Roman Eisner - Publications
Publications
M.Sc. Thesis: Predicting Protein Function Using Machine-Learned Hierarchical Classifiers
Refereed Publications:
Stretch C, Eastman T, Mandal R, Eisner R, Wishart DS, Mourtzakis M, Prado CM, Damaraju S, Ball RO, Greiner R, Baracos VE. Prediction of skeletal muscle and fat mass in patients with advanced cancer using a metabolomic approach. J Nutr. 2012 Jan;142(1):14-21. Epub 2011 Dec 7 (link).
Psychogios N, Hau DD, Peng J, Guo AC, Mandal R, Bouatra S, Sinelnikov I, Krishnamurthy R, Eisner R et al. The Human Serum Metabolome. PLoS ONE 6(2): e16957. doi:10.1371/journal.pone.0016957 (link).
Eisner R, Stretch C, Eastman T, Xia J, Hau D, Damaraju S, Greiner R, Wishart DS, Baracos VE. Learning to predict cancer-associated skeletal muscle wasting from 1H-NMR profiles of urinary metabolites. Metabolomics Volume 7, Issue 1 (2011), Page 25 (link).
Knox C, Law V, Jewison T, Liu P, Ly S, Frolkis A, Pon A, Banco K, Mak C, Neveu V, Djoumbou Y, Eisner R, Guo AC, Wishart DS. DrugBank 3.0: a comprehensive resource for 'omics' research on drugs. Nucleic Acids Res. 2011 Jan;39(Database issue):D1035-41. (link).
Wishart D, Knox C, Guo A, Eisner R, Young N et al. HMDB: A Knowledgebase for the Human Metabolome. Nucleic Acids Research 2009 Jan; 37(Database issue):D603-10 (link).
Wishart DS, Lewis MJ, Morrissey JA, Flegel MD, Jeroncic K, Xiong Y, Cheng D, Eisner R, Gautam B, Tzur D, Sawhney S, Bamforth F, Greiner R, Li L. The human cerebrospinal fluid metabolome. J Chromatogr B Analyt Technol Biomed Life Sci. 2008 Aug 15;871(2):164-73. Epub 2008 May 8 (link).
Wishart DS, Tzur D, Knox C, Eisner R, Guo AC, Young N, Cheng D, Jewell K, Arndt D, Sawhney S, Fung C, Nikolai L, Lewis M, Coutouly M-A, Forsythe I, Tang P, Shrivastava S, Jeroncic K, Stothard P, Amegbey G, Block D, Hau DD, Wagner J, Miniaci J, Clements M, Gebremedhin M, Guo N, Zhang Y, Duggan GE, Macinnis GD, Weljie AM, Dowlatabadi R, Bamforth F, Clive D, Greiner R, Li L, Marrie T, Sykes BD, Vogel HJ, Querengesser L. HMDB: The Human Metabolome Database. Nucleic Acids Research 2007 Jan;35:D521-6. ( pdf 858kb - BibTeX ).
Knox C, Shrivastava S, Stothard P, Eisner R, Wishart DS. BioSpider: a web server for automating metabolome annotations. Pacific Symposium on Biocomputing 12:145-156, 2007. ( pdf 444kb ).
B. Poulin, R. Eisner, D. Szafron, P. Lu, R. Greiner, D.S. Wishart, A. Fyshe, B. Pearcy, C. MacDonell and J. Anvik, Visual Explanation of Evidence in Additive Classifiers, 18th Conference on Innovative Applications of Artificial Intelligence (IAAI), July 2006. ( pdf 1.7mb - BibTeX ).
R. Eisner, B,.Poulin, D. Szafron, P. Lu and R. Greiner, Improving Protein Function Prediction using the Hierarchical Structure of the Gene Ontology, 2005 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, November 2005, 10 ms. ( pdf 480kb - BibTeX ).
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. ( BibTeX ).
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. ( pdf 780kb - BibTeX )
D. Szafron, P. Lu, R. Greiner, D. S. Wishart, B. Poulin, R. Eisner, Z. Lu, J. Anvik, C. Macdonell, A. Fyshe, and D. 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. ( pdf 422kb - BibTeX )
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. ( pdf 643kb )
Research Posters:
Eisner R, Knox C, Cheng D, Greiner R, Wishart DS. "Text Analysis in the Human Metabolome Project", poster presented at the 5th Annual Northern Lights Summer Conference on Metabolomics, Technologies & Applications, Waterloo ON, June 20-23, 2007.
Eisner R, Knox C, Cheng D, Greiner R, Wishart DS. "Text Analysis in the Human Metabolome Project", poster presented at the 3rd Annual Meeting of the Metabolomics Society, Manchester UK, June 11-14, 2007.
Eisner R, Knox C, Greiner R, Wishart DS. Predicting Chemical Properties of Small Molecules, The Second Annual Metabolomics Symposium: Exploring the Human Metabolome poster session, University of Alberta, October 12, 2006. ( pdf 477kb ) (Also presented at the 2006 ISMB (Intelligent Systems in Molecular Biology) Conference, Fortaleza, Brazil, August 4-7, 2006)
Tzur D, Jeroncic K, Jewell K, Block D, Knox C, Eisner R, Guo A, Stothard P, Forsythe I, Shrivastava S, Greiner R, Wishart DS. The Human Metabolome Database (HMDB), The Metabolomics Symposium: Understanding the Human Metabolome poster session, University of Alberta, Oct. 25, 2005. ( pdf 710kb )
Improving Protein Function Prediction using the Hierarchical Structure of the Gene Ontology by R. Eisner, B. Poulin, D. Szafron, P. Lu and R. Greiner, 2005 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, November 2005. ( pdf )
Predicting 400 GO Functions of Proteins by R. Eisner, A. Fyshe, R. Greiner, P. Lu, B. Pearcy, B. Poulin, D. Szafron and D. Wishart, Intelligent Systems for Molecular Biology Conference. June, 2005. ( pdf )
Custom Classifier Creation in Proteome Analyst by J.Anvik, R.Eisner, P.Lu, Z.Lu, C.MacDonell, B.Poulin, D.Szafron, and D.Wishart Canadian Proteomics Initiative Conference/Canadian Protein Engineering Network Annual General Meeting. May 2003. (Research Poster) ( pdf )
Using Proteome Analyst for Protein Sub-cellular Localization Prediction by Z.Lu, J.Anvik, R.Eisner, R.Greiner, P.Lu, C.MacDonnell, B.Poulin, D.Szafron, and D.Wishart Canadian Proteomics Initiative Conference/Canadian Protein Engineering Network Annual General Meeting. May 2003. (Research Poster) ( pdf 1.8mb )
Proteome Analyst . High-throughput Protein Function Prediction by Roman Eisner, Brett Poulin, Duane Szafron, Paul Lu, Russ Greiner, David Wishart and Bahram Habibi-Nazhad, Intelligent Systems for Molecular Biology Conference. August, 2002. ( pdf 246kb )
Proteome Analyst by Roman Eisner, Brett Poulin, Duane Szafron, Paul Lu, Russ Greiner, David Wishart and Bahram Habibi-Nazhad, Canadian Proteomics Initiative Conference/Canadian Protein Engineering Network Annual General Meeting. May 2002. ( pdf 371kb )
Using Motifs in Proteome Analyst by Brett Poulin, Roman Eisner, Duane Szafron and Paul Lu, Canadian Proteomics Initiative Conference/Canadian Protein Engineering Network Annual General Meeting. May 2002.
Technical Reports:
Szafron D, Greiner R, Lu P, Wishart D, MacDonell C, Anvik J, Poulin B, Lu Z and Eisner R (2003a) Explaining Naive Bayes classifications, TR03-09, Department of Computing Science, University of Alberta. ( pdf 1.9mb )