Publications in Peer-Refereed Conferences

  • Shabash Boris, and Wiese, Kay C. (2013) "pEvoSAT: a novel permutation based genetic algorithm for solving the boolean satisfiability problem", Genetic and Evolutionary Computation Conference (GECCO '13), pp. 861-868.
  • Shabash, Boris, Wiese, Kay and Glen, Edward (2012), "Improving the Portability and Performance of jViz.RNA, A Dynamic RNA Visualization Software", The 7th IAPR International Conference on Pattern Recognition in Bioinformatics PRIB '12), pp. 82-93.
  • Jiang, Wenbo and Wiese, Kay C. (2012), "Non-Coding RNA Gene Finding with Combined Partial Covariance Models", IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB '12), pp. 306-313.
  • Salekdeh, Amin Y. and Wiese, Kay C. (2011), "Improving splice-junctions classification employing a novel encoding schema and decision-tree", IEEE Congress on Evolutionary Computation (IEEE CEC '11), pp. 1302-1307.
  • Jiang, Wenbo and Wiese, Kay C. (2011), "Combined Covariance Model for Non-coding RNA Gene Finding" Proc. of the 2011 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB '11), pp. 22-26.
  • Erho, Nicholas and Wiese, Kay C. (2011), "Secondary Structure Element Voting for RNA Gene Finding", Proc. of the 2011 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB '11), pages 27-24, April 2011.
  • Tsang, Herbert H., Jiang, Tiancheng, Wiese, Kay C., and Jacob, Christian (2010), "A study of RNA secondary structure prediction using different mutation operators." IEEE Congress on Evolutionary Computation (IEEE/CEC 2011): 1-7.
  • Wiese, Kay C. and Hendriks, Andrew (2010). "Expanded Study of efn2 Thermodynamic Model Performance on RnaPredict, an Evolutionary Algorithm for RNA Folding, IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB '10), pp. 55-62.
  • Erho, Nicholas and Wiese, Kay C. (2010), "An Exploration of Individual RNA Structural Elements in RNA Gene Finding", IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB '10), pp. 203-211.
  • Wiese, Kay C. and Hendriks, Andrew (2009). "Impact of an Enhanced Thermodynamic Model on RnaPredict, an Evolutionary Algorithm for RNA Secondary Structure Prediction," IEEE Congress on Evolutionary Computation (IEEE CEC '09), Trondheim, Norway, pp. 2892 - 2899.
  • [48] Wiese, Kay C. and Hendriks, Andrew (2009). "RNA Pseudoknot Prediction via an Evolutionary Algorithm," IEEE Congress on Evolutionary Computation (IEEE CEC '09), Trondheim, Norway, 270 -276.
  • Dai, Denny C. and Wiese, Kay C. (2009). "Performance Prediction for RNA Design Using Parametric and Non-Parametric Regression Models", IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB '09), Nashville, TN, USA, pp. 16-23.
  • Tsang, Herbert H. and Wiese, Kay C. (2009). "SARNA-Ensemble-Predict: The Effect of Different Dissimilarity Metrics on a Novel Ensemble-based RNA Secondary Structure Prediction Algorithm", IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB '09), Nashville, TN, USA, pp. 8-15.
  • Dai, Denny C., Tsang, Herbert H. and Wiese, Kay C. (2009). "rnaDesign: Local Search for RNA Secondary Structure Design", IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB '09), Nashville, TN, USA, 1-7.
  • [44] Wiese, Kay C., and Hendriks, Andrew (2008). "A Hybrid Clustering/Evolutionary Algorithm for RNA Folding", IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB'08), Sun Valley, USA, pp. 15-21.
  • Tsang, Herbert H. and Wiese, Kay C. (2008). "SARNA-Predict-pk: Predicting RNA Secondary Structures Including Pseudoknots", IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB '08), Sun Valley, USA, pp. 1-8.
  • Smith, Scott and Wiese, Kay C. (2007). "Improved Covariance Model Parameter Estimation Using RNA Thermodynamic Properties", 2nd International Conference on Bio-Inspired Models of Network, Information, and Computing Systems BIONETICS 2007, Budapest, Hungary, Paper #2431 (7 pages).
  • Tsang, Herbert H. and Wiese, Kay C. (2007). "The Significance of Thermodynamic Models in the Accuracy Improvement of RNA Secondary Structure Prediction Using Permutation-based Simulated Annealing", Proceedings of the 2007 IEEE Congress on Evolutionary Computation (IEEE/CEC-2007), Singapore, pp. 3879-3885.
  • Tsang, Herbert H. and Wiese, Kay C. (2007). "SARNA-Predict: A Study in a Novel Approach for RNA Secondary Structure Prediction Using Different Annealing Schedules", Proceedings of the 2007 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB '07), Waikiki, USA, pp.239-246.
  • Wiese, Kay C., Hendriks, Andrew, and Deschênes, Alain (2006). "Analysis of Thermodynamic Models and Performance in RnaPredict - An Evolutionary Algorithm for RNA Folding", Proceedings of the 2006 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB '06), Toronto, Canada pp. 343-351.
  • Tsang, Herbert H. and Wiese, Kay C. (2006). "SARNA-Predict: A Simulated Annealing Algorithm for RNA Secondary Structure Prediction", Proceedings of the 2006 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB '06), Toronto, Canada, pp. 466-475.
  • Wiese, Kay C. and Hendriks, Andrew (2006). "A Detailed Analysis of Parallel Speedup in P-RnaPredict - An Evolutionary Algorithm for RNA Secondary Structure Prediction", Proceedings of the 2006 IEEE Congress on Evolutionary Computation (IEEE/CEC-2006), Vancouver, Canada, pp. 8087-8094.
  • Ebhardt, H. Alexander, Wiese, Kay C., and Unrau, Peter J. (2006). "Ebbie: Automated Analysis and Storage of Small RNA Cloning Data Using a Dynamic Web Server", Proceedings of the 11th Annual Meeting of the RNA Society (RNA 2006), Seattle, Washington, Abstract #207.
  • Wiese, Kay C. and Glen, Edward (2006). "jViz.Rna - An Interactive Graphical Tool for Visualizing RNA Secondary Structure Including Pseudoknots", Proceedings of the 19th IEEE International Symposium on Computer Based Medical-Systems (IEEE/CBMS-2006), Salt Lake City, Utah, pp. 659-664.
  • Wiese, Kay C., and Eicher, Christina (2006). "Graph Drawing Tools for Bioinformatics Research: An Overview", Proceedings of the 19th IEEE International Symposium on Computer Based Medical-Systems (IEEE/CBMS-2006), Salt Lake City, Utah, pp. 653-658.
  • Wiese, Kay C., Hendriks, Andrew, Deschênes, Alain, and Youssef, Belgacem B. (2005). "Significance of Randomness in P-RnaPredict - A Parallel Evolutionary Algorithm for RNA Folding", Proceedings of the 2005 IEEE Congress on Evolutionary Computation (IEEE/CEC-2005), Special Session on EC in Bioinformatics and Computational Biology, Edinburgh, Scotland, pp. 467-474.
  • Wiese, Kay C., Hendriks, Andrew, and Poonian, Jag (2005). "Algorithms for RNA Folding: a Comparison of Dynamic Programming and Parallel Evolutionary Algorithms", Proceedings of the 2005 IEEE Congress on Evolutionary Computation (IEEE/CEC-2005), Special Session on EC in Bioinformatics and Computational Biology, Edinburgh, Scotland, pp. 475-483.
  • Wiese, Kay C., Hendriks, Andrew, Deschênes, Alain, and Youssef, Belgacem B. (2005). "The Impact of Pseudorandom Number Quality on P-RnaPredict, a Parallel Genetic Algorithm for RNA Secondary Structure Prediction", Proceedings of the 2005 Genetic and Evolutionary Computation Conference (GECCO-2005) - Biological Applications Track, Washington, D.C., pp. 479-480 (Full paper published as GECCO late breaking paper on CD, 8 pages).
  • Deschênes, Alain, Wiese, Kay C., and Poonian, Jagdeep (2004). "Comparison of Dynamic Programming and Evolutionary Algorithms for RNA Secondary Structure Prediction", Proceedings of the 2004 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB'04), La Jolla, California, pp. 214-222, (Winner of Best Student Paper Award).
  • Hendriks, Andrew, Deschênes, Alain, and Wiese, Kay C. (2004). "A Parallel Evolutionary Algorithm for RNA Secondary Structure Prediction Using Stacking-Energies (INN and INN-HB)", Proceedings of the 2004 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB'04), La Jolla, California, pp. 223-230.
  • Noel, Kirt and Wiese, Kay C. (2004). "Using Stem-loop Characteristics as Means to Locate Structural RNA Genes", Proceedings of the IEEE Computer Society Computational Systems Bioinformatics Conference (IEEE/CSB), Stanford University, California, pp. 533-534.
  • Noel, Kirt and Wiese, Kay C. (2004). "Evaluating the Usefulness of Stem-loop Characteristics in Pinpointing Structural RNA Genes", Proceedings of the 12th Intelligent Systems for Molecular Biology Conference/3rd European Conference on Computational Biology ISMB/ECCB'04, Glasgow, Scotland, Abstract I-13.
  • Deschênes, Alain and Wiese, Kay C. (2004). "Using Stacking-Energies (INN and INN-HB) for Improving the Accuracy of RNA Secondary Structure Prediction with an Evolutionary Algorithm - A Comparison to Known Structures", Proceedings of the IEEE Congress on Evolutionary Computation (IEEE/CEC 2004), Portland, Oregon, pp. 598-606. (Nominated for Best Student Paper and Best Paper. It won the Best Student Paper Award).
  • Tang, Lenny, Wiese, Kay C., and Kumar, Vive (2004). "Genetic Algorithm Based OSPF Network Routing using LEDA", Proceedings of the 17th Conference of the Canadian Society for Computational Studies of Intelligence (Cdn. AI 2004), Lecture Notes in Artificial Intelligence LNAI Vol. 3060, Springer Verlag, Germany, pp. 571-572.
  • Hendriks, Andrew, Wiese, Kay C., and Glen, Edward (2004). "Comparison of Parallel and Serial Genetic Algorithms for RNA Secondary Structure Prediction", Proceedings of the 17th Conference of the Canadian Society for Computational Studies of Intelligence (Cdn. AI 2004), Lecture Notes in Artificial Intelligence LNAI Vol. 3060, Springer Verlag, Germany, pp. 554-555.
  • Deschênes, Alain, Wiese, Kay C., and Glen, Edward (2004). "Comparison of Permutation-based and Binary Representation in a Genetic Algorithm for RNA Secondary Structure Prediction", Proceedings of the 17th Conference of the Canadian Society for Computational Studies of Intelligence (Cdn. AI 2004), Lecture Notes in Artificial Intelligence LNAI Vol. 3060, Springer Verlag, Germany, pp. 549-550.
  • Wiese, Kay C., Deschênes, Alain, and Glen, Edward (2003). "Permutation-based RNA Secondary Structure Prediction via a Genetic Algorithm", Proceedings of the IEEE Congress on Evolutionary Computation (IEEE/CEC 2003), Special Session on EC in Bioinformatics and Computational Biology, Canberra, Australia, pp. 335-342.
  • Hendriks, Andrew, Wiese, Kay C., Glen, Edward, and Deschênes, Alain (2003). "A Distributed Genetic Algorithm for RNA Secondary Structure Prediction", Proceedings of the IEEE Congress on Evolutionary Computation (IEEE/CEC-2003), Special Session on EC in Bioinformatics and Computational Biology, Canberra, Australia, pp. 343-350.
  • Wiese, Kay C. and Glen, Edward (2003). "RNA Structure as Permutation: A GA Approach Comparing Different Genetic Sequencing Operators", Proceedings of the 14th International Symposium on Methodologies for Intelligent Systems (ISMIS-2003), Lecture Notes in Artificial Intelligence, Vol. 2871, Springer Verlag, Germany, pp. 511-520.
  • Wiese, Kay C. and Glen, Edward (2003). "A Genetic Algorithm Using Order Crossover for RNA Folding", Proceedings of the 7th IASTED International Conference in Artificial Intelligence and Softcomputing (ASC 2003), Henry Leung (Ed.), Banff, Canada, pp. 261-267.
  • Wiese, Kay C., Kyrylov, Vadim, Nesbit, John, and Calvert, Tom (2003). "Interactive Media and Team-Based Learning in a Computer Graphics Course Blending Online and Face-To-Face Delivery", Proceedings of the IASTED International Conference on Computers and Advanced Technology in Education (CATE 2003), Vladimir Uskov (Ed.), Rhodes, Greece, pp. 450-460.
  • Wiese, Kay C. and Glen, Edward (2002). "A Permutation Based Genetic Algorithm for RNA Secondary Structure Prediction", Frontiers in Artificial Intelligence and Applications, Vol. 87, Soft computing Systems, IOS Press, pp. 173-182.
  • Wiese, Kay C. and Kyrylov, Vadim (2002). "Teaching Computer Graphics On-line: Lessons Learned", Proceedings of the Western Computer Graphics Symposium (SkiGraph 2002), Vernon, B.C., Canada, pp. 93-101.
  • Wiese, Kay C., Nagarajan, Sivakumar, and Goodwin, Scott D. (2000). "ASERC - A Genetic Sequencing Operator for Asymmetric Permutation Problems", Proceedings of the 13th Biennial Conference of the Canadian Society for Computational Studies of Intelligence (AI 2000), Advances in Artificial Intelligence, Lecture Notes in Artificial Intelligence, Vol. 1822, Springer Verlag, Germany, pp. 201-213.
  • Wiese, Kay C. and Goodwin, Scott D. (1999). "Convergence Characteristics of Keep-Best Reproduction", Proceedings of the 1999 ACM Symposium on Applied Computing (SAC'99), Genetic Algorithms Track, pp. 312-318.
  • Wiese, Kay C., Nagarajan, Sivakumar, and Goodwin, Scott D. (1998). "Parallel Genetic Algorithms for Constrained Ordering Problems", Proceedings of the 11th International Florida Artificial Intelligence Research Symposium (FLAIRS'98), pp. 101-105.
  • Wiese, Kay C. and Goodwin, Scott D. (1998). "The Effect of Genetic Operator Probabilities and Selection Strategies on the Performance of a Genetic Algorithm", Proceedings of the 12th Biennial Conference of the Canadian Society for Computational Studies of Intelligence (AI'98) Advances in Artificial Intelligence, Lecture Notes in Artificial Intelligence, Vol. 1418, Springer Verlag, Germany, pp.141-153.
  • Wiese, Kay C. and Goodwin, Scott D. (1998). "Keep-Best Reproduction: A Selection Strategy for Genetic Algorithms", Proceedings of the 1998 ACM Symposium on Applied Computing (SAC'98), Genetic Algorithms Track, pp. 343-348.
  • Wiese, Kay C. and Goodwin, Scott D. (1997). "A New Selection Strategy for Genetic Algorithms that Yields Better Results", 3rd International Conference on Principles and Practice of Constraint Programming (CP'97), Workshop on Biocomputing and Bioinformatics.
  • Wiese, Kay C., Nagarajan, Sivakumar, and Goodwin, Scott D. (1997). "QDOOCS: A C++ Class Library for Solving Binary Constraint Satisfaction Problems", Proceedings of the 10th International Florida Artificial Intelligence Research Symposium (FLAIRS'97), pp. 443-448.