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Stephen Harris

Assistant Professor of Biology

Stephen Harris received his BS in molecular genetics from Ohio State University in 2006. After graduating he spent two years teaching high school science through the NYC Teaching Fellows and received his MA in science education from the City College of New York in 2009.  He then went back into research and received his PhD in evolutionary biology from the Graduate Center, City University of New York in 2015. His research uses genomics and bioinformatics to study the evolution, ecology, and behavior of natural populations in response to environmental change. 

His PhD research focused on urban ecology and investigated the population genomics of urban white-footed mice in New York City. Following his graduate studies, he completed one postdoctoral fellowship at Columbia University in the Ecology, Evolution, and Environmental Biology Department, studying local extinction in eusocial snapping shrimp across the Caribbean. He moved on to a postdoctoral researcher position at Metabiota and a visiting scholar appointment at Stanford University, where he used metagenomics and unbiased deep RNA sequencing to identify and track novel viruses from bats and rodents in Africa and Asia.

He has performed field work in urban ecosystems in New York City, coral reefs in the Florida Keys and Belize, and tropical forests in Indonesia, which has led to a passion for democratizing science by using the latest innovations in biotechnology to build portable, low-cost, and user-friendly sequencing labs for research and education.  In pursuing this mission, he also co-founded and runs Science-Corps,  a non-profit which sends recent PhD graduates abroad to teach science and build science capacity globally.

Research Interests

I study how organisms and natural populations are affected by anthropogenic environmental change. I combine field work, genomics, and computational biology to investigate plasticity/novel adaptations, range-shifts, and dietary/predator-prey interactions.  I use Oxford Nanopore Technologies and their handheld MinION device for all sequencing  projects, allowing our undergraduate Biology students to gain hands-on experience with Next-Generation Sequencing protocols.  I am increasingly focused on environmental DNA (eDNA) and metabarcoding/metagenomics to study regional biodiversity patterns around NYC. 

Representative Courses

  • Cell Biology Lecture (BIO3530)

  • Biotechnology II Lecture & Lab (BIO3205)

  • Molecular Biology (BIO4620)

  • Science in the Modern World: Frontiers of Biology (FRS1200)

  • Senior Project I & II (SPJ4990 & SPJ4991)

  • The Buzz About Bees (LBS3032)


  • Boehm JT, Bovee E, Harris SE, Eddins K, Akahoho I, Foster M, Pell SK, Hickerson MJ, Amato G, DeSalle R, Waldman J. (2023). The United States dried seahorse trade: A comparison of traditional Chinese medicine and ecommerce-curio markets using molecular identification. PLOS ONE 18:e0291874. DOI: 10.1371/journal.pone.0291874. Corresponding Author.
  • Chak, S. T. C., Harris, S. E., Hultgren, K. M., Duffy, J. E., & Rubenstein, D. R. (2022). Demographic inference provides insights into the extirpation and ecological dominance of eusocial snapping shrimps. Journal of Heredity, 1–16. Both authors contributed equally to this manuscript
  • Chak, S. T. C., Harris, S. E., Hultgren, K. M., Jeffery, N. W., & Rubenstein, D. R. (2021). Eusociality in snapping shrimps is associated with larger genomes and an accumulation of transposable elements. Proceedings of the National Academy of Sciences of the United States of America, 118(24), 1–10.
  • Bertola LD, Boehm JT, Putman NF, Xue AT, Robinson JD, Harris S, Baldwin CC, Overcast I, Hickerson MJ. (2020) Asymmetrical gene flow in five co- distributed syngnathids explained by ocean currents and rafting propensity. R. Soc. B 20200657.
  • Ntumvi N, F, Mbala Kingebeni P, Tamoufe U, Kumakamba C, Ndze V, Ngay Lukusa I, LeBreton M, Atibu Losoma J, Le Doux Diffo J, N’Kawa F, Takuo J, -M, Mulembakani P, Nwobegahay J, Makuwa M, Muyembe Tamfum J, J, Gillis A, Harris SE, Rimoin A, W, Hoff N, A, Fair J, M, Monagin C, Ayukekbong J, Rubin E, M, Wolfe N, D, Lange C. E. (2018) High Herpesvirus Diversity in Wild Rodent and Shrew Species in Central Africa. Intervirology. doi: 10.1159/000493796
  • Kumakamba C., Lukusa I.N., Kingebeni P.M., N’Kawa F., Losoma J.A., Mulembakani P.M., Makuwa M., Tamfum J.-J.M. Belais R., Gillis A., Harris SE., Rimoin A.W., Hoff N.A., Fair J.N., Monagin C., Ayukekbong J., Rubin E.M., Wolfe N.D., Lange C.E. (2018) DNA indicative of human bocaviruses detected in non-human primates in the Democratic Republic of the Congo. Journal of General Virology, 99, 676–681.
  • Harris SE, Munshi-South J (2017) Signatures of positive selection and local adaptation to urbanization in white-footed mice (Peromyscus leucopus). Molecular Ecology, 12, 3218–3221.
  • Izuogu AO, McNally KL, Harris SE et al. (2017) Interferon signaling in Peromyscus leucopus confers a potent and specific restriction to vector-borne flaviviruses. PLoS ONE, 12, 1–24.
  • Harris, S.E., Xue, X., Joseph, T., Alvarado, D., Hickerson, M.J., Munshi-South, J. (2016). Urbanization shapes the demographic history of a native rodent (the white-footed mouse, Peromyscus leucopus) in New York City. Biology Letters, 12 20150983, DOI: 1098/rsbl.2015.0983
  • Munshi-South, J., Zolnik, C. P., & Harris, S. E. (2016). Population genomics of the Anthropocene: urbanization reduces the evolutionary potential of small mammal populations. Evolutionary Applications, 9: 546–564.
  • Harris, S. E., O’Neill, R. J., & Munshi‐South, J. (2015). Transcriptome resources for the white‐footed mouse (Peromyscus leucopus): new genomic tools for investigating ecologically divergent urban and rural populations. Molecular Ecology Resources, 15(2), 382-394.
  • Harris, S.E., M. Bellino. (2013). DNA Barcoding from NYC to Belize. Science 342(6165):1462-1463.
  • Harris, S.E., Munshi-South, C. Obergfell, & R. O’Neill. (2013). Signatures of rapid evolution in urban and rural transcriptomes of white-footed mice (Peromyscus leucopus) in the New York metropolitan area. PLOS One 8(8): e74938.