Research

Michael D. Lee, PhD – Science Mercenary

Bioinformatician exploring microbial ecology and evolution

Email: Mike.Lee@nasa.gov
AstrobioMike
AstrobioMike
Orcid: 0000-0001-7750-9145

Current position
NASA Space Biology Postdoctoral Fellow

Affiliations
NASA
JCVI
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 👽

CV
Lee_CV_2019.pdf




Publications

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. (2019). Applications and considerations of GToTree: a user-friendly workflow for phylogenomics. Evolutionary Bioinformatics.
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Lee, M.D. (2019). Happy Belly Bioinformatics: an open-source resource dedicated to helping biologists utilize bioinformatics. The Journal of Open-Source Education.
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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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