Lee JA, Baugh AC, Shevalier NJ, Strand B, Stolyar S, Marx CJ. (2021) Cross-feeding of a toxic metabolite in a synthetic lignocellulose-degrading microbial community. Microorganisms 9: 321.

Bazurto JV, Nayak DD, Ticak T, Davlieva M, Lee JA, Hellenbrand CN, Lambert LB, Benski OJ, Quates CJ, Johnson JL, Patel JS, Ytreberg FM, Shamoo Y, and Marx CJ. (2021) EfgA is a conserved formaldehyde sensor that leads to bacterial growth arrest in response to elevated formaldehyde. PLOS Biology 19: e3001208.

Bazurto JV, Bruger EL, Lee JA, Lambert LB, Marx CJ. (2021) Formaldehyde-responsive proteins, TtmR and EfgA, reveal a tradeoff between formaldehyde resistance and efficient transition to methylotrophy in Methylorubrum extorquens. Journal of Bacteriology.

Lee JA, Boston PJ, Buckner D, Everroad RC, Ledford SM, Moores JE, Reitz G, Schuerger AC, Smith DJ, Stooke PJ, Wacker AL, and Wilhelm MB. (2020) SOTERIA: Searching for Organisms Through Equipment Recovery at Impact Areas. White paper submitted to the Planetary Science and Astrobiology Decadal Survey 2023-2032. [PDF]

Lee JA, Riazi S, Nemati SH, Vasdekis AE, Ridenhour BJ, Remien CH, Marx CJ. (2019) Microbial phenotypic heterogeneity in response to a metabolic toxin: continuous, dynamically shifting distribution of formaldehyde tolerance in Methylobacterium extorquens populations. PLOS Genetics 15(11): e1008458 [PDF]

Lee JA, Stolyar S, Marx CJ. (2019) An aerobic link between lignin degradation and C₁ metabolism: growth on methoxylated aromatic compounds by members of the genus Methylobacterium. bioRxiv 712836. [PDF]

Lee JA, Marx CJ. (2019) Tales from the crypt(ic). Science 365: 318–319. [PDF]

Lee JA, Francis CA. (2017) Deep nirS amplicon sequencing of San Francisco Bay sediments enables prediction of geography and environmental conditions from denitrifying community composition. Environmental Microbiology 19: 4897–4912. [PDF]

Lee JA, Francis CA. (2017) Spatiotemporal characterization of San Francisco Bay denitrifying communities: a comparison of nirK and nirS diversity and abundance. Microbial Ecology 73: 271–284. [PDF]

Seyfferth AL, Kocar BD, Lee JA, Fendorf S. (2013) Seasonal dynamics of dissolved silicon in a rice cropping system after straw incorporation. Geochimica et Cosmochimica Acta 123: 120–133.

Lee JA. (2010) Yeast Are People Too: Sourdough fermentation from the microbe’s point of view. In: Saberi H (ed). Cured, Smoked, and Fermented Foods: Proceedings of the Oxford Symposium on Food and Cookery 2010. Prospect Books, United Kingdom. [PDF]

Froyd CA, Lee JA, Anderson AJ, Haberle SG, Gasson PE, Willis KJ. (2010) Historic fuel wood use in the Galápagos Islands: identification of charred remains. Vegetation History and Archaeobotany 19: 207–217. [PDF]

Sullivan MB, Coleman ML, Quinlivan V, Rosenkrantz JE, DeFrancesco AS, Tan G, Fu R, Lee JA, Waterbury JB, Bielawski JP, Chisholm SW. (2008) Portal protein diversity and phage ecology. Environmental Microbiology 10: 2810–2823. [PDF]

Fricker MD, Lee JA, Boddy L, Bebber DP. (2008) The interplay between structure and function in fungal networks. Topologica 1: 004–004. [PDF]

Fricker MD, Lee JA, Bebber DP, Tlalka M, Hynes J, Darrah PR, Watkinson SC, Boddy L. (2008) Imaging complex nutrient dynamics in mycelial networks. Journal of Microscopy 231: 317–331.

Sullivan MB, Lindell D, Lee JA, Thompson LR, Bielawski JP, Chisholm SW. (2006) Prevalence and evolution of core Photosystem II genes in marine cyanobacterial viruses and their hosts. PLOS Biology 4: e234. [PDF]