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Project Publications: University of California-Berkeley: Data Science and Laboratory Core

Superfund Research Program

Data Science and Laboratory Core

Project Leader: Alan E. Hubbard
Co-Investigators: David L. Sedlak, Andres Cardenas (Stanford University)
Grant Number: P42ES004705
Funding Period: 2017-2022

Project-Specific Links



  • Beene D, Collender P, Cardenas A, Harvey CF, Huhmann LB, Lin Y, Lewis JL, Lolacono NJ, Navas-Acien A, Nigra AE, Steinmaus CM, van Geen AF. 2022. A mass-balance approach to evaluate arsenic intake and excretion in different populations. Environ Int 166:107371. doi:10.1016/j.envint.2022.107371 PMID:35809487
  • Bozack AK, Boileau P, Hubbard AE, Sille FC, Ferreccio Readi C, Steinmaus CM, Smith MT, Cardenas A. 2022. The impact of prenatal and early-life arsenic exposure on epigenetic age acceleration among adults in Northern Chile. Environ Epigenet 8(1):doi:10.1093/eep/dvac014 PMID:35769198 PMCID:PMC9235373
  • Phillips RV, Wei L, Cardenas A, Hubbard AE, McHale CM, Vermeulen R, Wei H, Smith MT, Zhang L, Lan Q, Rothman N. 2022. Epigenome-wide association studies of occupational exposure to benzene and formaldehyde. Epigenetics 1-19. doi:10.1080/15592294.2022.2115604 PMID:36017556
  • Ramaprasad AS, Smith MT, McCoy D, Hubbard AE, La Merrill MA, Durkin KA. 2022. Predicting the binding of small molecules to nuclear receptors using machine learning. Brief Bioinform 23(3):doi:10.1093/bib/bbac114 PMID:35383362 PMCID:PMC9116378


  • Bozack AK, Boileau P, Wei L, Hubbard AE, Sille FC, Ferreccio Readi C, Acevedo J, Hou L, Ilievski V, Steinmaus CM, Smith MT, Navas-Acien A, Gamble MV, Cardenas A. 2021. Exposure to arsenic at different life-stages and DNA methylation meta-analysis in buccal cells and leukocytes. Environ Health 20:79. doi:10.1186/s12940-021-00754-7 PMID:34243768 PMCID:PMC8272372
  • Bozack AK, Rifas-Shiman SL, Coull BA, Baccarelli A, Wright RO, Amarasiriwardena CJ, Gold DR, Oken E, Hivert M, Cardenas A. 2021. Prenatal metal exposure, cord blood DNA methylation and persistence in childhood: An epigenome-wide association study of 12 metals. Clin Epigenetics 13(1):208. doi:10.1186/s13148-021-01198-z PMID:34798907 PMCID:PMC8605513
  • Joyce BT, Gao T, Koss K, Zheng Y, Cardenas A, Heiss J, Just AC, Zhang K, van Horn L, Bai Allen N, Greenland P, Cohen S, Gordon-Larsen P, Mitchell C, McLanahan S, Schneper L, Notterman D, Rifas-Shiman SL, Oken E, Hivert M, Wright RO, Baccarelli A, Lloyd-Jones D, Hou L. 2021. Impact of paternal education on epigenetic ageing in adolescence and mid-adulthood: a multi-cohort study in the USA and Mexico. Int J Epidemiol PMID:34534313
  • McCoy D, Mgbara W, Horvitz N, Getz WM, Hubbard AE. 2021. Ensemble machine learning of factors influencing COVID-19 across US counties. Sci Rep 11(1):11777. doi:10.1038/s41598-021-90827-x PMID:34083563 PMCID:PMC8175420
  • Nwanaji-Enwerem JC, Jackson CL, Ottinger M, Cardenas A, James KA, Malecki K, Chen J, Geller AM, Mitchell UA. 2021. Adopting a 'compound' exposome approach in environmental aging biomarker research: A call to action for advancing racial health equity. Environ Health Perspect 129(4):4500. doi:10.1289/EHP8392 PMID:33822649 PMCID:PMC8043128
  • Smith A, Lin PD, Rifas-Shiman SL, Rahman ML, Gold DR, Baccarelli A, Claus Henn B, Amarasiriwardena CJ, Wright RO, Coull BA, Hivert M, Oken E, Cardenas A. 2021. Prospective associations of early pregnancy metal mixtures with mitochondria DNA copy number and telomere length in maternal and cord blood. Environ Health Perspect 129(11):117007. doi:10.1289/EHP9294 PMID:34797165 PMCID:PMC8604047
  • van der Laan L, Cardenas A, Vermeulen R, Fadadu RP, Hubbard AE, Phillips RV, Zhang L, Breeze C, Hu W, Wen C, Huang Y, Tang X, Smith MT, Rothman N, Lan Q. 2021. Epigenetic aging biomarkers and occupational exposure to benzene, trichloroethylene and formaldehyde. Environ Int 158:106871. doi:10.1016/j.envint.2021.106871 PMID:34560324
  • Zhao Y, Wei L, Tagmount A, Loguinov AV, Sobh A, Hubbard AE, McHale CM, Chang C, Vulpe CD, Zhang L. 2021. Applying genome-wide CRISPR to identify known and novel genes and pathways that modulate formaldehyde toxicity. Chemosphere 269:128701. doi:10.1016/j.chemosphere.2020.128701 PMID:33189395 PMCID:PMC7904579


  • Castriota F, Zushin PH, Sanchez SS, Phillips RV, Hubbard AE, Stahl A, Smith MT, Wang J, La Merrill MA. 2020. Chronic arsenic exposure impairs adaptive thermogenesis in male C57BL/6J mice. Am J Physiol Endocrinol Metab 318:E667-E677. doi:10.1152/ajpendo.00282.2019 PMID:32045263
  • Smith MT, Guyton KZ, Kleinstreuer N, Borrell A, Cardenas A, Chiu WA, Felsher DW, Gibbons CF, Goodson III WH, Houck K, Kane AB, La Merrill MA, Lebrec H, Lowe L, McHale CM, Minocherhomji S, Rieswijk L, Sandy MS, Sone H, Wang A, Zhang L, Zeise L, Fielden MR. 2020. The Key Characteristics of Carcinogens: Relationship to the Hallmarks of Cancer, Relevant Biomarkers, and Assays to Measure Them. Cancer Epidemiol Biomarkers Prev 29(10):doi:10.1158/1055-9965.EPI-19-1346 PMID:32152214 PMCID:PMC7483401


  • Gerlovina I, Hubbard AE. 2019. Computer algebra and algorithms for unbiased moment estimation of arbitrary order. Cogent Math Stat 6:doi:10.1080/25742558.2019.1701917 (accepted for publication)
  • Ju C, Benkeser D, van der Laan MJ. 2019. Robust inference on the average treatment effect using the outcome highly adaptive lasso. Biometrics doi:10.1111/biom.13121 PMID:31350906
  • Phillips RV, Rieswijk L, Hubbard AE, Vermeulen R, Zhang J, Hu W, Li L, Bassig BA, Wong JJ, Reiss B, Huang Y, Wen C, Purdue MP, Tang X, Smith MT, Rothman N, Lan Q. 2019. Human exposure to trichloroethylene is associated with increased variability of blood DNA methylation that is enriched in genes and pathways related to autoimmune disease and cancer. Epigenetics 14(11):1112-1124. doi:10.1080/15592294.2019.1633866 PMID:31241004 PMCID:PMC6773405
  • Sobh A, Loguinov AV, Yazici GN, Zeidan RS, Tagmount A, Hejazi NS, Hubbard AE, Zhang L, Vulpe CD. 2019. Functional profiling identifies determinants of arsenic trioxide cellular toxicity. Toxicol Sci 169:108-121. doi:10.1093/toxsci/kfz024 PMID:30815697 PMCID:PMC6484884
  • Zhang L, Rana L, Shaffer RM, Taioli E, Sheppard L. 2019. Exposure to glyphosate-based herbicides and risk for non-Hodgkin lymphoma: a meta-analysis and supporting evidence. Mutat Res Rev Mutat Res doi:10.1016/j.mrrev.2019.02.001 (in press)


  • Hejazi NS, Phillips RV, Hubbard AE, van der Laan MJ. 2018. Methyvim: targeted, robust, and model-free differential methylation analysis in R. F1000 Biol Rep 7:1424. doi:10.12688/f1000research.16047.1
  • Schiffman C, McHale CM, Hubbard AE, Zhang L, Thomas R, Vermeulen R, Li G, Shen M, Rappaport SM, Yin S, Lan Q, Smith MT, Rothman N. 2018. Identification of gene expression predictors of occupational benzene exposure. PLoS One 13(10):e0205427. doi:10.1371/journal.pone.0205427 PMID:30300410
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