Superfund Research Program

Alan E. Hubbard

University of California-Berkeley
Division of Biostatistics
School of Public Health
101 Haviland Hall #7358
Berkeley, California 94720-7358
Phone: 510-643-6160
Fax: 510-643-5163
Email: hubbard@stat.berkeley.edu

Projects

• University of California-Berkeley: Data Management and Analysis Core (DMAC) (2022-2027)
• University of California-Berkeley: Data Science and Laboratory Core (2017-2022)
• University of California-Berkeley: Quantitative Biology: Biostatistics, Bioinformatics, and Computation (2006-2017)

Publications

2023

• Hejazi NS, Boileau P, van der Laan MJ, Hubbard AE. 2023. A generalization of moderated statistics to data adaptive semiparametric estimation in high-dimensional biology. Stat Methods Med Res 32(3):539-554. doi:10.1177/09622802221146313 PMID:36573044
• McCoy D, Hubbard AE, van der Laan MJ. 2023. CVtreeMLE: efficient estimation of mixed exposures using data adaptive decision trees and cross-validated targeted maximum likelihood estimation in R. J Open Source Softw 8(82):4181. doi:10.21105/joss.04181 PMID:37398941 PMCID:PMC10312067
• McCoy D, Schuler A, Hubbard AE, van der Laan MJ. 2023. SuperNOVA: semi-parametric identification and estimation of interaction and effect modification in mixed exposure using stochastic interventions in R. J Open Source Softw 8(91):5422. doi:10.21105/joss.05422

2022

• 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

2021

• 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
• 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, Chung FF, van der Laan L, Novoloaca A, Cuenin C, Johansson H, Bonanni B, Hubbard AE, Smith MT, Hartman SJ, Cardenas A, Sears DD, Herceg Z. 2021. An epigenetic aging analysis of randomized metformin and weight loss interventions in overweight postmenopausal breast cancer survivors. Clin Epigenetics 13(1):224. doi:10.1186/s13148-021-01218-y PMID:34920739 PMCID:PMC8684118
• 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

2020

• 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

2019

• 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)
• 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

2018

• Daniels SI, Chambers JC, Sanchez SS, La Merrill MA, Hubbard AE, Macherone A, McMullin M, Zhang L, Elliott P, Smith MT, Kooner JS. 2018. Elevated levels of organochlorine pesticides in South Asian immigrants are associated with an increased risk of diabetes. J Endocr Soc 2(8):832-841. doi:10.1210/js.2017-00480 PMID:30019022 PMCID:PMC6041775
• 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

2017

• Lu SS, Grigoryan H, Edmands WM, Hu W, Iavarone A, Hubbard AE, Rothman N, Vermeulen R, Lan Q, Rappaport SM. 2017. Profiling the serum albumin Cys34 adductome of solid fuel users in Xuanwei and Fuyuan, China. Environ Sci Technol 51(1):46-57. doi:10.1021/acs.est.6b03955 PMID:27936627 PMCID:PMC5567851

2016

• Chambaz A, Hubbard AE, van der Laan MJ. 2016. Special issue on data-adaptive statistical inference. Int J Biostat 12(1):1. doi:10.1515/ijb-2016-0033 PMID:27227714
• Goldstein BA, Polley EC, Briggs F, van der Laan MJ, Hubbard AE. 2016. Testing the relative performance of data adaptive prediction algorithms: a generalized test of conditional risk differences. Int J Biostat 12(1):117-129. doi:10.1515/ijb-2015-0014 PMID:26529567 PMCID:PMC4854799
• Hubbard AE, Kherad-Pajouh S, van der Laan MJ. 2016. Statistical inference for data adaptive target parameters. Int J Biostat 12(1):3-19. doi:10.1515/ijb-2015-0013 PMID:27227715
• Perttula K, Edmands WM, Grigoryan H, Cai X, Iavarone A, Gunter MJ, Naccarati A, Polidoro S, Hubbard AE, Vineis P, Rappaport SM. 2016. Evaluating ultra-long-chain fatty acids as biomarkers of colorectal cancer risk. Cancer Epidemiol Biomarkers Prev 25(8):1216-1223. doi:10.1158/1055-9965.EPI-16-0204 PMID:27257090

2015

• Helb DA, Tetteh K, Felgner PL, Skinner J, Hubbard AE, Arinaitwe E, Mayanja-Kizza H, Ssewanyana I, Kamya M, Beeson JG, Tappero J, Smith DL, Crompton PD, Rosenthal P, Dorsey G, Drakeley C, Greenhouse B. 2015. Novel serologic biomarkers provide accurate estimates of recent Plasmodium falciparum exposure for individuals and communities. Proc Natl Acad Sci U S A 112(32):E4438-E4447. doi:10.1073/pnas.1501705112 PMID:26216993 PMCID:PMC4538641
• Lan Q, Smith MT, Tang X, Guo W, Vermeulen R, Ji Z, Hu W, Hubbard AE, Shen M, McHale CM, Qiu C, Liu S, Reiss B, Beane-Freeman L, Blair AE, Ge Y, Xiong J, Li L, Rappaport SM, Huang H, Rothman N, Zhang L. 2015. Chromosome-wide aneuploidy study of cultured circulating myeloid progenitor cells from workers occupationally exposed to formaldehyde. Carcinogenesis 36(1):160-167. doi:10.1093/carcin/bgu229 PMID:25391402 PMCID:PMC4291049
• Peters T, Miller A, Tourette C, Agren H, Hubbard AE, Hughes R. 2015. Genomic analysis of ATP efflux in Saccharomyces cerevisiae. G3 (Bethesda) 6(1):161-170. doi:10.1534/g3.115.023267 PMID:26585826 PMCID:PMC4704715

2014

• Cai X, Perttula K, Pajouh S, Hubbard AE, Nomura DK, Rappaport SM. 2014. Untargeted lipidomic profiling of human plasma reveals differences due to race, gender and smoking status. Metabolomics 4:131. doi:10.4172/2153-0769.1000131
• Thomas R, Hubbard AE, McHale CM, Zhang L, Rappaport SM, Lan Q, Rothman N, Vermeulen R, Guyton KZ, Jinot J, Sonawane B, Smith MT. 2014. Characterization of changes in gene expression and biochemical pathways at low levels of benzene exposure. PLoS One 9(5):e91828. doi:10.1371/journal.pone.0091828 PMID:24786086 PMCID:PMC4006721

2013

• McHale CM, Zhang L, Lan Q, Thomas R, Hubbard AE, Vermeulen R, Li G, Rappaport SM, Yin S, Smith MT, Rothman N. 2013. Toxicogenomic and systems biology approaches in the understanding of toxicity and leukemogenesis induced by benzene. The Toxicologist, Society of Toxicology Meeting, March 2013.
• Shuga J, Zeng Y, Novak R, Lan Q, Tang X, Rothman N, Vermeulen R, Li L, Hubbard AE, Zhang L, Mathies RA, Smith MT. 2013. Single molecule quantitation and sequencing of rare translocations using microfluidic nested digital PCR. Nucleic Acids Res 41(16):e159. doi:10.1093/nar/gkt613 PMID:23873959 PMCID:PMC3763562
• Thomas R, McHale CM, Lan Q, Hubbard AE, Zhang L, Vermeulen R, Li G, Rappaport SM, Yin S, Rothman N, Smith MT. 2013. Global gene expression response of a population exposed to benzene: A pilot study exploring the use of RNA-sequencing technology. Environ Mol Mutagen 54(7):566-573. doi:10.1002/em.21801 PMID:23907980 PMCID:PMC4353497

2012

• Godderis L, Thomas R, Hubbard AE, Tabish AM, Hoet P, Zhang L, Smith MT, Veulemans H, McHale CM. 2012. Effect of chemical mutagens and carcinogens on gene expression profiles in human TK6 cells. PLoS One 7(6):e39205. doi:10.1371/journal.pone.0039205 PMID:22723965 PMCID:PMC3377624
• Zhang L, Lan Q, Ji Z, Li G, Shen M, Guo W, Hubbard AE, McHale CM, Rappaport SM, Hayes RB, Linet MS, Yin S, Smith MT, Rothman N, Vermeulen R. 2012. Leukemia-specific chromosomal loss detected in hematopoietic progenitor cells of benzene-exposed workers. Leukemia 26(12):2494-2498. doi:10.1038/leu.2012.143 PMID:22643707 PMCID:PMC3472034

2011

• Hubbard AE, Jewell NP, van der Laan MJ. 2011. Direct Effects and Effect Among the Treated. Chapter 8 in: Targeted learning: causal inference for observational and experimental data. Springer, New York, NY. pp.133-143.
• McHale CM, Zhang L, Hubbard AE, Smith MT. 2011. Transcriptomic studies in human populations. Chapter 9 in: Applications of toxicogenomics in safety evaluation and risk assessment. John Wiley & Sons, Hoboken, NJ. pp.177-206.
• McHale CM, Zhang L, Lan Q, Vermeulen R, Li G, Hubbard AE, Porter KE, Thomas R, Portier CJ, Shen M, Rappaport SM, Yin S, Rothman N, Smith MT. 2011. Global gene expression profiling of a population exposed to a range of benzene levels. Environ Health Perspect 119:628-634. doi:10.1289/ehp.1002546 PMID:21147609 PMCID:PMC3094412
• North M, Tandon VJ, Thomas R, Loguinov AV, Gerlovina I, Hubbard AE, Zhang L, Smith MT, Vulpe CD. 2011. Genome-wide functional profiling reveals genes required for tolerance to benzene metabolites in yeast. PLoS One 6(8):e24205. doi:10.1371/journal.pone.0024205 PMID:21912624 PMCID:PMC3166172
• Zhang L, Lan Q, Guo W, Hubbard AE, Li G, Rappaport SM, McHale CM, Shen M, Vermeulen R, Yin S, Rothman N, Smith MT, Ji Z. 2011. Chromosome-wide aneuploidy study (CWAS) in workers exposed to an established leukemogen, benzene. Carcinogenesis 32:605-612. doi:10.1093/carcin/bgq286 PMID:21216845 PMCID:PMC3066415

2010

• Porter KE, Basu A, Hubbard AE, Bates MN, Kalman DA, Rey OA, Smith AH, Smith MT, Steinmaus CM, Skibola CF. 2010. Association of genetic variation in cystathionine-beta-synthase and arsenic metabolism. Environ Res 110(6):580-587. doi:10.1016/j.envres.2010.05.001 PMID:20670920 PMCID:PMC2913479
• Steinmaus CM, Yuan Y, Kalman DA, Rey OA, Skibola CF, Dauphine DC, Basu A, Porter KE, Hubbard AE, Bates MN, Smith MT, Smith AH. 2010. Individual differences in arsenic metabolism and lung cancer in a case-control study in Cordoba, Argentina. Toxicol Appl Pharmacol 247(2):138-145. doi:10.1016/j.taap.2010.06.006 PMID:20600216 PMCID:PMC3849353
• Zhang L, McHale CM, Rothman N, Li G, Ji Z, Vermeulen R, Hubbard AE, Ren X, Shen M, Rappaport SM, North M, Skibola CF, Yin S, Vulpe CD, Chanock SJ, Smith MT, Lan Q. 2010. Systems biology of human benzene exposure. Chem Biol Interact 184(1-2):86-93. doi:10.1016/j.cbi.2009.12.011 PMID:20026094 PMCID:PMC2846187
• Zhang L, Tang X, Rothman N, Vermeulen R, Ji Z, Shen M, Qiu C, Guo W, Liu S, Reiss B, Freeman LB, Ge Y, Hubbard AE, Hua M, Blair AE, Galvan N, Ruan X, Alter BP, Xin KX, Li S, Moore LE, Kim S, Xie Y, Hayes RB, Azuma M, Hauptmann M, Xiong J, Stewart P, Li L, Rappaport SM, Huang H, Fraumeni JF, Smith MT, Lan Q. 2010. Occupational exposure to formaldehyde, hematotoxicity, and leukemia-specific chromosome changes in cultured myeloid progenitor cells. Cancer Epidemiol Biomarkers Prev 19(1):80-88. doi:10.1158/1055-9965.EPI-09-0762 PMID:20056626 PMCID:PMC2974570

2009

• McHale CM, Zhang L, Lan Q, Li G, Hubbard AE, Forrest MS, Vermeulen R, Chen J, Shen M, Rappaport SM, Yin S, Smith MT, Rothman N. 2009. Changes in the peripheral blood transcriptome associated with occupational benzene exposure identified by cross-comparison on two microarray platforms. Genomics 93(4):343-349. doi:10.1016/j.ygeno.2008.12.006 PMID:19162166 PMCID:PMC2693268

2008

• Hubbard AE, van der Laan MJ. 2008. Population Intervention models In causal inference. Biometrika 95(1):35-47. doi:10.1093/biomet/asm097 PMID:18629347
• Johnson DR, Brodie EL, Hubbard AE, Andersen GL, Zinder SH, Alvarez-Cohen L. 2008. Temporal transcriptomic microarray analysis of "Dehalococcoides ethenogenes" strain 195 during the transition into stationary phase. Appl Environ Microbiol 74(9):2864-2872. doi:10.1128/AEM.02208-07 PMID:18310438 PMCID:PMC2394897
• Skibola CF, Nieters A, Bracci PM, Curry JD, Agana L, Skibola DR, Hubbard AE, Becker N, Smith MT, Holly EA. 2008. A functional TNFRSF5 gene variant is associated with risk of lymphoma. Blood 111(8):4348-4354. doi:10.1182/blood-2007-09-112144 PMID:18287517 PMCID:PMC2288730

2007

• Chen J, van der Laan MJ, Smith MT, Hubbard AE. 2007. A comparison of methods to control type I errors in microarray studies. Stat Appl Genet Mol Biol 6:Article28. doi:10.2202/1544-6115.1310 PMID:18052911
• Escobar PA, Smith MT, Vasishta A, Hubbard AE, Zhang L. 2007. Leukaemia-specific chromosome damage detected by comet with fluorescence in situ hybridization (comet-FISH). Mutagenesis 22(5):321-327. doi:10.1093/mutage/gem020 PMID:17575318
• McHale CM, Zhang L, Hubbard AE, Zhao X, Baccarelli A, Pesatori AC, Smith MT, Landi MT. 2007. Microarray analysis of gene expression in peripheral blood mononuclear cells from dioxin-exposed human subjects. Toxicology 229:101-113. PMID:17101203
• van der Laan MJ, Polley EC, Hubbard AE. 2007. Super Learning. Stat Appl Genet Mol Biol 6(1):25.
• Zhang L, Rothman N, Li G, Guo W, Yang W, Hubbard AE, Hayes RB, Yin S, Lu W, Smith MT. 2007. Aberrations in chromosomes associated with lymphoma and therapy-related leukemia in benzene-exposed workers. Environ Mol Mutagen 48(6):467-74. PMID:17584886

2006

• Birkner MD, Hubbard AE, van der Laan MJ, Skibola CF, Hegedus CM, Smith MT. 2006. Issues of processing and multiple testing of SELDI-TOF MS proteomic data. Stat Appl Genet Mol Biol 5:Article11. doi:10.2202/1544-6115.1198 PMID:16646865
• van der Laan MJ, Birkner MD, Hubbard AE. 2006. Empirical Bayes and resampling based multiple testing procedure controlling tail probability of the proportion of false positives. Stat Appl Genet Mol Biol 4(1):Article29. PMID:16646847
• van der Laan MJ, Hubbard AE. 2006. Quantile-function based null distribution in resampling based multiple testing. Stat Appl Genet Mol Biol 5:Article14. doi:10.2202/1544-6115.1199 PMID:17049025

2004

• Duramad P, McMahon CW, Hubbard AE, Eskenazi B, Holland NT. 2004. Flow cytometric detection of intracellular Th1/Th2 cytokines using whole blood: Validation of immunologic biomarker for use in epidemiologic studies. Cancer Epidemiol Biomarkers Prev 13(9):1452-1458. PMID:15342445

2002

• Holland NT, Duramad P, Rothman N, Figgs LW, Blair AE, Hubbard AE, Smith MT. 2002. Micronucleus frequency and proliferation in human lymphocytes after exposure to herbicide 2,4-dichlorophenoxyacetic acid in vitro and in vivo. Mutat Res 521(1-2):165-78. PMID:12438013
• Skibola CF, Smith MT, Hubbard AE, Shane B, Roberts AC, Law GR, Rollinson S, Roman E, Cartwright RA, Morgan GJ. 2002. Polymorphisms in the thymidylate synthase and serine hydroxymethyltransferase genes and risk of adult acute lymphocytic leukemia. Blood 99(10):3786-3791. PMID:11986237
• Skibola CF, Smith MT, Hubbard AE, Shane B, Roberts AC, Law GR, Rollinson S, Roman E, Cartwright RA, Morgan GJ. 2002. Polymorphisms in the thymidylate synthase and serine hydroxymethyltransferase genes increase the risk of adult acute leukemia. In: Proceedings of the Ninety Third (AACR) American Association for Cancer Research, April 6-10, 2002, San Francisco. San Franciso, CA. pp.3807.
• Yang W, Zhang L, Hubbard AE, Wang Y, Smith MT. 2002. Non-random chromosome damage may be important in chemical carinogenesis. In: Proceedings of the Ninety Third (AACR) American Association for Cancer Research, April 6-10, 2002, San Francisco. San Franciso, CA. pp.3451.
• Zhang L, Yang W, Hubbard AE, Wang Y, Smith MT. 2002. Is chromosomal aneuploidy induced by benzene metabolites random or selective?. Environ Mol Mutagen 39(Suppl33):230.

2000

• Smith MT, Zhang L, Jeng M, Wang Y, Guo W, Duramad P, Hubbard AE, Hofstadler G, Holland NT. 2000. Hydroquinone, a benzene metabolite, increases the level of aneusomy of chromosomes 7 and 8 in human CD34-positive blood progenitor cells. Carcinogenesis 21(8):1485-1490. PMID:10910948