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"Truly Interactive Textbooks for Computer Science Education",
Proceedings of the Sixth Program Visualization Workshop, Darmstadt, Germany, pp. 97-103, 06/2011.
"Getting algorithm visualizations into the classroom",
Proceedings of the 42nd ACM Technical Symposium on Computer Science Education - SIGCSE '11, Dallas, TX, USA, ACM Press, pp. 129, 2011.
"Building an online educational community for algorithm visualization",
Proceedings of the 41st ACM technical symposium on Computer science education, SIGCSE 2010, pp. 475-476, March, 2010.
"Algorithm visualization: The state of the field",
ACM Transactions on Computing Education, vol. 10, New York, NY, USA, ACM, pp. 9:1–9:22, August, 2010.
"Ensemble PDP-8: eight principles for distributed portals",
Proceedings of the 2010 Joint International Conference on Digital Libraries, JCDL 2010, Gold Coast, Queensland, Australia, ACM, pp. 341-344, 06/2010.
"Model Composition for Macromolecular Regulatory Networks",
IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 7, no. 2, pp. 278-287, 2010.
"Multistate modeling and simulation for regulatory networks",
2010 Winter Simulation Conference, pp. 631-642, 2010.
"Proceedings of the 2009 Spring Simulation Multiconference, SpringSim 2009",
2009 Spring Simulation Multiconference, SpringSim 2009, San Diego, California, USA, SCS/ACM, 03/2009.
"Stochastic cell cycle modeling for budding yeast",
Proceedings of 2009 Spring Simulation Multiconference: HPC, G. Wainer, M. Chinni, P. Roman, H. Rajaei, B. Zeigler, and C. Ribbens (eds.), Soc. for Modeling Simulation Internat., San Diego, CA, SCS, pp. 569-574, 03/2009.
"Cell cycle modeling for budding yeast with stochastic simulation algorithms",
Computer Modeling in Engineering and Sciences, vol. 51, pp. 27--52, 2009.
"Model aggregation: a building-block approach to creating large macromolecular regulatory networks",
Bioinformatics, vol. 25, no. 24, pp. 3289-3295, 2009.
"Modeling Molecular Regulatory Networks with JigCell and PET",
Systems Biology, no. 500: Humana Press, pp. 81-111, 2009.
"Converting Macromolecular Regulatory Models from Deterministic to Stochastic Formulation",
Proceedings of High Performance Computing and Simulation 2008 (HPCS 2008), pp. 385–392, April, 2008.
"Deterministic parallel global parameter estimation for a model of the budding yeast cell cycle",
Journal of Global Optimization, vol. 40, no. 4, Hingham, MA, USA, Kluwer Academic Publishers, pp. 719–738, 2008.
"Fusing and Composing Macromolecular Regulatory Network Models",
Proceedings of the 2007 High Performance Computing Symposium (HPC 2007), pp. 337–344, March, 2007.
"Defect detection on hardwood logs using high resolution laser scan data",
Proceedings of the 15th International Symposium on Non-Distructive Testing of Wood, August, 2007.
"Automated Detection of Severe Surface Defects on Barked Hardwood Logs",
Forest Product Journal, vol. 57, no. 4, pp. 50–56, April, 2007.
"Algorithm visualization: a report on the state of the field",
SIGCSE '07: Proceedings of the 38th SIGCSE technical symposium on Computer science education, New York, NY, USA, ACM, pp. 150–154, 2007.
"A Mathematical Programming Formulation for the Budding Yeast Cell Cycle",
Simulation, vol. 83, no. 7, San Diego, CA, USA, Society for Computer Simulation International, pp. 497–514, 2007.
"S4W: a problem-solving environment for wireless system design",
Software: Practice & Experience, vol. 37, no. 14, New York, NY, USA, John Wiley & Sons, Inc., pp. 1539–1558, 2007.
"Defect Detection on Hardwood Logs Using Laser Scanning",
Wood and Fiber Science, vol. 38, no. 4, pp. 682–695, October, 2006.
"Computer Evaluation of Network Dynamics Models with Application to Cell Cycle Control in Budding Yeast",
IEE Proceedings – Systems Biology, vol. 153, no. 1, pp. 13–21, January, 2006.
"Using External High-Resolution Log Scanning to Determine Internal Defect Characteristics",
Proceedings of the 15th Central Hardwood Forestry Conference, pp. 497–505, February, 2006.
"The JigCell Model Builder: A Spreadsheet Interface for Creating Biochemical Reaction Network Models",
IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. Vol. 3, no. 2, pp. 155–164, April-June, 2006.
"Challenges for modeling and simulation methods in systems biology",
WSC '06: Proceedings of the 38th conference on Winter simulation: Winter Simulation Conference, pp. 1720–1730, 2006.