Publications

PMN

- Chae. L., Kim, T., Nilo-Poyanco, R., Rhee, S.Y. (2014) Genomic Signatures of Specialized Metabolism in Plants. Science. 344(6183):510-513.
- Dreher, K. (2014) Putting the Plant Metabolic Network Pathway Databases to Work: Going Offline to Gain New Capabilities.
- 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.
- 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.

Papers that cite PMN resources

- 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
- 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
- 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.
- 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.
- 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.
- Seaver, S., Henry, C.S., and Hanson, A.D. (2012) Frontiers in metabolic reconstruction and modeling of plant genomes. Journal of Experimental Botany.
- 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).
- Lim, E.K., Bowles, D. (2012) Plant production systems for bioactive small molecules. Current Opinion in Biotechnology. 23(2):271-277.
- 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
- 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.
- 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.
- Schallau, K. and Junker, B.H. (2010) Simulating plant metabolic pathways with enzyme-kinetic models. Plant Physiology 152(4):1763-71
- Tohge, T. and Fernie, A. (2010) Combining genetic diversity, informatics and metabolomics to facilitate annotation of plant gene function. Nature Protocols. 5: - 1210-1227.

AraCyc

- 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.
- 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.
- Mueller, LA., Zhang, P., Rhee SY (2003) AraCyc. A Biochemical Pathway Database for Arabidopsis. Plant Physiology. 132(2):453-60.

Pathway Tools and BioCyc

- Caspi R., Dreher K., Karp P.D. (2013) The challenge of constructing, classifying, and representing metabolic pathways. FEMS Microbiol Lett. 2013 Jun 7.
- 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.
- 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.

MedicCyc

- Urbanczyk-Wochniak, E. and Sumner, L.W. (2007) MedicCyc: a biochemical pathway database for Medicago truncatula. Bioinformatics. 23(11):1418-1423

Sol Genomics Network

- 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.

Bioinformatics

- Rhee SY, Dickerson, J, and Xu, D (2006) Bioinformatics and its Applications in Plant Biology. Annual Review of Plant Biology. 57: 335-360
- Rhee SY and Crosby W. (2005) Biological Databases for Plant Research. Plant Physiology. Plant Physiology. 138(1):1-3.
- Rhee SY. (2005) Bioinformatics: Current Limitations and Insights for the Future. Plant Physiology. 138(2):569-70.
- 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.
- 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.

MetaCyc