Herbert H. Tsang:: Publications and Presentations

Scientific Publications and Presentations:

Book Authored

  • 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]
    SARNA-Predict.jpg

Refereed Journal Articles

In preparation / submitted

  • H. H. Tsang and K. C. Wiese, "Employing Permutation Based Simulated Annealing Algorithm to Predict Pseudoknotted RNA Secondary Structures" (in preparation)
  • H. H. Tsang and D. C. Dai, "RNA-DV: an interactive editing and visualization tool for RNA secondary structures" (in preparation)

2009

  • H. A. Ebhardt, H. H. Tsang, D. C. Dai, Y. Liu, B. Bostan and R. P. Fahlman, "Meta-analysis of small RNA sequencing errors reveals ubiquitous post transcriptional RNA modifications", Nucleic Acids Research, May 2009; 37(8):2461-70
  • 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

2008

  • H. H. Tsang and K. C. Wiese, "SARNA-Predict - Accuracy Improvement of RNA Secondary Structure Prediction Using Permutation-based Simulated Annealing", IEEE/ACM Transactions on Computational Biology and Bioinformatics (accepted for publication on September 1, 2008, total 14 pages) [ full paper | bibtex ]

2007

  • H. H. Tsang and K. C. Wiese, "A Study of Different Annealing Schedules in SARNA-Predict - a permutation based SA algorithm for RNA folding", International Journal of Information Technology and Intelligent Computing (accepted on June 4, 2007, total 26 pages). [ full paper | bibtex ]

Pre-2005

  • S. E. Qian, A. B. Hollinger, M. Dutkiewicz, H. Tsang, H. H. Zwick and J. Freemantle, “Effect of Lossy Vector Quantization Hyperspectral Data Compression on Retrieval of Red Edge Indices” IEEE Transactions on Geoscience and Remote Sensing, Volume: 39 Issue: 7, July 2001, P.1459 -1470 [ full paper | bibtex ]

Refereed Conference Papers

2011

  • H. H. Tsang and Christian Jacob, "RNADPCompare: An Algorithm for Comparing RNA Secondary Structures Based on Image Processing Techniques", Proceedings of the 2011 IEEE Congress on Evolutionary Computation, June 5-8, 2011, P. 1288 - 1295.
  • A. Alimadad, V. Dabbaghian, P. J. Giabbanelli, S. K. Singh and H. H. Tsang, "Modeling HIV Spread through Sexual Contact Using a Cellular Automaton" Proceedings of the 2011 IEEE Congress on Evolutionary Computation, June 5-8, 2011, P. 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, P. 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. Tsang, A. Park, M. Sun, and U. Glasser, “GENIUS: A Computational Modeling Framework for Counter-Terrorism Planning and Response", 2010 IEEE International Conferences on Intelligence and Security Informatics, Vancouver, BC, May 23-26, 2010, P. 71-76
  • H. H. Tsang, T. Jiang, K. C. Wiese, and C. Jacob, “A Study of RNA Secondary Prediction Using Different Mutation Operators”, 2010 IEEE World Congress on Computational Intelligence, Barcelona, Spain, July 18 - 23, 2010, P. 1-7
  • 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.
  • U. Glaesser, A. Park, M. Sun, and H. H. Tsang, “A Computational Framework to Simulate Human and Social Behaviors", the 10th International Probabilistic Safety Assessment and Management Conference, Seattle, Washington, USA, June 7 - 11, 2010 [accepted]

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”, 2009 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology - March 30 - April 2, 2009, Nashville, Tennessee, P. 8-15
  • D. C. Dai, H. H. Tsang and K. C. Wiese, “rnaDesign: Local Search for RNA Secondary Structure Design”, 2009 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology- March 30 - April 2, 2009, Nashville, Tennessee, P. 1-7
  • 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

2008

  • H. H. Tsang and K. C. Wiese, “SARNA-Predict-pk: Predicting RNA Secondary Structures Including Pseudoknots”, 2008 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB) - September 15-17, 2008, Sun Valley, Idaho, USA, P.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", 2007 IEEE Congress on Evolutionary Computation (CEC) - Singapore, September 25-28, 2007, Special Session on Evolutionary Computation in Bioinformatics and Computational Biology, P.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”, 2007 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB) - Honolulu, Hawaii, USA, April 1-5, 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”, Proceedings of the 2006 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB) - Toronto, Canada, Sept. 28-29, 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

  • 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]
MoCSSy-HIV_Poster_20090916.jpg
  • 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

  • "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.

Other Presentations

  • H. H. Tsang, R. D. Chamberlain, R. R. Krchnavek and W .D. Richard, "Optical System Synthesis of High-Performance Automobile Lighting", the Second Annual AGES (Association of Graduate Engineering Student) Research Fair, Washington University, St. Louis, Missouri , March 1995
  • H. H. Tsang, "Automated Segmentation using Deformable Template Matching Technique", Undergraduate Research Academy Symposium Southern Illinois University, Edwardsville, Illinois, May 1993

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Copyright © 2010, Herbert H. Tsang, http://www.herberttsang.org

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