2025
– Koper K., de Oliveira M.V.V., Huß S., Hataya S., Soleymani F., Hawkins C., Rhee S.Y., Takasuka T.E., Nikoloski N., Maeda H.A.* (2025) Mapping multi-substrate specificity of Arabidopsis aminotransferases. Nature Plants online.
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[PDF]
– Madera, M. A. et al., Zerbe, P. (2025). Genome-Wide Discovery and Characterization of Terpene Synthases Contributing to Strawberry Aroma Metabolism. bioRxiv, 2025-06.
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2024
– Hawkins, C., Xue, B., Yasmin, F., Wyatt, G., Zerbe, P., Rhee, S. Y. (2024) Plant Metabolic Network 16: expansion of underrepresented plant groups and experimentally supported enzyme data. Nucleic Acids Research 53(D1):D1606–D1613.
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– Koper K.#, Han S-W.#, Kothadia R., Salamon H., Yoshikuni Y.*, Maeda H.A.* (2024) Multi-substrate specificity shaped the complex evolution of the aminotransferase family across the tree of life. Proc. Natl. Acad. Sci. 121, e2405524121 bioRvix doi: 10.1101/2024.03.19.585368 See the DOE JGI News. #These authors contributed equally.
[HTML]
– Cowie AE et al., Zerbe P (2024) The crystal structure of Grindelia robusta 7,13-copalyl diphosphate synthase reveals active site features controlling catalytic specificity. JBC. doi:10.1016/j.jbc.2024.107921
[HTML]
– Wyatt G, Zerbe P, Tiedge K (2024) Characterization of switchgrass (Panicum virgatum L.) PvKSL1 as a levopimaradiene/abietadiene-type diterpene synthase. Plant Biol. https://doi.org/10.1111/plb.13708
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2023
– Murphy KM et al., Zerbe P (2023) A dolabralexin-deficient mutant provides insight into specialized diterpenoid metabolism in maize. Plant Physiol 192:1338.
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2022
– Koper K., Hataya S., Hall A.G., Takasuka T.E., Maeda H.A. (2022) Biochemical characterization of plant aromatic aminotransferases Methods Enzymol. 680, 35-83
[HTML]
– Koper K., Han S-W., Pastor D.C., Yoshikuni Y., Maeda H.A. (2022) Evolutionary Origin and Functional Diversification of Aminotransferases J. Biol. Chem. 298: 102122′
[HTML]
– Tiedge K et al., Zerbe P (2022) Comparative transcriptomics and metabolomics reveal specialized metabolite drought stress responses in switchgrass (Panicum virgatum). New Phytol 236:1393–1408.
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2021
– Hawkins, C., Ginzburg, D., Zhao, K., Dwyer, W., Xue, B., Xu, A., Rice, S., Cole, B., Paley, S., Karp, P., Rhee, S. Y. (2021) Plant Metabolic Network 15: A resource of genome-wide metabolism databases for 126 plants and algae. Journal of Integrative Plant Biology 63(11):1888-1905.
[HTML]
– Muchlinski A et al., Zerbe P (2021) Cytochrome P450-catalyzed biosynthesis of furanoditerpenoids in the bioenergy crop switchgrass (Panicum virgatum L.). Plant J 108:1053–68.
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2020
– Ding Y, Weckwerth PR, Poretsky E, Murphy KM, Sims J, Saldivar E, Christensen SA, Char SN, Yang B, Tong AD, Shen Z, Kremling KA, Buckler ES, Kono T, Nelson DR, Bohlmann J, Bakker MG, Vaughan MM, Khalil AS, Betsiashvili M, Dressano K, Köllner TG, Briggs SP, Zerbe P, Schmelz EA, Huffaker A (2020) Genetic elucidation of interconnected antibiotic pathways mediating maize innate immunity. Nat Plants. 6:1375-1388. doi: 10.1038/s41477-020-00787-9.
[HTML]
– Karunanithi PS et al., Zerbe P (2020) The foxtail millet (Setaria italica) terpene synthase gene family. Plant J 103:781–800.
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2019
– Ding Y et al., Zerbe P (2019) Multiple genes recruited from hormone pathways partition maize diterpenoid defences. Nat Plants 5:1043–56.
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2018
– Murphy KM, Ma LT, Ding Y, Schmelz EA, Zerbe P (2018) Functional Characterization of Two Class II Diterpene Synthases Indicates Additional Specialized Diterpenoid Pathways in Maize (Zea mays). Front Plant Sci. 9:1542. doi: 10.3389/fpls.2018.01542.
[HTML]
– Pelot KA et al., Zerbe P (2018) Functional diversity of diterpene synthases in switchgrass (Panicum virgatum). Plant Physiol 178:54–71.
[HTML]
– Mafu S et al., Zerbe P (2018) Discovery, Biosynthesis and Stress-Related Accumulation of Dolabradiene-Derived Defenses in Maize. Plant Physiol 176:2677–90.
[HTML]
2017
– Schlapfer, P., Zhang, P., Wang, C., Kim, T., Banf, M., Chae, L., Dreher, K., Chavali, A. K., Nilo-Poyanco, R., Bernard, T., Kahn, D., Rhee, S.Y. (2017) Genome-Wide Prediction of Metabolic Enzymes, Pathways, and Gene Clusters in Plants. Plant Physiology. 173(4):2041-2059.
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2014
– Chae. L., Kim, T., Nilo-Poyanco, R., Rhee, S.Y. (2014) Genomic Signatures of Specialized Metabolism in Plants. Science. 344(6183):510-513.
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– Dreher, K. (2014) Putting the Plant Metabolic Network Pathway Databases to Work: Going Offline to Gain New Capabilities.
[HTML]
2013
– Caspi R., Dreher K., Karp P.D. (2013) The challenge of constructing, classifying, and representing metabolic pathways. FEMS Microbiol Lett. 2013 Jun 7.
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2012
– Quanbeck, S.M., Brachova, L., Campbell, A.A., Guan, X., Perera, A., He, K., Rhee, S.Y., Bais, P., Dickerson, J.A., Dixon, P., Wohlgemuth, G., Fiehn, O., Barkan, L., Lange, I., Lange, B.M., Lee, I., Cortes, D., Salazar, C., Shuman, J., Shulaev, V., Huhman, (2012) Metabolomics as a Hypothesis-Generating Functional Genomics Tool for the Annotation of Arabidopsis thaliana Genes of “Unknown Function”. Frontiers in Plant Science. 3(15).
[HTML]
– Lim, E.K., Bowles, D. (2012) Plant production systems for bioactive small molecules. Current Opinion in Biotechnology. 23(2):271-277.
[HTML]
– Clark, S.T. and Verwoerd, W.S. (2012) A systems approach to identifying correlated gene targets for the loss of colour pigmentation in plants. BMC Bioinformatics. 12:343
[HTML]
– Bassel, G.W., Gaudinier A., Brady S.M., Hennig L., Rhee SY, and De Smet I. (2012) Systems analysis of plant functional, transcriptional, physical interaction, and metabolic networks. Plant Cell. 24(10)3859-3875.
[HTML]
– Seaver, S., Henry, C.S., and Hanson, A.D. (2012) Frontiers in metabolic reconstruction and modeling of plant genomes. Journal of Experimental Botany.
[HTML]
– Caspi, R., Altman, T., Dreher, K., Fulcher, C.A., Subhraveti, P., Kessler, I.M., Kothari, A., Krummenacker, M., Latendresse, M., Mueller, L.A., Ong, Q., Paley, S., Pujar, A., Shearer, A.G., Travers, M., Weerasinghe, D., Zhang, P., Karp, P.D. (2012) The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic Acids Research. 40(D1):F742-D753.
[HTML]
– Chae, L., Lee, I., Shin, J., and Rhee, S.Y. (2012) Towards understanding how molecular networks evolve in plants. Current Opinion in Plant Biology. 15(2):177-184.
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2011
– Hanada, K. Sawada, Y., Klausnitzer, R., Saito, K., Toyoda, T., Kazuo, S., Li, W-H., and Hirai, M. (2011) Functional Compensation of Primary and Secondary Metabolites by Duplicate Genes in Arabidopsis thaliana. Molecular Biology and Evolution. 28(1):377-82.
[HTML]
2010
– Bais, P. , Moon, S.M., He, K., Leitao R., Dreher K., Walk T., Sucaet Y., Barkan L., Wohlgemuth G., Roth M.R., Wurtele E.S., Dixon P., Fiehn O., Lange B.M., Shulaev V., Sumner L.W., Welti R., Nikolau B.J., Rhee S.Y., Dickerson J.A. et al (2010) PlantMetabolomics.org: A Web Portal for Plant Metabolomics Experiments. Plant Physiology. 152(4): 1807-1816.
[HTML]
– Schallau, K. and Junker, B.H. (2010) Simulating plant metabolic pathways with enzyme-kinetic models. Plant Physiology 152(4):1763-71
[HTML]
– Tohge, T. and Fernie, A. (2010) Combining genetic diversity, informatics and metabolomics to facilitate annotation of plant gene function. Nature Protocols. 5: – 1210-1227.
[HTML]
– Karp, PD., Paley, SM., Krummenacker, M., Latendresse, M., Dale, JM., Lee, TJ., Kaipa, P., Gilham, F., Spaulding, A., Popescu, L., Altman, T., Paulsen, I., Keseler, IM., and Caspi, R. (2010) Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology. Briefings in Bioinformatics. 11(1):40-79.
[HTML]
– Zhang, P., Dreher, K., Karthikeyan, A., Chi, A., Pujar, A., Caspi, R., Karp, P., Kirkup, V., Latendresse, M., Lee, C, Mueller, L.A., Muller, R., Rhee, S.Y. (2010) Creation of a Genome-Wide Metabolic Pathway Database for Populus trichocarpa Using a New Approach for Reconstruction and Curation of Metabolic Pathways for Plants. Plant Physiology 153(4): 1479-1491.
[HTML]
2009
– Charron, J.B.F., He, H., Elling, A.A., et al (2009) Dynamic Landscapes of Four Histone Modifications during Deetiolation in Arabidopsis. Plant Cell. 21(12): 3732-3748
[HTML]
– Lisec, J., Steinfath, M., Meyer, R.C., Selbig, J., Melchinger, A.E., Willmitzer, L., Altmann, T. (2009) Identification of heterotic metabolite QTL in Arabidopsis thaliana RIL and IL populations. Plant Journal.59(5):777-88
[HTML]
– Lysenko, A. Hindle, M.M., Taubert, J., Saqi, M., Rawlings C.J. (2009) Data integration for plant genomics-exemplars from the integration of Arabidopsis thaliana databases. Briefings in Bioinformatics. 10(6):676-693.
[HTML]
– Chaves, M.M., Flexas, J., and Pinheiro, C. (2009) Photosynthesis under drought and salt stress: regulation mechanisms from whole plant to cell. Annals of Botany. 103(4):551-560.
[HTML]
2007
– Urbanczyk-Wochniak, E. and Sumner, L.W. (2007) MedicCyc: a biochemical pathway database for Medicago truncatula. Bioinformatics. 23(11):1418-1423
[HTML]
2006
– Rhee SY, Dickerson, J, and Xu, D (2006) Bioinformatics and its Applications in Plant Biology. Annual Review of Plant Biology. 57: 335-360
[HTML]
2005
– Rhee SY, Zhang P, and Foerster H, and Tissier C (2005) AraCyc: Overview of an Arabidopsis Metabolism Database and Its Applications for Plant Research. In Biotechnology in Agriculture and Forestry: Plant Metabolomics. K. Saito, R. Dixon and L. Willmitzer ed., Springer. volume 57. pp. 141-153.
[HTML]
– Zhang, P, Foerster, H, Tissier, C, Mueller, L, Paley, S, Karp, P, Rhee, SY (2005) MetaCyc and AraCyc. Metabolic Pathway Databases for Plant Research. Plant Physiology 138: 27-37.
[HTML]
– Mueller LA, Solow TH, Taylor N, Skwarecki B, Buels R, Binns J, Lin C, Wright MH, Ahrens R, Wang Y, Herbst EV, Keyder ER, Menda N, Zamir D, Tanksley SD (2005) The SOL Genomics Network. A Comparative Resource for Solanaceae Biology and Beyond. Plant Physiology. 138(3):1310-7.
[HTML]
– Rhee SY and Crosby W. (2005) Biological Databases for Plant Research. Plant Physiology. Plant Physiology. 138(1):1-3.
[HTML]
– Rhee SY. (2005) Bioinformatics: Current Limitations and Insights for the Future. Plant Physiology. 138(2):569-70.
[HTML]
2003
– Mueller, LA., Zhang, P., Rhee SY (2003) AraCyc. A Biochemical Pathway Database for Arabidopsis. Plant Physiology. 132(2):453-60.
[HTML]
2002
– Reiser, L; Mueller, LA; and Rhee, SY (2002) Surviving in a sea of data: a survey of plant genome data resources and issues in building data management systems. Plant Molecular Biology. 48(1):59-74.
[HTML]
2000
– Rhee, SY. (2000) Bioinformatic resources, challenges, and opportunities using Arabidopsis thaliana as a model organism in post-genomic era. Plant Physiology.124(4):1460-4.
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