Publications

2009

Jia M, Swaminathan S, Wurtele E, Dickerson J, 2009. MetNetGE: Visualizing Biological Networks in Hierarchical Views and 3D Tiered Layouts. IEEE Computer Society Proceedings

El Kaissi M, Jia M, Dickerson J, Wurtele ES, Reiners D. 2009. Reaction centric layout for metabolic networks. Lecture Notes in Computer Science. Springer-Verlag,

El Kaissi M, Jia M, Dickerson J, Wurtele ES, Reiners D. 2009.Visualization of gene regulatory networks. Lecture Notes in Computer Science. Springer-Verlag.

Berleant D, Zhang L, Jing Ding J, Cao T, Xu J, Fulmer A, Wurtele ES. 2009. Text Empirics-Based Mining of Biomolecular Interactions from Texts: Theory and Application. BMC Bioinformatics. 11:S18 (software application)

Ding J, Berleant D, Xu J, Juhlin K, Wurtele ES, Fulmer A. (2009) GeneNarrator: Mining the Literaturome for Relations Among Genes. J Proteomics Bioinform 2: 360-371.

Li L, Foster C, Gan Q, Nettleton D, James MG, Myers AM, Wurtele ES.2009. Identification of the Novel Protein QQS as a component of the starch metabolic network in Arabidopsis leaves. Plant Journal. Online 2/09

Oliver, D.J. / Nikolau, B.J. / Wurtele, E.S. 2009. Life at the metabolic nexus. Plant Science, 176:597-601

2008

Berleant D, Ding J, Hughes L, Fulmer A, Wurtele ES, Viswanathan K, Schnable PS. 2008. PathBinderH: a tool for sentence-focused, plant taxonomy-sensitive access to the biological literature, chapter 5 in G. P. Rao, C. Wagner & R. K. Singh, eds., Application of Genomics and Bioinformatics in Plants, Studium Press LLC, Houston, pp 121-136.

Mentzen W, Wurtele ES. 2008. Regulon Organization of Arabidopsis. BMC Plant Biology. 8:99 Sept 30 highly accessed article

Mentzen W, Peng JL, Nikolau BJ, Wurtele ES. 2008. Articulation of Core Metabolic Processes in Arabidopsis. BMC Plant Biology 8:76.

Lawrence M, Cook D, Lee EK, Babka H, Wurtele ES. 2008. explorase: Multivariate Exploratory Analysis and Visualization. 25Apr

Kher S, Peng J, Wurtele ES, Dickerson J. 2008. A Symbolic Approach to Evidence Code Mapping for Biological Data Integration and Subjective Analysis for Reference Associations for Metabolic Pathways. NAFIPS 2008. Special Biosciences Section:1-6.

2007

Cook D., Hofmann H., Nikolau B., Wurtele ES, Lee Eun-kyung, Yang H. 2007. Exploring gene expressions using plots. J Data Science 5:151-181.

Xia T, Li J, Wurtele ES, Gu X: 2007. A tool for comprehensive analysis of protein interaction networks. In BIOCOMP 2007. Eds. Arabnia HR, Yang MQ, Yang JY. pp 523-527

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. 58:3323-3342

Call AB, Hernnstadt S, Dickerson J, Wurtele ES, Bassham D. 2007. Virtual Cell: A Pedagogical Convergence between Game Design and Science Education. Journal of Systemics, Cybernetics and Informatics. 5:27-31.

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.

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

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