Joshua Millstein, PhD

Associate Professor of Research Population and Public Health Sciences

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Dr. Millstein’s research is focused on developing and applying statistical methods to address the many challenges of high dimensional data, particularly in multi-omic population-based studies of the genome, epigenome, transcriptome, microbiome, etc., in the context of pathogenesis of complex diseases such as cancer. With massive amounts of data collected in typical studies due to these advancing technologies, it has become increasingly important to have computational tools able to sift through all the information to separate the signal of interest from the noise. Specific areas of methods development include, causal mediation (CIT), dimensionality reduction, causal networks, false discovery rates (FDR), and epistasis/statistical interactions.


  • Impact of genetic variants involved in the lipid metabolism pathway on progression free survival in patients receiving bevacizumab-based chemotherapy in metastatic colorectal cancer: a retrospective analysis of FIRE-3 and MAVERICC trials EClinicalMedicine. 2023 Mar; 57:101827. . View in PubMed
  • CausNet: generational orderings based search for optimal Bayesian networks via dynamic programming with parent set constraints BMC Bioinformatics. 2023 Feb 14; 24(1):46. . View in PubMed
  • Transcriptional Profiling and Consensus Molecular Subtype Assignment to Understand Response and Resistance to Anti-Epidermal Growth Factor Receptor Therapy in Colorectal Cancer JCO Precis Oncol. 2023 07; 7:e2200422. . View in PubMed
  • Breast cancer and neurotransmitters: emerging insights on mechanisms and therapeutic directions Oncogene. 2023 02; 42(9):627-637. . View in PubMed
  • Mutational analysis of microsatellite-stable gastrointestinal cancer with high tumour mutational burden: a retrospective cohort study Lancet Oncol. 2023 02; 24(2):151-161. . View in PubMed
  • CCNE1 and survival of patients with tubo-ovarian high-grade serous carcinoma: An Ovarian Tumor Tissue Analysis consortium study Cancer. 2023 03 01; 129(5):697-713. . View in PubMed
  • ACDC: a general approach for detecting phenotype or exposure associated co-expression Front Med (Lausanne). 2023; 10:1118824. . View in PubMed
  • Ambient air pollution exposure and increasing depressive symptoms in older women: The mediating role of the prefrontal cortex and insula Sci Total Environ. 2022 Jun 01; 823:153642. . View in PubMed
  • MCM3 is a novel proliferation marker associated with longer survival for patients with tubo-ovarian high-grade serous carcinoma Virchows Arch. 2022 Apr; 480(4):855-871. . View in PubMed
  • Neurotransmitter signaling: a new frontier in colorectal cancer biology and treatment Oncogene. 2022 10; 41(43):4769-4778. . View in PubMed
  • Genetic variants involved in the cGAS-STING pathway predict outcome in patients with metastatic colorectal cancer: Data from FIRE-3 and TRIBE trials Eur J Cancer. 2022 09; 172:22-30. . View in PubMed
  • Germline Polymorphisms in Genes Involved in the Antioxidant System Predict the Efficacy of Cetuximab in Metastatic Colorectal Cancer Patients Enrolled in FIRE-3 Trial Clin Colorectal Cancer. 2022 09; 21(3):259-266. . View in PubMed
  • Air quality improvement and cognitive decline in community-dwelling older women in the United States: A longitudinal cohort study PLoS Med. 2022 02; 19(2):e1003893. . View in PubMed
  • Molecular characteristics and clinical outcomes of patients with Neurofibromin 1-altered metastatic colorectal cancer Oncogene. 2022 01; 41(2):260-267. . View in PubMed
  • Germline polymorphisms in genes maintaining the replication fork predict the efficacy of oxaliplatin and irinotecan in patients with metastatic colorectal cancer Br J Cancer. 2022 01; 126(1):72-78. . View in PubMed
  • fdrci: FDR confidence interval selection and adjustment for large-scale hypothesis testing Bioinform Adv. 2022; 2(1):vbac047. . View in PubMed
  • Association of improved air quality with lower dementia risk in older women Proc Natl Acad Sci U S A. 2022 01 11; 119(2). . View in PubMed
  • Distinct genomic landscapes of gastroesophageal adenocarcinoma depending on PD-L1 expression identify mutations in RAS-MAPK pathway and TP53 as potential predictors of immunotherapy efficacy Ann Oncol. 2021 07; 32(7):906-916. . View in PubMed
  • Large-scale analysis of KMT2 mutations defines a distinctive molecular subset with treatment implication in gastric cancer Oncogene. 2021 07; 40(30):4894-4905. . View in PubMed
  • Germ line polymorphisms of genes involved in pluripotency transcription factors predict efficacy of cetuximab in metastatic colorectal cancer Eur J Cancer. 2021 06; 150:133-142. . View in PubMed
  • RNA-Binding Protein Polymorphisms as Novel Biomarkers to Predict Outcomes of Metastatic Colorectal Cancer: A Meta-analysis from TRIBE, FIRE-3, and MAVERICC Mol Cancer Ther. 2021 06; 20(6):1153-1160. . View in PubMed
  • Prevalence and risk factors for cisplatin-induced hearing loss in children, adolescents, and young adults: a multi-institutional North American cohort study Lancet Child Adolesc Health. 2021 04; 5(4):274-283. . View in PubMed
  • The Landscape of Alterations in DNA Damage Response Pathways in Colorectal Cancer Clin Cancer Res. 2021 06 01; 27(11):3234-3242. . View in PubMed
  • Random survival forests identify pathways with polymorphisms predictive of survival in KRAS mutant and KRAS wild-type metastatic colorectal cancer patients Sci Rep. 2021 06 09; 11(1):12191. . View in PubMed
  • Associations Between Air Pollution Exposure and Empirically Derived Profiles of Cognitive Performance in Older Women J Alzheimers Dis. 2021; 84(4):1691-1707. . View in PubMed
  • Molecular Characterization of Appendiceal Goblet Cell Carcinoid Mol Cancer Ther. 2020 12; 19(12):2634-2640. . View in PubMed
  • Immunogenic cell death pathway polymorphisms for predicting oxaliplatin efficacy in metastatic colorectal cancer J Immunother Cancer. 2020 11; 8(2). . View in PubMed
  • Prognostic gene expression signature for high-grade serous ovarian cancer Ann Oncol. 2020 09; 31(9):1240-1250. . View in PubMed
  • Correction to: Infectious mononucleosis, immune genotypes, and non-Hodgkin lymphoma (NHL): an InterLymph Consortium study Cancer Causes Control. 2020 06; 31(6):607. . View in PubMed
  • Infectious mononucleosis, immune genotypes, and non-Hodgkin lymphoma (NHL): an InterLymph Consortium study Cancer Causes Control. 2020 05; 31(5):451-462. . View in PubMed
  • Are Epithelial Ovarian Cancers of the Mesenchymal Subtype Actually Intraperitoneal Metastases to the Ovary? Front Cell Dev Biol. 2020; 8:647.. View in PubMed
  • partition: A fast and flexible framework for data reduction in R J Open Source Softw. 2020; 5(47). . View in PubMed
  • Partition: a surjective mapping approach for dimensionality reduction Bioinformatics. 2020 02 01; 36(3):676-681. . View in PubMed
  • Association of HLA Genotype With T-Cell Activation in Human Immunodeficiency Virus (HIV) and HIV/Hepatitis C Virus-Coinfected Women J Infect Dis. 2020 03 16; 221(7):1156-1166. . View in PubMed
  • Lactose-reduced infant formula with added corn syrup solids is associated with a distinct gut microbiota in Hispanic infants Gut Microbes. 2020 11 09; 12(1):1813534. . View in PubMed
  • Impact of polymorphisms within genes involved in regulating DNA methylation in patients with metastatic colorectal cancer enrolled in three independent, randomised, open-label clinical trials: a meta-analysis from TRIBE, MAVERICC and FIRE-3 Eur J Cancer. 2019 04; 111:138-147. . View in PubMed
  • Prognostic Effect of Adenosine-related Genetic Variants in Metastatic Colorectal Cancer Treated With Bevacizumab-based Chemotherapy Clin Colorectal Cancer. 2019 03; 18(1):e8-e19. . View in PubMed
  • High intake of dietary fructose in overweight/obese teenagers associated with depletion of Eubacterium and Streptococcus in gut microbiome Gut Microbes. 2019; 10(6):712-719. . View in PubMed
  • AMPK variant, a candidate of novel predictor for chemotherapy in metastatic colorectal cancer: A meta-analysis using TRIBE, MAVERICC and FIRE3 Int J Cancer. 2019 10 15; 145(8):2082-2090. . View in PubMed
  • Gene Coexpression Networks in Whole Blood Implicate Multiple Interrelated Molecular Pathways in Obesity in People with Asthma Obesity (Silver Spring). 2018 12; 26(12):1938-1948. . View in PubMed
  • Role of local CpG DNA methylation in mediating the 17q21 asthma susceptibility gasdermin B (GSDMB)/ORMDL sphingolipid biosynthesis regulator 3 (ORMDL3) expression quantitative trait locusJ Allergy Clin Immunol. 2018 06; 141(6):2282-2286. e6. . View in PubMed
  • Self-reported prenatal tobacco smoke exposure, AXL gene-body methylation, and childhood asthma phenotypes Clin Epigenetics. 2018 07 20; 10(1):98. . View in PubMed
  • Single-Cell Digital Lysates Generated by Phase-Switch Microfluidic Device Reveal Transcriptome Perturbation of Cell Cycle ACS Nano. 2018 05 22; 12(5):4687-4694. . View in PubMed
  • Genetic-Epigenetic Interactions in Asthma Revealed by a Genome-Wide Gene-Centric Search Hum Hered. 2018; 83(3):130-152. . View in PubMed
  • Association between AXL promoter methylation and lung function growth during adolescence Epigenetics. 2018; 13(10-11):1027-1038. . View in PubMed
  • Epigenetic regulation of AXL and risk of childhood asthma symptoms Clin Epigenetics. 2017; 9:121. . View in PubMed
  • Gene Expression Profiling in Blood Provides Reproducible Molecular Insights into Asthma Control Am J Respir Crit Care Med. 2017 01 15; 195(2):179-188. . View in PubMed
  • 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. . View in PubMed
  • cit: hypothesis testing software for mediation analysis in genomic applications Bioinformatics. 2016 08 01; 32(15):2364-5. . View in PubMed
  • 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. . View in PubMed
  • Alteration of select gene expression patterns in individuals infected with HIV-1 J Med Virol. 2014 Apr; 86(4):678-86. . View in PubMed
  • Computationally efficient permutation-based confidence interval estimation for tail-area FDR Front Genet. 2013; 4:179. . View in PubMed
  • Screening-testing approaches for gene-gene and gene-environment interactions using independent statistics Front Genet. 2013; 4:306. . View in PubMed
  • Mapping the genetic architecture of gene expression in human liver PLoS Biol. 2008 May 06; 6(5):e107. . View in PubMed
  • Health effects of the 2003 Southern California wildfires on children Am J Respir Crit Care Med. 2006 Dec 01; 174(11):1221-8. . View in PubMed
  • A testing framework for identifying susceptibility genes in the presence of epistasis Am J Hum Genet. 2006 Jan; 78(1):15-27. . View in PubMed
  • Identifying susceptibility genes by using joint tests of association and linkage and accounting for epistasis BMC Genet. 2005 Dec 30; 6 Suppl 1:S147. . View in PubMed
  • Testing association and linkage using affected-sib-parent study designs Genet Epidemiol. 2005 Nov; 29(3):225-33. . View in PubMed
  • 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. . View in PubMed
  • 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. . View in PubMed
  • Comparison of age-length and growth-increment general growth models of the Schnute type in the Pacific Blue Mussel, Mytilus trossulus Gould J Exp Mar Biol Ecol. 2001 Jul 30; 262(2):155-176. . View in PubMed