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Joshua Millstein, PhD

TitleAssistant Professor of Research Preventive Medicine
InstitutionUniversity of Southern California
DepartmentPreventive Medicine
AddressSSB 202N 2001 N. Soto Street
Health Sciences Campus
Los Angeles CA 90033
Phone+1 323 442 1450
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    Dr. Millstein first developed an interest in the analytic challenges arising from high throughput molecular data during his graduate studies at USC. As part of his dissertation he pioneered a two-stage analysis approach for identifying genes involved in epistasis in the context of case-control data. After a brief stint exploring the Gulf of Alaska and the Berring Sea as a Mathematical Statistician for the National Marine Fisheries Service (NMFS/NOAA), he joined Eric Schadt’s group at Rosetta Inpharmatics. There he became interested in integrative genomics studies, developing and applying methods for studies that included both genome-wide DNA and gene expression data. In 2009, Rosetta was dismantled by its owner, Merck & Co. Inc., which prompted Millstein to join the then new non-profit company, Sage Bionetworks, co-founded by Schadt and Stephen Friend, the previous Senior Vice President of Oncology at Merck. Millstein then migrated back to Los Angeles from Seattle in July 2011 to join his alma mater and continue his pursuit of the ‘missing heritability’.


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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
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    1. Gao L, Liu X, Millstein J, Siegmund KD, Dubeau L, Maguire RL, Jim Zhang J, Fuemmeler BF, Kollins SH, Hoyo C, Murphy SK, Breton CV. Self-reported prenatal tobacco smoke exposure, AXL gene-body methylation, and childhood asthma phenotypes. Clin Epigenetics. 2018 Jul 20; 10(1):98. PMID: 30029617.
      View in: PubMed
    2. Chen Y, Millstein J, Liu Y, Chen GY, Chen X, Stucky A, Qu C, Fan JB, Chang X, Soleimany A, Wang K, Zhong J, Liu J, Gilliland FD, Li Z, Zhang X, Zhong JF. Single-Cell Digital Lysates Generated by Phase-Switch Microfluidic Device Reveal Transcriptome Perturbation of Cell Cycle. ACS Nano. 2018 Apr 18. PMID: 29589910.
      View in: PubMed
    3. Kothari PH, Qiu W, Croteau-Chonka DC, Martinez FD, Liu AH, Lemanske RF, Ober C, Krishnan JA, Nicolae DL, Barnes KC, London SJ, Barraza-Villarreal A, White SR, Naureckas ET, Millstein J, Gauderman WJ, Gilliland FD, Carey VJ, Weiss ST, Raby BA. Role of local CpG DNA methylation in mediating the 17q21 asthma susceptibility gasdermin B (GSDMB)/ORMDL sphingolipid biosynthesis regulator 3 (ORMDL3) expression quantitative trait locus. J Allergy Clin Immunol. 2018 Jan 31. PMID: 29374573.
      View in: PubMed
    4. Gao L, Millstein J, Siegmund KD, Dubeau L, Maguire R, Gilliland FD, Murphy SK, Hoyo C, Breton CV. Epigenetic regulation of AXL and risk of childhood asthma symptoms. Clin Epigenetics. 2017; 9:121. PMID: 29177020.
      View in: PubMed
    5. Croteau-Chonka DC, Qiu W, Martinez FD, Strunk RC, Lemanske RF, Liu AH, Gilliland FD, Millstein J, Gauderman WJ, Ober C, Krishnan JA, White SR, Naureckas ET, Nicolae DL, Barnes KC, London SJ, Barraza-Villarreal A, Carey VJ, Weiss ST, Raby BA. Gene Expression Profiling in Blood Provides Reproducible Molecular Insights into Asthma Control. Am J Respir Crit Care Med. 2017 Jan 15; 195(2):179-188. PMID: 27494826.
      View in: PubMed
    6. Breton CV, Yao J, Millstein J, Gao L, Siegmund KD, Mack W, Whitfield-Maxwell L, Lurmann F, Hodis H, Avol E, Gilliland FD. Prenatal Air Pollution Exposures, DNA Methyl Transferase Genotypes, and Associations with Newborn LINE1 and Alu Methylation and Childhood Blood Pressure and Carotid Intima-Media Thickness in the Children's Health Study. Environ Health Perspect. 2016 12; 124(12):1905-1912. PMID: 27219456.
      View in: PubMed
    7. Millstein J, Chen GK, Breton CV. cit: hypothesis testing software for mediation analysis in genomic applications. Bioinformatics. 2016 08 01; 32(15):2364-5. PMID: 27153715; PMCID: PMC4965632 [Available on 08/01/17].
    8. Lawrenson K, Grun B, Lee N, Mhawech-Fauceglia P, Kan J, Swenson S, Lin YG, Pejovic T, Millstein J, Gayther SA. NPPB is a novel candidate biomarker expressed by cancer-associated fibroblasts in epithelial ovarian cancer. Int J Cancer. 2015 Mar 15; 136(6):1390-401. PMID: 25047817; PMCID: PMC4289413.
    9. Serrao E, Wang CH, Frederick T, Lee CL, Anthony P, Arribas-Layton D, Baker K, Millstein J, Kovacs A, Neamati N. Alteration of select gene expression patterns in individuals infected with HIV-1. J Med Virol. 2014 Apr; 86(4):678-86. PMID: 24482297.
      View in: PubMed
    10. Millstein J. Screening-testing approaches for gene-gene and gene-environment interactions using independent statistics. Front Genet. 2013; 4:306. PMID: 24416039; PMCID: PMC3874470.
    11. Millstein J, Volfson D. Computationally efficient permutation-based confidence interval estimation for tail-area FDR. Front Genet. 2013; 4:179. PMID: 24062767; PMCID: PMC3775454.
    12. Schadt EE, Molony C, Chudin E, Hao K, Yang X, Lum PY, Kasarskis A, Zhang B, Wang S, Suver C, Zhu J, Millstein J, Sieberts S, Lamb J, GuhaThakurta D, Derry J, Storey JD, Avila-Campillo I, Kruger MJ, Johnson JM, Rohl CA, van Nas A, Mehrabian M, Drake TA, Lusis AJ, Smith RC, Guengerich FP, Strom SC, Schuetz E, Rushmore TH, Ulrich R. Mapping the genetic architecture of gene expression in human liver. PLoS Biol. 2008 May 06; 6(5):e107. PMID: 18462017; PMCID: PMC2365981.
    13. Künzli N, Avol E, Wu J, Gauderman WJ, Rappaport E, Millstein J, Bennion J, McConnell R, Gilliland FD, Berhane K, Lurmann F, Winer A, Peters JM. Health effects of the 2003 Southern California wildfires on children. Am J Respir Crit Care Med. 2006 Dec 01; 174(11):1221-8. PMID: 16946126; PMCID: PMC2648104.
    14. Millstein J, Siegmund KD, Conti DV, Gauderman WJ. Identifying susceptibility genes by using joint tests of association and linkage and accounting for epistasis. BMC Genet. 2005 Dec 30; 6 Suppl 1:S147. PMID: 16451607; PMCID: PMC1866788.
    15. Millstein J, Conti DV, Gilliland FD, Gauderman WJ. A testing framework for identifying susceptibility genes in the presence of epistasis. Am J Hum Genet. 2006 Jan; 78(1):15-27. PMID: 16385446; PMCID: PMC1380213.
    16. Millstein J, Siegmund KD, Conti DV, Gauderman WJ. Testing association and linkage using affected-sib-parent study designs. Genet Epidemiol. 2005 Nov; 29(3):225-33. PMID: 16121357.
      View in: PubMed
    17. Salam MT, Millstein J, Li YF, Lurmann FW, Margolis HG, Gilliland FD. Birth outcomes and prenatal exposure to ozone, carbon monoxide, and particulate matter: results from the Children's Health Study. Environ Health Perspect. 2005 Nov; 113(11):1638-44. PMID: 16263524; PMCID: PMC1310931.
    18. Millstein J, Gilliland F, Berhane K, Gauderman WJ, McConnell R, Avol E, Rappaport EB, Peters JM. Effects of ambient air pollutants on asthma medication use and wheezing among fourth-grade school children from 12 Southern California communities enrolled in The Children's Health Study. Arch Environ Health. 2004 Oct; 59(10):505-14. PMID: 16425660.
      View in: PubMed
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