2008
Panning T.D., Watson L.T., Allen N.A., Chen K.C., Shaffer C.A., Tyson J.J.,
"Deterministic parallel global parameter estimation for a model of the budding yeast cell cycle",
J. of Global Optimization, vol. 40, no. 4, Hingham, MA, USA, Kluwer Academic Publishers, pp. 719–738, 2008.
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2007
Mishra D., Shaffer C.A., Ramakrishnan N., Watson L.T., Bae K.K., He J., Verstak A.A., Tranter W.H.,
"S4W: a problem-solving environment for wireless system design",
Softw. Pract. Exper., vol. 37, no. 14, New York, NY, USA, John Wiley & Sons, Inc., pp. 1539–1558, 2007.
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Thomas L., Shaffer C A., Mili L., Thomas E.,
"Automated Detection of Severe Surface Defects on Barked Hardwood Logs",
Forest Product Journal, vol. 57, no. 4, pp. 50–56, April, 2007.
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Randhawa R., Shaffer C A., Tyson J J.,
"Fusing and Composing Macromolecular Regulatory Network Models",
Proceedings of the 2007 High Performance Computing Symposium (HPC 2007), pp. 337–344, March, 2007.
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2006
Thomas L., Mili L., Thomas E., Shaffer C A.,
Wood and Fiber Science,
, vol. 38, no. 4, pp. 682–695, October, 2006.
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Vass M.T., Shaffer C.A., Ramakrishnan N., Watson L.T., Tyson J.J.,
"The JigCell Model Builder: A Spreadsheet Interface for Creating Biochemical Reaction Network Models",
IEEE/ACM Trans. Comput. Biol. Bioinformatics, vol. 3, no. 2, Los Alamitos, CA, USA, IEEE Computer Society Press, pp. 155–164, 2006.
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Allen N A., Chen K C., Shaffer C A., Tyson J J., Watson L T.,
IEE Proceedings – Systems Biology,
, vol. 153, no. 1, pp. 13–21, January, 2006.
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Sauro H.M., Harel D., Kwiatkowska M., Shaffer C.A., Uhrmacher A.M., Hucka M., Mendes P., Strömback L., Tyson J.J.,
"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.
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Vass M., Shaffer C A., Ramakrishnan N., Watson L T., Tyson J J.,
"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.
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2005
2004
Vass M., Allen N., Shaffer C.A., Ramakrishnan N., Watson L.T., Tyson J.J.,
"The JigCell Model Builder and Run Manager",
Bioinformatics, vol. 20, no. 18, Oxford, UK, Oxford University Press, pp. 3680–3681, 2004.
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Skidmore R.R., Verstak A., Ramakrishnan N., Rappaport T.S., Watson L.T., He J., Varadarajan S., Shaffer C.A., Chen J., Bae K., Jiang J., Tranter W.H.,
"Towards integrated PSEs for wireless communications: experiences with the S4W and SitePlanner\textregistered projects",
SIGMOBILE Mob. Comput. Commun. Rev., vol. 8, no. 2, New York, NY, USA, ACM, pp. 20–34, 2004.
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Saraiya P., Shaffer C.A., McCrickard S.D., North C.,
"Effective features of algorithm visualizations",
Proceedings of the 35th SIGCSE technical symposium on Computer Science Education, pp. 382 - 386, March , 2004.
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2003
Allen N A., Shaffer C A., Vass M T., Ramakrishnan N., Watson L T.,
"Improving the Development Process for Eukaryotic Cell Cycle Models with a Modeling support environment",
Simulation, vol. 79, no. 12, pp. 674–688, December, 2003.
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Rubin E J., Shaffer C A., Ramakrishnan N., Watson L T., Dymond R., Kibler D., Dietz R., Chanat J., Lohani V., Bosch D., Speir C.,
"From Landscapes to Waterscapes: A PSE for Landuse Change Analysis",
Engineering with Computers, vol. 19, no. 1, pp. 9–25, July, 2003.
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Verstak A., Ramakrishnan N., Watson L.T., He J., Shaffer C.A., Bae K., Jiang J., Tranter W.H., Rappaport T.S.,
"BSML: A binding schema markup language for data interchange in problem solving environments",
Sci. Program., vol. 11, no. 3, Amsterdam, The Netherlands, The Netherlands, IOS Press, pp. 199–224, 2003.
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Su Y., Murali T M., Pavlovic V., Schaffer M., Kasif S.,
"RankGene: identification of diagnostic genes based on expression data.",
Bioinformatics, vol. 19, no. 12, pp. 1578–9, 2003.
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Allen N., Calzone L., Chen K C., Ciliberto A., Ramakrishnan N., Shaffer C A., Sible J C., Tyson J J., Vass M., Watson L T., Zwolak J.,
"Modeling Regulatory Networks at Virginia Tech",
Omics Journal of Integrative Biology, vol. Vol. 7, no. 3, pp. pages 285–300, Fall, 2003.
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2002
He J., Watson L.T., Ramakrishnan N., Shaffer C.A., Verstak A., Jiang J., Bae K., Tranter W.H.,
"Dynamic Data Structures for a Direct Search Algorithm",
Comput. Optim. Appl., vol. 23, no. 1, Norwell, MA, USA, Kluwer Academic Publishers, pp. 5–25, 2002.
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Watson L T., Lohani V K., Kibler D F., Dymond R L., Ramakrishnan N., Shaffer C A.,
"Integrated Computing Environments for Watershed Management",
ASCE Journal of Computing in Civil Engineering, vol. 16, no. 4, pp. 259–268, October, 2002.
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2000
Shaffer C A., Watson L T., Kafura D G., Ramakrishnan N., Tentner A.,
"Features of Problem Solving Environments for Computational Science",
Proceedings of the 2000 High Performance Computing Symposium (HPC'00): Society for Computer Simulation International, pp. 242–247, 2000.
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Goel A., Phanouriou C., Kamke F A., Ribbens C.J., Shaffer C A., Watson L T.,
"WBCSim: A prototype PSE for wood-based composites simulations",
Enabling Technologies for Computational Science: Frameworks, Middleware and Environments, pp. 187-196, 2000.
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1996
Shaffer C.A., Heath L.S., Yang J.,
"Using the Swan data structure visualization system for computer science education",
SIGCSE '96: Proceedings of the twenty-seventh SIGCSE technical symposium on Computer science education, New York, NY, USA, ACM, pp. 140–144, 1996.
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1995
Fox E A., Barnette N D., Shaffer C A., Heath L., Wake W., Nowell L T., Lee J A N., Hix D., Hartson H R.,
"Progress in Interactive Learning with a Digital Library in Computer Science",
Proceedings ED-MEDIA 95, World Conf. on Educational Multimedia and Hypermedia, June, 1995.
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1994
Bright J S., Shaffer C A., Nagarkatti P S., Nagarkatti M.,
"Computer Simulation of the Immune System",
Proceedings of the Fourteenth Annual Seminar of Cancer Researchers in Virginia, pp. {17}., March, 1994.
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1993
1991
Shaffer C.A., Carstensen L.W., Miranda V.F., Kriss S.A., Morrill R.W., Fox E.A.,
Project GEOSIM: The First Two Modules,
, Blacksburg, VA, USA, Virginia Polytechnic Institute && State University, 1991.
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