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.
Tagged BibTex xml
2007
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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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.
Tagged BibTex xml
Panning T.D., Watson L.T., Shaffer C.A., Tyson J.J.,
"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.
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Shaffer C.A., Cooper M., Edwards S.H.,
"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.
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2006
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.
Tagged BibTex xml
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., 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.
Tagged BibTex xml
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.
Tagged BibTex xml
Shaffer C.A.,
"Experiences teaching a graduate research methods course",
SIGCSE Bull., vol. 38, no. 2, New York, NY, USA, ACM, pp. 97–101, 2006.
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2005
2004
He J., Sosonkina M., Shaffer C A., Tyson J J., Watson L T., Zwolak J W., Meyer J.,
"A Hierarchical Parallel Scheme for a Global Search Algorithm",
Proceedings of the 2004 High Performance Computing Symposium (HPC'04): Society for Modeling and Simulation International, pp. 43–50, 2004.
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He J., Verstak A., Watson L T., Stinson C A., Ramakrishnan N., Shaffer C A., Rappaport T S., Anderson C R., Bae K., Jiang J., Tranter W H.,
"Globally Optimal Transmitter Placement for Indoor Wireless Communication Systems",
IEEE Transactions on Wireless Communications, vol. 3, no. 6, pp. 1906–1911, November, 2004.
Tagged BibTex xml
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.
Tagged BibTex xml
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.
Tagged BibTex xml
Shaffer C.A.,
"Buffer pools and file processing projects for an undergraduate data structures course",
SIGCSE '04: Proceedings of the 35th SIGCSE technical symposium on Computer science education, New York, NY, USA, ACM, pp. 175–178, 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
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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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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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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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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2002
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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Ramakrishnan N., Watson L T., Kafura D G., Ribbens C.J., Shaffer C A.,
"Programming Environments for Multidisciplinary Grid Communities",
Concurrency and Computation: Practice and Experience, vol. 13–15, pp. 1241–1273, Nov–December, 2002.
Tagged BibTex xml
Colaso V., Kamal A., Saraiya P., North C., McCrickard S., Shaffer C.A.,
"Learning and Retention in Data Structures: A Comparison of Visualization, Text, and Combined Methods",
Proc. ED-MEDIA 2002, pp. 2, 2002.
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Vass M., Carroll J.M., Shaffer C.A.,
"Supporting creativity in problem solving environments",
C&C '02: Proceedings of the 4th conference on Creativity & cognition, New York, NY, USA, ACM, pp. 31–37, 2002.
Tagged BibTex xml
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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2001
Goel A., Baker C.A., Shaffer C.A., Grossman B., Watson L.T., Haftka R.T., Mason W.H.,
"VizCraft: a problem-solving environment for aircraft configuration design",
Comput. Sci. Eng., vol. 3, no. 1, Washington, DC, USA, IEEE Computer Society, pp. 56–66, 2001.
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Begole J., Smith R.B., Struble C.A., Shaffer C.A.,
"Resource sharing for replicated synchronous groupware",
IEEE/ACM Trans. Netw., vol. 9, no. 6, Piscataway, NJ, USA, IEEE Press, pp. 833–843, 2001.
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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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1999
Shaffer C A., Watson L T., Kafura D G.,
"Component Frameworks for Problem Solving Environments in Computational Science",
Proceedings of the 1st Symposium on Reusable Architectures and Components for Developing Distributed Information Systems (RACDIS'99), pp. 653–656, August, 1999.
Tagged BibTex xml
Goel A., Baker C., Shaffer C A., Grossman B., Haftka R., Mason W., Watson L.,
"VizCraft: A Multidimensional Visualization Tool for Aircraft Configuration Design",
VISUALIZATION '99: Proceedings of the 10th IEEE Visualization 1999 Conference (VIS '99), Washington, DC, USA, IEEE Computer Society, 1999.
Tagged BibTex xml
Goel A., Phanouriou C., Kamke F A., Ribbens C.J., Shaffer C A., Watson L T.,
"WBCSim: A Prototype Problem Solving Environment for Wood-Based Composites Simulations",
Engineering with Computers, vol. 15, no. 2, pp. 198–210, 1999.
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Begole J., Rosson M., Shaffer C.A.,
"Flexible collaboration transparency: supporting worker independence in replicated application-sharing systems",
ACM Trans. Comput.-Hum. Interact., vol. 6, no. 2, New York, NY, USA, ACM, pp. 95–132, 1999.
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1998
Begole J., Rosson M., Shaffer C.A.,
"Supporting worker independence in collaboration transparency",
UIST '98: Proceedings of the 11th annual ACM symposium on User interface software and technology, New York, NY, USA, ACM, pp. 133–142, 1998.
Tagged BibTex xml
Goel A., Phanouriou C., Kamke F A., Ribbens C J., Shaffer C A., Watson L T.,
WBCSim: A Prototype Problem Solving Environment for Wood-Based Composites Simulations,
, Blacksburg, VA, USA, Virginia Polytechnic Institute && State University, 1998.
Tagged BibTex xml
Begole J., Shaffer C.A.,
Flexible Collaboration Transparency,
, Blacksburg, VA, USA, Virginia Polytechnic Institute && State University, 1998.
Tagged BibTex xml
Koenemann J., Carroll J.M., Shaffer C.A., Rosson M., Abrams M.,
Designing collaborative applications for classroom use: the LiNC project,
, San Francisco, CA, USA, Morgan Kaufmann Publishers Inc., pp. 99–122, 1998.
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Shaffer C.A., Knill D.L., Watson L.T.,
"Visualization for multiparameter aircraft designs",
VIS '98: Proceedings of the conference on Visualization '98, Los Alamitos, CA, USA, IEEE Computer Society Press, pp. 491–494, 1998.
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1997
Begole J., Struble C.A., Shaffer C.A., Smith R.B.,
"Transparent sharing of Java applets: a replicated approach",
UIST '97: Proceedings of the 10th annual ACM symposium on User interface software and technology, New York, NY, USA, ACM, pp. 55–64, 1997.
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Begole J., Struble C.A., Shaffer C.A.,
"Leveraging Java Applets: Toward Collaboration Transparency in Java",
IEEE Internet Computing, vol. 1, no. 2, Piscataway, NJ, USA, IEEE Educational Activities Department, pp. 57–64, 1997.
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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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Yang J., Shaffer C.A., Heath L.S.,
"SWAN: A Data Structure Visualization System",
GD '95: Proceedings of the Symposium on Graph Drawing, London, UK, Springer-Verlag, pp. 520–523, 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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Jun Y., Shaffer C.A., Heath L.S.,
The Swan User''s Manual, Version 1.1,
, Blacksburg, VA, USA, Virginia Polytechnic Institute && State University, 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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Hines D.T., Begole J.M A., Klipsch C.A., Shaffer C.A.,
The GeoSim Interface Library (GIL): Programmer''s Manual, Version 1.0.1,
, Blacksburg, VA, USA, Virginia Polytechnic Institute && State University, 1994.
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Pemmaraju S.V., Shaffer C.A.,
"Analysis of the worst case space complexity of a PR quadtree",
Inf. Process. Lett., vol. 49, no. 5, Amsterdam, The Netherlands, The Netherlands, Elsevier North-Holland, Inc., pp. 263–267, 1994.
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1993
L.W. Carstensen J., Shaffer C A., Morrill R W., Fox E A.,
"GeoSim: A GIS-Based Simulation Laboratory for Introductory Geography",
Journal of Geography, vol. 92, no. 5, pp. 217–222, September/Octobe, 1993.
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Shaffer C.A.,
"Dissertation Abstracts in Computer Graphics",
SIGGRAPH Comput. Graph., vol. 27, no. 2, New York, NY, USA, ACM, pp. 86–98, 1993.
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Shaffer C.A., Brown P.R.,
"A Paging Scheme for Pointer-Based Quadtrees",
SSD '93: Proceedings of the Third International Symposium on Advances in Spatial Databases, London, UK, Springer-Verlag, pp. 89–104, 1993.
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1992
Shaffer C A.,
Data representations for Geographic Information Systems,
, vol. 27, Medford, NJ, American Society for Information Science, pp. 135–172, 1992.
Tagged BibTex xml
Shaffer C A.,
"Dissertation Abstracts in Computer Graphics",
SIGGRAPH Comput. Graph., vol. 26, no. 1, pp. 76–96, January, 1992.
Tagged BibTex xml
Shaffer C.A., Feustel C.D.,
Exact computation of 2–D intersections,
, San Diego, CA, USA, Academic Press Professional, Inc., pp. 188–192, 1992.
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1991
Shaffer C.A.,
"Real-time robot arm collision detection for telerobotics",
Comput. Electr. Eng., vol. 17, no. 3, Tarrytown, NY, USA, Pergamon Press, Inc., pp. 205–215, 1991.
Tagged BibTex xml
Shaffer C A.,
Getting Around on a Sphere,
, San Diego, CA, USA, Academic Press Professional, Inc., 1991.
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Brown P.R., Shaffer C.A., Webber R.E.,
"A paging scheme for pointer-based quadtrees",
CSC '91: Proceedings of the 19th annual conference on Computer Science, New York, NY, USA, ACM, pp. 687, 1991.
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Shaffer C.A., Stout Q.F.,
"Linear time distance transforms for quadtrees",
CVGIP: Image Underst., vol. 54, no. 2, Orlando, FL, USA, Academic Press, Inc., pp. 215–223, 1991.
Tagged BibTex xml
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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Lattanzi M.R., Shaffer C.A.,
"An optimal boundary to quadtree conversion algorithm",
CVGIP: Image Underst., vol. 53, no. 3, Orlando, FL, USA, Academic Press, Inc., pp. 303–312, 1991.
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1990
Shaffer C A.,
"A full resolution elevation representation requiring three bits per pixel",
SSD '90: Proceedings of the first symposium on Design and implementation of large spatial databases, New York, NY, USA, Springer-Verlag New York, Inc., pp. 45–64, 1990.
Tagged BibTex xml
Ang C -H., Samet H., Shaffer C A.,
"A New Region Expansion for Quadtrees",
IEEE Trans. Pattern Anal. Mach. Intell., vol. 12, no. 7, Washington, DC, USA, IEEE Computer Society, pp. 682–686, 1990.
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Oskard D N., Hong T -H., Shaffer C A.,
"Real-Time Algorithms and Data Structures for Underwater Mapping",
IEEE Transactions on Systems, Man, and Cybernetics, vol. 20, no. 6, pp. 1469–1475, November/Decembe, 1990.
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1988
Ang C -H., Samet H., Shaffer C A.,
"Fast Region Expansion for Quadtrees",
Proceedings of the Third International Symposium on Spatial Data Handling, pp. 19–38, August, 1988.
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1986
Shaffer C A.,
"An Empirical Comparison of Vectors, Rasters, and Quadtrees for Representing Geographic Data",
Proceedings of the International Colloquium on the Construction and Display of Geoscientific Maps Derived from Databases, Geologisches Jahrbuch A 104, pp. 99–115, December, 1986.
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Shaffer C A., Samet H.,
"An Optimal Quadtree Construction Algorithm",
Proceedings of the Eighth International Conference on Pattern Recognition, pp. 317–319, October, 1986.
Tagged BibTex xml
Samet H., Shaffer C A., Nelson R C., Huang Y -G., Fujimura K., Rosenfeld A.,
"Hierarchical Data Structures for Geographic Information",
Proceedings of the International Colloquium on the Construction and Display of Geoscientific Maps Derived from Databases, Geologisches Jahrbuch A 104, pp. 97–98, December, 1986.
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1985
Samet H., Shaffer C A., Webber R E.,
"The Segment Quadtree: A Linear Quadtree-Based Representation for Linear Features",
Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition (CVPR'85), pp. 385–389, June, 1985.
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1984
Samet H., Rosenfeld A., Shaffer C A., Webber R E.,
"Processing Geographic Data with Quadtrees",
Proceedings of the Seventh International Conference on Pattern Recognition, pp. 212–215, August, 1984.
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1983
Samet H., Rosenfeld A., Shaffer C A., Webber R E.,
"Quadtree Region Representation in Cartography: Experimental Results",
IEEE Transactions on Systems, Man, and Cybernetics, vol. 13, no. 6, pp. 1148–1154, November/Decembe, 1983.
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