Applied Research Lab:: Publications and Presentations

Book

  • H. H . Tsang, "SARNA-Predict – An Algorithm for RNA Folding”, VDM Verlag Dr. Müller Aktiengesellschaft & Co., ISBN 978-3-8364-9001-6, 2008. [order from Amazon.com, click here]

Book Chapters

2015

  • A. J. Park and H. H. Tsang, “A Systematic Approach to Develop a Computational Framework for Counter-terrorism and Public Safety” Martin Bouchard, editor, Social Networks, Terrorism and Counter-terrorism: Radical and Connected, Routledge, 2015, 196-217.

2014

  • H. H . Tsang, "How Can Experiential Computing Learning Make a Positive Impact in the World?”, Vivian Neal, editor, Experiential Learning Casebook, Teaching and Learning Centre, Simon Fraser University, 2014. LINK

Refereed Journal Articles

2015

2014

2012

2010

2009

  • H. A. Ebhardt, H. H. Tsang, and D. C. Dai, "Small RNA sequence analysis: a novel approach to decipher sequencing errors from RNA editing events", Biochemistry and Cell Biology, NRC Research Press, 87(1):370, 2009

Pre-2005

Refereed Conference Publications

2016

  • S. Sav, D. J. D. Hampson and H. H. Tsang. “SIMARD: A Simulated Annealing Based RNA Design Algorithm with Quality Pre-Selection Strategies", the IEEE Symposium Series on Computational Intelligence, 2016 (accepted).
  • D. J. D. Hampson, S. Sav, and H. H. Tsang. “Investigation of Multi-Objective Optimization Criteria for RNA Design", the IEEE Symposium Series on Computational Intelligence, 2016 (accepted)
  • A. J. Park, B. Beck, D. Fletche, P. Lam, and H. H. Tsang. “Temporal Analysis of Radical Dark Web Forum Users", in Proceedings of the International Symposium on Foundations of Open Source Intelligence and Security Informatics, San Francisco, CA, USA, August 18-21, 2016, pp. 880-883.
  • H. E. Erhan, S. Sav, S. Kalashnikov and H. H. Tsang. “Examining the Annealing Schedules for RNA Design Algorithm”, in Proceedings of the IEEE Congress on Evolutionary Computation, Vancouver, BC, Canada, July 24-29, 2016, pp. 1295-1302.
  • B. Chersinoff, H.H. Tsang, and V. Spicer. "iPatrol+: Patterns of Public Disorder from a Community Volunteer Perspective," in Proceedings of the 43rd Annual Conference of the Western Society of Criminology, Vancouver, BC, Canada, February 4 -6, 2016.

2015

2014

  • P. Grypma and H. H. Tsang. "SARNA-Predict: Using Adaptive Annealing Schedule and Inversion Mutation Operator for RNA Secondary Structure Prediction," in Proceedings of the IEEE Symposium Series on Computational Intelligence (SSCI) in Multi-Criteria Decision-Making, December 9-12, 2014, Orlando, FL, pp. 150-156.
  • C. K. Hobbs and H. H. Tsang, "Industry in the Classroom: Equipping Students with Real-World Experience," in Proceedings of the 19th Western Canadian Conference on Computing Education (WCCCE), May 2-3, 2014, Richmond, BC.

2013

  • A. J. Park and H. H. Tsang. "Detecting Key Players in Criminal Networks Using Dynalink," in Proceedings of the European Intelligence and Security Informatics Conference, August 12-14, 2013, Uppsala, Sweden, pp. 208-211.
  • P. Grypma, J. Babbitt, and H. H. Tsang. "A Study on the Effect of Different Thermodynamic Models for Predicting Pseudoknotted RNA Secondary Structures," in Proceedings of the IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, April 15-19, 2013, Singapore, pp.52-59.

2012

  • H. H. Tsang and D. C. Dai. “RNA-DV: An Interactive Tool for Editing and Visualizing RNA Secondary Structures,” in Proceedings of the ACM Conference on Bioinformatics, Computational Biology and Biomedicine, 2012, pp. 601-603.
  • A. J. Park, H. H. Tsangand P. L. Brantingham. "Dynalink: A Framework for Dynamic Criminal Network Visualization," in Proceedings of the European Intelligence and Security Informatics Conference, 2012, pp. 217-224.

2011

  • H. H. Tsangand C. Jacob. "RNADPCompare: An Algorithm for Comparing RNA Secondary Structures Based on Image Processing Techniques," in Proceedings of the IEEE Congress on Evolutionary Computation, 2011, pp. 1288 -1295.
  • A. Alimadad, V. Dabbaghian, S. K. Singh, and H. H. Tsang. "Modeling HIV Spread through Sexual Contact Using a Cellular Automaton," in Proceedings of the IEEE Congress on Evolutionary Computation, 2011, pp. 2345 - 2350.

2010

  • J. Kietzmann and H. H. Tsang"Minding the Gap: Bridging Computing Science and Business Studies with an Interdisciplinary Innovation Challenge", WCCCE 2010 - the 15th Western Canadian Conference on Computing Education, University of British Columbia, May 7 - 8, 2010, pp. 80-84
  • Christopher C. Yang, Daniel Zeng, Ke Wang, Antonio Sanfilippo, Herbert H. Tsang, Min-Yuh Day, Uwe Glässer, Patricia L. Brantingham, Hsinchun Chen. IEEE International Conference on Intelligence and Security Informatics, ISI 2010, Vancouver, BC, Canada, May 23-26, 2010, Proceedings. ISI'2010.
  • H. H. TsangA. Park, M. Sun, and U. Glasser. “GENIUS: A Computational Modeling Framework for Counter-Terrorism Planning and Response", in Proceedings of the IEEE International Conferences on Intelligence and Security Informatics, 2010, pp. 71-76.
  • H. H. Tsang, T. Jiang, K. C. Wiese, and C. Jacob. “A Study of RNA Secondary Prediction Using Different Mutation Operators,” in Proceedings of the IEEE World Congress on Computational Intelligence, 2010, pp. 684-690.
  • A. Park, H. H. Tsang, and E. Hwang. “Evacuation Simulation of Older Adults from High-Rise Buildings", the 7th World Conference of International Society for Gerontechnology, Vancouver, BC, May 27 – 30, 2010, 9(2):241 doi: http://dx.doi.org/10.4017/gt.2010.09.02.312.00

2009

  • H. H. Tsang and K. C. Wiese. “SARNA-Ensemble-Predict: The Effect of Different Dissimilarity Metrics on a Novel Ensemble-based RNA Secondary Structure Prediction Algorithm”, in Proceedings of the IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, 2009, pp. 8-15.
  • D. C. Dai, H. H. Tsang, and K. C. Wiese. “rnaDesign: Local Search for RNA Secondary Structure Design”, in Proceedings of the IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, 2009, pp. 1-7.
  • D. C. Dai, H. H. Tsang, and K. C. Wiese. “An Incremental Redundancy Estimation for the Sequence Neighborhood Boundary”, in Proceedings of the Fourth Canadian Student Conference on Biomedical Computing, 2009.

2008

  • H. H. Tsang and K. C. Wiese. “SARNA-Predict-pk: Predicting RNA Secondary Structures Including Pseudoknots”, in Proceedings of the IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB), 2008, pp.1-8. [ full paper | bibtex ]

2007

  • H. H. Tsang and K. C. Wiese. "The Significance of thermodynamic models in the accuracy improvement of RNA secondary structure prediction using permutation based simulated annealing", in Proceedings of the IEEE Congress on Evolutionary Computation (CEC), 2007, Special Session on Evolutionary Computation in Bioinformatics and Computational Biology, pp.3879 -3885. [ full paper | bibtex ]
  • H. H. Tsang and K. C. Wiese. “SARNA-Predict: A Study of RNA Secondary Structure Prediction Using Different Annealing Schedules”, in Proceedings of the IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB), 2007, pp.239-246. [ full paper | bibtex ]

2006

  • H. H. Tsang and K. C. Wiese. “SARNA-Predict: A Simulated Annealing Algorithm for RNA Secondary Structure Prediction”, in Proceedings of the IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB), 2006, pp.466-475. [ full paper | bibtex ]

Pre-2005

  • H. H. Tsang and J. McCracken, “Learning Musical Terms in Context: The Role for Rich Multimedia Learning Technologies”, Proceedings of the Seventh International Association of Science and Technology for Development (IASTED) Conference on Computers and Advanced Technology in Education (CATE), August 16-18, 2004, Kauai, Hawaii, USA, pp.27-31 (One of three finalists in the PhD student competition and best paper nomination) [ full paper | bibtex ]
  • M. Dutkiewicz, H. Tsang, H. H. Zwick, B. Robertson, S. E. Qian and A. B.Hollinger, “Web-Based Hyperspectral Image Analysis”, Proceedings of 2001 American Society for Photogrammetry and Remote Sensing Annual Convention, St. Louis, Missouri, April 23-27, 2001, CDROM unpaginated. PDF
  • S. E. Qian, A. B. Hollinger, M. Dutkiewicz, H. Tsang and H. H. Zwick, “A Tool for Hyperspectral Image Data Distribution by E-Commerce”, 14th International Conference & Workshops on Applied Geologic Remote Sensing, Las Vegas, Nevada, USA, November 2000
  • S. E. Qian, A. B. Hollinger, M. Dutkiewicz, H. Tsang and H. H. Zwick, “Fast Spectral Processing of Hyperspectral Image Cubes” 14th International Conference & Workshops on Applied Geologic Remote Sensing, Las Vegas, Nevada, USA, November 2000
  • M. Dutkiewicz, H. Tsang and H. H. Zwick, “Earth Under A Microscope”, 22nd Canadian Symposium on Remote Sensing, Victoria , BC , Canada , August, 2000
  • H. H. Tsang and K. R. Smith, “Automated Segmentation using Deformable Template Matching Technique”, Third Annual Argonne Symposium for Undergraduate in Science, Engineering and Mathematics Argonne National Laboratory, Argonne, Illinois, November 1992

Posters

  • G. Yang, V.L. Porter, C.K. Hobbs, H.H. Tsang, B.A. Siame, Y. Zhang, Q. Wang, K.Y. Leung, "Genome-wide search for type III secretion system effectors of Edwardsiella tarda using a meta-analytical approach", the 114th General Meeting of the American Society for Microbiology, Boston, Massachusetts, May 17-20, 2014.
  • V.L. Porter, G. Yang, C.K. Hobbs, H.H. Tsang, B.A. Siame, Y. Zhang, Q. Wang, K.Y. Leung, "Genome-wide search for type III secretion system effectors of Edwardsiella tarda using a meta-analytical approach", the Thompson Rivers University Annual Undergraduate Research & Innovation Conference, Kamloops, B.C. March 2014. LINK
  • V.L. Porter, G. Yang, C.K. Hobbs, H.H. Tsang, B.A. Siame, Y. Zhang, Q. Wang, K.Y. Leung, "Genome-wide search for type III secretion system effectors of Edwardsiella tarda using bioinformatics", the 22nd Annual Murdock College Science Research Conference, Vancouver, WA, November 7-9, 2013. LINK
  • S.W. Leung, C.K. Hobbs, H.A. Ebhardt, and H.H. Tsang, "PIVOT: Visualizing Protein Interactions", the Annual Undergraduate Research & Innovation Conference, 2013
  • S.W. Leung, C.K. Hobbs, and H.H. Tsang, "Visualizing Protein Interactions", the 21st Annual Murdock College Science Research Conference, Whitman College, Walla Walla, WA, October 26-27, 2012.
  • A. Alimadad, V. Dabbaghian, S. Singh and H. H. Tsang, “Examining HIV Transmission Rate through Sexual Contact with the Cellular Automata Model”, The Second Annual MoCSSy Symposium, The IRMACS Centre, Burnaby, BC, September 14, 2009 [Third prize winner in the poster competition]
  • A. Park, M. Sun, and H. H. Tsang, “A Computational Framework to Simulate Human and Social Behaviors”, The Second Annual MoCSSy Symposium, The IRMACS Centre, Burnaby, BC, September 14, 2009
  • D. C. Dai, H. H. Tsang and K. C. Wiese, “An Incremental Redundancy Estimation for the Sequence Neighborhood Boundary”, The Fourth Canadian Student Conference on Biomedical Computing, Vancouver, BC, March 12 - 14, 2009
  • H. A. Ebhardt, H. H. Tsang and D. C. Dai, "Small RNA sequence analysis: a novel approach to decipher sequencing errors from RNA editing events", Canadian Society of Biochemistry, Molecular and Cellular Biology's 51st Annual Meeting, Banff, Alberta, March 6-9, 2008

Invited Talks/Presentations

  • "Computational Intelligence and Bioinformatics", Science Seminar Series at Thompson Rivers University, Kamloops, BC, Canada, March 26, 2015.
  • "Computational Framework for Counter-terrorism and Public Safety”. Preliminary Research Findings from TSAS-sponsored projects, Ottawa, ON, Canada, 2014.
  • "A Systematic Approach to Develop a Computational Framework for Counter-terrorism and Public Safety”, Turning a New Leaf: Developments in Research and Policy on Terrorism & Counter-Terrorism, Ottawa, ON, Canada, 2013.
  • "How Can Computing Make a Positive Impact on the World?”, Experiential Education in Large Classes: A Dialogue, Burnaby, BC, Canada, 2013.
  • "Effective IT leadership and project management: Bridging Computing Science and Business Studies with an Interdisciplinary Innovation Challenge", the EDDE 804 - Project Management and Leadership class at Athabasca University, Alberta, Canada on April 7, 2011.
  • "A Framework for Examining the Impacts of the Built Environment for Seniors", the MoCSSy Symposium on Gerontological Research and Modelling, the Interdisciplinary Research in the Mathematical and Computational Sciences (IRMACS) Centre, Simon Fraser University, Burnaby, BC, Canada. November 25, 2009.
  • "The Modelling of Complex Social Systems (MoCSSy) Research and Training Program", the Workshop on Visualization and Communication of Climate Change Risk, the Climate-Change Impacts Research Consortium (CCIRC), the Interdisciplinary Research in the Mathematical and Computational Sciences (IRMACS) Centre, Simon Fraser University, Burnaby, BC, Canada. April 14, 2009.
  • "GENIUS: A Decision Support System for Counter-Terrorism Planning and Response", the 4th Annual IRMACS Day at the Interdisciplinary Research in the Mathematical and Computational Sciences (IRMACS) Centre, Simon Fraser University, Burnaby, BC, Canada. April 2, 2009.
  • "Bioinformatics: Structure Prediction and Visualization in the RNA World", Department of Electrical Engineering, Calvin College, Gradn Rapids, MI, USA. October 6, 2008.
  • "Introduction to Bioinformatics –Visualizing and folding of RNA", Institute for Canadian Urban Research Studies - ICURS Seminar, School of Criminology, Simon Fraser University, Burnaby, BC, Canada. June 2, 2008.
  • "The Road from Headlight Design to Bioinformatics", Computational Biology (COMBI) Research Group, School of Computing Science, Simon Fraser University, Burnaby, BC, Canada. March 31, 2008.
  • "Bioinformatics: Structure Prediction and Sequence Analysis in the RNA World", Department of Computing Science, University of Alabama in Huntsville, USA. March 13, 2008.
  • "SARNA-Predict: RNA Secondary Structure Prediction Using Permutation Based Simulated Annealing", Molecular and Computational Systems Biology Seminar, Simon Fraser University, Burnaby, BC, Canada. June 13, 2007.
  • "SARNA-Predict: A Simulated Annealing Algorithm for RNA Secondary Structure Prediction", BETA Lab Bioinformatics / Algorithmic Reading Group, University of British Columbia, Vancouver, BC. December 13, 2006.

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