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Clifford A. Shaffer - Publications

Affiliations: 
Virginia Polytechnic Institute and State University, Blacksburg, VA, United States 
Area:
Computer Science, Electronics and Electrical Engineering, Statistics
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51 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2020 Keating SM, Waltemath D, König M, Zhang F, Dräger A, Chaouiya C, Bergmann FT, Finney A, Gillespie CS, Helikar T, Hoops S, Malik-Sheriff RS, Moodie SL, Moraru II, Myers CJ, ... ... Shaffer CA, et al. SBML Level 3: an extensible format for the exchange and reuse of biological models. Molecular Systems Biology. 16: e9110. PMID 32845085 DOI: 10.15252/Msb.20199110  0.391
2020 Bart AC, Tibau J, Kafura D, Shaffer CA, Tilevich E. Design and Evaluation of a Block-based Environment with a Data Science Context Ieee Transactions On Emerging Topics in Computing. 8: 182-192. DOI: 10.1109/Tetc.2017.2729585  0.716
2019 Palmisano A, Hoops S, Watson LT, Jones TC, Tyson JJ, Shaffer CA. Efficiently Encoding Complex Biochemical Models with the Multistate Model Builder (MSMB). Methods in Molecular Biology (Clifton, N.J.). 1945: 119-139. PMID 30945244 DOI: 10.1007/978-1-4939-9102-0_5  0.351
2019 Manzoor H, Akhuseyinoglu K, Wonderly J, Brusilovsky P, Shaffer CA. Crossing the Borders: Re-Use of Smart Learning Objects in Advanced Content Access Systems Future Internet. 11: 160. DOI: 10.3390/Fi11070160  0.331
2018 Koh KH, Fouh E, Farghally MF, Shahin H, Shaffer CA. Experience Journal of Data and Information Quality. 9: 1-10. DOI: 10.1145/3148240  0.325
2017 Chen M, Amos B, Watson LT, Tyson J, Cao Y, Shaffer C, Trosset M, Oguz C, Kakoti G. Quasi-Newton Stochastic Optimization Algorithm for Parameter Estimation of a Stochastic Model of the Budding Yeast Cell Cycle. Ieee/Acm Transactions On Computational Biology and Bioinformatics. PMID 29990127 DOI: 10.1109/Tcbb.2017.2773083  0.317
2017 Bart AC, Tibau J, Tilevich E, Shaffer CA, Kafura D. BlockPy: An Open Access Data-Science Environment for Introductory Programmers Computer. 50: 18-26. DOI: 10.1109/Mc.2017.132  0.698
2016 Karavirta V, Shaffer CA. Creating Engaging Online Learning Material with the JSAV JavaScript Algorithm Visualization Library Ieee Transactions On Learning Technologies. 9: 171-183. DOI: 10.1109/Tlt.2015.2490673  0.355
2015 Palmisano A, Hoops S, Watson LT, Jones TC, Tyson JJ, Shaffer CA. JigCell Run Manager (JC-RM): a tool for managing large sets of biochemical model parametrizations. Bmc Systems Biology. 9: 95. PMID 26704692 DOI: 10.1186/S12918-015-0237-0  0.366
2015 Ahn TH, Sandu A, Watson LT, Shaffer CA, Cao Y, Baumann WT. A Framework to Analyze the Performance of Load Balancing Schemes for Ensembles of Stochastic Simulations International Journal of Parallel Programming. 43: 597-630. DOI: 10.1007/S10766-014-0309-6  0.31
2014 Palmisano A, Hoops S, Watson LT, Jones TC, Tyson JJ, Shaffer CA. Multistate Model Builder (MSMB): a flexible editor for compact biochemical models. Bmc Systems Biology. 8: 42. PMID 24708852 DOI: 10.1186/1752-0509-8-42  0.351
2014 Shaffer CA. Grand Challenges in Digital Education Frontiers in Ict. 1. DOI: 10.3389/Fict.2014.00005  0.305
2014 Akbar M, Shaffer CA, Fan W, Fox EA. Recommendation based on Deduced Social Networks in an educational digital library Proceedings of the Acm/Ieee Joint Conference On Digital Libraries. 29-38. DOI: 10.1109/JCDL.2014.6970147  0.496
2014 Cooper ML, Shaffer CA, Edwards SH, Ponce SP. Open source software and the algorithm visualization community Science of Computer Programming. 88: 82-91. DOI: 10.1016/J.Scico.2013.12.008  0.319
2014 Fouh E, Karavirta V, Breakiron DA, Hamouda S, Hall S, Naps TL, Shaffer CA. Design and architecture of an interactive eTextbook - The OpenDSA system Science of Computer Programming. 88: 22-40. DOI: 10.1016/J.Scico.2013.11.040  0.354
2013 Verstak A, Ramakrishnan N, Watson LT, He J, Shaffer CA, Grama AY. Using hierarchical data mining to characterize performance of wireless system configurations Advances in Engineering Software. 65: 66-77. DOI: 10.1016/J.Advengsoft.2013.05.012  0.312
2012 Liu Z, Pu Y, Li F, Shaffer CA, Hoops S, Tyson JJ, Cao Y. Hybrid modeling and simulation of stochastic effects on progression through the eukaryotic cell cycle. The Journal of Chemical Physics. 136: 034105. PMID 22280742 DOI: 10.1063/1.3677190  0.318
2012 Akbar M, Shaffer CA, Fox EA. Deduced social networks for an educational digital library Proceedings of the Acm/Ieee Joint Conference On Digital Libraries. 43-46. DOI: 10.1145/2232817.2232828  0.491
2012 Fouh E, Akbar M, Shaffer CA. The Role of Visualization in Computer Science Education Computers in the Schools. 29: 95-117. DOI: 10.1080/07380569.2012.651422  0.559
2011 Akbar M, Fan W, Cassel L, Delcambre L, Shaffer CA, Fox EA, Chen Y. How educators find educational resources online Iticse'11 - Proceedings of the 16th Annual Conference On Innovation and Technology in Computer Science. 367. DOI: 10.1145/1999747.1999880  0.472
2011 Shaffer CA, Akbar M, Alon AJD, Stewart M, Edwards SH. Getting algorithm visualizations into the classroom Sigcse'11 - Proceedings of the 42nd Acm Technical Symposium On Computer Science Education. 129-134. DOI: 10.1145/1953163.1953204  0.462
2011 Akbar M, Fan W, Shaffer CA, Chen Y, Cassel L, Delcambre L, Garcia DD, Hislop GW, Shipman F, Furuta R, Carpenter BS, Hsieh H, Siegfried B, Fox EA. Digital library 2.0 for educational resources Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 6966: 89-100. DOI: 10.1007/978-3-642-24469-8_11  0.487
2010 Randhawa R, Shaffer CA, Tyson JJ. Model composition for macromolecular regulatory networks. Ieee/Acm Transactions On Computational Biology and Bioinformatics / Ieee, Acm. 7: 278-87. PMID 20431147 DOI: 10.1109/Tcbb.2008.64  0.625
2010 Shaffer CA, Cooper ML, Alon AJD, Akbar M, Stewart M, Ponce S, Edwards SH. Algorithm Visualization: The state of the field Acm Transactions On Computing Education. 10. DOI: 10.1145/1821996.1821997  0.548
2010 Fox EA, Chen Y, Akbar M, Shaffer CA, Edwards SH, Brusilovsky P, Garcia D, Delcambre L, Decker F, Archer D, Furuta R, Shipman F, Carpenter S, Cassel L. Ensemble PDP-8: Eight principles for distributed portals Proceedings of the Acm International Conference On Digital Libraries. 341-344. DOI: 10.1145/1816123.1816174  0.432
2009 Randhawa R, Shaffer CA, Tyson JJ. Model aggregation: a building-block approach to creating large macromolecular regulatory networks. Bioinformatics (Oxford, England). 25: 3289-95. PMID 19880372 DOI: 10.1093/Bioinformatics/Btp581  0.628
2009 Shaffer CA, Zwolak JW, Randhawa R, Tyson JJ. Modeling molecular regulatory networks with JigCell and PET. Methods in Molecular Biology (Clifton, N.J.). 500: 81-111. PMID 19399431 DOI: 10.1007/978-1-59745-525-1_4  0.62
2009 Ahn TH, Watso LT, Cao Y, Shaffer CA, Baumann WT. Cell cycle modeling for budding yeast with stochastic simulation algorithms Cmes - Computer Modeling in Engineering and Sciences. 51: 27-52. DOI: 10.3970/Cmes.2009.051.027  0.338
2008 Wang P, Randhawa R, Shaffer CA, Cao Y, Baumann WT. Converting macromolecular regulatory models from deterministic to stochastic formulation Proceedings of the 2008 Spring Simulation Multiconference, Springsim'08. 385-392. DOI: 10.1145/1400549.1400608  0.592
2008 Panning TD, Watson LT, Allen NA, Chen KC, Shaffer CA, Tyson JJ. Deterministic parallel global parameter estimation for a model of the budding yeast cell cycle Journal of Global Optimization. 40: 719-738. DOI: 10.1007/S10898-007-9273-7  0.312
2007 Mishra D, Shaffer CA, Ramakrishnan N, Watson LT, Bae KK, He J, Verstak AA, Tranter WH. S 4 W: a problem-solving environment for wireless system design Software - Practice and Experience. 37: 1539-1558. DOI: 10.1002/Spe.V37:14  0.36
2006 Vass MT, Shaffer CA, Ramakrishnan N, Watson LT, Tyson JJ. The JigCell model builder: a spreadsheet interface for creating biochemical reaction network models. Ieee/Acm Transactions On Computational Biology and Bioinformatics / Ieee, Acm. 3: 155-64. PMID 17048401 DOI: 10.1109/Tcbb.2006.27  0.334
2006 Shaffer CA, Randhawa R, Tyson JJ. The role of composition and aggregation in modeling macromolecular regulatory networks Proceedings - Winter Simulation Conference. 1628-1635. DOI: 10.1109/WSC.2006.322937  0.559
2004 Vass M, Allen N, Shaffer CA, Ramakrishnan N, Watson LT, Tyson JJ. the JigCell model builder and run manager. Bioinformatics (Oxford, England). 20: 3680-1. PMID 15273159 DOI: 10.1093/Bioinformatics/Bth422  0.357
2004 Skidmore RR, Verstak A, Ramakrishnan N, Rappaport TS, Watson LT, He J, Varadarajan S, Shaffer CA, Chen J, Bae KK, Jiang J, Tranter WH. Towards integrated PSEs for wireless communications Acm Sigmobile Mobile Computing and Communications Review. 8: 20-34. DOI: 10.1145/997122.997128  0.373
2003 Allen NA, Calzone L, Chen KC, Ciliberto A, Ramakrishnan N, Shaffer CA, Sible JC, Tyson JJ, Vass MT, Watson LT, Zwolak JW. Modeling regulatory networks at Virginia Tech. Omics : a Journal of Integrative Biology. 7: 285-99. PMID 14583117 DOI: 10.1089/153623103322452404  0.382
2003 Verstak A, Ramakrishnan N, Watson LT, He J, Shaffer CA, Bae KK, Jiang J, Tranter WH, Rappaport TS. BSML: A binding schema markup language for data interchange in problem solving environments Scientific Programming. 11: 199-224. DOI: 10.1155/2003/314624  0.305
2003 Dymond R, Lohani V, Kibler D, Bosch D, Rubin EJ, Dietz R, Chanat J, Speir C, Shaffer CA, Ramakrishnan N, Watson LT. From landscapes to waterscapes: A PSE for landuse change analysis Engineering With Computers. 19: 9-25. DOI: 10.1007/S00366-002-0245-8  0.322
2002 Watson LT, Lohani VK, Kibler DF, Dymond RL, Ramakrishnan N, Shaffer CA. Integrated computing environments for watershed management Journal of Computing in Civil Engineering. 16: 259-268. DOI: 10.1061/(Asce)0887-3801(2002)16:4(259)  0.326
2002 He J, Watson LT, Ramakrishnan N, Shaffer CA, Verstak A, Jiang J, Bae K, Tranter WH. Dynamic data structures for a direct search algorithm Computational Optimization and Applications. 23: 5-25. DOI: 10.1023/A:1019992822938  0.342
2002 Ramakrishnan N, Watson LT, Kafura DG, Ribbens CJ, Shaffer CA. Programming environments for multidisciplinary grid communities Concurrency Computation Practice and Experience. 14: 1241-1273. DOI: 10.1002/Cpe.679  0.699
2001 Begole J, Smith RB, Struble CA, Shaffer CA. Resource sharing for replicated synchronous groupware Ieee/Acm Transactions On Networking. 9: 833-843. DOI: 10.1109/90.974535  0.351
1999 Begole J, Rosson MB, Shaffer CA. Flexible collaboration transparency: supporting worker independence in replicated application-sharing systems Acm Transactions On Computer-Human Interaction. 6: 95-132. DOI: 10.1145/319091.319096  0.325
1999 Goel A, Phanouriou C, Kamke FA, Ribbens CJ, Shaffer CA, Watson LT. WBCSim: A prototype problem solving environment for wood-based composites simulations Engineering With Computers. 15: 198-210. DOI: 10.1007/S003660050014  0.35
1997 Begole J, Struble CA, Shaffer CA. Leveraging Java applets: Toward collaboration transparency in Java Ieee Internet Computing. 1: 57-64. DOI: 10.1109/4236.601100  0.302
1993 Carstensen LW, Shaffer CA, Morrill RW, Fox EA. Geosim: A GIS-based simulation laboratory for introductory geography Journal of Geography. 92: 217-222. DOI: 10.1080/00221349308979656  0.343
1990 Shaffer CA, Sametj H, Nelson RC. Quilt; a geographic information system based on quadtrees International Journal of Geographical Information Systems. 4: 103-131. DOI: 10.1080/02693799008941534  0.31
1987 Samet H, Shaffer CA, Nelson RC, Huang YG, Rosenfeld A. Recent developments in linear quadtree-based geographic information systems Image and Vision Computing. 5: 187-197. DOI: 10.1016/0262-8856(87)90049-7  0.321
1987 Samet H, Shaffer CA, Webber RE. Digitizing the plane with cells of nonuniform size Information Processing Letters. 24: 369-375. DOI: 10.1016/0020-0190(87)90113-X  0.301
1986 Samet H, Shaffer CA. A Model for the Analysis of Neighbor Finding in Pointer-Based Quadtrees Ieee Transactions On Pattern Analysis and Machine Intelligence. 717-720. DOI: 10.1109/Tpami.1985.4767729  0.324
1984 Samet H, Rosenfeld A, Shaffer CA, Webber RE. A geographic information system using quadtrees Pattern Recognition. 17: 647-656. DOI: 10.1016/0031-3203(84)90018-9  0.302
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