2007

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

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

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.

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.

2006

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

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.

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.

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. 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 PathBinderH. 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.

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).

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.

2004

Jenkins H, Hardy N, Beckmann M, Draper J, Smith AR, Taylor J, Fiehn O, Goodacre R, 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. 2004. A proposed framework for the description of plant metabolomics experiments and their results. Nature Biotech 22:1601-1606.

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

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

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, Li J, Diao L, Zhang H, Foster CM, Fatland B, Julie Dickerson J, Brown A, Cox Z, Cook D, Lee E-K, Hofmann H. 2003. MetNet: Software to build and model the biogenetic lattice of Arabidopsis. Comp Funct Genom 4: 239-245.

Dickerson JA, Berleant, D, Cox Z, Qi, W, Ashlock D, Fulmer AW, Wurtele ES, 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. Chapter 9. pp. 1-33.

2002

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

Ding J, Berleant D, Nettleton D, E. Wurtele ES. 2002. Mining Medline: Abstracts, sentences, or phrases? Pacific Symposium on Biocomputing, 1-12. Pacific Symposium on Biocomputing (PSB 2002), Kaua'i, Hawaii, Jan. 3-7, pp. 326-337.

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