Refereed Publications - Bioinformatics

Babak Bostan, Russell Greiner, Duane Szafron and Paul Lu, Predicting Homologous Signaling Pathways Using Machine Learning, Volume 25 Issue 22, November 2009, pp. 2913-2920 2009. abstract or preprint pdf.

Alona Fyshe, Yifeng Liu, Duane Szafron, Russ Greiner and Paul Lu, Improving subcellular localization prediction using text classification and the gene ontology, Bioinformtics Volume 24, November 2008, pp. 2512-2517, abstract or browser version or pdf.

Luca Pireddu, Duane Szafron, Paul Lu, and Russell Greiner, The Path-A metabolic pathway prediction web server, Nucleic Acids Research, Volume 34, July 2006, pp. W714-W719, abstract or browser version or pdf.

Brett Poulin, Roman Eisner, Duane Szafron, Paul Lu, Russ Greiner, D.S. Wishart, Alona Fyshe, Brandon Pearcy, Cam MacDonell and John Anvik, Visual Explanation of Evidence in Additive Classifiers, 18th Conference on Innovative Applications of Arificial Intelligence (IAAI), July 2006, 1822-1829. abstract or pdf.

A. Fyshe and D. Szafron, Term Generalization and Synonym Resolution for Biological Abstracts: Using the Gene Ontology for Subcellular Localization Prediction, to appear in the BioNLP Workshop at the Human Language Technology conference - North American chapter of the Association for Computational Linguistics (HLT-NAACL), June 2006, 17-24. abstract or pdf.

A. Driga, P. Lu, J. Schaeffer, D. Szafron, K. Charter and I. Parsons. FastLSA: A Fast, Linear-Space, Parallel and Sequential Algorithm for Sequence Alignment, Algorithmica, 2006, 337-375. abstract or pdf.

Luca Pireddu, Brett Poulin, Duane Szafron, Paul Lu, and David Wishart, Pathway Analyst—Automated Metabolic Pathway Prediction, Proceedings of 2005 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, November 2005, pp. 243-250.abstract or pdf.

Roman Eisner, Brett Poulin, Duane Szafron, Paul Lu and Russ Greiner, Improving Protein Function Prediction using the Hierarchical Structure of the Gene Ontology, Proceedings of 2005 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, November 2005, pp. 354-363, abstract or pdf.

Gary H. Van Domselaar, Paul Stothard, Savita Shrivastava, Joseph A. Cruz, AnChi Guo, Xiaoli Dong, Paul Lu, Duane Szafron, Russ Greiner and David S. Wishart, BASys: A Web Server for Automated Bacterial Genome Annotation, Nucleic Acids Research, Volume 33, July 2005, pp. W455-W459, abstract or html or pdf.

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, pp. D147-D152, abstract or html or pdf.

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, pp. W365-W371, abstract or html or pdf.

Z. Lu, D. Szafron, R. Greiner, P. Lu, D.S. Wishart, B. Poulin, J. Anvik, C. Macdonell, and R. Eisner, Predicting Subcellular Localization of Proteins using Machine-Learned Classifiers, Bioinformatics, Volume 20, Issue 4, March 2004, pp. 547 - 556. abstract or pdf or preprint abstract or preprint pdf.

A. Driga, P. Lu, J. Schaeffer, D. Szafron, K. Charter and I. 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, abstract or pdf.

D. Szafron, P. Lu, R. Greiner, D. Wishart, Z. Lu, B. Poulin, R. Eisner, J. Anvik and C. 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, abstract or pdf.

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. abstract or pdf.

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. abstract or pdf

D. S. Wishart, S. Fortin, D. R. Woloschuk, W. Wong, T. Rosborough, G. Van Domselaar, J. Schaeffer and D. Szafron, A Platform-Independent Graphical User Interface for SEQSEE and XALIGN, Bioinformatics (formerly - Computer Applications in the Biosciences - CABIOS), Vol. 13, No. 5, 1997, pp. 561-562. abstract or pdf.

I. Goralwalla, M.T. Özsu, and D. Szafron, Modeling Medical Trials in Pharmacoeconomics using a Temporal Object Model, Computers in Biology and Medicine - Special Issue on Time Oriented Systems in Medicine, Vol. 27 No. 5,1997, pp. 369 - 387. abstract or pdf.