Tony Kusalik

Bioinformatics Research

Publications and Presentations

(Bioinformatics) Algorithms
Refereed Papers:

Biomolecular Structure:
Refereed Papers:
Supervised Theses: "A Framework for Comparing Flexible Objects Applied to Protein Structure Analysis" by Stephen O'Hearn, M.Sc. thesis, Department of Computer Science, University of Saskatchewan, December 1999.
Presentations: "Modelling and Predicting the Structure of Biomolecules Using Constraint-based Computational Techniques", CREFSIP (Centre de recherche sur la fonction, la structure et l'ingénierie des protéines), Université Laval, Québec, Québec, May 11, 2000. Invited lecture.

Gene Expression Analysis:
Refereed Papers:
Supervised Theses: "Microarray Analysis Using Pattern Discovery" by Matthew Bainbridge, M.Sc. thesis, Department of Computer Science, November 2004. U. of S. etd-12102004-091353.
"Computational Methods for Analysis and Modeling of Time-Course Gene Expression Data" by Fangxiang Wu, Ph.D. thesis, Division of Biomedical Engineering, August 2004. U. of S. etd-08302004-164807.
Posters: "cSAGE and the Serial Analysis of Gene Expression in Arabidopsis thaliana", C. Lewis, S. Robinson, A. Kusalik, and I. Parkin, poster at ISMB 2003, Brisbane, Australia, June 29 - July 3, 2003, Poster F-38.
Technical Reports: "Locally Optimal Parameter Settings for Pattern Discovery in Gene Expression Microarray Data", Matthew Bainbridge and Anthony Kusalik. Technical Report, Department of Computer Science, University of Saskatchewan, March 2003.

Refereed Papers: "Optimally-Connected Hidden Markov Models for Predicting MHC-Binding Peptides", by C. Zhang, M. G. Bickis, F.-X. Wu, and A. J. Kusalik in Journal of Bioinformatics and Computational Biology, Vol. 4, No. 5 (October 2006), pp. 959-980. DOI: 10.1142/S0219720006002314.
Supervised Theses: "An Improved Fully Connected Hidden Markov Model for Rational Vaccine Design" by Chenhong Zhang, M.Sc. thesis, Department of Computer Science, February 2005. U. of S. etd-02232005-121948.

Machine-Learning (applied to Bioinformatics)
Refereed Papers:
Posters: "Genetic Weighted K-means for Large-Scale Clustering Problems", F.-X. Wu, A. J. Kusalik, and W.-J. Zhang, poster at FLAIRS 2005, Clearwater Beach, FL, May 15-17, 2005. Two pages.

Sequence Analysis:    
Refereed Papers:
Supervised Theses: "Declarative Grammars and Constraints for Intelligent Biosequence Analysis" by Zhuan Chen, M.Sc. thesis, Department of Computer Science, University of Saskatchewan, May 2000.
Invited Presentations: "Advanced Computational Techniques for Triplex-DNA Engineering", by Z. Chen and A. Kusalik, presented at Colloque 101 (Biologie Informatique), 68e Congrès de l'Acfas, May 15-19, 2000, Montréal, Québec.

† - Note that presentation at computer science and most bioinformatics conferences is subject to peer review. Further, top-ranked bioinformatics and computer science conferences have reviewing standards as rigorous as journals in the area.