Research in our group focuses on understanding how microbial life impacts human health. We are working on studies of the complex communities of microbes that live in association with humans. We are interested in the development of the microbiome in infants and children, and the associations among environmental and dietary exposures, the human microbiota, and risk for infectious and other diseases. We develop novel computational approaches for exposing the interactions between the various components of the microbiome in order to enhance our understanding of its structure and responsiveness to perturbation. We work to link together the knowledge gained from different measures of microbiota composition and function to identify the microbial consortia that contribute to disease risk or protect health. 



Annie HOen, PhD

Annie completed her PhD in epidemiology and public health at Yale University and was a postdoctoral fellow at Harvard Medical School. She is currently an Assistant Professor of Epidemiology, Biomedical Data Science and Microbiology and Immunology at the Geisel School of Medicine at Dartmouth. 

ERIKA DADE, MS  Erika is the lab data wrangler. She has a background in GIS, oceanography, satellite remote sensing and real-time data acquisition. When not sitting in front of a computer, she is most likely out rowing or coaching rowing.


Erika is the lab data wrangler. She has a background in GIS, oceanography, satellite remote sensing and real-time data acquisition. When not sitting in front of a computer, she is most likely out rowing or coaching rowing.



Jie completed his PhD in statistics and mathematics at Xidian University, China. He has worked as postdoc in Dartmouth College since July 2018 with both the Hoen Lab and Professor Jiang Gui. He uses different statistical tools such as time series models and graphical models to decipher complex relationship within the human microbiome and metabolome and associated health outcomes.


Becky Lebeaux, BS

Becky is a PhD student in the Quantitative Biomedical Sciences (QBS) program. She graduated from Emory University with a degree in Anthropology and Human Biology. She is interested in exploring the consequences of antibiotics and vaccines on antimicrobial resistance and species-level taxonomy within the developing infant gut microbiome.


Quang Nguyen, bs

Quang is currently a PhD Student in the QBS program. He graduated from Bates College with a degree in Biochemistry and Mathematics. He is co-mentored by Dr. Anne Hoen and Dr. Robert Frost and is working to understand the relationship between microbial functional redundancy in the microbiome and health outcomes.



Jeffrey is a BA candidate at Dartmouth College majoring in Philosophy with a minor in Chemistry. He enjoys working with data and learning new things.


Sara Lundgren, PHD

Sara is a postdoctoral researcher at the Institute for Molecular Medicine Finland.


Margaret hilliard, ba

Margaret is a graduate of Marlboro College. With a BA in Biology and Biochemistry she is interested in the evolution of inter-individual differences in human breast milk composition and how maternal genetics and environmental exposures influence the development of the infant gut microbiome. She currently works with the Sela Lab at the University of Massachusetts Amherst.

WES viles, Phd

Wes is an Assistant Professor of Mathematics and Statistics at University of Southern Maine.


  1. Coker MO, Hoen AG, Dade E, Lundgren S, Li Z, Wong AD, Zens MS, Palys TJ, Morrison HG, Sogin ML, Baker ER, Karagas MR, Madan JC. Specific class of intrapartum antibiotics relates to maturation of the infant gut microbiota: a prospective cohort study. BJOG. 2019 Apr 21. doi: 10.1111/1471-0528.15799. [Epub ahead of print] PubMed PMID: 31006170.

  2. Singh SB, Madan J, Coker M, Hoen A, Baker ER, Karagas MR, Mueller NT. Does birth mode modify associations of maternal pre-pregnancy BMI and gestational weight gain with the infant gut microbiome? Int J Obes (Lond). 2019 Feb 14. doi: 10.1038/s41366-018-0273-0. [Epub ahead of print] PubMed PMID: 30765892.

  3. Li Z, Lee K, Karagas MR, Madan JC, Hoen AG, O'Malley AJ, Li H. Conditional regression based on a multivariate zero-inflated logistic-normal model for microbiome relative abundance data. Stat Biosci. 2018 Dec;10(3):587-608. doi: 10.1007/s12561-018-9219-2. Epub 2018 Jul 10. PubMed PMID: 30923584; PubMed Central PMCID: PMC6432796.

  4. Hoen AG, Madan JC, Li Z, Coker M, Lundgren SN, Morrison HG, Palys T, Jackson B, Sogin ML, Cottingham KL, Karagas MR. Sex-specific associations of infants’ gut microbiome with arsenic exposure in a US population. Scientific Reports. 2018 Aug 22;(8):12627. doi: 10.1038/s41598-018-30581-9.

  5. Lundgren SN, Madan JC, Emond JA, Morrison HG, Christensen BC, Karagas MR, Hoen AG. Maternal diet during pregnancy is related with the infant stool microbiome in a delivery mode-dependent manner. Microbiome. 2018 Jul 5;6(1):109. doi: 10.1186/s40168-018-0490-8. PubMed PMID: 29973274; PubMed Central PMCID: PMC6033232.

  6. Chernikova DA, Madan JC, Housman ML, Zain-Ul-Abideen M, Lundgren SN, Morrison HG, Sogin ML, Williams SM, Moore JH, Karagas MR, Hoen AG. The premature infant gut microbiome during the first 6 weeks of life differs based on gestational maturity at birth. Pediatr Res. 2018 May 23. doi: 10.1038/s41390-018-0022-z. [Epub ahead of print] PubMed PMID: 29795209.

  7. Wright PF, Connor RI, Wieland-Alter WF, Hoen AG, Boesch AW, Ackerman ME, Oberste MS, Gast C, Brickley EB, Asturias EJ, Rüttimann R, Bandyopadhyay AS. Vaccine-induced mucosal immunity to poliovirus: analysis of cohorts from an open-label, randomised controlled trial in Latin American infants. Lancet Infect Dis. 2016 Dec;16(12):1377-1384. doi: 10.1016/S1473-3099(16)30169-4. Epub 2016 Sep
    13. PubMed PMID: 27638357; PubMed Central PMCID: PMC5611465.

  8. Wright PF, Hoen AG, Ilyushina NA, Brown EP, Ackerman ME, Wieland-Alter W, Connor RI, Jegaskanda S, Rosenberg-Hasson Y, Haynes BC, Luke CJ, Subbarao K, Treanor JJ. Correlates of immunity to influenza as determined by challenge of children with live, attenuated influenza vaccine. Open Forum Infect Dis. 2016 May 23;3(2):ofw108. doi: 10.1093/ofid/ofw108. eCollection 2016 Apr. PubMed PMID: 27419180; PubMed Central PMCID: PMC4943547.

  9. Gossai A, Waterboer T, Nelson HH, Doherty JA, Michel A, Willhauck-Fleckenstein M, Farzan SF, Christensen BC, Hoen AG, Perry AE, Pawlita M, Karagas MR. Prospective study of human polyomaviruses and risk of cutaneous squamous cell carcinoma in the United States. Cancer Epidemiol Biomarkers Prev. 2016 May;25(5):736-44. doi: 10.1158/1055-9965.EPI-15-1111. Epub 2016 Feb 11. PubMed PMID: 26908434; PubMed Central PMCID: PMC4883679.

  10. Gossai A, Waterboer T, Hoen AG, Farzan SF, Nelson HH, Michel A, Willhauck-Fleckenstein M, Christensen BC, Perry AE, Pawlita M, Karagas MR. Human polyomaviruses and incidence of cutaneous squamous cell carcinoma in the New Hampshire skin cancer study. Cancer Med. 2016 Jun;5(6):1239-50. doi: 10.1002/cam4.674. Epub 2016 Feb 21. PubMed PMID: 26899857; PubMed Central PMCID: PMC4924382.

  11. Madan JC, Hoen AG, Lundgren SN, Farzan SF, Cottingham KL, Morrison HG, Sogin ML, Li H, Moore JH, Karagas MR. Association of Cesarean delivery and formula supplementation with the intestinal microbiome of 6-week-old infants. JAMA Pediatr. 2016 Mar;170(3):212-9. doi: 10.1001/jamapediatrics.2015.3732. PubMed PMID: 26752321; PubMed Central PMCID: PMC4783194.

  12. Gossai A, Waterboer T, Nelson HH, Michel A, Willhauck-Fleckenstein M, Farzan SF, Hoen AG, Christensen BC, Kelsey KT, Marsit CJ, Pawlita M, Karagas MR. Seroepidemiology of human polyomaviruses in a US population. Am J Epidemiol. 2016 Jan 1;183(1):61-9. doi: 10.1093/aje/kwv155. Epub 2015 Dec 13. PubMed PMID: 26667254; PubMed Central PMCID: PMC5006224.

  13. Hoen AG, Hladish TJ, Eggo RM, Lenczner M, Brownstein JS, Meyers LA. Epidemic wave dynamics attributable to urban community structure: a theoretical characterization of disease transmission in a large network. J Med Internet Res. 2015 Jul 8;17(7):e169. doi: 10.2196/jmir.3720. PubMed PMID: 26156032; PubMed Central PMCID: PMC4526984.

  14. Carpi G, Walter KS, Bent SJ, Hoen AG, Diuk-Wasser M, Caccone A. Whole genome capture of vector-borne pathogens from mixed DNA samples: a case study of Borrelia burgdorferi. BMC Genomics. 2015 Jun 6;16:434. doi: 10.1186/s12864-015-1634-x. PubMed PMID: 26048573; PubMed Central PMCID: PMC4458057.

  15. Hoen AG, Li J, Moulton LA, O'Toole GA, Housman ML, Koestler DC, Guill MF, Moore JH, Hibberd PL, Morrison HG, Sogin ML, Karagas MR, Madan JC. Associations between gut microbial colonization in early life and respiratory outcomes in cystic fibrosis. J Pediatr. 2015 Jul;167(1):138-47.e1-3. doi: 10.1016/j.jpeds.2015.02.049. Epub 2015 Mar 26. PubMed PMID: 25818499; PubMed Central PMCID: PMC4674690.

  16. Chernikova DA, Koestler DC, Hoen AG, Housman ML, Hibberd PL, Moore JH, Morrison HG, Sogin ML, Zain-Ul-Abideen M, Madan JC. Fetal exposures and perinatal influences on the stool microbiota of premature infants. J Matern Fetal Neonatal Med. 2016;29(1):99-105. doi: 10.3109/14767058.2014.987748. Epub 2015 Sep 4. PubMed PMID: 25394613; PubMed Central PMCID: PMC4476945.

  17. Ilyushina NA, Haynes BC, Hoen AG, Khalenkov AM, Housman ML, Brown EP, Ackerman ME, Treanor JJ, Luke CJ, Subbarao K, Wright PF. Live attenuated and inactivated influenza vaccines in children. J Infect Dis. 2015 Feb 1;211(3):352-60. doi: 10.1093/infdis/jiu458. Epub 2014 Aug 26. PubMed PMID: 25165161; PubMed Central PMCID: PMC4296173.

  18. Wright PF, Wieland-Alter W, Ilyushina NA, Hoen AG, Arita M, Boesch AW, Ackerman ME, van der Avoort H, Oberste MS, Pallansch MA, Burton AH, Jaffar MA, Sutter RW. Intestinal immunity is a determinant of clearance of poliovirus after oral vaccination. J Infect Dis. 2014 May 15;209(10):1628-34. doi: 10.1093/infdis/jit671. Epub 2014 Jan 23. PubMed PMID: 24459191.

  19. Messina JP, Brady OJ, Pigott DM, Brownstein JS, Hoen AG, Hay SI. A global compendium of human dengue virus occurrence. Sci Data. 2014 May 27;1:140004. doi: 10.1038/sdata.2014.4. eCollection 2014. PubMed PMID: 25977762; PubMed Central PMCID: PMC4322574.

  20. Aenishaenslin C, Hongoh V, Cissé HD, Hoen AG, Samoura K, Michel P, Waaub JP, Bélanger D. Multi-criteria decision analysis as an innovative approach to managing zoonoses: results from a study on Lyme disease in Canada. BMC Public Health. 2013 Sep 30;13:897. doi: 10.1186/1471-2458-13-897. PubMed PMID: 24079303; PubMed Central PMCID: PMC3850527.

  21. Charland KM, Buckeridge DL, Hoen AG, Berry JG, Elixhauser A, Melton F, Brownstein JS. Relationship between community prevalence of obesity and associated behavioral factors and community rates of influenza-related hospitalizations in the United States. Influenza Other Respir Viruses. 2013 Sep;7(5):718-28. doi: 10.1111/irv.12019. Epub 2012 Nov 8. PubMed PMID: 23136926; PubMed Central PMCID: PMC5781204.

  22. Bhatt S, Gething PW, Brady OJ, Messina JP, Farlow AW, Moyes CL, Drake JM, Brownstein JS, Hoen AG, Sankoh O, Myers MF, George DB, Jaenisch T, Wint GR, Simmons CP, Scott TW, Farrar JJ, Hay SI. The global distribution and burden of dengue. Nature. 2013 Apr 25;496(7446):504-7. doi: 10.1038/nature12060. Epub 2013  Apr 7. PubMed PMID: 23563266; PubMed Central PMCID: PMC3651993.

  23. Chan EH, Scales DA, Brewer TF, Madoff LC, Pollack MP, Hoen AG, Choden T, Brownstein JS. Forecasting high-priority infectious disease surveillance regions: a socioeconomic model. Clin Infect Dis. 2013 Feb;56(4):517-24. doi: 10.1093/cid/cis932. Epub 2012 Nov 1. PubMed PMID: 23118271; PubMed Central PMCID: PMC3552528.

  24. Hoen AG, Gardner SN, Moore JH. Identification of SNPs associated with variola virus virulence. BioData Min. 2013 Feb 14;6(1):3. doi: 10.1186/1756-0381-6-3. PubMed PMID: 23410064; PubMed Central PMCID: PMC3599518.

  25. Margos G, Tsao JI, Castillo-Ramírez S, Girard YA, Hamer SA, Hoen AG, Lane RS, Raper SL, Ogden NH. Two boundaries separate Borrelia burgdorferi populations in North America. Appl Environ Microbiol. 2012 Sep;78(17):6059-67. doi: 10.1128/AEM.00231-12. Epub 2012 Jun 22. PubMed PMID: 22729536; PubMed Central PMCID: PMC3416618.

  26. Brady OJ, Gething PW, Bhatt S, Messina JP, Brownstein JS, Hoen AG, Moyes CL, Farlow AW, Scott TW, Hay SI. Refining the global spatial limits of dengue virus transmission by evidence-based consensus. PLoS Negl Trop Dis. 2012;6(8):e1760. doi: 10.1371/journal.pntd.0001760. Epub 2012 Aug 7. PubMed PMID: 22880140; PubMed Central PMCID: PMC3413714.

  27. Egger JR, Hoen AG, Brownstein JS, Buckeridge DL, Olson DR, Konty KJ. Usefulness of school absenteeism data for predicting influenza outbreaks, United States. Emerg Infect Dis. 2012 Aug;18(8):1375-7. doi: 10.3201/eid1808.111538. PubMed PMID: 22840354; PubMed Central PMCID: PMC3414019.

  28. Hoen AG, Keller M, Verma AD, Buckeridge DL, Brownstein JS. Electronic event-based surveillance for monitoring dengue, Latin America. Emerg Infect Dis. 2012 Jul;18(7):1147-50. doi: 10.3201/eid1807.120055. PubMed PMID: 22709430; PubMed Central PMCID: PMC3376807.

  29. Pepin KM, Eisen RJ, Mead PS, Piesman J, Fish D, Hoen AG, Barbour AG, Hamer S, Diuk-Wasser MA. Geographic variation in the relationship between human Lyme disease incidence and density of infected host-seeking Ixodes scapularis nymphs in the Eastern United States. Am J Trop Med Hyg. 2012 Jun;86(6):1062-71. doi: 10.4269/ajtmh.2012.11-0630. PubMed PMID: 22665620; PubMed Central PMCID: PMC3366524.

  30. Margos G, Castillo-Ramírez S, Hoen AG. Phylogeography of Lyme borreliosis-group spirochetes and methicillin-resistant Staphylococcus aureus. Parasitology. 2012 Dec;139(14):1952-65. doi: 10.1017/S0031182012000741. Epub 2012 May 23. Review. PubMed PMID: 22617338.

  31. Diuk-Wasser MA, Hoen AG, Cislo P, Brinkerhoff R, Hamer SA, Rowland M, Cortinas R, Vourc'h G, Melton F, Hickling GJ, Tsao JI, Bunikis J, Barbour AG, Kitron U, Piesman J, Fish D. Human risk of infection with Borrelia burgdorferi, the Lyme disease agent, in eastern United States. Am J Trop Med Hyg. 2012 Feb;86(2):320-7. doi: 10.4269/ajtmh.2012.11-0395. PubMed PMID: 22302869; PubMed Central PMCID: PMC3269287.

  32. Hongoh V, Hoen AG, Aenishaenslin C, Waaub JP, Bélanger D, Michel P; Lyme-MCDA Consortium. Spatially explicit multi-criteria decision analysis for managing vector-borne diseases. Int J Health Geogr. 2011 Dec 29;10:70. doi: 10.1186/1476-072X-10-70. Review. PubMed PMID: 22206355; PubMed Central PMCID: PMC3315429.

  33. Charland KM, Brownstein JS, Verma A, Brewer T, Jones S, Hoen AG, Buckeridge DL. Increased influenza-related healthcare utilization by residents of an urban aboriginal community. Epidemiol Infect. 2011 Dec;139(12):1902-8. doi: 10.1017/S0950268810003109. Epub 2011 Jan 20. PubMed PMID: 21251347; PubMed Central PMCID: PMC4313877.

  34. Hoen AG, Buckeridge DL, Charland KM, Mandl KD, Quach C, Brownstein JS. Effect of expanded US recommendations for seasonal influenza vaccination: comparison of two pediatric emergency departments in the United States and Canada. CMAJ. 2011 Sep 20;183(13):E1025-32. doi: 10.1503/cmaj.110241. PubMed PMID: 21930745; PubMed Central PMCID: PMC3176865.

  35. Driscoll T, Gabbard JL, Mao C, Dalay O, Shukla M, Freifeld CC, Hoen AG, Brownstein JS, Sobral BW. Integration and visualization of host-pathogen data related to infectious diseases. Bioinformatics. 2011 Aug 15;27(16):2279-87. doi:  10.1093/bioinformatics/btr391. Epub 2011 Jun 27. PubMed PMID: 21712250; PubMed Central PMCID: PMC3150046.

  36. Brinkerhoff RJ, Bent SJ, Folsom-O'Keefe CM, Tsao K, Hoen AG, Barbour AG, Diuk-Wasser MA. Genotypic diversity of Borrelia burgdorferi strains detected in Ixodes scapularis larvae collected from North American songbirds. Appl Environ Microbiol. 2010 Dec;76(24):8265-8. doi: 10.1128/AEM.01585-10. Epub 2010 Oct 22. PubMed PMID: 20971869; PubMed Central PMCID: PMC3008240.

  37. Diuk-Wasser MA, Vourc’h G, Cislo P, Hoen AG, Melton F, Hamer S, Rowland M, Cortinas R, Hickling G, Tsao J, Kitron U, Piesman J and Fish D. Field and climate-based model for predicting the density of host-seeking Ixodes scapularis, an important vector of tick-borne agents in the eastern United States. Glob Ecol Biogeogr. 2010 19(4): 504-14.

  38. Hoen AG, Buckeridge DL, Chan EH, Freifeld CC, Keller M, Charland K, Donnelly CA, Brownstein JS. Characteristics of US public schools with reported cases of novel influenza A (H1N1). Int J Infect Dis. 2010 Sep;14 Suppl 3:e6-8. doi: 10.1016/j.ijid.2009.11.034. Epub 2010 Apr 2. PubMed PMID: 20363169; PubMed Central PMCID: PMC2914813.

  39. Barbour AG, Bunikis J, Travinsky B, Hoen AG, Diuk-Wasser MA, Fish D, Tsao JI. Niche partitioning of Borrelia burgdorferi and Borrelia miyamotoi in the same tick vector and mammalian reservoir species. Am J Trop Med Hyg. 2009 Dec;81(6):1120-31. doi: 10.4269/ajtmh.2009.09-0208. PubMed PMID: 19996447; PubMed Central PMCID: PMC2841027.

  40. Sasaki A, Hoen AG, Ozonoff A, Suzuki H, Tanabe N, Seki N, Saito R, Brownstein JS. Evidence-based tool for triggering school closures during influenza outbreaks, Japan. Emerg Infect Dis. 2009 Nov;15(11):1841-3. PubMed PMID: 19891880; PubMed Central PMCID: PMC2857248.

  41. Hoen AG, Margos G, Bent SJ, Diuk-Wasser MA, Barbour A, Kurtenbach K, Fish D. Phylogeography of Borrelia burgdorferi in the eastern United States reflects multiple independent Lyme disease emergence events. Proc Natl Acad Sci U S A. 2009 Sep 1;106(35):15013-8. doi: 10.1073/pnas.0903810106. Epub 2009 Aug 14. PubMed PMID: 19706476; PubMed Central PMCID: PMC2727481.

  42. Hoen AG, Rollend LG, Papero MA, Carroll JF, Daniels TJ, Mather TN, Schulze TL, Stafford KC 3rd, Fish D. Effects of tick control by acaricide self-treatment of white-tailed deer on host-seeking tick infection prevalence and entomologic risk for Ixodes scapularis-borne pathogens. Vector Borne Zoonotic Dis. 2009 Aug;9(4):431-8. doi: 10.1089/vbz.2008.0155. PubMed PMID: 19650738.

  43. Gatewood AG, Liebman KA, Vourc'h G, Bunikis J, Hamer SA, Cortinas R, Melton F, Cislo P, Kitron U, Tsao J, Barbour AG, Fish D, Diuk-Wasser MA. Climate and tick seasonality are predictors of Borrelia burgdorferi genotype distribution. Appl Environ Microbiol. 2009 Apr;75(8):2476-83. doi: 10.1128/AEM.02633-08. Epub 2009 Feb 27. PubMed PMID: 19251900; PubMed Central PMCID: PMC2675205.

  44. Movila A, Gatewood AG, Toderasa I, Ducaa M, Papero M, Uspenskaia I, Conovalova J, Fish D. Prevalence of Borrelia burgdorferi sensu lato in Ixodes ricinus and I. lividus ticks collected from wild birds in the Republic of Moldova. Int J Med Microbiol. 298(S1): 149-53.

  45. Margos G, Gatewood AG, Aanensen DM, Hanincová K, Terekhova D, Vollmer SA, Cornet M, Piesman J, Donaghy M, Bormane A, Hurn MA, Feil EJ, Fish D, Casjens S, Wormser GP, Schwartz I, Kurtenbach K. MLST of housekeeping genes captures geographic population structure and suggests a European origin of Borrelia burgdorferi. Proc Natl Acad Sci U S A. 2008 Jun 24;105(25):8730-5. doi: 10.1073/pnas.0800323105. Epub 2008 Jun 23. PubMed PMID: 18574151; PubMed Central PMCID: PMC2435589.

  46. Diuk-Wasser MA, Gatewood AG, Cortinas MR, Yaremych-Hamer S, Tsao J, Kitron U, Hickling G, Brownstein JS, Walker E, Piesman J, Fish D. Spatiotemporal patterns of host-seeking Ixodes scapularis nymphs (Acari: Ixodidae) in the United States.  J Med Entomol. 2006 Mar;43(2):166-76. PubMed PMID: 16619595.




Opportunities for postdoctoral training are currently available in the Hoen Lab. Possible projects include: 

  • 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 

To apply: Send a CV and list of references here


Opportunities for graduate training are available through the QBS and MCB graduate programs at Dartmouth College.


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