Tony Kusalik

Bioinformatics Research

Current Projects

Kinome Analysis
	Themes:	bioinformatics methods for creation of kinome peptide arrays, and analysis of data from such arrays; prediction of phosphorylation sites.
	Co-supervisors or Collaborators:	Dr. Scott Napper, VIDO and Biochemistry Dr. Philip Griebel, VIDO and the School of Public Health
	Students:	Brett Trost
	Former Students:
	Refereed^† Papers:	"A Systematic Approach for Analysis of Peptide Array Kinome Data", by Y. Li, R. J. Arsenault, B. Trost, J. Slind, P. J. Griebel, S. Napper, and A. Kusalik in Science Signaling, Vol. 5, No. 220 (17 April 2012), pl2. 16 pages. DOI: 10.1126/scisignal.2002429. Links to abstract, reprint, and full text.
	Theses:
	Presentations:

Immuno-informatics
	Themes:	proteome similarity as a factor in immunogenecity and vaccine design; improved methods for MHC binding prediction.
	Co-supervisors or Collaborators:	Dr. Mik Bickis, Math & Stats Dr. Darja Kanduc, U Bari Dr. Shawn Babiuk, CFIA Dr. Gary Kobinger, PHAC
	Students:	Brett Trost
	Former Students:	Chenhong Zhang (M.Sc.) Ying Li(M.Sc.) Yue Li
	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.
	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.
	Presentations:

(DNA Microarray) Gene Expression Analysis
	Themes:	determining models of transcription regulation incorporating delay from microarray data
	Co-supervisors or Collaborators:	Dr. Gopalan Selvaraj, NRC PBI Dr. Chris Zhang, Biomedical Engin.
	Students:
	Former Students:	Fangxiang Wu (Ph.D.) Matthew Bainbridge (M.Sc.) Chushin Koh (M.Sc.)
	Refereed^† Papers:	"On Determination of Minimum Sample Size for Discovery of Termporal Gene Expression Patterns", by F.-X. Wu, W.-J. Zhang, and A. J. Kusalik, Proceedings of the International Multi-Symposiums on Computer and Computational Science (IMSCCS), Hang Zhou, P.R. China, June 20-24, 2006, pp. 96-103. DOI: 10.1109/IMSCCS.2006.95.
	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.
	Presentations:
	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.

Past Projects

Proteomics
	Themes:	identifying differentially expressed proteins from mass spectrometry data
	Co-supervisors or Collaborators:	Dr. Gordon Gray, Plant Science
	Former Students:	Sudeep Mehrotra

Multiple Sequence Alignment
	Themes:	representation-independent models of MSA; PCR-primer design
	Co-supervisors or Collaborators:	Dr. Isobel Parkin, AAFC
	Former Students:	Christopher Lewis

Triplex DNA
	Themes:	Prediction and ranking of triplex-forming sequences
	Co-supervisors or Collaborators:	Dr. Peta Bonham-Smith, Biology
	Students:	Thomas Covello
	Former Students:	Zhuan Chen (M.Sc.)
	Refereed^† Papers:
	Theses:	"Declarative Grammars and Constraints for Intelligent Biosequence Analysis" by Zhuan Chen, M.Sc. thesis, Department of Computer Science, University of Saskatchewan, May 2000.
	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.

Clustering algorithms
	Themes:	improved `k`-means clustering algorithms
	Co-supervisors & Collaborators:	Dr. Chris Zhang, Biomedical Engin.
	Former Students:	Fangxiang Wu (Ph.D.)
	Refereed^† Papers:
	Theses:
	Presentations:
	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.

Motif-finding
	Themes:	Motif-finding in promoter sequences of rRNA genes
	Co-supervisors or Collaborators:	Dr. Peta Bonham-Smith, Biology
	Former Students:	Pinchao Ma Jason Truong Michael Grayson

(SAGE) Gene Expression Analysis
	Themes:	improved software systems for cSAGE analysis
	Co-supervisors & Collaborators:	Dr. Isobel Parkin, AAFC
	Former Students:	Christopher Lewis
	Refereed^† Papers:
	Theses:
	Presentations:
	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.

3D Protein Comparison
	Themes:	improved algorithm for 3-D structural and chemical similarity comparison of proteins
	Co-supervisors & Collaborators:	Dr. Joseph Angel, Biochemistry
	Former Students:	Stephen O'Hearn (M.Sc.)
	Refereed^† Papers:
	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:
	Posters:

Biomolecular Structure Prediction
	Themes:	3D structure prediction using constraints
	Co-supervisors or Collaborators:	Dr. Francois Major, U. Montréal
	Former Students:

All Bioinformatics-related Publications and Presentations

† - 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.