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Project Publications: University of California-Berkeley: Quantitative Biology: Biostatistics, Bioinformatics, and Computation

Superfund Research Program

Quantitative Biology: Biostatistics, Bioinformatics, and Computation

Project Leader: Mark J. van der Laan
Co-Investigator: Alan E. Hubbard
Grant Number: P42ES004705
Funding Period: 2006-2017
View this project in the NIH Research Portfolio Online Reporting Tools (RePORT)

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  • Ju C, Bibaut A, van der Laan MJ. 2018. The relative performance of ensemble methods with deep convolutional neural networks for image classification. Journal of Applied Statistics 45(15):2800-2818. doi:10.1080/02664763.2018.1441383


  • 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


  • 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


  • 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
  • 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


  • 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



  • 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, 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
  • Porter KE, Gruber S, van der Laan MJ, Sekhon JS. 2011. The Relative Performance of Targeted Maximum Likelihood Estimators. (non-peer reviewed)
  • Wang H, van der Laan MJ. 2011. Dimension reduction with gene expression data using targeted variable importance measurement. BMC Bioinformatics 12:312. doi:10.1186/1471-2105-12-312 PMID:21849016 PMCID:PMC3166941
  • 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


  • 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


  • 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



  • 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


  • 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
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