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Items: 50

1.

Integration of curated and high-throughput screening data to elucidate environmental influences on disease pathways.

Kosnik MB, Planchart A, Marvel SW, Reif DM, Mattingly CJ.

Comput Toxicol. 2019 Nov;12. pii: 100094. doi: 10.1016/j.comtox.2019.100094. Epub 2019 Jun 27.

PMID:
31453412
2.

The Comparative Toxicogenomics Database: update 2019.

Davis AP, Grondin CJ, Johnson RJ, Sciaky D, McMorran R, Wiegers J, Wiegers TC, Mattingly CJ.

Nucleic Acids Res. 2019 Jan 8;47(D1):D948-D954. doi: 10.1093/nar/gky868.

3.

Chemical-Induced Phenotypes at CTD Help Inform the Predisease State and Construct Adverse Outcome Pathways.

Davis AP, Wiegers TC, Wiegers J, Johnson RJ, Sciaky D, Grondin CJ, Mattingly CJ.

Toxicol Sci. 2018 Sep 1;165(1):145-156. doi: 10.1093/toxsci/kfy131.

4.

Cadmium exposure increases the risk of juvenile obesity: a human and zebrafish comparative study.

Green AJ, Hoyo C, Mattingly CJ, Luo Y, Tzeng JY, Murphy SK, Buchwalter DB, Planchart A.

Int J Obes (Lond). 2018 Jul;42(7):1285-1295. doi: 10.1038/s41366-018-0036-y. Epub 2018 Feb 20.

5.

Heavy Metal Exposure and Metabolic Syndrome: Evidence from Human and Model System Studies.

Planchart A, Green A, Hoyo C, Mattingly CJ.

Curr Environ Health Rep. 2018 Mar;5(1):110-124. doi: 10.1007/s40572-018-0182-3. Review.

6.

Accessing an Expanded Exposure Science Module at the Comparative Toxicogenomics Database.

Grondin CJ, Davis AP, Wiegers TC, Wiegers JA, Mattingly CJ.

Environ Health Perspect. 2018 Jan 18;126(1):014501. doi: 10.1289/EHP2873.

7.

Applying evolutionary genetics to developmental toxicology and risk assessment.

Leung MCK, Procter AC, Goldstone JV, Foox J, DeSalle R, Mattingly CJ, Siddall ME, Timme-Laragy AR.

Reprod Toxicol. 2017 Apr;69:174-186. doi: 10.1016/j.reprotox.2017.03.003. Epub 2017 Mar 4. Review.

8.

From the Cover: Embryonic Exposure to TCDD Impacts Osteogenesis of the Axial Skeleton in Japanese medaka, Oryzias latipes.

Watson AT, Planchart A, Mattingly CJ, Winkler C, Reif DM, Kullman SW.

Toxicol Sci. 2017 Feb;155(2):485-496. doi: 10.1093/toxsci/kfw229. Epub 2016 Nov 15.

9.

Informatics and Data Analytics to Support Exposome-Based Discovery for Public Health.

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.

Annu Rev Public Health. 2017 Mar 20;38:279-294. doi: 10.1146/annurev-publhealth-082516-012737. Epub 2016 Dec 23. Review.

10.

Advancing toxicology research using in vivo high throughput toxicology with small fish models.

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.

ALTEX. 2016;33(4):435-452. doi: 10.14573/altex.1601281. Epub 2016 Jun 21.

11.

The Comparative Toxicogenomics Database: update 2017.

Davis AP, Grondin CJ, Johnson RJ, Sciaky D, King BL, McMorran R, Wiegers J, Wiegers TC, Mattingly CJ.

Nucleic Acids Res. 2017 Jan 4;45(D1):D972-D978. doi: 10.1093/nar/gkw838. Epub 2016 Sep 19.

12.

Generating Gene Ontology-Disease Inferences to Explore Mechanisms of Human Disease at the Comparative Toxicogenomics Database.

Davis AP, Wiegers TC, King BL, Wiegers J, Grondin CJ, Sciaky D, Johnson RJ, Mattingly CJ.

PLoS One. 2016 May 12;11(5):e0155530. doi: 10.1371/journal.pone.0155530. eCollection 2016.

13.

Advancing Exposure Science through Chemical Data Curation and Integration in the Comparative Toxicogenomics Database.

Grondin CJ, Davis AP, Wiegers TC, King BL, Wiegers JA, Reif DM, Hoppin JA, Mattingly CJ.

Environ Health Perspect. 2016 Oct;124(10):1592-1599. Epub 2016 May 12.

14.

BioCreative V CDR task corpus: a resource for chemical disease relation extraction.

Li J, Sun Y, Johnson RJ, Sciaky D, Wei CH, Leaman R, Davis AP, Mattingly CJ, Wiegers TC, Lu Z.

Database (Oxford). 2016 May 9;2016. pii: baw068. doi: 10.1093/database/baw068. Print 2016.

15.

ToxEvaluator: an integrated computational platform to aid the interpretation of toxicology study-related findings.

Pelletier D, Wiegers TC, Enayetallah A, Kibbey C, Gosink M, Koza-Taylor P, Mattingly CJ, Lawton M.

Database (Oxford). 2016 May 9;2016. pii: baw062. doi: 10.1093/database/baw062. Print 2016.

16.

Assessing the state of the art in biomedical relation extraction: overview of the BioCreative V chemical-disease relation (CDR) task.

Wei CH, Peng Y, Leaman R, Davis AP, Mattingly CJ, Li J, Wiegers TC, Lu Z.

Database (Oxford). 2016 Mar 19;2016. pii: baw032. doi: 10.1093/database/baw032. Print 2016.

17.

Laying a Community-Based Foundation for Data-Driven Semantic Standards in Environmental Health Sciences.

Mattingly CJ, Boyles R, Lawler CP, Haugen AC, Dearry A, Haendel M.

Environ Health Perspect. 2016 Aug;124(8):1136-40. doi: 10.1289/ehp.1510438. Epub 2016 Feb 12.

18.

The Comparative Toxicogenomics Database's 10th year anniversary: update 2015.

Davis AP, Grondin CJ, Lennon-Hopkins K, Saraceni-Richards C, Sciaky D, King BL, Wiegers TC, Mattingly CJ.

Nucleic Acids Res. 2015 Jan;43(Database issue):D914-20. doi: 10.1093/nar/gku935. Epub 2014 Oct 17.

19.

BioC interoperability track overview.

Comeau DC, Batista-Navarro RT, Dai HJ, Do─čan 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.

Database (Oxford). 2014 Jun 30;2014. pii: bau053. doi: 10.1093/database/bau053. Print 2014. Review.

20.

Web services-based text-mining demonstrates broad impacts for interoperability and process simplification.

Wiegers TC, Davis AP, Mattingly CJ.

Database (Oxford). 2014 Jun 10;2014. pii: bau050. doi: 10.1093/database/bau050. Print 2014.

21.

A CTD-Pfizer collaboration: manual curation of 88,000 scientific articles text mined for drug-disease and drug-phenotype interactions.

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.

Database (Oxford). 2013 Nov 28;2013:bat080. doi: 10.1093/database/bat080. Print 2013.

22.

Text mining effectively scores and ranks the literature for improving chemical-gene-disease curation at the comparative toxicogenomics database.

Davis AP, Wiegers TC, Johnson RJ, Lay JM, Lennon-Hopkins K, Saraceni-Richards C, Sciaky D, Murphy CG, Mattingly CJ.

PLoS One. 2013 Apr 17;8(4):e58201. doi: 10.1371/journal.pone.0058201. Print 2013.

23.

Targeted journal curation as a method to improve data currency at the Comparative Toxicogenomics Database.

Davis AP, Johnson RJ, Lennon-Hopkins K, Sciaky D, Rosenstein MC, Wiegers TC, Mattingly CJ.

Database (Oxford). 2012 Dec 6;2012:bas051. doi: 10.1093/database/bas051. Print 2012.

24.

Collaborative biocuration--text-mining development task for document prioritization for curation.

Wiegers TC, Davis AP, Mattingly CJ.

Database (Oxford). 2012 Nov 22;2012:bas037. doi: 10.1093/database/bas037. Print 2012.

25.

Ranking transitive chemical-disease inferences using local network topology in the comparative toxicogenomics database.

King BL, Davis AP, Rosenstein MC, Wiegers TC, Mattingly CJ.

PLoS One. 2012;7(11):e46524. doi: 10.1371/journal.pone.0046524. Epub 2012 Nov 7.

26.

The Comparative Toxicogenomics Database: update 2013.

Davis AP, Murphy CG, Johnson R, Lay JM, Lennon-Hopkins K, Saraceni-Richards C, Sciaky D, King BL, Rosenstein MC, Wiegers TC, Mattingly CJ.

Nucleic Acids Res. 2013 Jan;41(Database issue):D1104-14. doi: 10.1093/nar/gks994. Epub 2012 Oct 23.

27.

MEDIC: a practical disease vocabulary used at the Comparative Toxicogenomics Database.

Davis AP, Wiegers TC, Rosenstein MC, Mattingly CJ.

Database (Oxford). 2012 Mar 20;2012:bar065. doi: 10.1093/database/bar065. Print 2012.

28.

Disease model curation improvements at Mouse Genome Informatics.

Bello SM, Richardson JE, Davis AP, Wiegers TC, Mattingly CJ, Dolan ME, Smith CL, Blake JA, Eppig JT.

Database (Oxford). 2012 Mar 20;2012:bar063. doi: 10.1093/database/bar063. Print 2012.

29.

Providing the missing link: the exposure science ontology ExO.

Mattingly CJ, McKone TE, Callahan MA, Blake JA, Hubal EA.

Environ Sci Technol. 2012 Mar 20;46(6):3046-53. doi: 10.1021/es2033857. Epub 2012 Mar 12.

30.

DiseaseComps: a metric that discovers similar diseases based upon common toxicogenomic profiles at CTD.

Davis AP, Rosenstein MC, Wiegers TC, Mattingly CJ.

Bioinformation. 2011;7(4):154-6. Epub 2011 Oct 14.

31.

The curation paradigm and application tool used for manual curation of the scientific literature at the Comparative Toxicogenomics Database.

Davis AP, Wiegers TC, Rosenstein MC, Murphy CG, Mattingly CJ.

Database (Oxford). 2011 Sep 20;2011:bar034. doi: 10.1093/database/bar034. Print 2011. Erratum in: Database (Oxford). 2012;2012:bas012. Rosenstein, Michael C [added].

32.

Aquatic models, genomics and chemical risk management.

Cheng KC, Hinton DE, Mattingly CJ, Planchart A.

Comp Biochem Physiol C Toxicol Pharmacol. 2012 Jan;155(1):169-73. doi: 10.1016/j.cbpc.2011.06.009. Epub 2011 Jun 28.

33.

The Comparative Toxicogenomics Database: update 2011.

Davis AP, King BL, Mockus S, Murphy CG, Saraceni-Richards C, Rosenstein M, Wiegers T, Mattingly CJ.

Nucleic Acids Res. 2011 Jan;39(Database issue):D1067-72. doi: 10.1093/nar/gkq813. Epub 2010 Sep 22.

34.

2,3,7,8-Tetrachlorodibenzo-p-dioxin upregulates FoxQ1b in zebrafish jaw primordium.

Planchart A, Mattingly CJ.

Chem Res Toxicol. 2010 Mar 15;23(3):480-7. doi: 10.1021/tx9003165.

35.

Text mining and manual curation of chemical-gene-disease networks for the comparative toxicogenomics database (CTD).

Wiegers TC, Davis AP, Cohen KB, Hirschman L, Mattingly CJ.

BMC Bioinformatics. 2009 Oct 8;10:326. doi: 10.1186/1471-2105-10-326.

36.

Perturbation of defense pathways by low-dose arsenic exposure in zebrafish embryos.

Mattingly CJ, Hampton TH, Brothers KM, Griffin NE, Planchart A.

Environ Health Perspect. 2009 Jun;117(6):981-7. doi: 10.1289/ehp.0900555. Epub 2009 Feb 22.

37.

Genetic and environmental pathways to complex diseases.

Gohlke JM, Thomas R, Zhang Y, Rosenstein MC, Davis AP, Murphy C, Becker KG, Mattingly CJ, Portier CJ.

BMC Syst Biol. 2009 May 5;3:46. doi: 10.1186/1752-0509-3-46.

38.

GeneComps and ChemComps: a new CTD metric to identify genes and chemicals with shared toxicogenomic profiles.

Davis AP, Murphy CG, Saraceni-Richards CA, Rosenstein MC, Wiegers TC, Hampton TH, Mattingly CJ.

Bioinformation. 2009 Oct 15;4(4):173-4.

39.

Marine organism cell biology and regulatory sequence discoveryin comparative functional genomics.

Barnes DW, Mattingly CJ, Parton A, Dowell LM, Bayne CJ, Forrest JN Jr.

Cytotechnology. 2004 Oct;46(2-3):123-37. doi: 10.1007/s10616-005-1719-5. Epub 2005 Nov 30.

40.

Chemical databases for environmental health and clinical research.

Mattingly CJ.

Toxicol Lett. 2009 Apr 10;186(1):62-5. doi: 10.1016/j.toxlet.2008.10.003. Epub 2008 Oct 18. Review.

41.

The Comparative Toxicogenomics Database facilitates identification and understanding of chemical-gene-disease associations: arsenic as a case study.

Davis AP, Murphy CG, Rosenstein MC, Wiegers TC, Mattingly CJ.

BMC Med Genomics. 2008 Oct 9;1:48. doi: 10.1186/1755-8794-1-48.

42.

Comparative Toxicogenomics Database: a knowledgebase and discovery tool for chemical-gene-disease networks.

Davis AP, Murphy CG, Saraceni-Richards CA, Rosenstein MC, Wiegers TC, Mattingly CJ.

Nucleic Acids Res. 2009 Jan;37(Database issue):D786-92. doi: 10.1093/nar/gkn580. Epub 2008 Sep 9.

43.

An evaluation of information content as a metric for the inference of putative conserved noncoding regions in DNA sequences using a genetic algorithms approach.

Congdon CB, Aman JC, Nava GM, Gaskins HR, Mattingly CJ.

IEEE/ACM Trans Comput Biol Bioinform. 2008 Jan-Mar;5(1):1-14. doi: 10.1109/TCBB.2007.1059.

PMID:
18245871
44.

The Comparative Toxicogenomics Database (CTD): a resource for comparative toxicological studies.

Mattingly CJ, Rosenstein MC, Colby GT, Forrest JN Jr, Boyer JL.

J Exp Zool A Comp Exp Biol. 2006 Sep 1;305(9):689-92. Review.

45.

The comparative toxicogenomics database: a cross-species resource for building chemical-gene interaction networks.

Mattingly CJ, Rosenstein MC, Davis AP, Colby GT, Forrest JN Jr, Boyer JL.

Toxicol Sci. 2006 Aug;92(2):587-95. Epub 2006 May 4.

46.

Promoting comparative molecular studies in environmental health research: an overview of the comparative toxicogenomics database (CTD).

Mattingly CJ, Colby GT, Rosenstein MC, Forrest JN Jr, Boyer JL.

Pharmacogenomics J. 2004;4(1):5-8. Review. No abstract available.

PMID:
14735110
47.

The Comparative Toxicogenomics Database (CTD).

Mattingly CJ, Colby GT, Forrest JN, Boyer JL.

Environ Health Perspect. 2003 May;111(6):793-5.

48.
49.
50.

Estrogen receptor reduces CYP1A1 induction in cultured human endometrial cells.

Ricci MS, Toscano DG, Mattingly CJ, Toscano WA Jr.

J Biol Chem. 1999 Feb 5;274(6):3430-8.

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