Publications

Liu, S., Chou, M.-Y., Benucci, G.M.N., Eudes, A. & Bonito, G. "Genetic modification of the shikimate pathway to reduce lignin content in switchgrass (Panicum virgatum L.) significantly impacts plant microbiomes." Microbiology Spectrum 13,1, e01546–24+ (2025). [DOI: 10.1128/spectrum.01546-24]

Lucas, M., Gil, J., Robertson, G.P., Ostrom, N.E. & Kravchenko, A. "Changes in soil pore structure generated by the root systems of maize, sorghum and switchgrass affect in situ N2O emissions and bacterial denitrification." Biology and Fertility of Soils 61,3, 367–383+ (2025). [DOI: 10.1007/s00374-023-01761-1]

Mandalika, A., Runge, T. & Ragauskas, A. "Membrane separations in biomass processing." ChemPlusChem 90,2, e202400497+ (2025). [DOI: 10.1002/cplu.202400497]

Martin, G., Austin, K., Lark, T., Lee, S. & Clark, C.M. "Tracking cropland transitions: a comparative analysis of U.S. land cover change data." PLOS ONE 20,3, e0313880+ (2025). [DOI: 10.1371/journal.pone.0313880]

McDonald, M.A., Larson, E.D., Greig, C. & Maravelias, C.T. "A control-inspired approach for energy transition planning under uncertainty." Computers & Chemical Engineering 200, 109176+ (2025). [DOI: 10.1016/j.compchemeng.2025.109176]

Metz, F., Allemann, M.N., Michener, J.K., Myers, K.S., Lu, F., Noguera, D.R. & Donohue, T.J. "RB-TnSeq barcode abundance data sets for Novosphingobium aromaticivorans grown on the β-5-linked aromatic dimer dehydrodiconiferyl alcohol." Microbiology Resource Announcements 14,1, e00844–24+ (2025). [DOI: 10.1128/mra.00844-24]

Miao, G., Li, H., Zhu, Y., Chen, S., Lu, F., Ralph, J. & Xu, F. "Deep eutectic solvents for efficient fractionation of lignocellulose to produce uncondensed lignin and high-quality cellulose." ACS Sustainable Chemistry & Engineering 13, 2197–2209+ (2025). [DOI: 10.1021/acssuschemeng.4c09673]

Miller, S.T., Macdonald, C.B. & Raman, S. "Understanding, inhibiting, and engineering membrane transporters with high-throughput mutational screens." Cell Chemical Biology 32,4, 529–542+ (2025). [DOI: 10.1016/j.chembiol.2025.03.003]

Min, K., Nuccio, E., Slessarev, E., Kan, M., McFarlane, K.J., Oerter, E., Jurusik, A., Sanford, G., Thelen, K.D., Pett-Ridge, J., et al. "Deep-rooted perennials alter microbial respiration and chemical composition of carbon in density fractions along soil depth profiles." Geoderma 455, 117202+ (2025). [DOI: 10.1016/j.geoderma.2025.117202]

Mottiar, Y., Tschaplinski, T.J., Ralph, J. & Mansfield, S.D. "Suppression of chorismate mutase 1 in hybrid poplar to investigate potential redundancy in the supply of lignin precursors." Plant Direct 9,3, e70053+ (2025). [DOI: 10.1002/pld3.70053]

Myers, K.S., Linz, A.M., Baumgart, L.A., Zhang, Y., Blaby, I., Mewalal, R., Ng, V., Noguera, D.R. & Donohue, T.J. "Using DNA affinity purification sequencing (DAP-seq) to identify in vitro binding sites of potential Novosphingobium aromaticivorans DSM12444 transcription factors." Microbiology Resource Announcements 14,8, e00260–25+ (2025). [DOI: 10.1128/mra.00260-25]

O’Neill, E.G., Lark, T.J., Xie, Y., Kim, S., Dale, B.E., Robertson, G.P., Basso, B. & Maravelias, C.T. "Available land for cellulosic biofuel production: a supply chain centered comparison." Environmental Research Letters 20,1, 014067+ (2025). [DOI: 10.1088/1748-9326/ada301]

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 Rio, 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 DOI:10.1021/acs.biochem.5c00417, (2025). [DOI: 10.1021/acs.biochem.5c00417]

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]

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 - Molecular Phylogeny and Evolution of Fungi 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]

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]