Ludwig, D.W., Guptil, C., Alexander, N.R., Zhalnina, K., Wipf, E.M.-L., Khasanova, A., Barber, N.A., Swingley, W., Walker, D.M., and Phillips, J.L. (2025) SetBERT: the deep learning platform for contextualized embeddings and explainable predictions from high-throughput sequencing, Bioinform, 41, btaf370.

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Bell, J.K., Swingley, W.D., and Midgley, M.G. (2025) Bison and burn timing shape arbuscular mycorrhizal diversity and community composition in tallgrass prairie restorations. Appl Soil Ecol, 206, 105895.

Swingley, W.D. (2024) Evolution: Spectral speciation. Curr Biol, 34, pR635-R637.

Mason, C.N., Shahar, S., Beals, K.K., Kelley, S.T., Lipson, D.A., Swingley, W.D., & Barber, N.A. (2023) Taxonomic and functional restoration of tallgrass prairie soil microbial communities in comparison to remnant and agricultural soils, FEMS Microbiol Ecol, 99, fiad120.

Barber, N.A., Klimek, D.M., Bell, J.K., & Swingley, W.D. (2023) Restoration age and reintroduced bison may shape soil bacterial communities in restored tallgrass prairies, FEMS Microbiol Ecol, 99, fiad007.

Kohata, R., Lim, H.-S., Kanamoto, Y., Murakami, A., Fujita, Y., Tanaka, A., Swingley, W., Ito, H., and Tanaka, R. (2022) Heterologous complementation systems verify the mosaic distribution of three distinct protoporphyrinogen IX oxidase in the cyanobacterial phylum, J of Plant Res, 136, 107-15.

 

Kiang, N.Y., Swingley, W.D., Gautam, D., Broddrick, J.T., Stolz, J., Repeta, D., Blankenship, R.E., Wolf, B.W., Detweiler, A., Bebout, L.E., Schladweiler, J., Miller, K.A., Lindemann, R., and Parenteau, M.N. (2022) Discovery of chlorophyll d: Isolation and characterization of a far-red cyanobacterium from the original site of Manning & Strain (1943) at Moss Beach, California, Microorganisms, 10, 819.

 

Sattley, W.M., Swingley, W.D., Burchell, B.M., Dewey, E.D., Hayward, M.K., Renbarger, T.L., Shaffer, K.N., Stokes, L.M., Gurbani, S.A., Kujawa, C.M., Nuccio, D.A., Schladweiler, J., Touchman, J.T., Wang-Otomo, Z.-Y., Blankenship, R.E., and Madigan, M.T. (2021) Complete genome of the thermophilic purple sulfur bacterium Thermochromatium tepidum compared to Allochromatium vinosum and other Chromatiaceae, Photosynth Res, 151, 125-42.

Nayfach, S., et al. (2021) A genomic catalog of Earth’s microbiomes, Nature Biotech, 39, 499-509
Lawrence, T.J., Amrine, K.C.H., Swingley, W.D., and Ardell, D.H. (2019) tRNA functional signatures classify plastids as late-branching cyanobacteria, BMC Evol Biol, 19, 224.

Ohlsson, J.O., Osvatic, J.T., Becraft, E.D., and Swingley, W.D. (2019) Microbial community in hyperalkaline steel slag-fill emulates serpentinizing springs, Diversity, 11, 103.
 

Becraft, E.D., Dodsworth, J.A., Murugapiran, S.K., Thomas, S.C., Ohlsson, J.I., Stepanauskas, R., Hedlund, B.P., and Swingley, W.D. (2017) Genomic comparison of two family-level groups of the uncultivated NAG1 archaeal lineage from chemically and geographically disparate hot springs. Front Microbiol. 8, 2082.

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Barber, N.A., Chantos-Davidson, K.M., Peralta, R.A., Sherwood, J.P., and Swingley, W.D. (2017) Soil microbial community composition in tallgrass prairie restorations converge with remnants across a 27-year chronosequence. Environ Microbiol. 8, 3118-31.

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Baker, J.M., Riester, C.J., Skinner, B.M., Newell, A.W., Swingley, W.D., Madigan, M.T., Jung, D.O., Asao, M., Chen, M., Loughlin, P., Pan, H., Lin, S., Li, N., Shaw, J., Prado, M., Sherman, C., Li, X., Tang, K.-H., Blankenship, R.E., Zhao, T., Touchman, J.W., and Sattley , W.M. (2017) Genome sequence of Rhodoferax antarcticus ANT.BRT, a psychrophilic purple nonsulfur bacterium from an Antarctic microbial mat. Microorganisms. 5, 8.

 

Wysocki, W.P., Burke, S.V., Swingley, W.D., and Duvall, M.R. (2016) The first complete plastid genome from Joinvilleaceae (J. ascendens; Poales) shows unique and unpredicted rearrangements. PLOS ONE. 11, e0163218.

 

Becraft, E.D., Dodsworth, J.A., Murugapiran, S.K., Ohlsson, J.I., Briggs, B.R., Kanbar, J., De Vlaminck, I., Quake, S.R., Dong, H., Hedlund, B.P., and Swingley, W.D. (2016) Single-Cell-Genomics-Facilitated Read Binning of Candidate Phylum EM19 Genomes from Geothermal Spring Metagenomes. Appl Environ Microbiol. 82, 992-1003.

 

Amrine, K.C.H., Swingley, W.D., and Ardell, D.H. (2014) tRNA signatures reveal a polyphyletic origin of SAR11 strains among Alphaproteobacteria. PLOS Comput Biol. 10, e1003454.

 

Sattley, W.M. and Swingley, W.D. (2013) “Properties and Evolutionary Implications of the Heliobacterial Genome,” In Genome Evolution of Photosynthetic Bacteria. ed Beatty, J.T. Elsevier, Amsterdam, The Netherlands. pp 67-98.

 

Dodsworth, J.A., Blainey, P.C., Murugapiran, S.K., Swingley, W.D., Ross, C.A., Tringe, S.G., Chain, P.S.G., Scholz, M.B., Lo, C.-C., Raymond, J., Quake, S.R., and Hedlund, B.P. (2013) Single-cell and metagenomic analyses indicate a fermentative and saccharolytic lifestyle for members of the OP9 lineage. Nat Commun. 4, 1854.         

 

Swingley. W.D., Meyer-Dombard, D.R., Shock, E.L., Alsop, E.B., Falenski, H.D., Havig, J.R., and Raymond, J. (2011) Coordinating environmental genomics and geochemistry reveals metabolic transitions in a hot spring ecosystem. PLoS ONE. 7, e38108.

 

Meyer-Dombard, D.R., Swingley, W., Raymond, J., Havig, J., Shock, E.L., and Summons, R.E. (2011) Hydrothermal ecotones and streamer biofilm communities in the Lower Geyser Basin, Yellowstone National Park. Environ Microbiol. 13, 2216-31.

 

Swingley, W.D., Iwai, M., Chen, Y., Ozawa, S.-I.,Takizawa, K., Takahashi, Y., and Minagawa, J. (2010) Characterization of photosystem I antenna proteins in the prasinophyte Ostreococcus tauri. Biochim Biophys Acta. 1797, 1458-64.

 

Lu Y.K., Marden J., Han M., Swingley W.D., Mastrian S.D., Chowdhury S.R., Hao J., Helmy T., Kim S., Kurdoglu A.A., Matthies H.J., Rollo D., Stothard P., Blankenship R.E., Bauer C.E., Touchman J.W. (2010) Metabolic flexibility revealed in the genome of the cyst-forming alpha-1 proteobacterium Rhodospirillum centenum. BMC Genomics. 11, 325.

 

Swingley, W.D., Blankenship, R.E., and Raymond, J. (2008) “Evolutionary Relationships Among Purple Photosynthetic Bacteria and the Origin of Proteobacterial Photosynthetic Systems,” In The Purple Phototrophic Bacteria. eds. Hunter, C.N., Daldal, F., Thurnauer, M.C., and Beatty, J.T. Springer, Dordrecht, The Netherlands. pp 17-29.

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Raymond, J. and Swingley, W.D. (2008) Phototroph genomics ten years on. Photosynth Res. 97, 5-19.

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Sattley, W.M., Madigan, M.T., Swingley, W.D., Cheung, P.C., Clocksin, K. M., Conrad, A.L., Dejesa, L.C., Honchak, B.M., Jung, D.O., Karbach, L.E., Kurdoglu, A., Lahiri, S., Mastrian, S.D., Page, L.E., Taylor, H.L., Wang, Z.T., Raymond, J., Chen, M., Blankenship, R.E., and Touchman, J.W. (2008) The genome of Heliobacterium modesticaldum, a phototrophic representative of the Firmicutes containing the simplest photosynthetic apparatus. J Bacteriol. 190, 4687-96.

 

Swingley, W.D., Blankenship, R.E., Raymond, J. (2008) Integrating Markov clustering and molecular phylogenetics to reconstruct the cyanobacterial species tree from conserved protein families. Mol Biol Evol. 25, 643-54.

 

Swingley, W.D., Chen, M., Cheung, P.C., Conrad, A.L., Dejesa, L.C., Hao, J., Honchak, B.M., Karbach, L.E., Kurdoglu, A., Lahiri, S., Mastrian, S.D., Miyashita, H., Page, L., Satoh, S., Sattley, W.M., Shimada, Y., Taylor, H.L., Tomo, T., Tsuchiya, T., Wang, Z.T., Raymond, J., Mimuro, M., Blankenship, R.E., and Touchman, J.W. (2008) Niche adaptation and genome expansion in the chlorophyll d-producing cyanobacterium Acaryochloris marina. Proc Natl Acad Sci USA. 105, 2005-10.

 

Swingley, W.D., Blankenship, R.E., and Raymond, J. (2008) “Insight into cyanobacterial evolution from comparative genomics,” In The Cyanobacteria: Molecular Biology, Genomics and Evolution. eds. Herrero, A. and Flores, E. Caister Academic Press, Norfolk, UK. pp 21-44.

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Soule, T., Stout, V., Swingley, W.D., Meeks, J.C., Garcia-Pichel, F. (2007) Molecular genetics and genomic analysis of scytonemin biosynthesis in Nostoc punctiforme ATCC 29133. J Bacteriol. 189, 4465-72.

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Swingley, W.D., Gholba, S., Mastrian, S.D., Matthies, H.J., Hao, J., Ramos, H., Acharya, C.R., Conrad, A.L., Taylor, H.L., Dejesa, L.C., Shah, M.K., O’Huallachain, M.E., Lince, M.T., Beatty, J.T., Blankenship, R.E. and Touchman, J.W. (2007) The complete genome sequence of Roseobacter denitrificans reveals a mixotrophic rather than photosynthetic metabolism. J Bacteriol. 189, 683-90.

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Swingley, W.D., Hohmann-Marriott, M.F., Le Olson, T., and Blankenship, R.E. (2005) Effect of iron on growth and ultrastructure of Acaryochloris marina. Appl Environ Microbiol. 71, 8606-10.