- Publications
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PMN publications
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. and 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 (in press)
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AraCyc publications
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.
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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.
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Mueller, LA., Zhang, P., Rhee SY (2003)
AraCyc. A Biochemical Pathway Database for Arabidopsis. Plant Physiology. 132(2):453-60.
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Papers that cite PMN resources
Schallau, K. and Junker, B.H. (2010)
Simulating plant metabolic pathways with enzyme-kinetic models. Plant Physiology 152(4):1763-71
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Bais, P. , Moon, S.M., He, K., et al (2010)
PlantMetabolomics.org: A Web Portal for Plant Metabolomics Experiments. Plant Physiology. 152(4): 1807-1816.
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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
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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.
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Pathway Tools and BioCyc publications
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.
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[additional publications]
MetaCyc publications
MedicCyc publications
Urbanczyk-Wochniak, E. and Sumner, L.W. (2007) MedicCyc: a biochemical pathway database for Medicago truncatula. Bioinformatics. 23(11):1418-1423
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Sol Genomics Network publications
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.
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Bioinformatics publications
Rhee SY, Dickerson, J, and Xu, D (2006) Bioinformatics and its Applications in Plant Biology. Annual Review of Plant Biology. 57: 335-360
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Rhee SY and Crosby W. (2005) Biological Databases for Plant Research. Plant Physiology. 138(1):1-3.
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Rhee SY. (2005) Bioinformatics: Current Limitations and Insights for the Future. Plant Physiology. 138(2):569-70.
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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.
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Rhee, SY. Bioinformatic resources, challenges, and opportunities using Arabidopsis thaliana as a model organism in post-genomic era. (2000) Plant Physiology.124(4):1460-4.
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