Carolyn Mattingly

Davis, A. P., Wiegers, T. C., Wiegers, J., Wyatt, B., Johnson, R. J., Sciaky, D., … Mattingly, C. J. (2023). CTD tetramers: a new online tool that computationally links curated chemicals, genes, phenotypes, and diseases to inform molecular mechanisms for environmental health. TOXICOLOGICAL SCIENCES, 195(2), 155–168. https://doi.org/10.1093/toxsci/kfad069

Green, A. J., Wall, A. R., Weeks, R. D., Mattingly, C. J., Marsden, K. C., & Planchart, A. (2023). Developmental cadmium exposure disrupts zebrafish vestibular calcium channels interfering with otolith formation and inner ear function. NEUROTOXICOLOGY, 96, 129–139. https://doi.org/10.1016/j.neuro.2023.04.006

Davis, A. P., Wiegers, T. C., Johnson, R. J., Sciaky, D., Wiegers, J., & Mattingly, C. J. (2022, September 28). Comparative Toxicogenomics Database (CTD): update 2023. NUCLEIC ACIDS RESEARCH, Vol. 9. https://doi.org/10.1093/nar/gkac833

Davis, A. P., Wiegers, T. C., Wiegers, J., Grondin, C. J., Johnson, R. J., Sciaky, D., & Mattingly, C. J. (2021). CTD anatomy: Analyzing chemical-induced phenotypes and exposures from an anatomical perspective, with implications for environmental health studies. CURRENT RESEARCH IN TOXICOLOGY, 2, 128–139. https://doi.org/10.1016/j.crtox.2021.03.001

Davis, A. P., Grondin, C. J., Johnson, R. J., Sciaky, D., Wiegers, J., Wiegers, T. C., & Mattingly, C. J. (2021). Comparative Toxicogenomics Database (CTD): update 2021. NUCLEIC ACIDS RESEARCH, 49(D1), D1138–D1143. https://doi.org/10.1093/nar/gkaa891

Grondin, C. J., Davis, A. P., Wiegers, J. A., Wiegers, T. C., Sciaky, D., Johnson, R. J., & Mattingly, C. J. (2021). Predicting molecular mechanisms, pathways, and health outcomes induced by Juul e-cigarette aerosol chemicals using the Comparative Toxicogenomics Database. CURRENT RESEARCH IN TOXICOLOGY, 2, 272–281. https://doi.org/10.1016/j.crtox.2021.08.001

Pinkhasova, D. V., Jameson, L. E., Conrow, K. D., Simeone, M. P., Davis, A. P., Wiegers, T. C., … Leung, M. C. K. (2021). Regulatory status of pesticide residues in cannabis: Implications to medical use in neurological diseases. CURRENT RESEARCH IN TOXICOLOGY, 2, 140–148. https://doi.org/10.1016/j.crtox.2021.02.007

Hollander, J. A., Cory-Slechta, D. A., Jacka, F. N., Szabo, S. T., Guilarte, T. R., Bilbo, S. D., … Ladd-Acosta, C. (2020). [Review of Beyond the looking glass: recent advances in understanding the impact of environmental exposures on neuropsychiatric disease]. NEUROPSYCHOPHARMACOLOGY, 45(7), 1086–1096. https://doi.org/10.1038/s41386-020-0648-5

Davis, A. P., Wiegers, T. C., Grondin, C. J., Johnson, R. J., Sciaky, D., Wiegers, J., & Mattingly, C. J. (2020). Leveraging the Comparative Toxicogenomics Database to Fill in Knowledge Gaps for Environmental Health: A Test Case for Air Pollution-induced Cardiovascular Disease. TOXICOLOGICAL SCIENCES, 177(2), 392–404. https://doi.org/10.1093/toxsci/kfaa113

Davis, A. P., Grondin, C. J., Johnson, R. J., Sciaky, D., McMorran, R., Wiegers, J., … Mattingly, C. J. (2019). The Comparative Toxicogenomics Database: update 2019. NUCLEIC ACIDS RESEARCH, 47(D1), D948–D954. https://doi.org/10.1093/nar/gky868

Grondin, C. J., Davis, A. P., Wiegers, T. C., Wiegers, J. A., & Mattingly, C. J. (2018). Accessing an Expanded Exposure Science Module at the Comparative Toxicogenomics Database. ENVIRONMENTAL HEALTH PERSPECTIVES, 126(1). https://doi.org/10.1289/ehp2873

Green, A. J., Hoyo, C., Mattingly, C. J., Luo, Y., Tzeng, J.-Y., Murphy, S. K., … Planchart, A. (2018). Cadmium exposure increases the risk of juvenile obesity: a human and zebrafish comparative study. International Journal of Obesity, 42(7), 1285–1295. https://doi.org/10.1038/s41366-018-0036-y

Davis, A. P., Wiegers, T. C., Wiegers, J., Johnson, R. J., Sciaky, D., Grondin, C. J., & Mattingly, C. J. (2018). Chemical-Induced Phenotypes at CTD Help Inform the Predisease State and Construct Adverse Outcome Pathways. TOXICOLOGICAL SCIENCES, 165(1), 145–156. https://doi.org/10.1093/toxsci/kfy131

Planchart, A., Green, A., Hoyo, C., & Mattingly, C. J. (2018). Heavy Metal Exposure and Metabolic Syndrome: Evidence from Human and Model System Studies. Current Environmental Health Reports, 5(1), 110–124. https://doi.org/10.1007/s40572-018-0182-3

Leung, M. C. K., Procter, A. C., Goldstone, J. V., Foox, J., DeSalle, R., Mattingly, C. J., … Timme-Laragy, A. R. (2017). [Review of Applying evolutionary genetics to developmental toxicology and risk assessment]. REPRODUCTIVE TOXICOLOGY, 69, 174–186. https://doi.org/10.1016/j.reprotox.2017.03.003

Manrai, A. K., Cui, Y., Bushel, P. R., Hall, M., Karakitsios, S., Mattingly, C. J., … Patel, C. J. (2017). Informatics and Data Analytics to Support Exposome-Based Discovery for Public Health. ANNUAL REVIEW OF PUBLIC HEALTH, VOL 38, Vol. 38, pp. 279–294. https://doi.org/10.1146/annurev-publhealth-082516-012737

Davis, A. P., Grondin, C. J., Johnson, R. J., Sciaky, D., King, B. L., McMorran, R., … Mattingly, C. J. (2017). The Comparative Toxicogenomics Database: update 2017. NUCLEIC ACIDS RESEARCH, 45(D1), D972–D978. https://doi.org/10.1093/nar/gkw838

Grondin, C. J., Davis, A. P., Wiegers, T. C., King, B. L., Wiegers, J. A., Reif, D. M., … Mattingly, C. J. (2016). Advancing Exposure Science through Chemical Data Curation and Integration in the Comparative Toxicogenomics Database. Environmental Health Perspectives, 124(10), 1592–1599. https://doi.org/10.1289/ehp174

Planchart, A., Mattingly, C. J., Allen, D., Ceger, P., Casey, W., Hinton, D., … Hamm, J. (2016). Advancing toxicology research using in vivo high throughput toxicology with small fish models. Altex-Alternatives to Animal Experimentation, 33(4), 435–452.

Wei, C.-H., Peng, Y., Leaman, R., Davis, A. P., Mattingly, C. J., Li, J., … Lu, Z. (2016). Assessing the state of the art in biomedical relation extraction: overview of the BioCreative V chemical-disease relation (CDR) task. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION. https://doi.org/10.1093/database/baw032

Li, J., Sun, Y. P., Johnson, R. J., Sciaky, D., Wei, C. H., Leaman, R., … al. (2016). BioCreative V CDR task corpus: a resource for chemical disease relation extraction. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION. https://doi.org/10.1093/database/baw068

Watson, A. L. T. D., Planchart, A., Mattingly, C. J., Winkler, C., Reif, D. M., & Kullman, S. W. (2016). From the Cover: Embryonic Exposure to TCDD Impacts Osteogenesis of the Axial Skeleton in Japanese medaka,Oryzias latipes. Toxicological Sciences, 155(2), 485–496. https://doi.org/10.1093/toxsci/kfw229

Davis, A. P., Wiegers, T. C., King, B. L., Wiegers, J., Grondin, C. J., Sciaky, D., … Mattingly, C. J. (2016). Generating Gene Ontology-Disease Inferences to Explore Mechanisms of Human Disease at the Comparative Toxicogenomics Database. PLOS ONE, 11(5). https://doi.org/10.1371/journal.pone.0155530

Mattingly, C. J., Boyles, R., Lawler, C. P., Haugen, A. C., Dearry, A., & Haendel, M. (2016). [Review of Laying a Community-Based Foundation for Data-Driven Semantic Standards in Environmental Health Sciences]. ENVIRONMENTAL HEALTH PERSPECTIVES, 124(8), 1136–1140. https://doi.org/10.1289/ehp.1510438

Pelletier, D., Wiegers, T. C., Enayetallah, A., Kibbey, C., Gosink, M., Koza-Taylor, P., … Lawton, M. (2016). ToxEvaluator: an integrated computational platform to aid the interpretation of toxicology study-related findings. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION. https://doi.org/10.1093/database/baw062

Mattingly, C. J. (2015). Integrating literature-based curated data to predict mechanisms of toxicity. Presented at the OpenTox USA 2015, Baltimore, MD.

Davis, A. P., Grondin, C. J., Lennon-Hopkins, K., Saraceni-Richards, C., Sciaky, D., King, B. L., … Mattingly, C. J. (2015). The Comparative Toxicogenomics Database's 10th year anniversary: update 2015. NUCLEIC ACIDS RESEARCH, 43(D1), D914–D920. https://doi.org/10.1093/nar/gku935

Comeau, D. C., Batista-Navarro, R. T., Dai, H.-J., Dogan, R. I., Yepes, A. J., Khare, R., … Wilbur, W. J. (2014). BioC interoperability track overview. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION. https://doi.org/10.1093/database/bau053

Wiegers, T. C., Davis, A. P., & Mattingly, C. J. (2014). Web services-based text-mining demonstrates broad impacts for interoperability and process simplification. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION. https://doi.org/10.1093/database/bau050

Davis, A. P., Wiegers, T. C., Roberts, P. M., King, B. L., Lay, J. M., Lennon-Hopkins, K., … Mattingly, C. J. (2013). A CTD-Pfizer collaboration: manual curation of 88 000 scientific articles text mined for drug-disease and drug-phenotype interactions. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION. https://doi.org/10.1093/database/bat080

Davis, A. P., Wiegers, T. C., Johnson, R. J., Lay, J. M., Lennon-Hopkins, K., Saraceni-Richards, C., … Mattingly, C. J. (2013). Text Mining Effectively Scores and Ranks the Literature for Improving Chemical-Gene-Disease Curation at the Comparative Toxicogenomics Database. PLOS ONE, 8(4). https://doi.org/10.1371/journal.pone.0058201

Cheng, K. C., Hinton, D. E., Mattingly, C. J., & Planchart, A. (2012). Aquatic models, genomics and chemical risk management. Comparative Biochemistry and Physiology Part C: Toxicology & Pharmacology, 155(1), 169–173. https://doi.org/10.1016/j.cbpc.2011.06.009

Wu, C. H., Arighi, C. N., Cohen, K. B., Hirschman, L., Krallinger, M., Lu, Z. Y., … al. (2012, December 5). BioCreative-2012 Virtual Issue. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION. https://doi.org/10.1093/database/bas049

Wiegers, T. C., Davis, A. P., & Mattingly, C. J. (2012). Collaborative biocuration--text-mining development task for document prioritization for curation. Database, 2012(0), bas037–bas037. https://doi.org/10.1093/database/bas037

Mattingly, J. (2012). Computation of Neutron Multiplicity Statistics Using Deterministic Transport. IEEE TRANSACTIONS ON NUCLEAR SCIENCE, 59(2), 314–322. https://doi.org/10.1109/tns.2012.2185060

Bello, S. M., Richardson, J. E., Davis, A. P., Wiegers, T. C., Mattingly, C. J., Dolan, M. E., … Eppig, J. T. (2012). Disease model curation improvements at Mouse Genome Informatics. Database, 2012(0), bar063–bar063. https://doi.org/10.1093/database/bar063

Davis, A. P., Wiegers, T. C., Rosenstein, M. C., & Mattingly, C. J. (2012). MEDIC: a practical disease vocabulary used at the Comparative Toxicogenomics Database. Database, 2012(0), bar065–bar065. https://doi.org/10.1093/database/bar065

Mattingly, C. J., McKone, T. E., Callahan, M. A., Blake, J. A., & Hubal, E. A. C. (2012). Providing the Missing Link: the Exposure Science Ontology ExO. ENVIRONMENTAL SCIENCE & TECHNOLOGY, 46(6), 3046–3053. https://doi.org/10.1021/es2033857

King, B. L., Davis, A. P., Rosenstein, M. C., Wiegers, T. C., & Mattingly, C. J. (2012). Ranking Transitive Chemical-Disease Inferences Using Local Network Topology in the Comparative Toxicogenomics Database. PLOS ONE, 7(11). https://doi.org/10.1371/journal.pone.0046524

Davis, A. P., Johnson, R. J., Lennon-Hopkins, K., Sciaky, D., Rosenstein, M. C., Wiegers, T. C., & Mattingly, C. J. (2012). Targeted journal curation as a method to improve data currency at the Comparative Toxicogenomics Database. Database-The Journal of Biological Databases and Curation.

Davis, A. P., Murphy, C. G., Johnson, R., Lay, J. M., Lennon-Hopkins, K., Saraceni-Richards, C., … Mattingly, C. J. (2012). The Comparative Toxicogenomics Database: update 2013. Nucleic Acids Research, 41(D1), D1104–D1114. https://doi.org/10.1093/nar/gks994

Davis, A. P., Rosenstein, M. C., Wiegers, T. C., & Mattingly, C. J. (2011). DiseaseComps: a metric that discovers similar diseases based upon common toxicogenomic profiles at CTD. Bioinformation, 7(4), 154–156. https://doi.org/10.6026/97320630007154

Davis, A. P., Wiegers, T. C., Murphy, C. G., & Mattingly, C. J. (2011). The curation paradigm and application tool used for manual curation of the scientific literature at the Comparative Toxicogenomics Database. Database, 2011(0), bar034–bar034. https://doi.org/10.1093/database/bar034

Planchart, A., & Mattingly, C. J. (2010). 2,3,7,8-Tetrachlorodibenzo-p-dioxin Upregulates FoxQ1b in Zebrafish Jaw Primordium. Chemical Research in Toxicology, 23(3), 480–487. https://doi.org/10.1021/tx9003165

Davis, A. P., King, B. L., Mockus, S., Murphy, C. G., Saraceni-Richards, C., Rosenstein, M., … Mattingly, C. J. (2010). The Comparative Toxicogenomics Database: update 2011. Nucleic Acids Research, 39(Database), D1067–D1072. https://doi.org/10.1093/nar/gkq813

Mattingly, C. J. (2010). Understanding environment-disease connections: An introduction to the comparative toxicogenomics database (ctd). In Nature Pathway Interaction Database.

Mattingly, C. J. (2009). Chemical databases for environmental health and clinical research. Toxicology Letters, 186(1), 62–65. https://doi.org/10.1016/j.toxlet.2008.10.003

Davis, A. P., Murphy, C. G., Saraceni-Richards, C. A., Rosenstein, M. C., Wiegers, T. C., & Mattingly, C. J. (2009). Comparative Toxicogenomics Database: a knowledgebase and discovery tool for chemical-gene-disease networks. Nucleic Acids Research, 37(Database), D786–D792. https://doi.org/10.1093/nar/gkn580

Davis, A. P., Murphy, C. G., Saraceni-Richards, C. A., Rosenstein, M. C., Wiegers, T. C., Hampton, T. H., & Mattingly, C. J. (2009). GeneComps and ChemComps: a new CTD metric to identify genes and chemicals with shared toxicogenomic profiles. Bioinformation, 4(4), 173–174. https://doi.org/10.6026/97320630004173

Gohlke, J. M., Thomas, R., Zhang, Y., Rosenstein, M. C., Davis, A. P., Murphy, C., … Portier, C. J. (2009). Genetic and environmental pathways to complex diseases. BMC Systems Biology, 3(1), 46. https://doi.org/10.1186/1752-0509-3-46

Mattingly, C. J., Hampton, T. H., Brothers, K. M., Griffin, N. E., & Planchart, A. (2009). Perturbation of Defense Pathways by Low-Dose Arsenic Exposure in Zebrafish Embryos. Environmental Health Perspectives, 117(6), 981–987. https://doi.org/10.1289/ehp.0900555

Wiegers, T. C., Davis, A. P., Cohen, K. B., Hirschman, L., & Mattingly, C. J. (2009). Text mining and manual curation of chemical-gene-disease networks for the Comparative Toxicogenomics Database (CTD). BMC Bioinformatics, 10(1). https://doi.org/10.1186/1471-2105-10-326

Bates Congdon, C., Aman, J. C., Nava, G. M., Gaskins, H. R., & Mattingly, C. J. (2008). 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 Transactions on Computational Biology and Bioinformatics, 5(1), 1–14. https://doi.org/10.1109/tcbb.2007.1059

Davis, A. P., Murphy, C. G., Rosenstein, M. C., Wiegers, T. C., & Mattingly, C. J. (2008). The Comparative Toxicogenomics Database facilitates identification and understanding of chemical-gene-disease associations: arsenic as a case study. BMC Medical Genomics, 1(1). https://doi.org/10.1186/1755-8794-1-48

Congdon, C. B., Gaskins, H. R., Nava, G. M., & Mattingly, C. (2007). Towards Interactive Visualization for Exploring Conserved Motifs in Noncoding DNA Sequence. 2007 Frontiers in the Convergence of Bioscience and Information Technologies. Presented at the 2007 Frontiers in the Convergence of Bioscience and Information Technologies. https://doi.org/10.1109/fbit.2007.149

Mattingly, C. J., Rosenstein, M. C., Colby, G. T., Forrest Jr, J. N., & Boyer, J. L. (2006). The Comparative Toxicogenomics Database (CTD): a resource for comparative toxicological studies. Journal of Experimental Zoology Part A: Comparative Experimental Biology, 305A(9), 689–692. https://doi.org/10.1002/jez.a.307

Mattingly, C. J., Rosenstein, M. C., Davis, A. P., Colby, G. T., Forrest, J. N., Jr, & Boyer, J. L. (2006). The Comparative Toxicogenomics Database: A Cross-Species Resource for Building Chemical-Gene Interaction Networks. Toxicological Sciences, 92(2), 587–595. https://doi.org/10.1093/toxsci/kfl008

Congdon, C. B., Fizer, C. W., Smith, N. W., Gaskins, H. R., Aman, J., Nava, G. M., & Mattingly, C. (2005). Preliminary Results for GAMI: A Genetic Algorithms Approach to Motif Inference. 2005 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology. Presented at the 2005 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology. https://doi.org/10.1109/cibcb.2005.1594904

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(2), 111–120. https://doi.org/10.1089/zeb.2004.1.111

Barnes, D. W., Mattingly, C. J., Parton, A., Dowell, L. M., Bayne, C. J., & Forrest, J. N., Jr. (2004). Marine Organism Cell Biology and Regulatory Sequence Discoveryin Comparative Functional Genomics. Cytotechnology, 46(2-3), 123–137. https://doi.org/10.1007/s10616-005-1719-5

Mattingly, C. J., Colby, G. T., Rosenstein, M. C., Forrest, J. N., & Boyer, J. L. (2004). Promoting comparative molecular studies in environmental health research: an overview of the comparative toxicogenomics database (CTD). The Pharmacogenomics Journal, 4(1), 5–8. https://doi.org/10.1038/sj.tpj.6500225

Mattingly, C. J., Colby, G. T., Forrest, J. N., & Boyer, J. L. (2003). The Comparative Toxicogenomics Database (CTD). Environmental Health Perspectives, 111(6), 793–795. https://doi.org/10.1289/ehp.6028

Mattingly, C. J., McLachlan, J. A., & Toscano, W. A., Jr. (2001). Green fluorescent protein (GFP) as a marker of aryl hydrocarbon receptor (AhR) function in developing zebrafish (Danio rerio). Environmental Health Perspectives, 109(8), 845–849. https://doi.org/10.1289/ehp.01109845

Mattingly, C. J., & Toscano, W. A. (2001). Posttranscriptional silencing of cytochrome P4501A1 (CYP1A1) during zebrafish (Danio rerio) development. Developmental Dynamics, 222(4), 645–654. https://doi.org/10.1002/dvdy.1215

Ricci, M. S., Toscano, D. G., Mattingly, C. J., & Toscano, W. A., Jr. (1999). Estrogen Receptor Reduces CYP1A1 Induction in Cultured Human Endometrial Cells. Journal of Biological Chemistry, 274(6), 3430–3438. https://doi.org/10.1074/jbc.274.6.3430