.1016/j.comtox.2019.100094. Epub 2019 Jun 27. PMID: 31453412; PMCID:
PMC6709694.
Davis AP, Wiegers J, Wiegers TC, Mattingly CJ. Public data sources to
support systems toxicology applications. Curr Opin Toxicol. 2019 Aug;16:17-24.
doi: 10.1016/j.cotox.2019.03.002. Epub 2019 Mar 11. PMID: 33604492; PMCID:
PMC7889036.
Davis AP, Grondin CJ, Johnson RJ, Sciaky D, McMorran R, Wiegers J, Wiegers
TC, Mattingly CJ. The Comparative Toxicogenomics Database: update 2019. Nucleic Acids Res. 2019 Jan 8;47(D1):D948-D954. doi: 10.1093/nar/gky868. PMID: 30247620; PMCID: PMC6323936.
Davis AP, Wiegers TC, Wiegers J, Johnson RJ, Sciaky D, Grondin CJ, Mattingly
CJ. Chemical-Induced Phenotypes at CTD Help Inform the Predisease State and
Construct Adverse Outcome Pathways. Toxicol Sci. 2018 Sep 1;165(1):145-156. doi:10.1093/toxsci/kfy131. PMID: 29846728; PMCID: PMC6111787.
Green AJ, Hoyo C, Mattingly CJ, Luo Y, Tzeng JY, Murphy SK, Buchwalter DB,
Planchart A. Cadmium exposure increases the risk of juvenile obesity: a human
and zebrafish comparative study. Int J Obes (Lond). 2018 Jul;42(7):1285-1295.
doi: 10.1038/s41366-018-0036-y. Epub 2018 Feb 20. PMID: 29511319; PMCID:
PMC6054604.
Planchart A, Green A, Hoyo C, Mattingly CJ. Heavy Metal Exposure and
Metabolic Syndrome: Evidence from Human and Model System Studies. Curr Environ Health Rep. 2018 Mar;5(1):110-124. doi: 10.1007/s40572-018-0182-3. PMID:29460222; PMCID: PMC6053628.
Grondin CJ, Davis AP, Wiegers TC, Wiegers JA, Mattingly CJ. Accessing an
Expanded Exposure Science Module at the Comparative Toxicogenomics Database.
Environ Health Perspect. 2018 Jan 18;126(1):014501. doi: 10.1289/EHP2873. PMID:29351546; PMCID: PMC6014688.
Watson AT, Planchart A, Mattingly CJ, Winkler C, Reif DM, Kullman SW. From
the Cover: Embryonic Exposure to TCDD Impacts Osteogenesis of the Axial Skeleton in Japanese medaka, Oryzias latipes. Toxicol Sci. 2017 Feb;155(2):485-496. doi:10.1093/toxsci/kfw229. Epub 2016 Nov 15. PMID: 28077779; PMCID: PMC5291214.
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.
Informatics and Data Analytics to Support Exposome-Based Discovery for Public
Health. Annu Rev Public Health. 2017 Mar 20;38:279-294. doi: 10.1146/annurev-
publhealth-082516-012737. Epub 2016 Dec 23. PMID: 28068484; PMCID: PMC5774331.
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. Advancing toxicology research using in vivo high
throughput toxicology with small fish models. ALTEX. 2016;33(4):435-452. doi:
10.14573/altex.1601281. Epub 2016 Jun 21. PMID: 27328013; PMCID: PMC5270630.
Davis AP, Grondin CJ, Johnson RJ, Sciaky D, King BL, McMorran R, Wiegers J,
Wiegers TC, Mattingly CJ. The Comparative Toxicogenomics Database: update 2017.Nucleic Acids Res. 2017 Jan 4;45(D1):D972-D978. doi: 10.1093/nar/gkw838. Epub 2016 Sep 19. PMID: 27651457; PMCID: PMC5210612.
Davis AP, Wiegers TC, King BL, Wiegers J, Grondin CJ, Sciaky D, Johnson RJ,
Mattingly CJ. Generating Gene Ontology-Disease Inferences to Explore Mechanisms
of Human Disease at the Comparative Toxicogenomics Database. PLoS One. 2016 May12;11(5):e0155530. doi: 10.1371/journal.pone.0155530. PMID: 27171405; PMCID:PMC4865041.
Grondin CJ, Davis AP, Wiegers TC, King BL, Wiegers JA, Reif DM, Hoppin JA,
Mattingly CJ. Advancing Exposure Science through Chemical Data Curation and
Integration in the Comparative Toxicogenomics Database. Environ Health Perspect.
2016 Oct;124(10):1592-1599. doi: 10.1289/EHP174. Epub 2016 May 12. PMID:
27170236; PMCID: PMC5047769.
Li J, Sun Y, Johnson RJ, Sciaky D, Wei CH, Leaman R, Davis AP, Mattingly CJ,
Wiegers TC, Lu Z. BioCreative V CDR task corpus: a resource for chemical disease
relation extraction. Database (Oxford). 2016 May 9;2016:baw068. doi:
10.1093/database/baw068. PMID: 27161011; PMCID: PMC4860626.
Pelletier D, Wiegers TC, Enayetallah A, Kibbey C, Gosink M, Koza-Taylor P,
Mattingly CJ, Lawton M. ToxEvaluator: an integrated computational platform to
aid the interpretation of toxicology study-related findings. Database (Oxford).
2016 May 9;2016:baw062. doi: 10.1093/database/baw062. PMID: 27161010; PMCID: PMC4860628.
Wei CH, Peng Y, Leaman R, Davis AP, Mattingly CJ, Li J, Wiegers TC, Lu Z.
Assessing the state of the art in biomedical relation extraction: overview of
the BioCreative V chemical-disease relation (CDR) task. Database (Oxford). 2016
Mar 19;2016:baw032. doi: 10.1093/database/baw032. PMID: 26994911; PMCID:
PMC4799720.
Mattingly CJ, Boyles R, Lawler CP, Haugen AC, Dearry A, Haendel M. Laying a
Community-Based Foundation for Data-Driven Semantic Standards in Environmental
Health Sciences. Environ Health Perspect. 2016 Aug;124(8):1136-40. doi:
10.1289/ehp.1510438. Epub 2016 Feb 12. PMID: 26871594; PMCID: PMC4977056.
Davis AP, Grondin CJ, Lennon-Hopkins K, Saraceni-Richards C, Sciaky D, King
BL, Wiegers TC, Mattingly CJ. The Comparative Toxicogenomics Database’s 10th
year anniversary: update 2015. Nucleic Acids Res. 2015 Jan;43(Database
issue):D914-20. doi: 10.1093/nar/gku935. Epub 2014 Oct 17. PMID: 25326323;
PMCID: PMC4384013.
Comeau DC, Batista-Navarro RT, Dai HJ, Doğan 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. BioC interoperability track overview. Database
(Oxford). 2014 Jun 30;2014:bau053. doi: 10.1093/database/bau053. PMID: 24980129; PMCID: PMC4074764.
Wiegers TC, Davis AP, Mattingly CJ. Web services-based text-mining
demonstrates broad impacts for interoperability and process simplification.
Database (Oxford). 2014 Jun 10;2014:bau050. doi: 10.1093/database/bau050. PMID: 24919658; PMCID: PMC4207221.
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. A CTD-Pfizer collaboration: manual curation of 88,000 scientific
articles text mined for drug-disease and drug-phenotype interactions. Database
(Oxford). 2013 Nov 28;2013:bat080. doi: 10.1093/database/bat080. PMID: 24288140; PMCID: PMC3842776.
Davis AP, Wiegers TC, Johnson RJ, Lay JM, Lennon-Hopkins K, Saraceni-
Richards C, Sciaky D, Murphy CG, Mattingly CJ. Text mining effectively scores
and ranks the literature for improving chemical-gene-disease curation at the
comparative toxicogenomics database. PLoS One. 2013 Apr 17;8(4):e58201. doi:
10.1371/journal.pone.0058201. PMID: 23613709; PMCID: PMC3629079.
Davis AP, Johnson RJ, Lennon-Hopkins K, Sciaky D, Rosenstein MC, Wiegers TC,
Mattingly CJ. Targeted journal curation as a method to improve data currency at
the Comparative Toxicogenomics Database. Database (Oxford). 2012 Dec
6;2012:bas051. doi: 10.1093/database/bas051. PMID: 23221299; PMCID: PMC3515863.
Wiegers TC, Davis AP, Mattingly CJ. Collaborative biocuration–text-mining
development task for document prioritization for curation. Database (Oxford).
2012 Nov 22;2012:bas037. doi: 10.1093/database/bas037. PMID: 23180769; PMCID: PMC3504477.
King BL, Davis AP, Rosenstein MC, Wiegers TC, Mattingly CJ. Ranking
transitive chemical-disease inferences using local network topology in the
comparative toxicogenomics database. PLoS One. 2012;7(11):e46524. doi:
10.1371/journal.pone.0046524. Epub 2012 Nov 7. PMID: 23144783; PMCID:
PMC3492369.
Davis AP, Murphy CG, Johnson R, Lay JM, Lennon-Hopkins K, Saraceni-Richards
C, Sciaky D, King BL, Rosenstein MC, Wiegers TC, Mattingly CJ. The Comparative
Toxicogenomics Database: update 2013. Nucleic Acids Res. 2013 Jan;41(Database
issue):D1104-14. doi: 10.1093/nar/gks994. Epub 2012 Oct 23. PMID: 23093600;
PMCID: PMC3531134.
Davis AP, Wiegers TC, Rosenstein MC, Mattingly CJ. MEDIC: a practical
disease vocabulary used at the Comparative Toxicogenomics Database. Database
(Oxford). 2012 Mar 20;2012:bar065. doi: 10.1093/database/bar065. PMID: 22434833;
PMCID: PMC3308155.
Bello SM, Richardson JE, Davis AP, Wiegers TC, Mattingly CJ, Dolan ME, Smith
CL, Blake JA, Eppig JT. Disease model curation improvements at Mouse Genome
Informatics. Database (Oxford). 2012 Mar 20;2012:bar063. doi:
10.1093/database/bar063. PMID: 22434831; PMCID: PMC3308153.
Mattingly CJ, McKone TE, Callahan MA, Blake JA, Hubal EA. Providing the
missing link: the exposure science ontology ExO. Environ Sci Technol. 2012 Mar
20;46(6):3046-53. doi: 10.1021/es2033857. Epub 2012 Mar 12. PMID: 22324457;
PMCID: PMC3314380.
Davis AP, Rosenstein MC, Wiegers TC, Mattingly CJ. DiseaseComps: a metric
that discovers similar diseases based upon common toxicogenomic profiles at CTD.
Bioinformation. 2011;7(4):154-6. doi: 10.6026/97320630007154. Epub 2011 Oct 14. PMID: 22125387; PMCID: PMC3220301.
Davis AP, Wiegers TC, Rosenstein MC, Murphy CG, Mattingly CJ. The curation
paradigm and application tool used for manual curation of the scientific
literature at the Comparative Toxicogenomics Database. Database (Oxford). 2011
Sep 20;2011:bar034. doi: 10.1093/database/bar034. Erratum in: Database (Oxford).
2012;2012:bas012. Rosenstein, Michael C [added]. PMID: 21933848; PMCID:
PMC3176677.
Cheng KC, Hinton DE, Mattingly CJ, Planchart A. Aquatic models, genomics and
chemical risk management. Comp Biochem Physiol C Toxicol Pharmacol. 2012
Jan;155(1):169-73. doi: 10.1016/j.cbpc.2011.06.009. Epub 2011 Jun 28. PMID:
21763781; PMCID: PMC4104604.
Davis AP, King BL, Mockus S, Murphy CG, Saraceni-Richards C, Rosenstein M,
Wiegers T, Mattingly CJ. The Comparative Toxicogenomics Database: update 2011.
Nucleic Acids Res. 2011 Jan;39(Database issue):D1067-72. doi:
10.1093/nar/gkq813. Epub 2010 Sep 22. PMID: 20864448; PMCID: PMC3013756.
Planchart A, Mattingly CJ. 2,3,7,8-Tetrachlorodibenzo-p-dioxin upregulates
FoxQ1b in zebrafish jaw primordium. Chem Res Toxicol. 2010 Mar 15;23(3):480-7.
doi: 10.1021/tx9003165. PMID: 20055451; PMCID: PMC2839046.
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;10:326. doi:
10.1186/1471-2105-10-326. PMID: 19814812; PMCID: PMC2768719.
Mattingly CJ, Hampton TH, Brothers KM, Griffin NE, Planchart A. Perturbation
of defense pathways by low-dose arsenic exposure in zebrafish embryos. Environ
Health Perspect. 2009 Jun;117(6):981-7. doi: 10.1289/ehp.0900555. Epub 2009 Feb 22. PMID: 19590694; PMCID: PMC2702417.
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;3:46. doi: 10.1186/1752-0509-3-46. PMID:
19416532; PMCID: PMC2680807.
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. doi: 10.6026/97320630004173. PMID: 20198196; PMCID: PMC2825594.
Barnes DW, Mattingly CJ, Parton A, Dowell LM, Bayne CJ, Forrest JN Jr.
Marine organism cell biology and regulatory sequence discoveryin comparative
functional genomics. Cytotechnology. 2004 Oct;46(2-3):123-37. doi:
10.1007/s10616-005-1719-5. Epub 2005 Nov 30. PMID: 19003267; PMCID: PMC3449718.
Mattingly CJ. Chemical databases for environmental health and clinical
research. Toxicol Lett. 2009 Apr 10;186(1):62-5. doi:
10.1016/j.toxlet.2008.10.003. Epub 2008 Oct 18. PMID: 18996453; PMCID:
PMC2727625.
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;1:48. doi: 10.1186/1755-8794-1-48. PMID: 18845002; PMCID: PMC2576347.
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. doi: 10.1093/nar/gkn580. Epub 2008 Sep 9. PMID: 18782832; PMCID: PMC2686584.
Congdon CB, Aman JC, Nava GM, Gaskins HR, Mattingly CJ. 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. doi:
10.1109/TCBB.2007.1059. PMID: 18245871.
Mattingly CJ, Rosenstein MC, Colby GT, Forrest JN Jr, Boyer JL. The
Comparative Toxicogenomics Database (CTD): a resource for comparative
toxicological studies. J Exp Zool A Comp Exp Biol. 2006 Sep 1;305(9):689-92.
doi: 10.1002/jez.a.307. PMID: 16902965; PMCID: PMC1586110.
Mattingly CJ, Rosenstein MC, Davis AP, Colby GT, Forrest JN Jr, Boyer JL.
The comparative toxicogenomics database: a cross-species resource for building
chemical-gene interaction networks. Toxicol Sci. 2006 Aug;92(2):587-95. doi:
10.1093/toxsci/kfl008. Epub 2006 May 4. PMID: 16675512; PMCID: PMC1586111.
Mattingly CJ, Colby GT, Rosenstein MC, Forrest JN Jr, 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. doi: 10.1038/sj.tpj.6500225. PMID: 14735110.
Mattingly CJ, Colby GT, Forrest JN, Boyer JL. The Comparative Toxicogenomics
Database (CTD). Environ Health Perspect. 2003 May;111(6):793-5. doi:
10.1289/ehp.6028. PMID: 12760826; PMCID: PMC1241500.
Mattingly CJ, Toscano WA. Posttranscriptional silencing of cytochrome
P4501A1 (CYP1A1) during zebrafish (Danio rerio) development. Dev Dyn. 2001
Dec;222(4):645-54. doi: 10.1002/dvdy.1215. PMID: 11748833.
Mattingly CJ, McLachlan JA, Toscano WA Jr. Green fluorescent protein (GFP)
as a marker of aryl hydrocarbon receptor (AhR) function in developing zebrafish
(Danio rerio). Environ Health Perspect. 2001 Aug;109(8):845-9. doi:
10.1289/ehp.01109845. PMID: 11564622; PMCID: PMC1240414.
Ricci MS, Toscano DG, Mattingly CJ, Toscano WA Jr. Estrogen receptor reduces
CYP1A1 induction in cultured human endometrial cells. J Biol Chem. 1999 Feb
5;274(6):3430-8. doi: 10.1074/jbc.274.6.3430. PMID: 9920887.
