Publications

2026

Dumontet, L., Han, S.-R., Lee, J. H., Oh, T.-J., & Kang, M. (2026). Trustworthy prediction of enzyme commission numbers using a hierarchical interpretable transformer. Nature Communications, 17(1), 1146. https://doi.org/10.1038/s41467-026-68727-3

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

Khanal, A., Han, S.-R., Lee, J. H., & Oh, T.-J. (2026). Genomic insights into abiotic stress tolerance in polar lichen-associated Sphingomonas sp. PAMC26617 and Sphingomonas sp. PAMC26621. Extremophiles, 30(1), 9. https://doi.org/10.1007/s00792-026-01419-4

Kim, K.-H., Yaganapu, A., Kosaraju, S., Bhatt, A., Luo, Y. L., Parsa, S. P., Park, J., Lee, H., Lee, J. H., Oh, T.-J., & Kang, M. (2026). Prediction of bacterial protein–compound interactions with only positive samples. Bioinformatics, 42(3), btag067. https://doi.org/10.1093/bioinformatics/btag067

Lee, Y. K. (2026). Chromosome numbers, ploidy levels, and available genome size data of Svalbard plants. Journal of Ecology and Environment, 50. https://doi.org/10.5141/jee.25.100

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

Ueda, M., Todaka, D., Takahashi, S., Ishida, J., Tanaka, M., Ikeda, T., Suzuki, K., Miwa, M., Uchiyama, T., Ishimaru, Y., Sayama, K., Uozumi, N., Matsuyama, S., Nagano, A. J., Kikuno, H., & Seki, M. (2026). Requirement of Trichome Formation for the Growth-promoting Effects of Olivine for Enhanced Weathering in Arabidopsis thaliana. Journal of Plant Growth Regulation. https://doi.org/10.1007/s00344-026-12048-8

2025

Ahmed, R. A. H., Abdellatif, I. M. Y., Oka, N., Kobayashi, M., Fuhrmann-Aoyagi, M. B., Todaka, D., Seki, M., & 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), 32388. https://doi.org/10.1038/s41598-025-17929-8

Bang, J., Kim, B., Lee, Y. M., Do, H., Lee, J. H., & 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), e01160-25. https://doi.org/10.1128/mra.01160-25

Bashir, K., Todaka, D., Sako, K., Ueda, M., Aziz, F., & Seki, M. (2025). Chemical application improves stress resilience in plants. Plant Molecular Biology, 115(2), 47. 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., … 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), 1205–1224. https://doi.org/10.1111/nph.70525

Gurung, S., Lee, C.-M., Weon, H.-Y., Han, S.-R., & 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), e70121. 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., & Do, H. (2025). Ice affinity purification system for recombinant proteins using a DUF3494 ice-binding protein. International Journal of Biological Macromolecules, 315, 144378. 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., & Ohme-Takagi, M. (2025). TCP3-mediated regulation of cell expansion in Arabidopsis thaliana. New Phytologist, 248(6), 2981–2995. 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., … Wishart, D. S. (2025). MiMeDB 2.0: The Human Microbial Metabolome Database for 2026. Nucleic Acids Research, 54(D1), D623–D634. https://doi.org/10.1093/nar/gkaf1272

Kuwayama, S., Hayashi, M., Takahashi, K., Hayashi, Y., Fukatsu, K., Murakami, K., Aihara, Y., Sato, A., & 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), 1020–1029. 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., … Rhee, S. Y. (2025). Life on the dry side: A roadmap to understanding desiccation tolerance and accelerating translational applications. Nature Communications, 16(1), 3284. https://doi.org/10.1038/s41467-025-58656-y

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

Min, K., Sulaiman, S., Lee, J., Seo, S., Arora, R., & 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), 30. 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., & Skirycz, A. (2025). Characterization of the cyclic dipeptide cyclo(His-Pro) in Arabidopsis. Plant Physiology, 198(1), kiaf174. https://doi.org/10.1093/plphys/kiaf174

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

Paudel, L., Pardhe, B. D., Han, S.-R., Lee, J., & 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, 100773. https://doi.org/10.1016/j.carpta.2025.100773

Paudel, P., Regmi, K. P., Kim, K.-H., & Oh, T.-J. (2025). Discovery of a novel CYP107E41 from Streptoalloteichus sp. KCCM40925 for advancing steroid hydroxylation catalysis. Archives of Biochemistry and Biophysics, 773, 110595. 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., & Rhee, S. Y. (2025). Building climate-resilient crops: Genetic, environmental, and technological strategies for heat and drought stress tolerance. Journal of Experimental Botany, 76(16), 4395–4413. 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., & Rhee, S. Y. (2025). Photosynthetic acclimation is a key contributor to exponential growth of a desert plant in Death Valley summer. Current Biology, 35(22), 5502–5520. 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., & 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), e70349. https://doi.org/10.1111/tpj.70349

Saldivar, E. V., Field, S., & Rhee, S. Y. (2025). Cellular view of metabolism: Metabolic biomolecular condensates. New Phytologist, 248(2), 555–562. https://doi.org/10.1111/nph.70474

Seo, S., Ahn, Y.-Y., Kim, K., Lee, J. H., Min, K., & 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, 105325. https://doi.org/10.1016/j.cryobiol.2025.105325

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

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

Suzuki, T., Takayama, M., Sumiyoshi, M., & 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), 1266–1273. https://doi.org/10.1021/acsagscitech.4c00572

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

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

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

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

Yuan, X., Smith, N. S. S., & Moghe, G. D. (2025). Analysis of plant metabolomics data using identification-free approaches. Applications in Plant Sciences, 13(4), e70001. 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., & Assmann, S. M. (2025). Apoplastic metabolomics reveals sugars as mesophyll messengers regulating guard cell ion transport under red light. Nature Plants, 11(9), 1847–1862. https://doi.org/10.1038/s41477-025-02078-7