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Anne G Hoen, PhD

Associate Professor of Epidemiology
Associate Professor of Biomedical Data Science
Associate Professor of Microbiology and Immunology

Biomedical Data Science
Microbiology and Immunology

Molecular and Cellular Biology Graduate Programs
Quantitative Biomedical Sciences


Contact Information

Dartmouth-Hitchcock Medical Center
One Medical Center Drive
HB 7927
Lebanon NH 03756

Phone: 603-653-6087

Professional Interests

Dr. Hoen's research focus is on the development of the microbiome in infants and children, and the associations between environmental and dietary exposures, the microbiome, and risk for infectious and other diseases. She has a broad interest in the predictors of disease risk and microbial colonization dynamics in human populations and the environment as reflected in microbial genetic sequence variation and health informatics streams over space and time. Interdisciplinary approaches used in her research include spatial and time-series statistics, population genetics and novel disease surveillance methodologies along with tools from the fields of microbial ecology, molecular epidemiology and landscape epidemiology.

Rotations and Thesis Projects

Development of novel computational methods for studying the human microbiota
Investigating the environmental drivers of infant intestinal microbiome development
Associations between patterns of infant intestinal microbiome establishment and health outcomes in children
Functional characterization of the developing infant gut microbiota using metabolomics

Grant Information

K01LM011985: Bioinformatics strategies for early life microbiomics
R01LM012723: Multi-omic functional integration using networks

Courses Taught

QBS 136 Applied Epidemiologic Methods I
QBS 137 Applied Epidemiologic Methods II


Dr. Hoen completed her PhD in epidemiology and public health at Yale University and received post-doctoral training at Children's Hospital Boston, Harvard Medical School and McGill University. She has broad training in biostatistics, epidemiology and public health with research experience in the evaluation of interventions, understanding infectious disease emergence and spread, and evaluating associations between the microbiome and human health. Her research uses advanced statistical methods as well as informatics and complex systems approaches. Past studies include modeling the timing and spread of influenza to estimate the effects of interventions targeting children, modeling the evolutionary ecology of the Lyme disease agent, Borrelia burgdorferi and characterizing the initial development of the human microbiome in early life and its associations with common exposures and infectious outcomes.

Selected Publications


CBEA: Competitive balances for taxonomic enrichment analysis.
Nguyen QP, Hoen AG, Frost HR
PLoS Comput Biol. 2022 May 18;18(5):e1010091. doi: 10.1371/journal.pcbi.1010091. Epub 2022 May 18.
PMID: 35584140

Impact of antibiotics on off-target infant gut microbiota and resistance genes in cohort studies.
Lebeaux RM, Madan JC, Nguyen QP, Coker MO, Dade EF, Moroishi Y, Palys TJ, Ross BD, Pettigrew MM, Morrison HG, Karagas MR, Hoen AG
Pediatr Res. 2022 May 14; doi: 10.1038/s41390-022-02104-w. Epub 2022 May 14.
PMID: 35568730

Viles WD, Madan JC, Li H, Karagas MR, Hoen AG
Ann Appl Stat. 2021 Dec;15(4):1788-1807. doi: 10.1214/21-aoas1449. Epub 2021 Dec 21.
PMID: 35342498

Using Satellite Images and Deep Learning to Identify Associations Between County-Level Mortality and Residential Neighborhood Features Proximal to Schools: A Cross-Sectional Study.
Levy JJ, Lebeaux RM, Hoen AG, Christensen BC, Vaickus LJ, MacKenzie TA
Front Public Health. 2021;9:766707. doi: 10.3389/fpubh.2021.766707. Epub 2021 Nov 5.
PMID: 34805078

Chemical exposures assessed via silicone wristbands and endogenous plasma metabolomics during pregnancy.
Doherty BT, McRitchie SL, Pathmasiri WW, Stewart DA, Kirchner D, Anderson KA, Gui J, Madan JC, Hoen AG, Sumner SJ, Karagas MR, Romano ME
J Expo Sci Environ Epidemiol. 2022 Mar;32(2):259-267. doi: 10.1038/s41370-021-00394-6. Epub 2021 Oct 26.
PMID: 34702988

Association of Cesarean Delivery and Formula Supplementation with the Stool Metabolome of 6-Week-Old Infants.
Hoen AG, Coker MO, Madan JC, Pathmasiri W, McRitchie S, Dade EF, Doherty BT, Sumner S, Karagas MR
Metabolites. 2021 Oct 13;11(10) pii: 702. doi: 10.3390/metabo11100702. Epub 2021 Oct 13.
PMID: 34677417

Associations between the gut microbiome and metabolome in early life.
Nguyen QP, Karagas MR, Madan JC, Dade E, Palys TJ, Morrison HG, Pathmasiri WW, McRitche S, Sumner SJ, Frost HR, Hoen AG
BMC Microbiol. 2021 Aug 28;21(1):238. doi: 10.1186/s12866-021-02282-3. Epub 2021 Aug 28.
PMID: 34454437

The infant gut resistome is associated with E. coli and early-life exposures.
Lebeaux RM, Coker MO, Dade EF, Palys TJ, Morrison HG, Ross BD, Baker ER, Karagas MR, Madan JC, Hoen AG
BMC Microbiol. 2021 Jul 2;21(1):201. doi: 10.1186/s12866-021-02129-x. Epub 2021 Jul 2.
PMID: 34215179

Infant Feeding Alters the Longitudinal Impact of Birth Mode on the Development of the Gut Microbiota in the First Year of Life.
Coker MO, Laue HE, Hoen AG, Hilliard M, Dade E, Li Z, Palys T, Morrison HG, Baker E, Karagas MR, Madan JC
Front Microbiol. 2021;12:642197. doi: 10.3389/fmicb.2021.642197. Epub 2021 Apr 7.
PMID: 33897650

Information enhanced model selection for Gaussian graphical model with application to metabolomic data.
Zhou J, Hoen AG, Mcritchie S, Pathmasiri W, Viles WD, Nguyen QP, Madan JC, Dade E, Karagas MR, Gui J
Biostatistics. 2021 Mar 15; pii: kxab006. doi: 10.1093/biostatistics/kxab006. Epub 2021 Mar 15.
PMID: 33720330

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