Research projects and interests.

Broadly speaking, I’m interested in developing variable selection and feature engineering methods that leverages prior biological knowledge for machine learning and statistical analysis in the context of high dimensional genomic data sets. I hope to deploy these tools to help assist in generating meaningful mechanistically driven hypotheses from population-level surveys.

First-author manuscripts

Associations between the gut microbiome and the metabolome in early life
Quang P Nguyen, Margaret R. Karagas, Juliette C. Madan, Erika Dade, Tom J. Palys, Hilary G. Morrison, Wimal W. Pathmasiri, Susan McRitche, Susan J. Sumner, H. Robert Frost, Anne G. Hoen
[Source Code] [Manuscript]
Abstract: The infant intestinal microbiome plays an important role in metabolism and immune development with impacts on lifelong health. The linkage between the taxonomic composition of the microbiome and its metabolic phenotype is undefined and complicated by redundancies in the taxon-function relationships within microbial communities. To inform a more mechanistic understanding of the relationship between the microbiome and health, we performed an integrative statistical and machine learning-based analysis of microbe taxonomic structure and metabolic function in order to characterize the taxa-function relationship in early life.

cILR: Competitive isometric log-ratio for taxonomic enrichment analysis
Quang P Nguyen, Anne G. Hoen, H. Robert Frost
[Analysis Code] [Package] [Pre-print]
Abstract: High-dimensionality and sparsity are challenging problems in statistical analysis of microbiome relative abundance data. One approach is to aggregate taxa to sets, most commonly to Linnean taxonomic categories identified through classification of representative sequences. However, most researchers perform aggregation through the pairwise summation of counts, preventing comparison across sets of different sizes. We developed a taxa set enrichment method based on the isometric log-ratio transformation (cILR) for microbiome relative abundance data. Our method generates sample-specific taxa set enrichment scores with a well-defined null hypothesis corresponding to the Q2 competitive null hypothesis in the gene set testing literature. Significance testing was performed by estimating the empirical null distribution accounting for variance inflation due to inter-taxa correlation.

Co-author manuscripts

Rebecca M Lebeaux, Juliette C Madan, Quang P Nguyen, Modupe O Coker, Erika F Dade, Yuka Moroishi, Thomas J Palys, Benjamin D Ross, Melinda M Pettigrew, Hilary G Morrison, Margaret R Karagas, Anne G Hoen. Impact of antibiotics to off-target infant gut microbiota and resistance genes in cohort studies. medRxiv, 2021. doi:

Jie Zhou, Anne G Hoen, Susan Mcritchie, Wimal Pathmasiri, Weston D Viles, Quang P Nguyen, Juliette C Madan, Erika Dade, Margaret R Karagas, Jiang Gui. Information enhanced model selection for Gaussian graphical model with application to metabolomic data. Biostatistics, 2021;, kxab006,

Robert A. Shumsky, Laurens Debo, Rebecca M. Lebeaux, Quang P. Nguyen, Anne G. Hoen. Retail store customer flow and COVID-19 transmission. Proceedings of the National Academy of Sciences Mar 2021, 118 (11) e2019225118; DOI: 10.1073/pnas.2019225118

Winterbottom, E.F., Moroishi, Y., Halchenko, Y., (incl. Nguyen Q.P.). Prenatal arsenic exposure alters the placental expression of multiple epigenetic regulators in a sex-dependent manner. Environ Health 18, 18 (2019).

Nguyen HL, Ha DA, Goldberg RJ, Kiefe CI, Chiriboga G, Ly HN, et al. (incl. Nguyen, Q.P.) (2018) Culturally adaptive storytelling intervention versus didactic intervention to improve hypertension control in Vietnam- 12 month follow up results: A cluster randomized controlled feasibility trial. PLoS ONE 13(12): e0209912.

Nguyen, H.L., Allison, J.J., Ha, D.A. et al (incl. Nguyen, Q.P.). Culturally adaptive storytelling intervention versus didactic intervention to improve hypertension control in Vietnam: a cluster-randomized controlled feasibility trial. Pilot Feasibility Stud 3, 22 (2017).