Paul Den Uyl

Bioinformatics Specialist

4840 South State Street
Ann Arbor, MI 48108-9719

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Paul’s research primarily revolves around the implementation of microbiological and bioinformatic methods, such as metagenomics, amplicon sequencing, and qPCR, to investigate microbial life present in the Great Lakes. He earned his M.S. in Earth and Environmental Sciences from the University of Michigan in 2024, employing metagenomic tools to characterize saxitoxin biosynthesis in Western Lake Erie.
In his previous role as a research specialist with CIGLR from 2018 to 2022, Paul analyzed ‘omics datasets collected by uncrewed systems. From 2015 to 2018, he served as a research associate in the DeLong Lab at the University of Hawai’i. Paul earned a B.S. in Geological Science with a concentration in Oceanography from the University of Michigan in 2013, where he conducted research on harmful algal blooms (HABs) and the coral disease known as black band disease following graduation.
    • M.S., Earth and Environmental Sciences, University of Michigan
    • B.S., Geological Science – Oceanography Concentration, University of Michigan
Research Interests/Area of Expertise: 
    • Microbial Ecology
    • Cyanotoxins
    • Bioinformatics Tools/Pipelines
    • Uncrewed Systems
In the News: 


Boegehold, A.G., Burtner, A.M., Camilleri, A.C., Carter, G., Den Uyl, P.A., Fanslow, D., Fyffe Semenyuk, D., Godwin, C.M., Gossiaux, D., Johengen, T.H., Kelchner, H., Kitchens, C., Mason, L.A., McCabe, K., Palladino, D., Stuart, D., Vanderploeg, H. and Errera, R. 2023. Routine monitoring of western Lake Erie to track water quality changes associated with cyanobacterial harmful algal blooms. Earth System Science Data. (DOI:10.5194/essd-15-3853-2023).

Thompson, L.R., S.R. Anderson, P.A Den Uyl, N.V Patin, S. Jean Lim, G. Sanderson, K.D. Goodwin. 2022, Tourmaline: A containerized workflow for rapid and iterable amplicon sequence analysis using QIIME 2 and Snakemake. GigaScience. 11:giac066. (DOI:10.1093/gigascience/giac066).

Den Uyl, P.A., L.R. Thompson, R.M. Errera, J.M. Birch, C.M. Preston, W. Usslerlll, C.E. Yancey, S.R. Chaganti, S.A. Ruberg, G.J. Doucette, G.J. Dick, C.A. Scholin, K.D. Goodwin. 2022. Lake Erie Field Trials to Advance Autonomous Monitoring of Cyanobacterial Harmful Algal blooms. Frontiers in Marine Science. 9:1021952. (DOI:10.3389/fmars.2022.1021952). [Altmetric Score]

Yancey, C.E.; D.J. Smith; P.A. Den Uyl; O.G. Mohamed; F. Yu; S.A. Ruberg; J.D. Chaffin; K.D. Goodwin; A. Tripathi; D.H. Sherman; G.J. Dick. 2022. Metagenomic and metatranscriptomic insights into population diversity of microcystis blooms: spatial and temporal dynamics of mcy genotypes, including a partial operon that can be abundant and expressed. Environmental Microbiology. (DOI:10.1128/aem.02464-21).

Den Uyl. P.A., S.B. Harrison, C.M. Godwin, M.D. Rowe, J.R. Strickler and H.A.Vanderploeg. 2021. Comparative Analysis of Microcystis Buoyancy in Western Lake Erie and Saginaw Bay of Lake Huron. Harmful Algae. 108. (DOI:10.1016/j.hal.2021.102102).

Beaulaurier, J., E. Luo, J.M. Eppley, P.A. Den Uyl, X. Dai, A. Burger, D.J. Turner, M. Pendelton, S. Juul, E.D. Harrington, E.F. DeLong. 2020. Assembly-free single-molecule sequencing recovers complete virus genomes from natural microbial communities. Genome Research. gr.251686.119. (DOI:10.1101/gr.251686.119). [Altmetric Score]

Den Uyl, P.A., L.L. Richardson, S. Jain, G.J. Dick. 2016. Unraveling the Physiological Roles of the Cyanobacterium Geitlerinema sp. BBD and Other Black Band Disease Community Members through Genomic Analysis of a Mixed Culture. PLoS One. 11(6):e0157953. (DOI:10.1371/journal.pone.0157953). [Altmetric Score]

Berry, M.A., T.W. Davis, R.M. Cory, M.B. Duhaime, T.H. Johengen, G.W. Kling, J.A. Marino, P.A. Den Uyl, D. Gossiaux, G.J. Dick, V.J. Denef. 2016. Cyanobacterial harmful algal blooms are a biological disturbance to western Lake Erie bacterial communities. Environmental Microbiology. kiju1462-2920. (DOI:10.1111/1462-2920.13640). [Altmetric Score]

Kinsman-Costello, L.E., C.S. Sheik, N.D. Sheldon, G.A. Burton, D.M. Costello, D. Marcus, P.A. Den Uyl, G.J. Dick. 2016. Groundwater shapes sediment biogeochemistry and microbial diversity in a submerged Great Lake sinkhole. Geobiology. 1472-4669. (DOI:10.1111/gbi.12215). [Altmetric Score]

Sheik, C.S., E.I. Stevenson, P.A. Den Uyl, G.J. Dick, and S.M. Aciego. 2015. Microbial communities of the Lemon Creek Glacier show subtle structural variation yet stable phylogenetic composition over space and time. Frontiers in Microbiology. 6:495. (DOI:10.3389/fmicb.2015.00495). [Altmetric Score]