What is bioinformatics?

Bioinformatics is a field of science at the interface of numerical discipline (informatics, mathematics) and the life sciences (biochemistry, biology, microbiology, ecology, epidemiology). Since life scientists produce growing numbers of data on genomes, biomolecules, organisms, their interactions and evolution, there is a growing demand for informatics approaches for storage, visualization and analysis of these often very complex datasets.

In addition, bioinformatics plays an important role in biomedical research. Research work in the area of genetic diseases and medical genomics is rapidly increasing and the future of personalized medicine depends on bioinformatics approaches. As a consequence, the job market for bioinformaticians is excellent.

What is it?

In short, bioinformatics is an interdisciplinary skill-set that combines computer science and mathematics with the various flavors of biological sciences, ranging from genetics, microbiology and ecology, to epidemiology and pharmacology.

Young field in turmoil, innovative, hybrid and dynamic!!

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:

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.

A window to the future

We have entered an era of unprecedented progress in the biological and biomedical sciences. The recent reports on the human genome sequence have received most public interest and have brought into focus the vast opportunities now open to identify and characterize genes. But the human genome is by no means the only genome that has been determined. The genomes of fruit fly, flatworm, thale cress, baker’s yeast and other single-celled eukaryotes, numerous bacteria and archaebacteria, as well as of mitochondria and chloroplasts that are comprised in the eukaryotic cell have also been sequenced entirely.

Because many of the genes that participate in the processes of human cells are also found in organisms that are easier to study, much can be learned about how our cells work by comparison to these simpler systems. In addition to sequence data, genome-wide gene function data are becoming available for a number of organisms. These include data on gene expression, protein-protein interactions and gene ablation (or knock-out).

* How can we analyze the data from large-scale, genome-wide experiments and interpret them in terms of biological function?

* What do we need to know in order to design such experiments in the most rational way?

What does it deal with ?

First, there are the obvious questions that bear on the extraction of meaningful information from huge data sets. For example, specialized bioinformatics tools allow us to reconstruct the evolutionary history and trends that have shaped today’s genomes on the basis of a broad sampling of genome sequence data. Likewise, the two-dimensional structure of RNA molecules can be predicted and complex epidemiological data can, when organized and categorized in an structured way, make possible systematic analyses of cause and effect.

Questions in biology can be addressed by studying how things work today, as well as asking how they evolved. Comparisons of networks of interacting genes, how they function and how they have evolved different functions during evolution, provide the broad understanding needed to describe how organisms work today.

But bioinformatics can also address questions at a much more general level. For example, are there defined and efficient principles or are living cells like “Rube Goldberg” devices, that is, the most complicated machineries possible to perform simple tasks? What we know today would suggest the later over the former. Biochemical networks (e.g. chemotactic signaling pathways) seem to have developed once and then diversified to take on new functions. These networks are robust on small time scales, but variable on evolutionary time scales. Further, progressive evolutionary selection of increasingly favorable outcomes seems to occur by repeated cycles of selection. Examples of such behavior include protein folding, assembly of the chromosome segregation machinery, chemotaxis, nervous systems, and evolution of organisms.

Research activities

The Université de Montréal (UdeM) houses long-standing and internationally recognized computational biology research activities in comparative genome analysis for more than two decades and provides a unique environment for bioinformatics research and training.

In order to underline the importance of the bioinformatic research, the Université de Montréal officially inaugurated in January 2004 the Robert Cedergren Centre.

Ongoing research

Ongoing bioinformatics activities at the UdeM bear on:

  • Bioinformatics: Use of software for acquiring, organizing, processing and analysis of biological data
  • Medical Bioinformatics: Genetics and Medical Genomics, disease diagnosis, personalized medicine
  • Engineering bioinformatics: software development based on established algorithms
  • Theoretical Bioinformatics: Development of algorithms and processes that describe the logical framework for solutions to specific biological problems