From the origins to 2001…
The founder of bioinformatics research at the UdeM was the late Robert J. Cedergren, who was a professor in the biochemistry department from 1966-1999. He attracted informaticians, mathematicians, physicists and chemists to join him in exploring RNA structure and evolution, which resulted in the seminal 1976 Nature publication on the evolutionary origin of 5.8S ribosomal RNA, which was co-authored by David Sankoff (UdeM, Centre de Recherches Mathématiques). Dr. Cedergren’s pioneering work led to a steady expansion of interdisciplinary research, much of this in collaboration with Sankoff and Guy Lapalme (UdeM, DIRO). In the past 25 years, Sankoff has become one of the best-known computational biologists, who has supervised together with Cedergren and Lapalme, numerous students in – what was in the beginning – the exotic field of bioinformatics. Amongst the students, who are today carrying on research in this area are Serguei Chteinberg (UdeM, biochemistry), F. Major, N. El-Mabrouk (both UdeM, DIRO), D. Bryant, M. Hallet (McGill), and many more.
Various research units contribute to bioinformatics research at the UdeM. More information of the particular contribution is available:
- Biochemistry Department
- Computer science Department
- Biology Department
- Pediatrics Department
- Department of Environmental and Occupational Health
- Mathematics Department
The contribution of the Biochemistry Department
The department of biochemistry has continuously expanded research in the areas of comparative, structural and functional genomics, and simultaneously consolidated bioinformatics research applied to these fields. In 1986, B. Franz Lang joined the biochemistry department, enhancing the focus on phylogenetic and genomics research issues, and in 1989, Gertraud Burger.
The creation of an interdisciplinary collaboration in organelle genomics (OGMP) between Cedergren, Lang, Burger (biochemistry department UdeM), Sankoff, Golding (McMaster University, Hamilton), Gray (Dalhousie University, Halifax), Lemieux and Turmel (Université Laval, Quebec City), which was centred in the biochemistry department of the UdeM, has further enhanced UdeM’s stake in bioinformatics.
These researchers are all affiliated with the Canadian Institute for Advanced Research Program in Evolutionary Biology (CIAR-evolBiol), is a group engaged in the most fundamental of questions, the origins of the living cell and how life evolved into the forms in that it exists today. Serguei Chteinberg was initially a post-doc student and then a collaborator of R. Cedergren for many years. Since 1998, he has been a faculty member of the biochemistry department. His research is focused on the modeling of RNA secondary structures and molecular interactions of RNA, including experimental testing of structural predictions. Stephen Michnick came to the UdeM in 1995. His research bridges the gap between genome and function. His group is developing experimental and informatics tools to define the functions of genes and how they are organized to perform the many structural and biochemical processes of the cell. To further expand bioinformatics research at the UdeM, the biochemistry department reaches out world-wide for young scientists in this field. Hervé Philippe from Paris, France, has received a prestigious Canada Research Chair (Evolutionary Bioinformatics and Genomics) to join the biochemistry department in September 2002.
The contribution of the Computer Science Department
The informatics department at the UdeM (DIRO) has steadily enhanced its activities in computational biology, by hiring François Major (1994) who works on the modelling of the 3-dimensional structure of small RNA molecules.
In 1998, Nadia El-Mabrouk took on her current position in the DIRO. She is interested in developing parsimony methods for gene order comparison and phylogenetic reconstruction based on genomic rearrangements, but she also designs algorithms to identify structured motifs of RNAs. Recently, Miklos Csürös (2001) joined the DIRO. He has a strong interest in evolutionary tree reconstruction, algorithmic problems associated with the use of clone arrays and the application of machine learning algorithms to gene expression and genotyping data.
The contribution of the Biology Department
The UdeM biology department is also active in the field of bioinformatics. François-Joseph Lapointe is developing and comparing statistical methods for validating and combining phylogenetic trees. Recently, his research has focussed on phylogenetic methods that allow for lateral gene transfer and other reticulation events.
Pierre Legendre (UdeM, biology) is widely known for his research in numerical ecology, for which he has received several Canadian and international prizes. He is the author of the founding textbook of this new field, and of ~150 scientific papers on quantitative ecology and phylogenetics. His lab develops statistical methods for the analysis of ecological and phylogenetic data and distributes the corresponding computer programs.
Anne Bruneau joined the biology department in 1995 as a researcher at the Institut de recherche en Biologie Végétale. She is interested in systematics and evolutionary mechanisms in plants, primarily through the study of molecular phylogenies, as well as in the theory of cladistics and in methods allowing for the combination of molecular and morphological data.
The contribution of the Pediatrics department
Damian Labuda and Daniel Sinnett, both from the Department of Pediatrics, UdeM, have been collaborating since 1995. They have developed a strong interest in genetic epidemiology and population genetics studies, particularly gene-gene and gene-environment interaction in the etiology of complex diseases. D. Labuda conducts haplotype studies in humans to trace back the origin and early migration of man kind. In addition, his group develops bioinformatic tools for formal genetic analysis and database management. D. Sinnett has recently received a Canada Research Chair to study the etiology of cancer and to develop the required bioinformatics instrumentarium.
The contribution of the department of Environmental and Occupational Health and the Mathematics department
Gaétan Carrier (Department of Environmental and Occupational Health, UdeM) and Robert Brunet (Department of Mathematics, UdeM) are collaborating since 1993. By combining expertise in medicine, toxicology, engineering and mathematics, these two researchers are developping new approaches to toxico-kinetic modeling.