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Michel Dumontier, Ph.D.
Associate Professor (tenured)
Department of Biology
School of Computer Science
Institute of Biochemistry
Affiliations:
Ottawa Institute of Systems Biology
Ottawa-Carleton Institute for Biomedical Engineering
Département d’informatique et de génie logiciel, Université Laval
Dr. Michel Dumontier is an Associate Professor of Bioinformatics at Carleton University in the Department of Biology, the Institute of Biochemistry and School of Computer Science. His research aims to improve our ability to represent and reason about biomedical knowledge, from experimental data to general textbook knowledge, towards building predictive systems for personalized medicine. Dr. Dumontier is an expert in developing and applying Semantic Web technologies in the biomedical and life sciences and currently serves as a co-chair for the World Wide Web Consortium Semantic Web in Health Care and Life Sciences Interest Group (W3C HCLSIG). With over 50 research publications in workshops, conferences, and journals, his innovative research is developing exciting opportunities towards pharmacogenomic based knowledge discovery.
Background 
Dr. Michel Dumontier's career in research began in the summer following his second year of undergraduate study at the University of Manitoba. Working for Dr. Jim Jamieson and Dr. Gro Thorne-Tjomsland, he investigated the transport of cargo in the Golgi Apparatus by building 3D models of the Golgi from serial section electron micrographs. After graduating in 1998 with a Bachelor of Science in Biochemistry, he worked as a research associate at Munich's Max Planck Institute for Biochemistry where he studied Rac1A actin-cytoskeleton reorganization and signalling in the slime mold Dictyostelium discoideum. Following this work, Dumontier earned his PhD in 2004 from the University of Toronto with advisor Christopher Hogue. His thesis uncovered species-specific optimizations in proteins of 150 completely sequenced organisms and has implications for taxonomic identification, sequence alignment, secondary structure and protein structure prediction. During his 9 month tenure as a Post-Doctoral fellow with the Genome Canada funded Blueprint Initiative (2004-2005), he worked on SMID and SMID-Genomes, tools to predict small molecule binding across genomes. Hired in July 2005, Dr. Dumontier leads his research group in semantic systems biology at Carleton University and offers courses in Biochemistry, Bioinformatics and Computational Systems Biology.
Graduate Students
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| Alison Callahan |
PhD |
Biology |
Knowledge Discovery from Natural Language |
| Jose Miguel Cruz-Toledo |
PhD |
Biology |
Aptamer Prediction |
| Tanya Hiebert |
MSc |
Biology |
Drug repositioning |
Gordana Lenert
part-time |
MSc |
Biology |
Pharmacogenomics |
Glen Newton
part-time |
MSc |
Biology |
Large Scale Text Search and Visualization |
Marc-Alexandre Nolin
part-time |
PhD |
CS |
Biological Knowledge Discovery |
Alumni Graduate Students
- Dana Klassen. MSc (Biology). 2012. Formal Representation of Toxicology Knowledge Towards Toxicity Prediction and Data Mining
- Mykola Konyk. Masters in Computer Science. 2011. Framework for cell simulation and particle simulation plug-in.
- Natalia Villanueva-Rosales. PhD (Computer Science). 2011. Formalizing Relational Databases as OWL Ontologies
- Leonid Chepelev. PhD (Biology). 2011. A Semantically Enabled Framework for Small Molecule Metabolic Fate Prediction: the Web as a Biochemical Reactor.
- Xueying Chen. PhD (Computer Science). 2011. Distributed Ontology Systems for OWL Ontologies with Large Number of Instances.
Undergraduate Students
2012-2013
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| Hala Al-Hafez | Aptamer Biotechnology | BIOL4908 |
| Holly Surins | Drug-Drug Interactions | BIOL4908 |
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2011-2012
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| Jessie Thuswaldner | Pathway Data Mining | summer student |
| Hala Al-Hafez | Aptamer Biotechnology | BIOL4901 |
| Sara Temkit | Drug Profiling | summer student |
| Holly Surins | Drug Profiling | BIOL4901 |
| Rhian Baldwin | Pharmacogenomics of Parkinson's disease | BIOC4908 |
| Phuong Ho | Aptamer Binding | BIOL4908 |
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2010-2011
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| Nichealla Keath | Comparative Genomics | COMP4901, COMP4905 |
| William Greenwood | Nucleic Acid motifs | COMP4901 |
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2009-2010
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| Muhammed Faizan | Molecular Electrostatics | COMP4901, COMP4905 |
| Alexander Gawronski | Chemical Semantic Web Service | COMP4901 |
| Matthew Chan | Aptamer Database | NSERC USRA |
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2008-2009
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| Hoang Tran | SPARQL Navigator | COMP4905 |
| Christina Dumitrescu | Legacy Data Mapping | COMP4905 |
| Alexander Gawronski | Protein Surfaces | COMP4905 |
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2007-2008
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| Mykola Konyk | SPARQL-DL Reasoning | COMP4905 |
| Andrej Vasilj | SNP Function Prediction | BIOL4908 |
| Alex De Leon | Biochemical Mashup | BIOL4901 |
| Jingjing Wang | User Interfaces | COMP4901, COMP4905 |
| Jordan Pleet | Experiment Capture | USRA1 |
| William Greenwood | Aptamer Design | SURI2 |
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2006-2007
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| Mykola Konyk | Chemical Knowledge Representation | COMP4901 |
| Muhammed Faizan | Disease Pathways | CWP CO-OP |
| Joseph Obeng | Pharmacogenomics of Obesity | CWP CO-OP |
| Alison Callahan | NLP Driven Ontology Design | NSERC-USRA |
| Jennifer Crutchley | Mutation Analysis | BIOL 4908 |
| Alex De Leon | Infrastructure for the Semantic Web | COMP4905 |
| Faris Matani | State of the Art in Ontology Management Tools | COMP4905 |
| Design Patterns for Temporal Reasoning in OWL | COMP4901 |
| Anne Taylor | Methods in Semantic Data Integration | COMP4905 |
| Biological Semantic Web | COMP4901 |
| Myroslav Palenychka | Persistent RDF Storage | COMP4905 |
| Evaluation of SPARQL Capable Triple Stores | COMP4901 |
| Gokulan Murukiah | Pattern Matching with the Cell BE Processor | COMP4905 |
| Hardware Accelerated Architectures | COMP4901 |
| Kirill Levitski | Ontology-Guided Queries | COMP4905 |
| Colin Bellinger | OWL/Jess Inference Query Plugin for Protege 3.2  | COMP4905 |
| Roberta Annan | Pharmacogenomics Data Mining | BIOL4908 |
| Yisu Li | Biochemical Ontologies | BIOL4901 |
| Fernando Villalobos | Biochemical Ontologies | CHEM4908 |
| Gavin Hamilton | Biochemical Ontologies | BIOL4908 |
| Janet Aika Matemu | Application of the Semantic Web to the Life Sciences | BIOL4901 |
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2005-2006
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| Jose Miguel Cruz Toledo | Ortholog Interactions | BIOL4908, Summer |
| Daniel Oropeza | Effect of Genetic Variation on Ligand Binding | BIOL4908, BIOL4901, Summer |
| Zhen Liu | Pathway Comparison Algorithms | CWP CO-OP |
| Salim Qadri | Genome Synteny | BIOL4901 |
| Roberta Annan | Pharmacogenomics and Pharmacodynamics | BIOL4901 |
| Latifa Haider | Disease Interaction Networks | BIOL4901 |
| Christian Leger | OWL Biological Ontologies | COMP5108 |
| Kevin Osbahr | Yeast Knowledge Base | INSC4908 |
| Maria Villota | Murine Blood Biomarkers | CWP CO-OP |
| Nuha Jabakhanji | Ontology Survey | BIOL4901 |
1 NSERC Undergraduate Student Research Award
2 Carleton University Summer Undergraduate Research Internship
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Collaborators
James Cheetham (Synaptic Signalling),
Frank Dehne (HPC),
Leo Ferres (Statistical Graphs),
Daniel Figeys (PTM prediction),
Ashkan Golshani (Yeast Bioinformatics),
Jim Green (Hardware Acceleration),
Warren Gross (Cell Simulation),
Christopher Hogue (Small Molecule Biochemistry),
Iain Lambert (Toxicogenomics),
Paul White (Toxicogenomics),
Carole Yauk (Toxicogenomics),
Myron Smith (Yeast Bioinformatics),
Gabriel Wainer (Cellular process simulation),
Bill Willmore (Hypoxia pathways)
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