Superfund Research Program

Data Management and Analysis Core

Project Leader: Katrina M. Waters (Pacific Northwest National Laboratory)
Co-Investigator: Sara Gosline (Pacific Northwest National Laboratory)
Grant Number: P42ES016465
Funding Period: 2009-2025

Project-Specific Links

Publications

2024

• Bramer L, Dixon HM, Degnan D, Rohlman D, Herbstman JB, Anderson KA, Waters KM. 2024. Expanding the access of wearable silicone wristbands in community-engaged research through best practices in data analysis and integration. Pac Symp Biocomput 29:170-186. PMID:38160278 PMCID:PMC10766083
• Bramer L, Dixon HM, Rohlman D, Scott RP, Miller RL, Kincl L, Herbstman JB, Waters KM, Anderson KA. 2024. PM2.5 is insufficient to explain personal PAH exposure. Geohealth 8(2):doi:10.1029/2023gh000937 PMID:38344245 PMCID:10858395

2023

• Gosline S, Kim DN, Pande P, Thomas DG, Truong L, Hoffman PD, Barton ML, Loftus J, Moran A, Hampton S, Dowson S, Franklin L, Degnan D, Anderson LN, Thessen AE, Tanguay RL, Anderson KA, Waters KM. 2023. The Superfund Research Program Analytics Portal: linking environmental chemical exposure to biological phenotypes. Sci Data 10(1):151. doi:10.1038/s41597-023-02021-5 PMID:36944655 PMCID:PMC1003089
• McClure RS, Rericha Y, Waters KM, Tanguay RL. 2023. 3' RNA-seq is superior to standard RNA-seq in cases of sparse data but inferior at identifying toxicity pathways in a model organism. Front Bioinform 3:1234218. doi:10.3389/fbinf.2023.1234218 PMID:37576716 PMCID:PMC10414111
• Rude CI, Tidwell LG, Tilton SC, Waters KM, Anderson KA, Tanguay RL. 2023. Coupling environmental whole mixture toxicity screening with unbiased RNA-Seq reveals site-specific biological responses in zebrafish. Toxics 11(3):201. doi:10.3390/toxics11030201 PMID:36976966 PMCID:PMC1005377

2022

• Dixon HM, Bramer LM, Scott RP, Calero L, Holmes D, Gibson EA, Cavalier HM, Rohlman D, Miller RL, Calafat AM, Kincl L, Waters KM, Herbstman JB, Anderson KA. 2022. Evaluating predictive relationships between wristbands and urine for assessment of personal PAH exposure. Environ Int 163:doi:10.1016/j.envint.2022.107226 PMID:35405507 PMCID:PMC8978533
• Evoy R, Kincl L, Rohlman D, Bramer LM, Dixon HM, Hystad P, Bae H, Barton ML, Phillips AR, Miller RL, Waters KM, Herbstman JB, Anderson KA. 2022. Impact of acute temperature and air pollution exposures on adult lung function: A panel study of asthmatics. PLoS One 17(6):e0270412. doi:10.1371/journal.pone.0270412 PMID:35763502 PMCID:PMC9239441
• Rivera BN, Wilson LB, Kim DN, Pande P, Anderson KA, Tilton SC, Tanguay RL. 2022. A comparative multi-system approach to characterizing bioactivity of commonly occurring chemicals. Int J Environ Res Public Health 19(7):3829. doi:10.3390/ijerph19073829 PMID:35409514 PMCID:PMC8998123
• Shankar P, Garcia GR, La Du JK, Sullivan CM, Dunham CL, Goodale BC, Waters KM, Stanisheuski S, Maier C, Thunga P, Reif DM, Tanguay RL. 2022. The Ahr2-Dependent wfikkn1 gene influences zebrafish transcriptome, proteome, and behavior. Toxicol Sci doi:10.1093/toxsci/kfac037 PMID:35377459
• Wilson LB, McClure RS, Waters KM, Simonich MT, Tanguay RL. 2022. Concentration-response gene expression analysis in zebrafish reveals phenotypically-anchored transcriptional responses to retene. Front Toxicol 4:950503. doi:10.3389/ftox.2022.950503 PMID:36093370 PMCID:PMC9453431

2021

• Mansouri K, Karmaus AL, Fitzpatrick J, Patlewicz G, Pradeep P, Alberga D, Alepee N, Allen TE, Allen D, Alves VM, Andrade CH, Auernhammer TR, Ballabio D, Bell S, Benfenati E, Bhattacharya S, Bastos JV, Boyd SA, Brown BJ, Capuzzi SJ, Chushak Y, Ciallella H, Clark AM, Consonni V, Daga PR, Ekins S, Farag S, Fedorov M, Fourches D, Gadaleta D, Gao F, Gearhart JM, Goh G, Goodman JM, Grisoni F, Grulke CM, Hartung T, Hirn M, Karpov P, Korotcov A, Lavado GJ, Lawless M, Luechtefeld T, Li X, Lunghini F, Mangiatordi GF, Marcou G, Marsh DE, Martin T, Mauri A, Muratov EN, Myatt GJ, Nguyen D, Nicolotti O, Note R, Pande P, Parks AK, Peryea T, Polash AH, Rallo R, Roncaglioni A, Rowlands C, Ruiz P, Russo DP, Sayed A, Sayre R, Sheils T, Siegel C, Silva AC, Simeonov A, Sosnin S, Southall N, Strickland J, Tang Y, Teppen BJ, Tetko IV, Thomas DG, Tkachenko V, Todeschini R, Toma C, Tripodi I, Trisciuzzi D, Tropsha A, Varnek A, Vukovic K, Wang Z, Wang L, Waters KM, Wedlake AJ, Wijeyesakere SJ, Wilson D, Xiao Z, Yang H, Zahoranszky-Kohalmi G, Zakharov AV, Zhang F, Zhang Z, Zhao T, Zhu H, Zorn KM, Casey W, Kleinstreuer N. 2021. CATMoS: Collaborative Acute Toxicity Modeling Suite. Environ Health Perspect 129(4):47013. doi:10.1289/EHP8495 PMID:33929906 PMCID:PMC8086800
• Shankar P, McClure RS, Waters KM, Tanguay RL. 2021. Gene co-expression network analysis in zebrafish reveals chemical class specific modules. BMC Genomics 22:doi:10.1186/s12864-021-07940-4 PMID:34517816 PMCID:PMC8438978

2019

• Brown J, Phillips AR, Lewis DA, Mans M, Chang Y, Tanguay RL, Peterson ES, Waters KM, Tilton SC. 2019. Bioinformatics Resource Manager: a systems biology web tool for microRNA and omics data integration. BMC Bioinformatics 20:255. doi:10.1186/s12859-019-2805-6 PMID:31101000
• Chang Y, Siddens LK, Heine L, Sampson D, Yu Z, Fischer K, Lohr CV, Tilton SC. 2019. Comparative mechanisms of PAH toxicity by benzo a pyrene and dibenzo def,p chrysene in primary human bronchial epithelial cells cultured at air-liquid interface. Toxicol Appl Pharmacol 379:114644. doi:10.1016/j.taap.2019.114644 PMID:31255691 PMCID:PMC6708476
• Dixon HM, Armstrong G, Barton ML, Bergmann AJ, Bondy M, Halbleib ML, Hamilton W, Haynes E, Herbstman JB, Hoffman PD, Jepson PC, Kile ML, Kincl L, Laurienti PJ, North P, Paulik LB, Petrosino J, Points GL, Poutasse C, Rohlman D, Scott RP, Smith BW, Tidwell LG, Walker C, Waters KM, Anderson KA. 2019. Discovery of common chemical exposures across three continents using silicone wristbands. R Soc Open Sci 6(2):181836. doi:10.1098/rsos.181836 PMID:30891293 PMCID:PMC6408398
• Madeen E, Siddens LK, Uesugi S, McQuistan TJ, Corley RA, Smith JN, Waters KM, Tilton SC, Anderson KA, Ognibene T, Turteltaub KW, Williams DE. 2019. Toxicokinetics of benzo[a]pyrene in humans: Extensive metabolism as determined by UPLC-accelerator mass spectrometry following oral micro-dosing. Toxicol Appl Pharmacol 364:97-105. doi:10.1016/j.taap.2018.12.010 PMID:30582946 PMCID:PMC6369707
• Shankar P, Geier MC, Truong L, McClure RS, Pande P, Waters KM, Tanguay RL. 2019. Coupling genome-wide transcriptomics and developmental toxicity profiles in zebrafish to characterize polycyclic aromatic hydrocarbon (PAH) hazard. Int J Mol Sci 20:2570. doi:10.3390/ijms20102570 PMID:31130617 PMCID:PMC6566387
• Thomas DG, Shankaran H, Truong L, Tanguay RL, Waters KM. 2019. Time-dependent behavioral data from zebrafish reveals novel signatures of chemical toxicity using point of departure analysis. Comput Toxicol 9:50-60. doi:10.1016/j.comtox.2018.11.001 PMID:31485548 PMCID:PMC6726397

2018

• Dixon HM, Scott RP, Holmes D, Calero L, Kincl L, Waters KM, Camann D, Calafat AM, Herbstman JB, Anderson KA. 2018. Silicone wristbands compared with traditional polycyclic aromatic hydrocarbon exposure assessment methods. Anal Bioanal Chem 410(13):3059-3071. doi:10.1007/s00216-018-0992-z PMID:29607448 PMCID:PMC5910488
• Garcia GR, Shankar P, Dunham CL, Garcia A, La Du JK, Truong L, Tilton SC, Tanguay RL. 2018. Signaling events downstream of AHR activation that contribute to toxic responses: The functional role of an AHR-dependent long noncoding RNA (slincR) using the zebrafish model. Environ Health Perspect 126(11):117002. doi:10.1289/EHP3281 PMID:30398377 PMCID:PMC6371766
• Geier MC, Minick DJ, Truong L, Tilton SC, Pande P, Anderson KA, Teeguardan J, Tanguay RL. 2018. Systematic developmental neurotoxicity assessment of a representative PAH Superfund mixture using zebrafish. Toxicol Appl Pharmacol 354:115-125. doi:10.1016/j.taap.2018.03.029 PMID:29630969 PMCID:PMC6087484
• Haggard DE, Noyes PD, Waters KM, Tanguay RL. 2018. Transcriptomic and phenotypic profiling in developing zebrafish exposed to thyroid hormone receptor agonists. Reprod Toxicol 77:80-93. doi:10.1016/j.reprotox.2018.02.006 PMID:29458080 PMCID:PMC5878140
• Hummel JM, Madeen E, Siddens LK, Uesugi S, McQuistan TJ, Anderson KA, Turteltaub KW, Ognibene T, Bench G, Krueger SK, Harris S, Smith JN, Tilton SC, Baird WM, Williams DE. 2018. Pharmacokinetics of [(14)C]-Benzo[a]pyrene (BaP) in humans: Impact of Co-Administration of smoked salmon and BaP dietary restriction. Food Chem Toxicol 115:136-147. doi:10.1016/j.fct.2018.03.003 PMID:29518434 PMCID:PMC5935529

2017

• Curtis L, Bravo CF, Bayne CJ, Tilton F, Arkoosh MR, Lambertini E, Loge FJ, Collier TK, Meador J, Tilton SC. 2017. Transcriptional changes in innate immunity genes in head kidneys from Aeromonas salmonicida-challenged rainbow trout fed a mixture of polycyclic aromatic hydrocarbons. Ecotoxicol Environ Saf 142:157-163. doi:10.1016/j.ecoenv.2017.03.044 PMID:28407501
• Davie-Martin C, Stratton KG, Teeguarden J, Waters KM, Simonich SL. 2017. Implications of bioremediation of polycyclic aromatic hydrocarbon contaminated soils for human health and cancer risk. Environ Sci Technol 51:9458-9468. doi:10.1021/acs.est.7b02956 PMID:28836766
• Ehrlich AK, Pennington J, Tilton SC, Wang X, Marshall NB, Rohlman D, Funatake C, Punj S, O'Donnell EF, Yu Z, Kolluri SK, Kerkvliet NI. 2017. AhR activation increases IL-2 production by alloreactive CD4+ T cells initiating the differentiation of mucosal-homing Tim3+ Lag3+ Tr1 cells. Eur J Immunol 47(11):1989-2001. doi:10.1002/eji.201747121 PMID:28833046
• Madeen E, Lohr CV, Siddens LK, Krueger SK, Dashwood RH, Gonzalez FJ, Baird WM, Ho E, Bramer LM, Waters KM, Williams DE, You H. 2017. Dibenzo[def,p]chrysene transplacental carcinogenesis in wild-type, Cyp1b1 knockout, and CYP1B1 humanized mice. Mol Carcinog 56(1):163-171. doi:10.1002/mc.22480 PMID:26990437
• Nguyen H, Tilton SC, Kemp CJ. 2017. Non-monotonic pathway gene expression analysis reveals oncogenic role of p27/Kip1 at intermediate dose. Cancer Inform 16:1176935117740132. doi:10.1177/1176935117740132 PMID:29162974 PMCID:PMC5692148
• Wittwehr C, Aladjov H, Ankley GT, Byrne H, de Knecht J, Heinzle E, Klambauer G, Landesmann b, Luijten M, MacKay C, Maxwell G, Meek MB, Paini A, Perkins EJ, Sobanski T, Villeneuve DL, Waters KM, Whelan M. 2017. How adverse outcome pathways can aid the development and use of computational prediction models for regulatory toxicology. Toxicol Sci 155(2):326-336. doi:10.1093/toxsci/kfw207 PMID:27994170 PMCID:PMC5340205

2016

• Haggard DE, Noyes PD, Waters KM, Tanguay RL. 2016. Phenotypically anchored transcriptome profiling of developmental exposure to the antimicrobial agent, triclosan, reveals hepatotoxicity in embryonic zebrafish. Toxicol Appl Pharmacol 308:32-45. doi:10.1016/j.taap.2016.08.013 PMID:27538710 PMCID:PMC5023494
• Teeguarden J, Tan Y, Edwards SW, Leonard JA, Anderson KA, Corley RA, Kile ML, Simonich SL, Stone D, Tanguay RL, Waters KM, Harper SL, Williams DE. 2016. Completing the link between exposure science and toxicology for improved environmental health decision making: the aggregate exposure pathway framework. Environ Sci Technol 50(9):4579-4586. doi:10.1021/acs.est.5b05311 PMID:26759916 PMCID:PMC4854780

2015

• Goodale BC, La Du JK, Tilton SC, Sullivan CM, Bisson WH, Waters KM, Tanguay RL. 2015. Ligand-specific transcriptional mechanisms underlie aryl hydrocarbon receptor-mediated developmental toxicity of oxygenated PAHs. Toxicol Sci 147(2):397-411. doi:10.1093/toxsci/kfv139 PMID:26141390 PMCID:PMC4612346
• Lafontaine S, Schrlau J, Butler J, Jia Y, Harper B, Harris S, Bramer LM, Waters KM, Harding A, Simonich SL. 2015. Relative influence of trans-Pacific and regional atmospheric transport of PAHs in the Pacific Northwest, US. Environ Sci Technol 49(23):13807-13816. doi:10.1021/acs.est.5b00800 PMID:26151337 PMCID:PMC4666789
• Siddens LK, Bunde KL, Harper TA, McQuistan TJ, Lohr CV, Bramer LM, Waters KM, Tilton SC, Krueger SK, Williams DE, Baird WM. 2015. Cytochrome P450 1b1 in polycyclic aromatic hydrocarbon (PAH)-induced skin carcinogenesis: Tumorigenicity of individual PAHs and coal-tar extract, DNA adduction and expression of select genes in the Cyp1b1 knockout mouse. Toxicol Appl Pharmacol 287(2):149-160. doi:10.1016/j.taap.2015.05.019 PMID:26049101 PMCID:PMC4689210
• Tilton SC, Siddens LK, Krueger SK, Larkin A, Lohr CV, Williams DE, Baird WM, Waters KM. 2015. Mechanism-based classification of PAH mixtures to predict carcinogenic potential. Toxicol Sci 146(1):135-145. doi:10.1093/toxsci/kfv080 PMID:25908611 PMCID:PMC4476464

2013

• Franzosa JA, Bugel SM, Tal TL, La Du JK, Tilton SC, Waters KM, Tanguay RL. 2013. Retinoic acid-dependent regulation of miR-19 expression elicits vertebrate axis defects. FASEB J 27(12):4866-4876. doi:10.1096/fj.12-225524 PMID:23975936 PMCID:PMC3834785
• Goodale BC, Tilton SC, Corvi MM, Wilson GR, Janszen DB, Anderson KA, Waters KM, Tanguay RL. 2013. Structurally distinct polycyclic aromatic hydrocarbons induce differential transcriptional responses in developing zebrafish. Toxicol Appl Pharmacol 272(3):656-670. doi:10.1016/j.taap.2013.04.024 PMID:23656968 PMCID:PMC4098828
• Knecht AL, Goodale BC, Truong L, Simonich MT, Swanson AJ, Matzke MM, Anderson KA, Waters KM, Tanguay RL. 2013. Comparative developmental toxicity of environmentally relevant oxygenated PAHs. Toxicol Appl Pharmacol 271(2):266-275. doi:10.1016/j.taap.2013.05.006 PMID:23684558 PMCID:PMC3976560
• Motorykin O, Matzke MM, Waters KM, Simonich SL. 2013. Association of carcinogenic polycyclic aromatic hydrocarbon emissions and smoking with lung cancer mortality rates on a global scale. Environ Sci Technol 47(7):3410-3416. doi:10.1021/es305295d PMID:23472838 PMCID:PMC3634325
• Saili KS, Tilton SC, Waters KM, Tanguay RL. 2013. Global gene expression analysis reveals pathway differences between teratogenic and non-teratogenic exposure concentrations of bisphenol A and 17β-estradiol in embryonic zebrafish. Reprod Toxicol 38:89-101. doi:10.1016/j.reprotox.2013.03.009 PMID:23557687 PMCID:PMC3690774

2012

• Forsberg ND, Stone D, Harding A, Harper B, Harris S, Matzke MM, Cardenas A, Waters KM, Anderson KA. 2012. Effect of Native American fish smoking methods on dietary exposure to polycyclic aromatic hydrocarbons and possible risks to human health. J Agric Food Chem 60(27):6899-6906. doi:10.1021/jf300978m PMID:22690788 PMCID:PMC3567306
• Goodale BC, La Du JK, Bisson WH, Janszen DB, Waters KM, Tanguay RL. 2012. AHR2 mutant reveals functional diversity of aryl hydrocarbon receptors in Zebrafish. PLoS One 7(1):e29346. doi:10.1371/journal.pone.0029346 PMID:22242167 PMCID:PMC3252317
• Hobbie KA, Peterson ES, Barton ML, Waters KM, Anderson KA. 2012. Integration of data systems and technology improves research and collaboration for a Superfund Research Center. J Lab Autom 17(4):275-283. doi:10.1177/2211068212448428 PMID:22651935 PMCID:PMC3460553
• Matzke MM, Allan SE, Anderson KA, Waters KM. 2012. An approach for calculating a confidence interval from a single aquatic sample for monitoring hydrophobic organic contaminants. Environ Toxicol Chem 31(12):2888-2892. doi:10.1002/etc.2014 PMID:22997050 PMCID:PMC3581149
• Shorey LE, Castro DJ, Baird WM, Siddens LK, Lohr CV, Matzke MM, Waters KM, Corley RA, Williams DE. 2012. Transplacental carcinogenesis with dibenzo[def,p]chrysene (DBC): Timing of maternal exposures determines target tissue response in offspring. Cancer Lett 317(1):49-55. doi:10.1016/j.canlet.2011.11.010 PMID:22085489 PMCID:PMC3269513
• Siddens LK, Larkin A, Krueger SK, Bradfield CA, Waters KM, Tilton SC, Pereira CB, Lohr CV, Arlt VM, Phillips DH, Williams DE, Baird WM. 2012. Polycyclic aromatic hydrocarbons as skin carcinogens: comparison of benzo[a]pyrene, dibenzo[def,p]chrysene and three environmental mixtures in the FVB/N mouse. Toxicol Appl Pharmacol 264(3):377-386. doi:10.1016/j.taap.2012.08.014 PMID:22935520 PMCID:PMC3483092
• Tal TL, Franzosa JA, Tilton SC, Philbrick KA, Iwaniec UT, Turner RT, Waters KM, Tanguay RL. 2012. MicroRNAs control neurobehavioral development and function in zebrafish. FASEB J 26(4):1452-1461. doi:10.1096/fj.11-194464 PMID:22253472 PMCID:PMC3316906
• Tilton SC, Tal TL, Scroggins SM, Franzosa JA, Peterson ES, Tanguay RL, Waters KM. 2012. Bioinformatics resource manager v2.3: an integrated software environment for systems biology with microRNA and cross-species analysis tools. BMC Bioinformatics 13(1):311. doi:10.1186/1471-2105-13-311 PMID:23174015 PMCID:PMC3534564