Publications

Publications in Peer-Refereed Journals

  • Erho, Nicholas, and Wiese, Kay C. "RNA Gene Discovery and Classification of RNA Secondary Structure Elements", in preparation
  • Shabash Boris and Wiese, Kay C. "jComp.Rna - A Visualization Tool for RNA Secondary Structure Including Pseudo-knots and Comparisons of Multiple Structures", in preparation
  • Shabash Boris, and Wiese, Kay C. (2015). "Diploidy in Evolutionary Algorithms for Dynamic Optimization Problems - A Best-Chromosome-Wins Dominance Mechanism", in preparation.
  • Shabash, Boris, and Wiese, Kay C. (2015). "RNA Visualization: Relevance and the Current State-of-the-art Focusing on Pseudoknots", IEEE/ACM Transactions on Computational Biology and Bioinformatics, accepted subject to revisions.
  • Tsang, Herbert, and Wiese, Kay C. (2015), "A Permutation Based Simulated Annealing Algorithm to Predict Pseudoknotted RNA Secondary Structures", International Journal of Bioinformatics Research and Applications, Vol. 11(4), in print.
  • Tsang, Herbert and Wiese, Kay C. (2015). "A Study of Different Annealing Schedules in SARNA-Predict - A Permutation Based SA-Algorithm for RNA Folding", International Journal of Intelligent Computing and Cybernetics, Vol. 8(2), in print.
  • Tsang, Herbert and Wiese, Kay C. (2010). "SARNA-Predict - RNA Secondary Structure Prediction Using Permutation-based Simulated Annealing", IEEE/ACM Transactions on Computational Biology and Bioinformatics, Vol. 7 (4), October 2010, pp. 727-740, (ISI Impact Factor: 1.842 (5 year, 2013)).
  • Scott F. Smith and Wiese, Kay C. (2008), "Integrating Thermodynamic and Observed-Frequency Data for Non-coding RNA Gene Search", Springer Transactions on Computational Systems Biology, Vol. 10, pp. 124-142.
  • Wiese, Kay C., Deschênes, Alain, and Hendriks, Andrew (2008). "RnaPredict - An Evolutionary Algorithm for RNA Secondary Structure Prediction", IEEE/ACM Transactions on Computational Biology and Bioinformatics, Vol. 5(1), pp. 25-41, (ISI Impact Factor: 1.842 (5 year, 2013)), Featured Article of Vol. 5 (1)).
  • 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", BMC Bioinformatics, 7:185, 18 pages, (ISI Impact factor: 3.491 (5 year, 2013)).
  • Wiese, Kay C. and Hendriks, Andrew (2006). "Comparison of P-RnaPredict and Mfold - Algorithms for RNA Secondary Structure Prediction", Bioinformatics Vol. 22 (8), pp. 934-942 (Acceptance Rate: ~20%, ISI Impact Factor: 6.968 (5 year, 2013)).
  • Wiese, Kay C. (2006). Review of "The Ten Most Wanted Solutions in Protein Bioinformatics", BMC BioMedical Engineering OnLine, 2006, 5:1, (ISI Impact Factor: 1.872 (5 year, 2013)).
  • Wiese, Kay C., Hendriks, Andrew, Deschênes, Alain, and Youssef Belgacem B. (2005). "P-RnaPredict - A Parallel Evolutionary Algorithm for RNA Folding: Effects of Pseudorandom Number Quality", IEEE Transactions on NanoBioscience, Vol. 4 (3), pp. 219-227, (Acceptance Rate: ~29%, ISI Impact Factor: 1.842 (2013)).
  • Wiese, Kay C., Glen, Edward. and Vasudevan, Anna (2005). "jViz.Rna - A Java Tool for RNA Secondary Structure Visualization", IEEE Transactions on NanoBioscience, Vol. 4(3), pp. 212-218, (Acceptance Rate: ~29%, ISI Impact Factor: 1.842 (5 year, 2013)).
  • Wiese, Kay C. and Glen, Edward (2003). "A Permutation-Based Genetic Algorithm for the RNA Folding Problem: A Critical Look at Selection Strategies, Crossover Operators, and Representation Issues", BioSystems - Special Issue on Computational Intelligence in Bioinformatics, Vol. 72 (1-2), Gary Fogel and David Corne (Eds.), Elsevier Science, pp. 29 - 41, (Acceptance Rate: ~45%, ISI Impact Factor: 1.584 (5 year, 2013)).
  • Wiese, Kay C. and Goodwin, Scott D. (2001). "Keep-Best Reproduction: A Local Family Competition Selection Strategy and the Environment it Flourishes in", Constraints, Vol. 6 (4), pp. 399 - 422, (Acceptance Rate: ~33%, ISI Impact Factor: 1.151 (5 year, 2013)).
  • Snider, Bonnie S., Asmundson, Gord J.G., and Wiese, Kay C. (2000). "Automatic and Strategic Processing of Threat Cues in Patients With Chronic Pain: A Modified-Stroop Evaluation", Clinical Journal of Pain, Vol. 16, pp.144 - 154 (ISI Impact factor: 3.148 (5 year, 2013).

Peer-Refereed Book Chapters

  • Wiese, Kay C. (2008). "Introduction to Evolutionary Design in Biology", in Design by Evolution - Advances in Evolutionary Design, Philip F. Hingston, Luigi C. Barone, Zbigniew Michalewicz (Eds.), Natural Computing Series, Springer Verlag, pp. 1-6
  • Noel, Kirt and Wiese, Kay C. (2008). "Considering Stem-loops as Sequence Signals for Finding Structural RNA Genes", Applications of Computational Intelligence in Bioinformatics and Biomedicine: Current Trends and Open Problems, Tomasz G. Smolinski, Mariofanna M. Milanova, Aboul-Ella Hassanien (eds.), Springer Studies on Computational Intelligence, Chapter 14, pp. 337-358.
  • Wiese, Kay C., Deschênes, Alain, and Hendriks, Andrew (2007). "RNA Secondary Structure Prediction Employing Evolutionary Algorithms", Computational Intelligence in Bioinformatics, Gary Fogel, David Corne, Yi Pan (eds.), IEEE Wiley (Publishers), pp. 197-223

Publications in Peer-Refereed Conference Proceedings

  • 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.

Theses

  • Wiese, Kay C. (1999). "On Genetic Selection and Sequencing", PhD Thesis, Department of Computer Science, University of Regina, Canada.
  • Wiese, Kay C. (1994). "Parallelization of LLL-Algorithms for Lattice Basis Reduction, an Implementation on an Intel iPSC/860 Hypercube", Masters Thesis (in German), Department of Computer Science, Universität des Saarlandes, Germany.

Other Publications

  • Wiese, Kay C. (2007), "Bioinformatics and Bioengineering Technical Committee", Computational Intelligence Magazine, Vol. 2 (2), Gary Yen (Editor in Chief), invited article, pp. 72-73.
  • Wiese, Kay C. (2006). "IEEE Computational Intelligence Society Tour de China", IEEE Computational Intelligence Magazine, Vol. 1 (4), Gary Yen (Editor in Chief), invited article, pp. 15-17.
  • 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", 16th Penn State Plant Symposium--RNA Biology: Novel Insights from Plant Systems, (Poster).
  • 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, GECCO Late Breaking Paper CD (8 pages).
  • Calvert, Tom, Donaldson, Toby, Hatala, Marek, Kyrylov, Vadym, Popowich, Fred, and Wiese, Kay (2000). "Intelligent Systems Research at TechBC", Canadian AI Society Magazine, No. 47, pp. 5-8.
  • Wiese, Kay C., Nagarajan, Sivakumar, and Goodwin, Scott D. (1996). "QDOOCS, A C++ Class Library for Solving Binary Constraint Satisfaction Problems, Technical Report CS-96-08, Department of Computer Science, University of Regina.

Software and Online Materials Developed

  • jViz.RNA - A Java tool for RNA secondary structure visualization including pseudoknots, available from http://jviz.cs.sfu.ca/ . jViz.Rna is used by hundreds of research labs in the US, Canada, and Europe. We receive about 10 inquiries per month and user responses have been very favorable. Users include Biochemists, Microbiologists, and Medical Researchers. Images of jViz.Rna are found in many RNA related technical publications including the cover pages of the IEEE/ACM Transactions of Computational Biology and Bioinformatics and the book Computational Intelligence in Bioinformatics (Wiley)
  • ITEC 306: Operating Systems. Online course including animations and learning objects, 2001
  • QDOOCS, A C++ Class Library for Solving Binary Constraint Satisfaction Problems, 1996