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National Institute of Environmental Health Sciences

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Your Environment. Your Health.

Project Publications: University of North Carolina-Chapel Hill: Data Management and Analysis Core (DMAC)

Superfund Research Program

Data Management and Analysis Core (DMAC)

Project Leader: Stanley Carlton Ahalt
Co-Investigators: Fei Zou, Julia E. Rager, Haibo Zhou, William Christopher Lenhardt
Grant Number: P42ES031007
Funding Period: 2020-2025
View this project in the NIH Research Portfolio Online Reporting Tools (RePORT)

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Publications

2023

  • Carberry C, Bangma J, Koval L, Keshava D, Hartwell HJ, Sokolsky M, Fry RC, Rager JE. 2023. Extracellular vesicles altered by a per- and polyfluoroalkyl substance mixture: in vitro dose-dependent release, chemical content, and MicroRNA signatures involved in liver health. Toxicol Sci doi:10.1093/toxsci/kfad108 PMID:37851381
  • Eaves LA, Keil AP, Jukic AM, Dhingra R, Brooks JL, Manuck TA, Rager JE, Fry RC. 2023. Toxic metal mixtures in private well water and increased risk for preterm birth in North Carolina. Environmental Health 22(1):69. doi:10.1186/s12940-023-01021-7 PMID:37845729 PMCID:PMC10577978
  • Eaves LA, Lanier P, Enggasser AE, Chung G, Turla T, Rager JE, Fry RC. 2023. Generation of the Chemical and Social Stressors Integration Technique (CASS-IT) to identify areas of holistic public health concern: an application to North Carolina. Sci Total Environ 862:160409. doi:10.1016/j.scitotenv.2022.160409 PMID:36436630
  • Freedman AN, Clark J, Eaves LA, Roell K, Oran A, Koval L, Rager JE, Santos HP, Kuban K, Joseph RM, Frazier JA, Marsit CJ, Burt AA, O'Shea TM, Fry RC. 2023. A multi-omic approach identifies an autism spectrum disorder (ASD) regulatory complex of functional epimutations in placentas from children born preterm. Autism Res 16(5):918-934. doi:10.1002/aur.2915 PMID:36938998 PMCID:PMC10192070
  • Payton A, Roell K, Rebuli ME, Valdar W, Rager JE. 2023. Navigating the bridge between wet and dry lab toxicology research to address current challenges with high-dimensional data. Front Toxicol 5:1171175. doi:10.3389/ftox.2023.1171175 PMID:37304253 PMCID:PMC10250703
  • Rager JE, Rider CV. 2023. Wrangling whole mixtures risk assessment: Recent advances in determining sufficient similarity. Curr Opin Toxicol 35:100417. doi:10.1016/j.cotox.2023.100417
  • Vitucci EC, Carberry C, Payton A, Herring L, Mordant AL, McCullough S, Rager JE. 2023. Characterizing the extracellular vesicle proteomic landscape of the human airway using in vitro organotypic multi-cellular models. iScience 26(11):108162. doi:10.1016/j.isci.2023.108162 PMID:37920665 PMCID:PMC10618692
  • Yan F, Liu Y, Cai J, Zhou H. 2023. Estimated quadratic inference function for correlated failure time data. Biometrics 79(2):1145-1158. doi:10.1111/biom.13633 PMID:35146750 PMCID:PMC9365883

2022

  • Avery CL, Howard AG, Ballou AF, Buchanan VL, Collins JM, Downie CG, Engel SM, Graff M, Highland HM, Lee MP, Lilly AG, Lu K, Rager JE, Staley BS, North KE, Gordon-Larsen P. 2022. Strengthening Causal Inference in Exposomics Research: Application of Genetic Data and Methods. Environ Health Perspect 130(5):55001. doi:10.1289/EHP9098 PMID:35533073 PMCID:PMC9084332
  • Carberry C, Ferguson SS, Beltran AS, Fry RC, Rager JE. 2022. Using liver models generated from human-induced pluripotent stem cells (iPSCs) for evaluating chemical-induced modifications and disease across liver developmental stages. Toxicol Vitro 83:doi:10.1016/j.tiv.2022.105412 PMID:35688329
  • Carberry C, Keshava D, Payton A, Smith GJ, Rager JE. 2022. Approaches to incorporate extracellular vesicles into exposure science, toxicology, and public health research. J Expo Sci Environ Epidemiol 32(5):647-659. doi:10.1038/s41370-022-00417-w PMID:35217808 PMCID:PMC9402811
  • Carberry C, Koval L, Payton A, Hartwell HJ, Kim YH, Smith GJ, Reif DM, Jaspers I, Gilmour MI, Rager JE. 2022. Wildfires and extracellular vesicles: Exosomal MicroRNAs as mediators of cross-tissue cardiopulmonary responses to biomass smoke. Environ Int 167:doi:10.1016/j.envint.2022.107419 PMID:35863239 PMCID:PMC9389917
  • Carberry C, Rager JE. 2022. The impact of environmental contaminants on extracellular vesicles and their key molecular regulators: A literature and database-driven review. Environ Mol Mutagen doi:10.1002/em.22522 PMID:36502378
  • Carberry C, Turla T, Koval L, Hartwell HJ, Fry RC, Rager JE. 2022. Chemical mixtures in household environments: In silico prediction and in vitro testing of potential join action on PPARy in human liver cells. Toxics 10(5):199. doi:10.3390/toxics10050199 PMID:35622613 PMCID:PMC9146550
  • Chao A, Grossman J, Carberry C, Lai Y, Williams AJ, Minucci JM, Purucker ST, Szilagyi JT, Lu K, Boggess K, Fry RC, Sobus JR, Rager JE. 2022. Integrative exposomic, transcriptomic, epigenomic analyses of human placental samples links understudied chemicals to preeclampsia. Environ Int 167:107385. doi:10.1016/j.envint.2022.107385 PMID:35952468 PMCID:PMC9552572
  • Freedman AN, Eaves LA, Rager JE, Gavino-Lopez N, Smeester L, Bangma J, Santos HP, Joseph RM, Kuban KC, O'Shea TM, Fry RC. 2022. The placenta epigenome-brain axis: placental epigenomic and transcriptomic responses that preprogram cognitive impairment. Epigenomics 14(15):897-911. doi:10.2217/epi-2022-0061 PMID:36073148
  • Johnson KJ, Auerbach SS, Stevens T, Barton-Maclaren TS, Costa E, Currie RA, Wilk DD, Haq S, Rager JE, Reardon AJ, Wehmas L, Williams A, O'Brien J, Yauk C, LaRocca JL, Pettit S. 2022. A transformative vision for an omics-based regulatory chemical testing paradigm. Toxicol Sci 190(2):127-132. doi:10.1093/toxsci/kfac097 PMID:36165699 PMCID:PMC9702989
  • Koval L, Carberry C, Kim YH, McDermott E, Hartwell HJ, Jaspers I, Gilmour MI, Rager JE. 2022. Wildfire variable toxicity: identifying biomass smoke exposure groupings through transcriptomic similarity scoring. Environ Sci Technol 56(23):17131-17142. doi:10.1021/acs.est.2c06043 PMID:36399130
  • Koval L, Dionisio KL, Friedman KP, Isaacs KK, Rager JE. 2022. Environmental mixtures and breast cancer: identifying co-exposure patterns between understudied vs breast cancer-associated chemicals using chemical inventory informatics. J Expo Sci Environ Epidemiol doi:10.1038/s41370-022-00451-8 PMID:35710593
  • Mahung C, Stepp WH, Long C, Malfitano M, Saklayici I, Wallet SM, Zhou LY, Zhou H, Cairns BA, Maile R. 2022. Early expression of IL-10, IL-12, ARG1, and NOS2 genes in peripheral blood mononuclear cells synergistically correlate with patient outcome after burn injury. J Trauma Acute Care Surg 93(5):702-711. doi:10.1097/TA.0000000000003602 PMID:35363228 PMCID:PMC9522922
  • Mahung C, Wallet SM, Jacobs JE, Zhou LY, Zhou H, Cairns BA, Maile R. 2022. Multiplexed human gene expression analysis reveals a central role of the TLR/mTOR/PPARy and NFkB axes in burn and inhalation injury-induced changes in systemic immunometabolism and long-term patient outcomes. Int J Mol Sci 23(16):9418. doi:10.3390/ijms23169418 PMID:36012680 PMCID:PMC9409318
  • Payton A, Perryman AN, Hoffman JR, Avula V, Wells H, Robinette C, Alexis N, Jaspers I, Rager JE, Rebuli ME. 2022. Cytokine signature clusters as a tool to compare changes associated with tobacco product use in upper and lower airway samples. Am J Physiol Lung Cell Mol Physiol 322(5):L722-L736. doi:10.1152/ajplung.00299.2021 PMID:35318855 PMCID:PMC9054348
  • Roell K, Koval L, Boyles R, Patlewicz G, Ring C, Rider CV, Ward-Caviness C, Reif DM, Jaspers I, Fry RC, Rager JE. 2022. Development of the InTelligence and Machine LEarning (TAME) Toolkit for introductory data science, chemical-biological analyses, predictive modeling, and database mining for environmental health research. Front Toxicol 4:doi:10.3389/ftox.2022.893924 PMID:35812168 PMCID:PMC9257219
  • Wambaugh J, Rager JE. 2022. Exposure forecasting - ExpoCast - for data-poor chemicals in commerce and the environment. J Expo Sci Environ Epidemiol doi:10.1038/s41370-022-00492-z PMID:36347934
  • Zhabotynsky V, Huang L, Little P, Hu Y, Pardo-Manuel de Villena F, Zou F, Sun W. 2022. eQTL mapping using allele-specific count data is computationally feasible, powerful, and provides individual-specific estimates of genetic effects. PLoS Genet 18:doi:10.1371/journal.pgen.1010076 PMID:35286297 PMCID:PMC8947591
  • Zou B, Santos HP, Xenakis JG, O'Shea M, Fry RC, Zou F. 2022. A mixed-effects two-part model for twin-data and an application on identifying important factors associated with extremely preterm children's health disorders. PLoS One 17(6):doi:10.1371/journal.pone.0269630 PMID:35696398 PMCID:PMC9191696

2021

  • Chang Y, Rager JE, Tilton SC. 2021. Linking coregulated gene modules with polycyclic aromatic hydrocarbon-related cancer risk in the 3D human bronchial epithelium. Chem Res Toxicol 34(6):1445-1455. doi:10.1021/acs.chemrestox.0c00333 PMID:34048650
  • Clark J, Avula V, Ring C, Eaves LA, Howard T, Santos HP, Smeester L, Bangma J, O'Shea TM, Fry RC, Rager JE. 2021. Comparing the predictivity of human placental gene, microRNA, and CpG methylation signatures in relation to perinatal outcomes. Toxicol Sci 183(2):269-284. doi:10.1093/toxsci/kfab089 PMID:34255065 PMCID:PMC8478332
  • Clark J, Eaves LA, Gaona AR, Santos HP, Smeester L, Bangma J, Rager JE, O'Shea TM, Fry RC. 2021. Pre-pregnancy BMI-associated miRNA and mRNA expression signatures in the placenta highlight a sexually-dimorphic response to maternal underweight status. Sci Rep 11(1):15743. doi:10.1038/s41598-021-95051-1 PMID:34344912 PMCID:PMC8333418
  • Eaves LA, Keil A, Rager JE, George A, Fry RC. 2021. Analysis of the novel NCWELL database highlights two decades of co-occurrence of toxic metals in North Carolina private well water: Public health and environmental justice implications. Sci Total Environ 812:151479. doi:10.1016/j.scitotenv.2021.151479 PMID:34767890 (ahead of print)
  • Liu Y, Wu Y, Zhang J, Zhou H. 2021. Cox regression analysis for distorted covariates with an unknown distortion function. Biom J 63(5):doi:10.1002/bimj.202000209 PMID:33687092 (ahead of print)
  • Manuck TA, Eaves LA, Rager JE, Sheffield-Abdullah K, Fry RC. 2021. Nitric oxide-related gene and microRNA expression in peripheral blood in pregnancy vary by self-reported race. Epigenetics 1-15. doi:10.1080/15592294.2021.1957576 PMID:34308756
  • Manuck TA, Lai Y, Ru H, Glover AV, Rager JE, Fry RC, Lu K. 2021. Metabolites from mid-trimester plasma of pregnant patients at high-risk for preterm birth. Am J Obstet Gynecol 3(4):doi:10.1016/j.ajogmf.2021.100393 PMID:33991707 (ahead of print)
  • Mischler A, Karakis V, Mahinthakumar J, Carberry C, San Miguel A, Rager JE, Fry RC, Rao BM. 2021. Two distinct trophectoderm lineage stem cells from human pluripotent stem cells. J Biol Chem 296:100386. doi:10.1016/j.jbc.2021.100386 PMID:33556374 PMCID:PMC7948510
  • Rager JE, Clark J, Eaves LA, Avula V, Niehoff NM, Kim YH, Jaspers I, Gilmour MI. 2021. Mixtures modeling identifies chemical inducers versus repressors of toxicity associated with wildfire smoke. Sci Total Environ 775:145749. doi:10.1016/j.scitotenv.2021.145759 PMID:33611182 PMCID:PMC8243846
  • Ring C, Sipes N, Hsieh J, Carberry C, Koval L, Klaren WD, Harris M, Auerbach SS, Rager JE. 2021. Predictive modeling of biological responses in the rat liver using in vitro Tox21 bioactivity: Benefits from high-throughput toxicokinetics. Comput Toxicol 18:doi:10.1016/j.comtox.2021.100166 PMID:34013136 PMCID:PMC8130852
  • Yan F, Zhu L, Liu Y, Cai J, Zhou H. 2021. Semiparametric regression based on quadratic inference function for multivariate failure time data with auxiliary information. Lifetime Data Analysis 27:269-299. doi:10.1007/s10985-020-09513-1 PMID:33420545 PMCID:PMC7943434
  • Yu J, Zhou H, Cai J. 2021. Accelerated failure time model for data from outcome-dependent sampling. Lifetime Data Analysis 27:15-37. doi:10.1007/s10985-020-09508-y PMID:33044612 PMCID:PMC7856009
  • Zhang J, Zhou H, Liu Y, Cai J. 2021. Conditional screening for ultrahigh-dimensional survival data in case-cohort studies. Lifetime Data Analysis 27(4):doi:10.1007/s10985-021-09531-7 PMID:34417679 (ahead of print)
  • Zhou Q, Cai J, Zhou H. 2021. Semiparametric regression analysis of case-cohort studies with multiple interval-censored disease outcomes. Stat Med 40(13):doi:10.1002/sim.8962 PMID:33783001 (ahead of print)

2020

  • Eaves LA, Nguyen HT, Rager JE, Sexton K, Howard T, Smeester L, Freedman AN, Aagaard KM, Shope C, Lefer B, Flynn JH, Erickson MH, Fry RC, Vizuete W. 2020. Identifying the Transcriptional Response of Cancer and Inflammation-Related Genes in Lung Cells in Relation to Ambient Air Chemical Mixtures. Environ Sci Technol 1380713816.
  • Eaves LA, Phookphan P, Rager JE, Bangma J, Santos H, Smeester L, O'Shea TM, Fry RC. 2020. A role for microRNAs in the epigenetic control of sexually dimorphic gene expression in the human placenta. Epigenomics 12:doi:10.2217/epi-2020-0062 PMID:32901510
  • Gomez JL, Chen A, Diaz M, Zirn N, Gupta A, Britto C, Sauler M, Yan X, Stewart E, Santerian K, Grant N, Liu Q, Fry RC, Rager JE, Cohn L, Alexis N, Chupp GL. 2020. A network of sputum microRNAs is associated with neutrophilic airway inflammation in asthma. Am J Respir Crit Care Med 1:51-64. doi:10.1164/rccm.201912-2360OC PMID:32255668 PMCID:PMC7328332
  • Payton A, Clark J, Eaves LA, Santos H, Smeester L, Bangma J, O'Shea TM, Fry RC, Rager JE. 2020. Placental genomic and epigenomic signatures associated with infant birth weight highlight mechanisms involved in collagen and growth factor signaling. Reprod Toxicol 96:221-230. doi:10.1016/j.reprotox.2020.07.007 PMID:32721520 PMCID:PMC7855285
  • Rager JE, Bangma J, Carberry C, Chao A, Grossman J, Lu K, Manuck TA, Sobus JR, Szilagyi JT, Fry RC. 2020. Review of the environmental prenatal exposome and its relationship to maternal and fetal health. Reprod Toxicol 98:1-12. doi:10.1016/j.reprotox.2020.02.004 PMID:32061676 PMCID:PMC7442624
  • Wang T, Wang X, George SL, Zhou H. 2020. Design and analysis of biomarker-integrated clinical trials with adaptive threshold detection and flexible patient enrichment. Journal of Biopharmaceutical Statistics 30:1060-1076. doi:10.1080/10543406.2020.1832110 PMID:33175640 PMCID:PMC7954851
  • Zavala J, Freedman AN, Szilagyi JT, Jaspers I, Wambaugh J, Higuchi M, Rager JE. 2020. New Approach Methods to Evaluate Health Risks of Air Pollutants: Critical Design Considerations for In Vitro Exposure Testing. Int J Environ Res Public Health 6:2124. doi:10.3390/ijerph17062124 PMID:32210027 PMCID:PMC7143849
  • Zhang J, Zhou H, Liu Y, Cai J. 2020. Feature screening for case-cohort studies with failure time outcome. Scandinavian Journal of Statistics doi:10.1111/sjos.12503 (ahead of print)
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