Publications

Oliveira, D.M., Saleme, M. de L.S., Smith, R.A., Vangeel, T., Lima, M. de F., Chanoca, A.A., Mota, T.R., Vanhevel, Y., Coussens, G., Van Aelst, K., et al. "CRISPR/Cas9 editing of p-COUMAROYL-CoA:MONOLIGNOL TRANSFERASE 1 in maize alters phenolic metabolism, lignin structure, and lignin-first biomass processing." Trends in Biotechnology 43,5, 1166–1195+ (2025). [DOI: 10.1016/j.tibtech.2025.01.006]

Pandeya, P.R., Black, I.M., Karlen, S.D., Heiss, C., Tseng, Y.-C., Downie, B., Azadi, P. & Schendel, R.R. "Hempseed cell wall polysaccharides are dominated by linear xylans and cellulose: comprehensive structural profiling of ten cultivars of industrial hemp, Cannabis sativa L." Carbohydrate Polymers 361, 123635+ (2025). [DOI: 10.1016/j.carbpol.2025.123635]

Rajbangshi, J., Sener, C. & Van Lehn, R.C. "Effect of solvents on lignin-surface interactions via molecular dynamics." Journal of Physical Chemistry B 129,36, 9175–9189+ (2025). [DOI: 10.1021/acs.jpcb.5c02943]

Reed, D.E., Chu, H., Peter, B.G., Chen, J., Abraha, M., Amiro, B., Anderson, R.G., Arain, A., Arruda, P., Barron-Gafford, G.A., et al. "Network of networks: time series clustering of AmeriFlux sites." Agricultural and Forest Meteorology 372, 110686+ (2025). [DOI: 10.1016/j.agrformet.2025.110686]

Rencoret, J., Ralph, J. & del Río, J.C. "cis-p-Coumarates acylate the lignin sidechain in grasses and other plants." Industrial Crops & Products 236, 121903+ (2025). [DOI: 10.1016/j.indcrop.2025.121903]

Vazquez, J.R., Trujillo, E., Wenger, Z., Botts, M., Coon, J.J. & Amador-Noguez, D. "Physiological and metabolic responses of Zymomonas mobilis to lignocellulosic hydrolysate." Microbiology Spectrum 13,10, e00610–25+ (2025). [DOI: 10.1128/spectrum.00610-25]

Rivett, E.D., Finders, C.M., Haslun, J.A., Gandhi, H., Kahle, M., Ädelroth P., Ostrom, P.H., Ostrom, N.E. & Hegg, E.L. "Isoptopic fractionation and kinetic isotope effects of a purified bacterial nitric oxide reductase (NOR)." Biochemistry 64,20, 4327–4340+ (2025). [DOI: 10.1021/acs.biochem.5c00417]

Rodriguez-Castro, L., Myers, K.S., Linz, A.M., Mettert, E.L., Camp, W., Kiley, P.J., Noguera, D.R. & Donohue, T.J. "Novosphingobium aromaticivorans LigR coordinates transcription of genes involved in metabolism of multiple types of aromatics." mSystems 10,12, e01469–25+ (2025). [DOI: 10.1128/msystems.01469-25]

Rodriguez-Castro, L., Myers, K.S., Noguera, D.R. & Donohue, T.J. "Transcriptomic data sets for Novosphingobium aromaticivorans DSM12444 and a ΔSARO_RS14285 mutant grown in the presence of glucose and either protocatechuic, vanillic, syringic, or 4-coumaric acid." Microbiology Resource Announcements 14,9, e00264–25+ (2025). [DOI: 10.1128/mra.00264-25]

Sener, C., Timokhin, V.I., Hellinger, J., Ralph, J. & Karlen, S.D. "Pd/C promotes C–H bond activation and oxidation of p-hydroxybenzoate during hydrogenolysis of poplar." Nature Communications 16,1, 5259+ (2025). [DOI: 10.1038/s41467-025-60270-x]

Serrano, L.R., Mellors, S., Thompson, W., Lancaster, N.M., Robinson, M.L., Overmyer, K.A., Quarmby, S.T. & Coon, J.J. "SPE-CZE-MS quantifies zeptomole amounts of phosphorylated peptides." Journal of Proteome Research 24,6, 3049–3061+ (2025). [DOI: 10.1021/acs.jproteome.5c00194]

Shen, G., Guber, A., Khosrozadeh, S., Ghaderi, N., Kravchenko, A. & Bladgodatskaya, E. "Plant-microbial interplay for organic nitrogen mediated by functional specificity of root compartments." Rhizosphere 33, 101024+ (2025). [DOI: 10.1016/j.rhisph.2025.101024]

Silva, M.R., Paraíso F., Al-Oboudi, J., Abegg, M.A., Aires, A., Barros, K.O., Brito, P.H., Jarzyna, M., Sylvester, K., Langdon, Q.K., et al. "A taxogenomic view of the genus Torulaspora: an expansion from ten to twenty-two species." Persoonia 54,1, 265–283+ (2025). [DOI: 10.3114/persoonia.2025.54.08]

Singhal, R., Izquierdo, P., Ranaweera, T., Abá, K.S., Brown, B.N.I., Lehti-Shiu, M.D. & Shiu, S.-H. "Using supervised machine-learning approaches to understand abiotic stress tolerance and design resilient crops." Philosophical Transactions of the Royal Society B 380, 20240252+ (2025). [DOI: 10.1098/rstb.2024.0252]

Tejera-Nieves, M.D., Córdova, C., Sears, M., Thelen, K.D., Robertson, P. & Walker, B.J. "Switchgrass (Panicum virgatum) and miscanthus (Miscanthus × Giganteus) long-term yield patterns reveal consistent productivity declines." Global Change Biology Bioenergy 17,12, e70088+ (2025). [DOI: 10.1111/gcbb.70088]

Tian, Y., Kim, B., Pamukçu, I., Turumtay, E.A., Tan, A.H., Saini, V., Chavez, A.I., Tang, A., Su, A.Z., Baidoo, E.E.K., et al. "Engineered accumulation of protocatechuate in corn biomass to enhance biomanufacturing." ACS Sustainable Chemistry & Engineering 13,46, 20204–20214+ (2025). [DOI: 10.1021/acssuschemeng.5c09025]

Tran, P.M., O’Neill, E.G. & Maravelias, C.T. "Complexity reduction methods for large-scale spatially explicit biofuels network design." Industrial & Engineering Chemistry Research 64, 12724–12736+ (2025). [DOI: 10.1021/acs.iecr.5c00439]

VanWallendael, A., Wijewardana, C., Bonnette, J., Vormwald, L., Fritschi, F.B., Boe, A., Chambers, S., Mitchell, R.B., Rouquette, F.M., Jr., Wu, Y., et al. "Local adaptation of both plant and pathogen: an arms-race compromise in switchgrass rust." New Phytologist 248,3, 1527–1541+ (2025). [DOI: 10.1111/nph.70313]

Venkataraman, M., Infante, V., Sabat, G., Sanos-Giles, K., Ané, J.-M. & Pfleger, B.F. "A novel membrane-associated protein aids bacterial colonization of maize." ACS Synthetic Biology 14,1, 206–215+ (2025). [DOI: 10.1021/acssynbio.4c00489]

Wang, N., Takada, M., Sakamoto, S., Vanholme, R., Goeminne, G., Kim, H., Nagano, S., Takata, N., Kamimura, N., Uesugi, M., et al. "Effects of feruloyl-CoA 6’-hydroxylase 1 overexpression on lignin and cell wall characteristics in transgenic hybrid aspen." Frontiers in Plant Science 16, 1543168+ (2025). [DOI: 10.3389/fpls.2025.1543168]

Wang, P., Meng, F., Del Azodi, C.B., Abá, K.S., Casler, M.D. & Shiu, S.-H. "Optimizing genomic prediction for complex traits via investigating multiple factors in switchgrass." Plant Physiology 198,3, kiaf188+ (2025). [DOI: 10.1093/plphys/kiaf188]

Yu, K.M.J., Weers, B.D., McKinley, B.A., Glenn, P.D., Kurtz, E., Rooney, W.L. & Mullet, J.E. "Bioenergy sorghum stem density increases threefold following internode elongation due to continued accumulation of lignified cell walls and complex regulation of genes involved in cell wall biosynthesis." Biotechnology for Biofuels and Bioproducts 18,1, 58+ (2025). [DOI: 10.1186/s13068-025-02659-w]

Zhang, J., Kang, L., Shen, W., Collings, C., Gong, H., Meulen, K.V., Fox, B.G., Gilcher, E., Dumesic, J.A. & Ding, S.-Y. "Lignin removal in subcellular location of poplar cell wall during pretreatment significantly impacts cellulose digestibility." ACS Sustainable Chemistry & Engineering 13,21, 7781–7788+ (2025). [DOI: 10.1021/acssuschemeng.5c00692]

Zhou, S., Garcia-Mancilla, M., Clar, J.F., Runge, T.M., Donohue, T.J., Noguera, D.R. & Karlen, S.D. "Biotransformation of phenolics in spent liquor from aqueous ammonia pretreatment." ChemSusChem 18,22, e202500881+ (2025). [DOI: 10.1002/cssc.202500881]

Zou, H., Chen, J., Li, X., Zhu, J., Liu, X., Tian, Z., Chen, Z., Dai, J., Xue, Z. & Robertson, P. "Contributions of vegetation heterogeneity within tower footprint to CO2 flux estimations through graph neural network modeling." Remote Sensing of Environment 329, 114952+ (2025). [DOI: 10.1016/j.rse.2025.114952]