University of Alberta
Department of Computer Science
2009
Babak Bostan, Russell Greiner, Duane Szafron and Paul Lu Predicting Homologous Signaling Pathways Using Machine Learning Bioinformatics, 2009, doi: 10.1093/bioinformatics/btp532.
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H. Alexander Ebhardt, Herbert H. Tsang, Denny C. Dai, Yifeng Liu, Babak Bostan and P. Fahlman Meta-analysis of small RNA-sequencing errors reveals ubiquitous post-transcriptional RNA modifications Nucleic Acids Research, March 2009, doi:10.1093/nar/gkp093.
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2008
Alona Fyshe, Yifeng Liu, Duane Szafron, Russell Greiner, Paul Lu. Improving Subcellular Localization Prediction using Text Classification and the Gene Ontology. Bioinformatics, August 2008, doi:10.1093/bioinformatics/btn463.
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2006
Luca Pireddu, Duane Szafron, Paul Lu, Russell Greiner, The Path-A metabolic pathway prediction web server, Nucleic Acids Research, Oxford Journals Online, Volume 34, Number (Web Server Issue), Pages W714 -- W719, July 2006
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D. Szafron, B. Poulin, R. Eisner, P. Lu, R. Greiner, D. Wishart, A. Fyshe, B. Pearcy, C. Macdonell, J. Anvik, Visual Explanation of Evidence in Additive Classifiers, Innovative Applications of Artificial Intelligence, July 2006
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2005
Paul Lu, Duane Szafron, Russell Greiner, David S. Wishart, Alona Fyshe, Brandon Pearcy, Brett Poulin, Roman Eisner, Danny Ngo, and Nicholas Lamb, PA-GOSUB: A Searchable Database of Model Organism Protein Sequences With Their Predicted GO Molecular Function and Subcellular Localization, Nucleic Acids Research, Volume 33, January 2005, ms. 6.
Roman Eisner, Brett Poulin, Duane Szafron, Paul Lu, Russell Greiner, Improving Protein Function Prediction using the Hierarchical Structure of the Gene Ontology, IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, San Diego, November 2005
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2004
Duane Szafron, Paul Lu, Russell Greiner, David S. Wishart, Brett Poulin, Roman Eisner, Zhiyong Lu, John Anvik, Cam Macdonell, Alona Fyshe, and David Meeuwis, Proteome Analyst: Custom Predictions with Explanations in a Web-based Tool for High-throughput Proteome Annotations, Nucleic Acids Research, Volume 32, July 2004, 7 ms.
Zhiyong Lu, Duane Szafron, Russell Greiner, Paul Lu, David S. Wishart, Brett Poulin, John Anvik, Cam Macdonell, and Roman Eisner, Predicting Subcellular Localization of Proteins using Machine-Learned Classifiers, Bioinformatics, Volume 20, Issue 4, March 2004, pp. 547 - 556.
2003
Adrian Driga, Paul Lu, Jonathan Schaeffer, Duane Szafron, Kevin Charter and Ian Parsons, FastLSA: A Fast, Linear-Space, Parallel and Sequential Algorithm for Sequence Alignment, International Conference on Parallel Processing (ICPP), October 2003, Kaohsiung, Taiwan, pp. 48-57.
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Duane Szafron, Paul Lu, Russell Greiner, David S. Wishart, Zhiyong Lu, Brett Poulin, Roman Eisner, John Anvik and Cam Macdonell, Proteome Analyst - Transparent High-throughput Protein Annotation: Function, Localization and Custom Predictors, International Conference on Machine Learning Workshop on Machine Learning in Bioinformatics (ICML Workshop - Bioinformatics), August 2003, Washington, U.S.A., pp. 2-10.
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2002
Matthew McNaughton, Paul Lu, Jonathan Schaeffer and Duane Szafron, Memory-Efficient A* Heuristics for Multiple Sequence Alignment, Proceedings of Nineteenth National Conference on Artificial Intelligence (AAAI'2002), July 2002, Edmonton Canada, pp. 737- 743.
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2000
Kevin Charter, Jonathan Schaeffer, Duane Szafron, Sequence Alignment using FastLSA, Proceedings of The 2000 International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences (METMBS'2000), June 2000, Las Vegas, Nevada, pp 239-245.
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2009
Babak Bostan, Predicting Homologous Signaling Pathways Using Machine Learning, Fall 2009.
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Bibtex
2008
Peng Wang, Hierarchical Prediction of Protein Function in The Gene Ontology Using Graphical Models, Spring 2008.
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Bibtex
2007
Alona Fyshe Term Generalization and Synonym Resolution for Biological Abstracts: Using the Gene Ontology for Subcellular Localization Prediction, Spring 2007
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Bibtex
2005
Roman Eisner, Predicting Protein Function using Machine-Learned Hierarchical Classifiers, Fall 2005.
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Bibtex
Luca Pireddu, Pathway Analyst - Automating Biochemical Pathway Prediction, Fall 2005.
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Bibtex
2004
Brett Poulin, Sequence-based protein function prediction, 2004.
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Bibtex
2003
Zhiyong Lu, Predicting Protein SUB-Cellular Localization From Homologs Using Machine Learning Algorithms, Fall 2003.
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Bibtex
 
2008
H. Alexander Ebhardt, Yifeng Liu, Duane Szafron, Homology Based miRNA Prediction. 51th Annual Meeting of the Canadian Society of Biochemistry and Molecular & Cellular Biology, Banff, AB, Canada, March 6-9, 2008.
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2007
Yifeng Liu, Alona Fyshe, Duane Szafron, Protein Subcellular Localization Prediction: A Natural Language Processing Approach. the Seventh International Conference of the Canadian Proteomics Initiative, Ottawa, ON, Canada, June 16-18, 2007.
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2005
Roman Eisner, Alona Fyshe, Russell Greiner, Paul Lu, Brandon Pearcy, Brett Poulin, Duane Szafron, and David S. Wishart, Predicting 400 GO Functions of Proteins: Part of the Proteome Analyst Suit of Tools, ISMB 2005
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Alona Fyshe, Paul Lu, Duane Szafron, Russell Greiner, David S. Wishart, Brandon Pearcy, Brett Poulin, Roman Eisner, Danny Ngo, and Nicholas Lamb, PA-GOSUB: Gene Ontology Molecular Function and Subcellular Localization Predictions for Model Organisms, ISMB 2005
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Alona Fyshe, Paul Lu, Duane Szafron, Russell Greiner, David S. Wishart, Brandon Pearcy, Brett Poulin, Roman Eisner, Danny Ngo, and Nicholas Lamb, Proteome Analyst: Machine learning for protein annotation, ISMB 2005
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Brandon Pearcy, Paul Lu, Duane Szafron, Russell Greiner, David S. Wishart, Alona Fyshe, Brett Poulin, Roman Eisner, Danny Ngo, and Nicholas Lamb, PA-GOSUB: Gene Ontology Molecular Function (GO) and Subcellular Localization (SUB) Predictions for Model Organisms, CPI 2005 (Second Place Poster)
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Luca Pireddu, Brett Poulin, Duane Szafron, and Paul Lu, Pathway Analyst, CPI 2005
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Brett Poulin, Duane Szafron, Russell Greiner, Roman Eisner, and Paul Lu, RAMMER: Accelerating Protein Function Prediction, CPI 2005
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2004
Alona Fyshe, Roman Eisner, Russell Greiner, Paul Lu, David Meeuwis, Brett Poulin, Duane Szafron, David S. Wishart, and Chris Upton, Proteome Analyst: An Overview, PENCE 2004 (Second Place Poster)
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Roman Eisner, Alona Fyshe, Russell Greiner, Paul Lu, David Meeuwis, Brett Poulin, Duane Szafron, Chris Upton, and David S. Wishart, Proteome Analyst - Gene Ontology Protein Function Prediction, CPI 2004
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2002
Roman Eisner, Brett Poulin, Duane Szafron, Paul Lu, Russell Greiner, David S. Wishart, and Bahram Habibi-Nazhad, Proteome Analyst, CPI 2002
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Roman Eisner, Brett Poulin, Duane Szafron, Paul Lu, Russell Greiner, David S. Wishart, and Bahram Habibi-Nazhad, An Overview of Proteome Analyst, ISMB 2002
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Zhiyong Lu, Xiaomeng Wu, and Russell Greiner, Protein Sequence Classification in Proteome Analyst, ISMB 2002
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Brett Poulin, Jennifer Listgarten, Russ Greiner, Sambasivarao Damaraju, Thomas Kolacz, Xiang Wan, David S. Wishart, and Brent Zanke, Cancer, SNPs and Machine Learning, ISMB 2002
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2005
Brett Poulin, Duane Szafron, Paul Lu, Russell Greiner, David S. Wishart, Roman Eisner, Alona Fyshe, Brandon Pearcy, and Luca Pireddu, The Proteome Analyst Suite of Automated Function Prediction Tools, AAAI 2005
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