= EDUCATION = ||1998-2002||University of Toronto||Toronto, Ontario|| ||'''Ph.D. Biochemistry'''||Bioinformatics|| || || 1997-1998 University of Toronto Toronto, Ontario Non-degree student • Computer Science (3rd year) 1993 - 1997 McGill University Montreal, Quebec B.Sc. Biochemistry Distinction Achieved Languages: English (native), French Computer Languages: Java, C, Perl, wide-ranging technical computer expertise RESEARCH Apr 2006-present Assistant Professor, Banting and Best Department of Medical Research Terrence Donnelly Centre for Cellular and Biomolecular Research University of Toronto Associate Investigator position at the Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto Focus: Biological pathway and network analysis, protein interaction prediction, network evolution. Dec 2002-Mar 2006 Computational Biology Center, Memorial Sloan-Kettering Cancer Center Post-doctoral Research Supervisor: Dr. Chris Sander Topic: Biological pathway and network informatics, protein interaction prediction Sep 1998-Oct 2002 University of Toronto, The Samuel Lunenfeld Research Institute Ph.D. Program Supervisor: Dr. Christopher W.V. Hogue Topic: Development and use of the Biomolecular Interaction Network Database (BIND) TEACHING June, 2004 Lecturer for Graduate Course in “Bioinformatics and Computational Biomedicine” at Weill Medical College of Cornell University, New York (Lecture on pathways, protein interactions) August 2003 (repeated August 2004) Lecturer for Graduate Course in “Introduction to Computational Biomedicine” at Weill Medical College of Cornell University, New York (Lecture on pathways, protein interactions) Apr 29-May 4, 2002 Teaching Assistant/Lecturer for Canadian Bioinformatics Workshop Proteomics Course Windsor, Ontario, Canada Jun 11-16, 2001 Teaching Assistant for Canadian Bioinformatics Workshop Proteomics Course Edmonton, Alberta, Canada Jun 26 – July 1, 2000 Teaching Assistant for Canadian Bioinformatics Workshop Developing the Tools Course Montreal, Quebec, Canada [:Publications:JOURNAL PUBLICATIONS] THESIS Bader GD Design and use of the Biomolecular Interaction Network Database (BIND) for storing and analyzing protein-protein interaction data Dissertation 2003 University of Toronto TEXTBOOK CHAPTERS 2006 Gary D. Bader, Michael Cary, Chris Sander BioPAX - Biological Pathway Data Exchange Format Encyclopedia of Genomics, Proteomics and Bioinformatics (in press) Humana Press, New Jersey 2005 Rowan Christmas, Iliana Avila-Campillo, Hamid Bolouri, Benno Schwikowski, Mark Anderson, Ryan Kelley, Nerius Landys, Chris Workman, Trey Ideker, Ethan Cerami, Rob Sheridan, Gary D. Bader, and Chris Sander Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks Am Assoc Cancer Res Educ Book 2005: 12-16. Gary D. Bader, Amy Tong, Lan V. Zhang, Frederick P. Roth, Brenda Andrews and Charles Boone Exploiting Synthetic Genetic Interactions to Predict Pathways and Complexes Protein-Protein Interactions: A Molecular Cloning Manual, 2nd Edition. Ed. Erica Golemis Cold Spring Harbor Laboratory Press, New York 2004 Gary D. Bader, Christopher W.V. Hogue Protein Interaction Databases Handbook of Genome Research: Genomics, Proteomics, Metabolomics, Bioinformatics, Ethical and Legal Issues. Ed. Christoph W. Sensen Volume 5B of the Series: Biotechnology, 2nd Edition. Eds Rehm, H.-J., Reed, G., Pühler, A., Stadler, P. Wiley-VCH, Germany Gary D. Bader, Anton J. Enright Intermolecular Interactions and Biological Pathways Bioinformatics 3E, Eds. Andreas D. Baxevanis and B.F.Francis Ouellette. Wiley, New York Anton J. Enright, Lucy Skrabanek, Gary D. Bader Computational Prediction of Protein-Protein Interactions The Proteomics Protocols Handbook, Ed. John M. Walker Humana Press, New Jersey 2003 Gary D. Bader, Amy Hin Yan Tong, Gianni Cesareni, Christopher W.V. Hogue, Stanley Fields, Charles Boone Peptide Recognition Module Networks: Combining Phage Display with Two-hybrid Analysis to Define Protein-Protein Interactions Handbook of Cell Signaling, Eds. Ralph Bradshaw and Edward Dennis. Academic/Elsevier Press, San Diego 2002 Gary D. Bader, Christopher W.V. Hogue Interaction Databases, in Genomics and Bioinformatics Volume 5B of the Series: Biotechnology, 2nd Edition. Eds Rehm, H.-J., Reed, G., Pühler, A., Stadler, P. Wiley-VCH, Germany ABSTRACTS AND POSTER PRESENTATIONS 2005 (Poster) BioPAX Workgroup BioPAX – A Data Exchange Format for Biological Pathways ISMB 2005, Detroit, MI, USA (Poster) Bader, GD, Cerami, E, Sander C cPath Biological Pathway Research Support ISMB 2005, Detroit, MI, USA 2004 (Poster) BioPAX Workgroup BioPAX – A Data Exchange Format for Biological Pathways ISMB 2004, Glasgow, Scotland, UK (Poster) Bader, GD, Cerami, E, Sheridan, R, Sander C Biological Pathway Research Support: The cBio Pathway Information Resource (cPath) ISMB 2004, Glasgow, Scotland, UK 2003 (Poster) BioPAX Workgroup BioPAX – A Data Exchange Format for Biological Pathways ISMB 2003, Brisbane, Australia (Poster) BioPAX Workgroup BioPAX Data Exchange Ontology for Biological Pathway Databases ISMB 2003, Brisbane, Australia 2002 (Poster) Bader GD, Pawson T, and Hogue, CWV BIND – The Biomolecular Interaction Network Database as a Research Tool Canadian Proteomics Initiative Conference, Edmonton, Alberta 2001 (Poster) Wolting CD, Bader GD, Donaldson IM, Baskin B, Pawson T, Hogue CWV Mapping Biological Pathways Onto the BIND Data Structure Signaling in Normal and Cancer Cells, Banff, Alberta (Poster) Donaldson IM, de Bruijn B, Bader GD, Wolting C, Baskin B, Martin J, Pawson T, Hogue CWV PreBIND: Mining the Scientific Literature for Biomolecular Interaction Data Signaling in Normal and Cancer Cells, Banff, Alberta (Poster) Bader GD, Donaldson I, Wolting I, Ouellette BFF, Pawson T, and Hogue CWV BIND – The Biomolecular Interaction Network Database Canadian Society of Biochemistry, Molecular & Cellular Biology (CSBMCB) Summer Meeting – From the Genome to Structure and Function, Alliston, Ontario 2000 (Poster) Bader GD, Donaldson I, Baskin B, Pawson T, and Hogue CWV BIND – A Database For Storing Biomolecular Interactions, Biochemistry and Kinetics Biophysical Journal 78 1(2) 908-Pos (Poster) Bader GD, Donaldson I, Baskin B, Pawson T, and Hogue CWV BIND – A Database For Storing Biomolecular Interactions, Biochemistry and Kinetics Keystone Signal Transduction Meeting 1999 (Poster) Bader GD, Pawson T, and Hogue CWV A Biomolecular Interaction Network Database Biophysical Journal 76 2(2) M-Pos 270 (Poster) Bader GD, Pawson T, and Hogue CWV A Biomolecular Interaction Network Database 5th Annual Symposium “Pathways of Development and Disease” – Samuel Lunenfeld Research Institute (http://www.mshri.on.ca/develop/rossant/mshrisym/sympposters.html) (Abstract) Bader GD and Hogue CWV Extending the ASN.1 biological data model to manage biomolecular interactions IBM CASCON 1999 (Poster) Bader GD, Pawson T, and Hogue CWV The Biomolecular Interaction Network Database (BIND) as a Resource and a Research Tool 2nd Georgia Tech International Conference on Bioinformatics – In Silico Biology, Sequence & Structure & Function – Atlanta, GA (http://genemark.biology.gatech.edu/conference/poster_abstracts.html) INVITED LECTURES 2006 Bader GD Pathway Information for Systems Biology (Apr 3, 2006) SRI, Menlo Park, CA Bader GD Gene Ontology, Pathway, and Interaction Databases (Apr 2, 2006) FASEB Experimental Biology, San Francisco, CA Bader GD Gene Ontology, Pathway, and Interaction Databases (Apr 1, 2006) 97th American Association for Cancer Research Annual Meeting, Washington, DC 2005 Bader GD BioPAX – A Data Exchange Format for Biological Pathways (Nov 18, 2005) Biological Pathways: communication and analysis, Tokyo, Japan Bader GD Predicting Links in Biological Systems (Aug 11, 2005) MODULAR PROTEIN DOMAINS from Functional Plasticity to Protein Linguistics, Seefeld, Austria Bader GD BioPAX – A Data Exchange Format for Biological Pathways (June 28, 2005) Intelligent Systems for Molecular Biology (ISMB), Detroit, MI, USA Bader GD BioPAX – A Data Exchange Format for Biological Pathways (June 24, 2005) Intelligent Systems for Molecular Biology (ISMB) - 7th BioPathways Satellite meeting, Detroit, MI, USA 2004 Bader GD BioPAX – A Data Exchange Format for Biological Pathways (July 30, 2004) Intelligent Systems for Molecular Biology (ISMB) - 6th BioPathways Satellite meeting, Glasgow, Scotland, UK Bader GD Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks (July 29, 2004) Intelligent Systems for Molecular Biology (ISMB) - 6th BioPathways Satellite meeting, Glasgow, Scotland, UK 2003 Bader GD BioPAX – A Data Exchange Format for Biological Pathways (Nov 4, 2003) NIST Information Science Standards to Enable Biomedical Research - NIH, Bethesda, MD Bader GD Protein Complex Detection in Large Protein Interaction Networks (May 21, 2003) New York Computational Biology Society, NYAS – New York, NY Bader GD BioPAX – Data Exchange Format for Pathway Databases (Jan 22, 2003) Proteomics Standards Initiative meeting – Hinxton, UK Bader GD Computational Methods for Generating Protein Interaction Networks (Jan 20, 2003) Understanding Phage Display 2003 - Vancouver, BC 2001 Bader GD Data Mining the Biomolecular Interaction Network Database (Oct 18, 2001) Functional Genomics - Satellite meeting of the 8th International Conference on Environmental Mutagens - Seattle, WA Bader GD The Biomolecular Interaction Network Database (Aug 14, 2001) The 2001 FASEB Summer Conference on Protein Kinases and Phosphorylation - Snowmass, CO 1999 Bader GD, Pawson T and Hogue CWV BIND, A Database System For Storing Biomolecular Interactions (Nov 18, 1999) 3rd Annual Conference on Computational Genomics – Baltimore, MD (http://www.hbcg.utmb.edu/genomics/3rdanngenconf.html) Bader GD and Hogue CWV BIND Database Specification for Storing Biomolecular Interactions, Molecular Complexes and Pathways (Nov 15, 1999) National Center for Biotechnology Information (NCBI), National Institutes of Health, Bethesda, MD (http://www.ncbi.nlm.nih.gov/CBBresearch/Seminar/1999Autumn/11151100) ORGANIZATION OF CONFERENCES 2004 September 8-9, 2004 The 2nd Annual Cytoscape Conference (~40 participants) MSKCC, New York, NY 2003-present 13 BioPAX workshops (co-organized with Michael Cary, ~15-30 participants) New York, Chicago, San Francisco, Denver, Detroit, Tokyo AD-HOC REVIEWER FOR Applied Bioinformatics, Bioessays, Biosilico, Bioinformatics, BMC Bioinformatics, Briefings in Bioinformatics, Expert Opinion on Therapeutic Targets, FEBS Letters, Genome Biology, Molecular and Cellular Proteomics, Nucleic Acids Research, Nature, Nature Biotechnology, Nature Molecular Systems Biology, Pacific Symposium on Biocomputing, PLoS Biology, PNAS, Science ORGANIZATIONS Biological Pathway Exchange Standards Initiative (BioPAX) http://www.biopax.org/ Proteomics Standards Initiative Molecular Interactions (PSI-MI) http://psidev.sourceforge.net/ Board Member, Protein Modules Consortium http://www.proteinmodules.org/