Publications

Stewart, R.D., Myers, K.S., Amstadt, C., Seib, M., McMahon, K.D. & Noguera, D.R. "Refinement of the "Candidatus Accumulibacter" genus based on metagenomic analysis of biological nutrient removal (BNR) pilot-scale plants operated with reduced aeration." mSystems 9,3, e01188–23+ (2024). [DOI: 10.1128/msystems.01188-23]

Su, Y., Mangus, A.M., Cordell, W.T. & Pfleger, B.F. "Overcoming barriers to medium-chain fatty alcohol production." Current Opinion in Biotechnology 85, 103063+ (2024). [DOI: 10.1016/j.copbio.2023.103063]

Sun, L., David, K.T., Wolters, J.F., Karlen, S.D., Goncalves, C., Opulente, D.A., LaBella, A.L., Groenewald, M., Zhou, X., Shen, X.-X., et al. "Functional and evolutionary integration of a fungal gene with a bacterial operon." Molecular Biology and Evolution 41,4, msae045+ (2024). [DOI: 10.1093/molbev/msae045]

Taifan, G.S.P. & Maravelias, C.T. "Multi-technology separation system synthesis." Computers & Chemical Engineering 183, 108616+ (2024). [DOI: 10.1016/j.compchemeng.2024.108616]

Tejera-Nieves, M., Seong, D.Y., Reist, L. & Walker, B.J. "The Dynamic Assimilation Technique measures photosynthetic CO2 response curves with similar fidelity as steady-state approaches in half the time." Journal of Experimental Biology 75,10, 2819–2828+ (2024). [DOI: 10.1093/jxb/erae057]

Thibault, E. & Brandizzi, F. "Post-translational modifications: emerging directors of cell-fate decisions during endoplasmic reticulum stress in Arabidopsis thaliana." Biochemical Society Transactions 52,2, 831–848+ (2024). [DOI: 10.1042/BST20231025]

Tilhou, N.W., Bonnette, J., Boe, A.R., Fay, P.A., Fritschi, F.B., Mitchell, R.B., Rouquette, F.M., Jr., Wu, Y., Jastrow, J.D., Ricketts, M., et al. "Genomic prediction of regional-scale performance in switchgrass (Panicum virgatum) by accounting for genotype-by-environment variation and yield surrogate traits." G3: Genes | Genomes | Genetics 14,10, jkae159+ (2024). [DOI: 10.1093/g3journal/jkae159]

Turumtay, E.A., Turumtay, H., Tian, Y., Lin, C.-Y., Chai, Y.N., Louie, K.B., Chen, Y., Lipzen, A., Harwood, T., Kumar, K.S., et al. "Expression in poplar of dehydroshikimate dehydratase induces transcriptional and metabolic changes in the phenylpropanoid pathway." Journal of Experimental Botany 75,16, 4960–4977+ (2024). [DOI: 10.1093/jxb/erae251]

Aragon, N.U., Xie, Y., Bigelow, D., Lark, T.J. & Eagle, A.J. "The realistic potential of soil carbon sequestration in U.S. croplands for climate mitigation." Earth’s Future 12,6, e2023EF003866+ (2024). [DOI: 10.1029/2023EF003866]

Unda, F., de Vries, L., Karlen, S.D., Rainbow, J., Zhang, C., Bartley, L.E., Kim, H., Ralph, J. & Mansfield, S.D. "Enhancing monolignol ferulate conjugate levels in poplar lignin via OsFMT1." Biotechnology for Biofuels and Bioproducts 17,1, 97+ (2024). [DOI: 10.1186/s13068-024-02544-y]

Vilbert, A.C., Kontur, W.S., Gille, D., Noguera, D.R. & Donohue, T.J. "Engineering Novosphingobium aromaticivorans to produce cis,cis-muconic acid from biomass aromatics." Applied and Environmental Microbiology 90,1, e01660–23+ (2024). [DOI: 10.1128/aem.01660-23]

Vizza, C., Belanger, M.A., Jones, J., Murphy, S.J., Buckley, D.H., Robertson, P. & Roley, S.S. "Rainfall events stimulate episodic associative nitrogen fixation in switchgrass." Biogeochemistry 167, 1409–1424+ (2024). [DOI: 10.1007/s10533-024-01180-w]

Walters, K.A., Myers, K.S., Donohue, T.J. & Noguera, D.R. "Metagenome-assembled genomes from microbiomes fermenting dairy coproducts." Microbiology Resource Announcements 13,7, e00173–24+ (2024). [DOI: 10.1128/mra.00173-24]

Walters, K.A., Myers, K.S., Ingle, A.T., Donohue, T.J. & Noguera, D.R. "Effect of temperature and pH on microbial communities fermenting a dairy coproduct mixture." Fermentation 10,8, 422+ (2024). [DOI: 10.3390/ fermentation10080422]

Wang, P., Lehti-Shiu, M.D., Lotreck, S., Abá, K.S., Krysan, P.J. & Shiu, S.-H. "Prediction of plant complex traits via integration of multi-omics data." Nature Communications 15,1, 6856+ (2024). [DOI: 10.1038/s41467-024-50701-6]

Weeda, E.P., Holland, C.M., de Bueren, J.B., Yuan, Z., Alherech, M., Coplien, J., Haak, D., Hegg, E.L., Luterbacher, J., Root, T.W., et al. "O2-permeable membrane reactor for continuous oxidative depolymerization of lignin." Joule 8,12, P3336–3346+ (2024). [DOI: 10.1016/j.joule.2024.08.015]

Wilkes, R.A., Borchert, A.J., Garcia, V.E., Geiselman, G.M., Liu, S., Guss, A.M., Michener, J.K., Noguera, D.R., Masai, E., Gladden, J.M., et al. "Comparison of microbial strains as candidate hosts and genetic reservoirs for the valorization of lignin streams." Green Chemistry 26,24, 12053–12069+ (2024). [DOI: 10.1039/D4GC03876B]

Xie, Y., Spawn-Lee, S.A., Radeloff, V.C., Yin, H., Robertson, P. & Lark, T.J. "Cropland abandonment between 1986 and 2018 across the United States: spatiotemporal patterns and current land uses." Environmental Research Letters 19, 044009+ (2024). [DOI: 10.1088/1748-9326/ad2d12]

Yoshioka, K., Kim, H., Lu, F., De Ridder, N., Vanholme, R., Kajita, S., Boerjan, W. & Ralph, J. "Hydroxycinnamaldehyde-derived benzofuran components in lignins." Plant Physiology 194,3, 1370–1382+ (2024). [DOI: 10.1093/plphys/kiad514]

Zavala, B., Dineen, L., Fisher, K.J., Opulente, D.A., Harrison, M.-C., Wolters, J.F., Shen, X.-X., Zhou, X., Groenewald, M., Hittinger, C.T., et al. "Genomic factors shaping codon usage across the Saccharomycotina subphylum." G3: Genes | Genomes | Genetics 14,11, jkae207+ (2024). [DOI: 10.1093/g3journal/jkae207]

Zou, H., Chen, J., Li, X., Abraha, M., Zhao, X. & Tang, J. "Modeling net ecosystem exchange of CO2 with gated recurrent unit neural networks." Agricultural and Forest Meteorology 350, 109985+ (2024). [DOI: 10.1016/j.agrformet.2024.109985]

Casler, M.D., Lee, D., Mitchell, R.B., Moore, K.J., Adler, P.R., Sulc, M., Johnson, K.D., Kallenbach, R.L., Boe, A.R., Mathison, R.D., et al. "Biomass quality responses to selection for increased biomass yield in perennial energy grasses." BioEnergy Research 16,2, 877–885+ (2023). [DOI: 10.1007/s12155-022-10513-2]

Dong, X., Mayes, H.B., Morreel, K., Katahira, R., Li, Y., Ralph, J., Black, B.A. & Beckham, G.T. "Energy-resolved mass spectrometry as a tool for identification of lignin depolymerization products." ChemSusChem 16,1, e202201441+ (2023). [DOI: 10.1002/cssc.202201441]

Hellinger, J., Kim, H., Ralph, J. & Karlen, S.D. "p-Coumaroylation of lignin occurs outside of commelinid monocots in the eudicot genus Morus (mulberry)." Plant Physiology 191,2, 854–861+ (2023). [DOI: 10.1093/plphys/kiac485]

Ko, D.K. & Brandizzi, F. "Coexpression network construction and visualization from transcriptomes underlying ER stress responses." in Plant Proteostasis. Methods in Molecular Biology. (eds. Lois, L. M. & Trujillo, M.) vols. 2581 385–401+ (Humana, 2023). [DOI: 10.1007/978-1-0716-2784-6_27]