Recent Publications

Invited book chapters:

Wurtele ES. 2005. Analysis of metabolic networks in Arabidopsis. Plant Metabolomics. Kluwer Academic Publishers.

Nikolau BJ, Xu L, Ilarslan H, Schmidt J, Allred C, Wurtele ES. 2005. Review: Juxtaposition of the biotin network on the regulation of fatty acid biosynthesis. J Lipid Res. In Press.

Other publications:

2007

Nikolau BJ, Wurtele ES. 2007. Concepts in Plant Metabolomics. Springer. 297 pgs, pp 145-158.

Wurtele ES, Li L, Berleant D, Cook D, Dickerson JA, Ding J, Hofmann H, Lawrence M, Lee EK, Li J, Mentzen W, Miller L, Nikolau BJ, Ransom N, Wang Y, 2007. MetNet: Systems Biology Software for Arabidopsis. In: Concepts in Plant Metabolomics. Springer. pp 145-158.

Birt DF, Widrlechner MP, LaLone CA, Wu L, Bae J, Solco AK, Kraus GA, Murphy PA, Wurtele ES, Leng Q, Hebert SC, Maury WJ, Price JP. 2007. Echinacea in Infection. American Journal of Clinical Nutrition In Press

Gatlin DM, Barrows FT, Brown P, Dabrowski K, Gaylord TG, Hardy RW, Herman E, Hu G, Krogdah J, Nelson R, Overturf K, Rust M, Sealey W, Skonberg D, Souza EJ, Stone D, Wilson R Wurtele E. 2007. Expanding the Utilization of Sustainable Plant Products in Aquafeeds: a Review. Aquaculture Research, 38:551-579

Li L, Ilarslan HH, James MG, Myers AM, Wurtele ES. 2007. Genome-Wide Co-Expression Among the Starch Debranching Enzyme Genes AtISA1, AtISA2, and AtISA3 in Arabidopsis Thaliana. J Exp Bot. online Sept 2007

Zhai Z, Liu Y, Wu L, Senchina DS, Wurtele ES, Murphy PA, Kohut ML, Cunnick JE. 2007. Enhancement of Innate and Adaptive Immune Functions by Multiple Echinacea Species. J Medicinal Food. 10:423-434.

Zhai Z, Haney D, Wu L, Solco A, Murphy PA, Wurtele ES, Kohut ML, Cunnick JE. 2007. Alcohol Extracts of Echinacea Inhibit Production of Nitric Oxide and Tumor Necrosis Factor-Alpha by Macrophages in Vitro. Food Agric Immunol. In press: 1-16

LaLone C, Hammer K, Wu L, Bae J, Layva N, Liu Y, Sia-Solco A, Kraus G, Murphy P, Wurtele ES, Kim OK, Seo K, Widrlechner MP, Birt DF. 2007. Echinacea Species and Alkamides Inhibit Prostaglandin E2 Production in RAW264.7 Mouse Macrophage Cells. J Agric Food Chem. In Press.

Hammer K, Hillwig M, Solco A, Dixon P, Delate K, Murphy P, Wurtele ES, Birt DF. 2007. Inhibition of Prostaglandin E2 Production by Anti-Inflammatory Hypericum Perforatum Extracts and Constituents in RAW264.7 Mouse Macrophage Cells. J Agric Food Chem. 55:7323 -7331

Call AB, Hernnstadt S, Wurtele ES, Bassham D. J. 2007. Virtual Cell: A Pedagogical Convergence between Game Design and Science Education. Systemics, Cybernetics and Informatics. In press.

Kraus GA, J Bae J, Wu L, Wurtele ES. 2007. The Synthesis and Natural Distribution of the Major Ketone Constituents in Echinacea Pallida. Molecules 12, 406-414.

Cook D., Hofmann H., Nikolau B., Wurtele E., Lee Eun-kyung, Yang H.. 2007. Exploring Gene Expression Data Using Plots. Journal of Data Science, J Data Science 5:151-181.

2006

Senchina DS, Wu L, Flinn GN, Konopka del N, McCoy JA, Widrelechner MP, Wurtele ES, Kohut ML. 2006. Year-and-a-Half Old, Dried Echinacea Roots Retain Cytokine-Modulating Capabilities in an in vitro Human Older Adult Model of Influenza Vaccination. Planta Med. 72:1440-1447.

Lawrence M, Lee e-K, Cook D, Hofmann H, Wurtele ES. 2006. exploRase: Exploratory Data Analysis of Systems Biology Data. Fourth International Conference on Coordinated and Multiple Views in Exploratory Visualization (CMV'06) 14-20.

Kraus GA, Bae J, Wu L, Wurtele ES. 2006. Synthesis and Natural Distribution of Anti-Inflammatory Alkamides from Echinacea. Molecules. 11, 758-767.

Yang Y, Wurtele ES, Cruz-Neira C, and Dickerson JA. 2006. Hierarchical Visualization of Metabolic Networks Using Virtual Reality. In Proc. ACM Intl. Conf. on Virtual Reality Continuum and Its Applications (Hong Kong, China). VRCIA '06. ACM Press, New York, NY, 377-381

Call AB, Herrnstadt S, Wurtele ES, and Bassham D. 2006. Virtual Cell: A Pedagogical Convergence between Game Design and Science Education. 4th International Conference on Education and Information Systems, Technologies and Applications, Orlando, FL, USA.

Ding J, Hughes L, Berleant D, Fulmer A, Wurtele ES. 2006. PubMed Assistant: A Biologist-Friendly Interface for Enhanced PubMed Search. Bioinformatics. 22: 378-380

Yang Y, Engin L, Wurtele ES, Dickerson JA. 2006. A 3D Compound Graph Layout Algorithm for Metabolic Network Visualization using Virtual Reality. submitted

2005

Dickerson JA, Berleant DA, Du P, Ding J, Foster CM, Ling L, Wurtele ES. 2005. in Medical Informatics. Eds. H Chen, SS Fuller, C Friedman, W Hirsch. Springer Verlag. 491-518.

Dickerson JA, Berleant DA, Du P, Ding J, Foster CM, Ling L, Wurtele ES. 2005. Creating, Modeling, and Visualizing Metabolic Networks. In Medical Informatics. Eds. H Chen, SS Fuller, C Friedman, W Hirsch. Springer Verlag. 491-518

Yang Y, Engin L, Wurtele ES, Cruz-Neira C, Dickerson JA. 2005. Integration of Metabolic Networks and Gene Expression in Virtual Reality. Bioinformatics. 21:3645-3650.

DeCook R, Nettleton D, Foster CM, Wurtele ES. 2005. Identifying Differentially Expressed Genes in Unreplicated Multiple-Treatment Microarray Timecourse Experiments. http://www.stat.unipg.it/IASC/Misc-stat-journ-CSDA.html Computational Statistics and Data Analysis. In press.

Ding J, Viswanathan K, Berleant D, Hughes L, Wurtele ES, Ashlock D, Dickerson JA, Fulmer A, Schnable PS, 2005. Using the Biological Taxonomy to Access Biological Literature with PathBinder. Bioinformatics. 21:2560-2562.

Du P, Gong J, Wurtele ES, Dickerson JA, Modeling Gene Expression Networks using Fuzzy Logic. 2005 IEEE Trans. On Systems, Man and Cybernetics, Part B. In press.

Fatland B, Nikolau BJ, Wurtele ES. 2005. Reverse Genetic Characterization of Cytosolic Acetyl-CoA Generation by ATP-citrate lyase in Arabidopsis. Plant Cell. 2005 Jan; 17(1):182-203. Epub 2004 Dec 17.

Jenkins H, Hardy N, Beckmann M, Draper J, Smith AR, Taylor J, Fiehn O, Goodacre R, Raoul Bino R, Hall R, Kopka J, Lange BM, Liu JR, Mendes P, Nikolau BJ, Oliver SG, Paton NW, Roessner-Tunali U, Saito K, Smedsgaard J, Sumner LW, Wurtele ES, Kell DB. 2005. A proposed framework for the description of plant metabolomics experiments and their results. Nature Biotech 22 (January Issue).

2004

J. A. Dickerson, P. Du, E. Wurtele, J. Li. 2004. Fuzzy modeling of metabolic maps in MetNetDB. NAFIPS04.

Wu L, Bae J, Kraus G, Wurtele ES. 2004. Diacetylenic isobutylamides of Echinacea: Synthesis and natural distribution. Phytochemistry 65:2477-2484.

Lee E-K, Cook D, Hofmann H, Eve Wurtele, Dongshin Kim, Jihong Kim, and Hogeun An. 2004 GeneGobi : Visual Data Analysis Tools For Microarray Data. COMPSTAT'2004 Symposium. Physica-Verlag/Springer

Bino RJ, Hall RD, Fiehn O, Kopka J, Saito K, Draper J, Nikolau BJ, Mendes P, Roessner-Tunali U, Beale MH, Trethewey RN, Lange BM, Wurtele ES, Sumner LW. 2004. Potential of metabolomics as a functional genomics tool. Trends Plant Sci. 9:418-425.

Du P, Gong J, Wurtele ES, Dickerson JA. 2004. Modeling Gene Expression Networks using Fuzzy Logic. IEEE In press.

2003

DeCook, R., Nettleton, D., Foster, C., and Wurtele, E.Shttp://metnetdb.org 2005. Identifying differentially expressed genes in unreplicated multiple-treatment microarray timecourse experiments. Computational Statistics and Data Analysis. In press.

Dickerson JA, Yang Y, Blom K, Reinot A, Lie J, Cruz-Neira C, Wurtele ES. 2003. Using Virtual Reality to Understand Complex Metabolic Networks. Atlantic Symposium on Computational Biology and Genomic Information Systems and Technology, September. 950-953.

Wurtele ES, Dickerson JD, Cook D, Hofmann H, Li J, Diao L. 2003. MetNet: software to build and model the biogenetic lattice of Arabidopsis. Comparative and Functional Genomics. 4:239-245.

Nikolau BJ, Ohlrogge JB, Wurtele ES. 2003. Plant Biotin-Containing Carboxylases. Arch Biochem Biophys. 414:211-222.

Dickerson JA, Berleant, D, Cox Z, Qi, W, Ashlock D, Wurtele ES, Fulmer AW. 2003. Creating and Modeling Metabolic and Regulatory Networks Using Text Mining and Expert Knowledge, in Computational Biology and Genome Informatics, edited by Cathy H. Wu, Paul Wang, Jason T. L. Wang, World Scientific.

2002

Ding J, Berleant D, Nettleton D, E. Wurtele ES. 2002. Mining Medline: Abstracts, sentences, or phrases? Pacific Symposium on Biocomputing, 1-12.

Fatland BF, Ke J, Anderson M, Mentzen W, Cui LW, Allred C, Johnston JL, Nikolau BJ, Wurtele ES. 2002. Molecular Characterization of a Novel Heteromeric ATP-Citrate Lyase that Generates Cytosolic Acetyl-CoA in Arabidopsis. Plant Physiol. 130:740-756.

Oliver DJ, Nikolau BJ. Wurtele ES. 2002. Functional Genomics: High throughput mRNA, protein, and metabolite analyses. Metabolic engineering. 4:98-108.

2001

Dickerson, JA, Cox Z, Wurtele ES, Fulmer AW. 2001. Creating metabolic and regulatory network models using fuzzy cognitive maps. IFSA World Congress and 20th North American Fuzzy Information Processing Society (NAFIPS) International Conference, Vancouver, British Columbia, Volume 4, 2171-2176, July, 2001.

2000

Ke J-S, Behal B, Yunkers S, Nikolau BJ, Wurtele ES, Oliver DJ. 2000. The role of pyruvate dehydrogenase and acetyl-CoA synthetase in fatty acid synthesis in developing Arabidopsis seeds. Plant Physiol 123:497-508.

Ke J-S, Wen T-N, Achenbach S, Nikolau BJ, Wurtele ES. 2000. Coordinate regulation of the nuclear and plastidic genes coding for the subunits of the heteromeric acetyl-CoA carboxylase. Plant Physiol 122: 1057-1071.

Wurtele ES, Nikolau BJ. 2000. Methylcrotonyl-CoA Carboxylase. Methods in Enzymology 324:280-292.

McKean AL, Ke J-S, Song J, Achenbach S, Nikolau BJ, Wurtele ES. 2000. Molecular characterization of the non-biotin-containing subunit of 3-methylcrotonyl-CoA carboxylase. Journal of Biological Chemistry. 275:5582-5590.

1999

Guan X, Diez T, Prasad KT, Nikolau BJ, Wurtele ES. 1999. Discovery and characterization of geranoyl-CoA carboxylase in plants. Archives Biochem Biophys 362:12-21.

1998

Anderson MD, Che P, Song J, Nikolau BJ, Wurtele ES. 1998. 3-Methylcrotonyl-CoA carboxylase is a component of the mitochondrial leucine catabolic pathway in plants. Plant Physiol 118: 1127-1138.

1997

Ke J, Choi JK, Smith M, Horner HT, Nikolau BJ, Wurtele ES. 1997. Structure of the CAC1 gene and in situ characterization of its expression: The Arabidopsis thaliana gene coding for the biotin-containing subunit of the plastidic acetyl-CoA carboxylase. Plant Physiol 113:357-365.

Sun J, Ke J, Johnson JL, Nikolau BJ, Wurtele ES. 1997. Molecular cloning and characterization of CAC2: The Arabidopsis thaliana gene coding for the biotin carboxylase subunit of the plastidic acetyl-CoA carboxylase. Plant Physiol 115:1371-1383.