Michael D. Lee, PhD – Science Mercenary

Bioinformatician exploring microbial ecology and evolution

Email: Mike.Lee(AT)nasa(DOT)gov
Phone: 732-691-6402
ORCID iD iconOrcid: 0000-0001-7750-9145

Current position
NASA Space Biology Postdoctoral Fellow

University of Southern California

Research summary
I’m a bioinformatician currently at NASA’s Ames Research Center in northern California, USA. I focus primarily on microbial ecology and evolution in all kinds of different systems ranging from the bottoms of our oceans up to the International Space Station 👽



Lee, M.D. (2019). GToTree: a user-friendly workflow for phylogenomics. Bioinformatics
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Software lives here; documentation lives here.

Lee, M.D., Ahlgren, N.A., Kling, J. D., Walworth, N.G., Rocap, G., Saito, M.A., Hutchins, D.A., and Webb, E.A. (2019). Marine Synechococcus isolates representing globally abundant genomic lineages demonstrate a unique evolutionary path of genome reduction without a decrease in GC content. Environmental Microbiology.
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Lee, M.D., Webb, E.A., Walworth, N.G., Fu, F.-X., Held, N.A., Saito, M.A., and Hutchins, D.A. (2017). Transcriptional activities of the microbial consortium living with the marine nitrogen-fixing cyanobacterium Trichodesmium reveal potential roles in community-level nitrogen cycling. Applied and Environmental Microbiology.
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Lee, M.D., Walworth, N.G., McParland, E.L., Fu, F.-X., Mincer, T.J., Levine, N.M., Hutchins, D.A., and Webb, E.A. (2017). The Trichodesmium consortium: conserved heterotrophic co-occurrence and genomic signatures of potential interactions. ISMEJ.
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Lee, M.D., Walworth, N.G., Sylvan, J.B., Edwards, K.J., and Orcutt, B.N. (2015). Microbial communities on seafloor basalts at Dorado Outcrop reflect level of alteration and highlight global lithic clades. Frontiers in Microbiology.
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Lee, M.D., Kling, J.D., Araya, R., and Ceh, J. (2018). Jellyfish life stages shape associated microbial communities, while a core microbiome is maintained across all. Frontiers in Microbiology.
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Walworth, N.G. and Lee, M.D., Suffridge, C., Qu, P., Fu., F-X., Saito, M.A., Webb, E.A., Sañudo-Wilhelmy, S.A., and Hutchins, D.A (2017). Functional genomics and phylogenetic evidence suggest genus-wide cobalamin production by the globally distributed marine nitrogen fixer Trichodesmium. Frontiers in Microbiology.
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Walworth, N.G., Fu., F-X., Lee, M.D., Cai, X., Saito, M.A., Webb, E.A., and Hutchins, D.A (2017). Nutrient co-limited Trichodesmium as nitrogen source or sink in a future ocean. Applied and Environmental Microbiology.
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Hutchins, D.A., Fu, F.-X., Walworth, N.G., Lee, M.D., Saito, M.A., and Webb, E.A. (2017). Comment on “The complex effects of ocean acidification on the prominent N2-fixing cyanobacterium Trichodesmium. Science.
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Walworth, N.G., Hutchins, D.A., Dolzhenko, E., Lee, M.D., Fu., F-X., Smith, A.D., and Webb, E.A. (2017). Biogeographic conservation of the cytosine epigenome in the globally important marine, nitrogen-fixing cyanobacterium Trichodesmium. Environmental Microbiology.
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Momper, L.M., Jungbluth, S.P., Lee, M.D., and Amend, J.P. (2017). Energy and carbon metabolisms in a deep terrestrial subsurface fluid microbial community. ISMEJ.
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Ramirez, G.A., Hoffman, C.L., Lee, M.D., Lesniewski, R.A., Barco, R., Garber, A., Toner, B.M., Wheat, C.G., Edwards, K.J., Orcutt, B.N. (2016). Assessing marine microbial induced corrosion monitored in Santa Catalina Island, California. Frontiers in Microbiology.
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Walworth, N.G., Lee, M.D., Fu, F.-X., Hutchins, D.A., and Webb, E.A. (2016). Molecular and physiological evidence of genetic assimilation to high CO2 in the marine nitrogen fixer Trichodesmium. PNAS.
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Walworth, N.G., Fu, F.-X., Webb, E.A., Saito, M.A., Moran, D., McIlvin, M.R., Lee, M.D., and Hutchins, D.A. (2016). Mechanisms of increased Trichodesmium fitness under iron and phosphorus co-limitation in the present and future ocean. Nature Communications.
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