Publications

2026

Dumontet, L., Han, S.-R., Prouvost, A., Lee, J.H., Oh, T.-J. and Kang, M. (2026) “Interpretable Kolmogorov-Arnold networks for enzyme commission number prediction,” npj Artificial Intelligence, 2(1), p. 11. Available at: https://doi.org/10.1038/s44387-025-00059-x.

Paudel, L., Pardhe, B.D., Gupta, S., Han, S.-R., Lee, J.H. and Oh, T.-J. (2026) “Functional characterization and effect of polysaccharides on the activity of GH16 β-agarase from Gelidibacter salicanalis PAMC21136,” Carbohydrate Research, 559, p. 109719. Available at: https://doi.org/10.1016/j.carres.2025.109719.

2025

Ahmed, R.A.H., Abdellatif, I.M.Y., Oka, N., Kobayashi, M., Fuhrmann-Aoyagi, M.B., Todaka, D., Seki, M. and Miura, K. (2025) “Application of 4-CPA or ethanol enhances plant growth and fruit quality of phyA mutant under heat stress,” Scientific Reports, 15(1), p. 32388. Available at: https://doi.org/10.1038/s41598-025-17929-8.

Bang, J., Kim, B., Lee, Y.M., Do, H., Lee, J.H. and Oh, T.-J. (2025) “Complete genome sequence of Rahnella sp. PAMC25559, a psychrophilic plant growth-promoting bacterium isolated from an Alpine glacier,” Microbiology Resource Announcements, 0(0), pp. e01160-25. Available at: https://doi.org/10.1128/mra.01160-25.

Bashir, K., Todaka, D., Sako, K., Ueda, M., Aziz, F. and Seki, M. (2025) “Chemical application improves stress resilience in plants,” Plant Molecular Biology, 115(2), p. 47. Available at: https://doi.org/10.1007/s11103-025-01566-w.

Fan, Y., Noble, D.W.A., Medlyn, B.E., Monson, R.K., Sage, R.F., Smith, N.G., Ainsworth, E.A., Busch, F.A., Danila, F.R., Ermakova, M., Friesen, P., Furbank, R.T., Gan, S.H., Ghannoum, O., Griffith, D.M., Gu, L., Jacob, V., Knauer, J., Leakey, A.D.B., Li, S., Lombardozzi, D.L., Ludwig, M., Pathare, V.S., Peixoto, M.M., Prado, K., Sonawane, B.V., Still, C.J., von Caemmerer, S., Woodford, R. and Way, D.A. (2025) “Environmental factors have a greater influence on photosynthetic capacity in C4 plants than biochemical subtypes or growth forms,” New Phytologist, 248(3), pp. 1205–1224. Available at: https://doi.org/10.1111/nph.70525.

Gurung, S., Lee, C.-M., Weon, H.-Y., Han, S.-R. and Oh, T.-J. (2025) “Comparative Genome Analysis of Three Halobacillus Strains Isolated From Saline Environments Reveal Potential Salt Tolerance and Algicidal Mechanisms,” Environmental Microbiology Reports, 17(3), p. e70121. Available at: https://doi.org/10.1111/1758-2229.70121.

Hoang, T., Nguyen, D.L., Kim, B., Choi, W., Cho, S.M., Kim, H.-W., Han, S.J., Kim, K., Lee, J.H. and Do, H. (2025) “Ice affinity purification system for recombinant proteins using a DUF3494 ice-binding protein,” International Journal of Biological Macromolecules, 315, p. 144378. Available at: https://doi.org/10.1016/j.ijbiomac.2025.144378.

Koyama, T., Kunieda, T., Toyonaga, H., Nobuhara, M., Mitsuda, N., Soga, K., Ishida, J., Seki, M., Takahashi, K., Kinoshita, T., Bessho, A., Demura, T. and Ohme-Takagi, M. (2025) “TCP3-mediated regulation of cell expansion in Arabidopsis thaliana,” New Phytologist, n/a(n/a). Available at: https://doi.org/10.1111/nph.70631.

Kruger, R., Oler, E., Saha, S., Poelzer, J., Han, S., Punsalan, M.P., Green, B., Bushra, F., Kyes, M., Disu, F., Wakoli, J., Woudstra, R., Tejol, E., Fakutan, O., Wang, F., Lee, B.L., Sajed, T., Tian, S., Torres-Calzada, C., Berjanskii, M., MacKay, S., Karu, N., Kadurrah-Daouk, R. and Wishart, D.S. (2025) “MiMeDB 2.0: the Human Microbial Metabolome Database for 2026,” Nucleic Acids Research, p. gkaf1272. Available at: https://doi.org/10.1093/nar/gkaf1272.

Kuwayama, S., Hayashi, M., Takahashi, K., Hayashi, Y., Fukatsu, K., Murakami, K., Aihara, Y., Sato, A. and Kinoshita, T. (2025) “The protein kinase inhibitor, tyrphostin AG126, and its derivatives suppress phosphorylation of plasma membrane H+-ATPase and light-induced stomatal opening,” Plant and Cell Physiology, 66(7), pp. 1020–1029. Available at: https://doi.org/10.1093/pcp/pcaf050.

Marks, R.A., Ekwealor, J.T.B., Artur, M. a. S., Bondi, L., Boothby, T.C., Carmo, O.M.S., Centeno, D.C., Coe, K.K., Dace, H.J.W., Field, S., Hutt, A., Porembski, S., Thalhammer, A., van der Pas, L., Wood, A.J., Alpert, P., Bartels, D., Boeynaems, S., Datar, M.N., Giese, T., Seidou, W.I., Kirchner, S.M., Köhler, J., Kumara, U.G.V.S.S., Kyung, J., Lyall, R., Mishler, B.D., Ndongmo, J.B.V.T., Otegui, M.S., Reddy, V., Rexroth, J., Tebele, S.M., VanBuren, R., Verdier, J., Vothknecht, U.C., Wittenberg, M.F., Zokov, E., Oliver, M.J. and Rhee, S.Y. (2025) “Life on the dry side: a roadmap to understanding desiccation tolerance and accelerating translational applications,” Nature Communications, 16(1), p. 3284. Available at: https://doi.org/10.1038/s41467-025-58656-y.

Mérai, Z., Xu, F., Hajdu, A., Kozma-Bognár, L. and Dolan, L. (2025) “Phytochrome A is required for light-inhibited germination of Aethionema arabicum seed,” New Phytologist, 247(5), pp. 2134–2146. Available at: https://doi.org/10.1111/nph.70344.

Min, K., Sulaiman, S., Lee, J., Seo, S., Arora, R. and Lee, H. (2025) “Differential response of plasma membrane versus chloroplast functions to freeze–thaw stress by Antarctic species, Deschampsia antarctica and Colobanthus quitensis, as explored through freeze-injury and post-thaw recovery,” Planta, 263(1), p. 30. Available at: https://doi.org/10.1007/s00425-025-04899-4.

Minen, R.I., Camalle, M.D., Schwertfeger, T.J., Abdulhakim, F., Reish, H., Perez de Souza, L., Moreno, J.C., Schilmiller, A., Thirumalaikumar, V.P., Agarwal, P., Plecki, C.F., Fernie, A.R., Hirt, H., Schroeder, F.C. and Skirycz, A. (2025) “Characterization of the cyclic dipeptide cyclo(His-Pro) in Arabidopsis,” Plant Physiology, 198(1), p. kiaf174. Available at: https://doi.org/10.1093/plphys/kiaf174.

Nguyen, D.L., Saha, S., Thacharodi, A., Singh, B.B., Mitra, S., Do, H. and Kumaraswami, M. (2025) “Environmental pH controls antimicrobial production by human probiotic Streptococcus salivarius,” Journal of Bacteriology, 207(6), pp. e00059-25. Available at: https://doi.org/10.1128/jb.00059-25.

Paudel, L., Pardhe, B.D., Han, S.-R., Lee, J. and Oh, T.-J. (2025) “CAZyme analysis and functional characterization of a new GH18 chitin hydrolase from Gelidibacter salicanalis PAMC21136,” Carbohydrate Polymer Technologies and Applications, 10, p. 100773. Available at: https://doi.org/10.1016/j.carpta.2025.100773.

Paudel, P., Regmi, K.P., Kim, K.-H. and Oh, T.-J. (2025) “Discovery of a novel CYP107E41 from Streptoalloteichus sp. KCCM40925 for advancing steroid hydroxylation catalysis,” Archives of Biochemistry and Biophysics, 773, p. 110595. Available at: https://doi.org/10.1016/j.abb.2025.110595.

Prado, K., Holland, B.L., McSpadden Gardener, B., Lundquist, P.K., Santiago, J.P., VanBuren, R. and Rhee, S.Y. (2025) “Building climate-resilient crops: genetic, environmental, and technological strategies for heat and drought stress tolerance,” Journal of Experimental Botany, p. eraf111. Available at: https://doi.org/10.1093/jxb/eraf111.

Prado, K., Xue, B., Johnson, J.E., Field, S., Stata, M., Hawkins, C.L., Hsia, R.-C., Liu, H., Cheng, S. and Rhee, S.Y. (2025) “Photosynthetic acclimation is a key contributor to exponential growth of a desert plant in Death Valley summer,” Current Biology, 0(0). Available at: https://doi.org/10.1016/j.cub.2025.10.004.

Robertson, S.M., Sakariyahu, S.K., Gan, E., Maqsood, O., Pasha, A., Provart, N.J. and Wilkins, O. (2025) “Growth-limiting drought increases sensitivity of Asian rice (Oryza sativa) leaves to heat shock through physiological and spatially distinct transcriptomic responses,” The Plant Journal, 123(2), p. e70349. Available at: https://doi.org/10.1111/tpj.70349.

Saldivar, E.V., Field, S. and Rhee, S.Y. (2025) “Cellular view of metabolism: metabolic biomolecular condensates,” New Phytologist, 248(2), pp. 555–562. Available at: https://doi.org/10.1111/nph.70474.

Seo, S., Ahn, Y.-Y., Kim, K., Lee, J.H., Min, K. and Lee, H. (2025) “Exogenous abscisic acid enhances freeze-thaw stress tolerance in Antarctic moss Sanionia uncinata through coordinated antioxidant defense and osmoprotectant accumulation,” Cryobiology, 121, p. 105325. Available at: https://doi.org/10.1016/j.cryobiol.2025.105325.

Shrestha, P., Kim, B., Han, S.-R., Lee, H. and Oh, T.-J. (2025) “Unraveling the genetic mechanisms of UV radiation resistance in Bacillus through biofilm formation, sporulation, and carotenoid production,” Genomics, 117(4), p. 111066. Available at: https://doi.org/10.1016/j.ygeno.2025.111066.

Shrestha, S.K., Ghimire, N., Lee, W.-H., Kim, H.-J. and Oh, T.-J. (2025) “Characterization of O-methyltransferase in Streptomyces sp. KCCM12257 and bioactivity assessment of polyphenols,” International Journal of Biological Macromolecules, 319, p. 145520. Available at: https://doi.org/10.1016/j.ijbiomac.2025.145520.

Suzuki, T., Takayama, M., Sumiyoshi, M. and Ezura, H. (2025) “Characterization of the Fruit Quality and Yield of a Genome-Edited High-GABA Tomato Cultivar (Solanum lycopersicum) Cultivated under Salt Stress Conditions,” ACS Agricultural Science & Technology, 5(7), pp. 1266–1273. Available at: https://doi.org/10.1021/acsagscitech.4c00572.

Thapa, G., Gurung, S., Han, S.-R. and Oh, T.-J. (2025) “In-silico and biochemical insights into MHET biodegradation by Arctic Pseudomonas MHET hydrolase,” International Journal of Biological Macromolecules, 321, p. 146195. Available at: https://doi.org/10.1016/j.ijbiomac.2025.146195.

Tiedge, K.J., Roda, F., Smith, S.D. and Moghe, G.D. (2025) “Advances in analyzing and engineering plant metabolic diversity,” Applications in Plant Sciences, 13(4), p. e70017. Available at: https://doi.org/10.1002/aps3.70017.

Wang, Z., Cara, S., Rhee, S.Y. and Hauser, B.A. (2025) “Tetratricopeptide Repeat 2 Is a Quantitative Trait Locus That Controls Seed Size,” International Journal of Molecular Sciences, 26(17), p. 8310. Available at: https://doi.org/10.3390/ijms26178310.

Xue, B., Prado, K., Rhee, S.Y. and Stata, M. (2025) “UnigeneFinder: An Automated Pipeline for Gene Calling From Transcriptome Assemblies Without a Reference Genome,” Plant Direct, 9(4), p. e70056. Available at: https://doi.org/10.1002/pld3.70056.

Yuan, X., Smith, N.S.S. and Moghe, G.D. (2025) “Analysis of plant metabolomics data using identification-free approaches,” Applications in Plant Sciences, 13(4), p. e70001. Available at: https://doi.org/10.1002/aps3.70001.

Zait, Y., Zhu, M., Ando, E., Zhou, Y., Yaaran, A., Yon, S., Okamoto, M., Hayashi, Y., Hirai, M.Y., Jegla, T., Kinoshita, T., Chen, S. and Assmann, S.M. (2025) “Apoplastic metabolomics reveals sugars as mesophyll messengers regulating guard cell ion transport under red light,” Nature Plants, 11(9), pp. 1847–1862. Available at: https://doi.org/10.1038/s41477-025-02078-7.