Publications

Li, J. & Van Lehn, R.C. "Effects of acid dissociation and ionic solutions on the aggregation of 2-pyrone-4,6-dicarboxylic acid." ACS Omega 9,39, 40759–40768+ (2024). [DOI: 10.1021/acsomega.4c05431]

Li, J., Van Lehn, R.C. & Maravelias, C.T. "An explainable classification framework for determining and understanding the suitability of solvent extraction for bioproduct recovery." ACS Sustainable Chemistry & Engineering 12,14, 5436–5446+ (2024). [DOI: 10.1021/acssuschemeng.3c07129]

Li, Z., Kravchenko, A.N., Cupples, A., Guber, A.K., Kuzyakov, Y., Robertson, P. & Blagodatskaya, E. "Composition and metabolism of microbial communities in soil pores." Nature Communications 15,1, 3578+ (2024). [DOI: 10.1038/s41467-024-47755-x]

Lindstrom, J.K., Peterson, C.A., Ciesielski, P.N., Ralph, J., Chen, M., Jakes, J.E., Johnston, P.A., Rollag, S.A. & Brown, R.C. "Structural and chemical changes in hardwood cell walls during early stages of flash pyrolysis." Frontiers in Energy Research 12, 1348464+ (2024). [DOI: 10.3389/fenrg.2024.1348464]

Liu, C., Zhou, X., Li, Y., Hittinger, C.T., Pan, R., Huang, J., Chen, X.- xin, Rokas, A., Chen, Y. & Shen, X.-X. "The influence of the number of tree searches on maximum likelihood inference in phylogenomics." Systematic Biology 73,5, 807–822+ (2024). [DOI: 10.1093/sysbio/syae031]

Mathieu, D., Bryson, A.E., Hamberger, B., Singan, V., Keymanesh, K., Wang, M., Barry, K., Mondo, S., Pangilinan, J., Koriabine, M., et al. "Multilevel analysis between Physcomitrium patens and Mortierellaceae endophytes explores potential long-standing interaction among land plants and fungi." The Plant Journal 118,2, 304–343+ (2024). [DOI: 10.1111/tpj.16605]

McDonald, M.A. & Maravelias, C.T. "Sequential decision-making under uncertainty for long-term energy transition planning." iScience 27,12, 111288+ (2024). [DOI: 10.1016/j.isci.2024.111288]

Metz, F., Myers, K.S., Lu, F., Noguera, D.R. & Donohue, T.J. "Transcriptomic data sets for Novosphingobium aromaticivorans grown with the β-5-linked aromatic dimer dehydrodiconiferyl alcohol and the related G-aromatic monomers vanillin and ferulic acid." Microbiology Resource Announcements 13,11, e00845–24+ (2024). [DOI: 10.1128/mra.00845-24]

Metz, F., Olsen, A.M., Lu, F., Myers, K.S., Allemann, M.N., Michener, J.K., Noguera, D.R. & Donohue, T.J. "Catabolism of β-5 linked aromatics by Novosphingobium aromaticivorans." mBio 15,8, e01718–24+ (2024). [DOI: 10.1128/mbio.01718-24]

Misra, J., Mettert, E.L. & Kiley, P.J. "Functional analysis of the methylerythritol phosphate pathway terminal enzymes IspG and IspH from Zymomonas mobilis." Microbiology Spectrum 12,7, e04256–23+ (2024). [DOI: 10.1128/spectrum.04256-23]

Mosier, S., Kelly, L., Ozlu, E. & Robertson, P. "Switchgrass (Panicum virgatum L.) cultivars have similar impacts on soil carbon and nitrogen stocks and microbial function." Global Change Biology – Bioenergy 16,3, e13125+ (2024). [DOI: 10.1111/gcbb.13125]

Myers, K.S., Place, M., Gasch, A.P., Noguera, D.R. & Donohue, T.J. "Auto-MuRCiS: a streamlined software package for analysis of multiplex, randomized CRISPR interference sequencing data." Microbiology Resource Announcements 13,9, e00356–24+ (2024). [DOI: 10.1128/mra.00356-24]

Nishikawa, K.K., Chen, J., Acheson, J.F., Harbaugh, S.V., Huss, P., Frenkel, M., Novy, N., Sieren, H.R., Lodewyk, E.C., Lee, D.H., et al. "Highly multiplexed design of an allosteric transcription factor to sense new ligands." Nature Communications 15,1, 10001+ (2024). [DOI: 10.1038/s41467-024-54260-8]

O’Neill, E.G., Geissler, C.H. & Maravelias, C.T. "Large-scale spatially explicit analysis of carbon capture at cellulosic biorefineries." Nature Energy 9, 828–838+ (2024). [DOI: 10.1038/s41560-024-01532-8]

Omolabake, S., Holland, C., Dülger, D.N., Yuan, Z., Hegg, E.L., Hodge, D.B. & Stahl, S.S. "Recovery of p-hydroxybenzoic acid from Cu-catalyzed alkaline hydrogen peroxide pretreatment of hybrid poplar." ACS Sustainable Chemistry & Engineering 12,15, 5726–5730+ (2024). [DOI: 10.1021/acssuschemeng.3c08032]

Opulente, D.A., Labella, A.L., Harrison, M.-C., Wolters, J.F., Liu, C., Li, Y., Kominek, J., Steenwyk, J.L., Stoneman, H.R., VanDenAvond, J., et al. "Genomic factors shape carbon and nitrogen metabolic niche breadth across Saccharomycotina yeasts." Science 384,6694, eadj4503+ (2024). [DOI: 10.1126/science.adj4503]

Parrell, D., Olson, J., Lemke, R.A., Donohue, T.J. & Wright, E.R. "Quantitative analysis of Rhodobacter sphaeroides storage organelles via cryo-electron tomography and light microscopy." Biomolecules 14,8, 1006+ (2024). [DOI: 10.3390/ biom14081006]

Pastor-Cantizano, N., Angelos, E.R., Ruberti, C., Jiang, T., Weng, X., Reagan, B.C., Haque, T., Juenger, T.E. & Brandizzi, F. "Programmed cell death regulator BAP2 is required for IRE1-mediated unfolded protein response in Arabidopsis." Nature Communications 15,1, 5804+ (2024). [DOI: 10.1038/s41467-024-50105-6]

de Lima, A.E.P., Coplien, J., Anthony, L.C., Sato, T.K., Zhang, Y., Karlen, S.D., Hittinger, C.T. & Maravelias, C.T. "On the synthesis of biorefineries for high-yield isobutanol production: from biomass-to-alcohol experiments to system level analysis." RSC Sustainability 2,9, 2532–2540+ (2024). [DOI: 10.1039/d4su00283k]

Pontes, A., Paraiso, F., Liu, Y.-C., Limtong, S., Jindamorakot, S., Jespersen, L., Goncalves, C., Rosa, C.A., Tsai, I.J., Rokas, A., et al. "Tracking alternative versions of the galactose gene network in the genus Saccharomyces and their expansion after domestication." iScience 27,2, 108987+ (2024). [DOI: 10.1016/j.isci.2024.108987]

Postma, K., Mane, S., Shen, M., Kussainova, M., Beisenova, R., Nanda, A., Dong, G. & Chen, J. "Water loss through evapotranspiration after precipitation events in bioenergy crops grown in similar climatic conditions." Frontiers in Environmental Science 12, 1463852+ (2024). [DOI: 10.3389/fenvs.2024.1463852]

Qin, S., Omolabake, S., Diaby, A., Li, J., González, L.D., Holland, C.M., Zavala, V.M., Stahl, S.S. & Van Lehn, R.C. "Identifying green solvent mixtures for bioproduct separation using Bayesian experimental design." ACS Sustainable Chemistry & Engineering 12,52, 18634–18647+ (2024). [DOI: 10.1021/acssuschemeng.4c07423]

Rapp, J.T., Bremer, B.J. & Romero, P.A. "Self-driving laboratories to autonomously navigate the protein fitness landscape." Nature Chemical Engineering 1, 97–107+ (2024). [DOI: 10.1038/s44286-023-00002-4]

Renna, L., Stefano, G., Puggioni, M.P., Kim, S.-J., Lavell, A., Froehlich, J.E., Burkart, G., Mancuso, S., Benning, C. & Brandizzi, F. "ER-associated VAP27-1 and VAP27-3 proteins functionally link the lipid-binding ORP2A at the ER-chloroplast contact sites." Nature Communications 15,1, 6008+ (2024). [DOI: 10.1038/s41467-024-50425-7]

Vazquez, J.R., Trujillo, E., Williams, J., She, F., Getahun, F., Callaghan, M.M., Coon, J.J. & Amador-Noguez, D. "Lipid membrane remodeling and metabolic response during isobutanol and ethanol exposure in Zymomonas mobilis." Biotechnology for Biofuels and Bioproducts 17,1, 14+ (2024). [DOI: 10.1186/s13068-023-02450-9]