Olivier Gascuel : Inria – French Académie des sciences Grand Prize

Publish on 29/01/2020

Thirty years ago, biology was basically test tubes, microscopes and Petri dishes. Today scientists are just as likely to be sitting at a computer, thanks in part to Olivier Gascuel, a pioneer in bioinformatics, who is now Director of the Institut Pasteur Center of Bioinformatics, Biostatistics and Integrative Biology (C3BI).

Olivier Gascuel does not only have fond memories of his years as a mathematics student at ENS Cachan. “I wasn’t a very good student.I found the discipline too abstract. I wanted to do things that were 'useful'!" After completing his Master’s he hesitated between ecology and architecture. In the end he went with architecture, but at the same time took a course in computer science, which led to a dissertation on artificial intelligence applied to medicine, which he defended in 1981. However, the following year, Olivier Gascuel moved to Africa as an architect. “When I came back to France in 1983 I was a little lost. Since my PhD had been well-received, I decided to pursue research. I applied to the CNRS and was accepted. Two years later, I joined a medical computer science unit at the French National Institute of Health and Medical Research (Inserm).There, while working with researchers from the Institut Pasteur including Antoine Danchin, I discovered molecular biology, which was a fast-growing field. That’s how I caught the bioinformatics bug! ”

Did you say bioinformatics?

In the mid-1980s, the subject didn’t generate any excitement. The term probably didn’t even exist yet. “We had no support and the academic community was somewhat wary of us.When I wanted to obtain my Research Director accreditation (HdR) in informatics, I was advised to keep my work in biology quiet!As for Des Higgins, who I met around the same time, he saw his research on sequence alignment as a hobby. We were a long way from thinking that his program, Clustal, would become a “classic” in bioinformatics and that one of his articles on the subject would one day become one of the Top 10 of the most cited papers of all time! ”

On course for molecular phylogenetics

Everything changed in 1990 with the launch of the Human Genome project. “France worked actively on the subject and I would like to underline that Inria was on the forefront, thanks to François Rechenmann. ” For Olivier Gascuel, things began to take shape. In 1987, he began working at the Montpellier Laboratory of Informatics, Robotics and Microelectronics (LIRMM) and made a decisive shift towards molecular phylogenetics, a discipline focused on reconstructing the evolutionary history of species by comparing DNA sequences or proteins. “This field combines theoretical and applied aspects and has allowed me to explore many subjects, such as the future of biodiversity or the development of viral epidemics, significant challenges affecting both science and society, which makes our research even more exciting. On the mathematics and informatics side, phylogenetic trees were new objects and the inference of trees from data raised numerous algorithmic and statistical problems, the basis of which we explored. These solid bases are what made the success of our future programs and software."

Research, publish, supervise...

The range of Olivier Gascuel’s work is marked by a number of high points, including being awarded a silver medal from the French National Center for Scientific Research (CNRS) in 2009. What is he most proud of? “In no particular order I would say my collaboration with Stéphane Guindon (CNRS-LIRMM) on the PhyMLprogram, a phylogenetic tree building software program now used in a range of fields, from genomics to ecology and medicine, with a high number of citations (over 20,000); the contribution to deciphering one of the main vectors of malaria, or the role I played in discovering the 10^th gene of HIV, which opened the door to new treatments. ” He also says that he was very happy to have actively participated in the development, structuring and recognition of bioinformatics, whether through his research papers, software programs or by launching a number of conferences that have become pillars in the field of bioinformatics (JOBIM, WABI, Mathematical and Computational Evolutionary Biology, etc.).

In March 2015, Olivier Gascuel became Director of the Institut Pasteur’s Center of Bioinformatics, Biostatistics and Integrative Biology (C3BI), which makes a significant contribution to the field, by recruiting research units and numerous bioinformaticians. “I oversee a unit dedicated to evolutionary bioinformatics. Our activities are centred on theoretical research, including statistics tests and selecting phylogenetic models, and developing molecular epidemiology methods, particularly within the framework of the H2020 Virogenesis programme. My overall goal is to continue pursuing transversal research combining biology, mathematics and computer science. The Investissement d’Avenir Convergences project, INCEPTION, which I oversee, will offer the perfect platform for this. ”

Testimonies

Alain Denise, professor at Université Paris-Sud, former member of Inria's AMIB team

"I got to know Olivier Gascuel over 15 years ago during a workshop. At the time, I was still a 'die-hard' computer scientist and Olivier Gascuel - who was already one of the major 'facilitators' of the bioinformatics community - was one of the people who helped me to get a foot on the ladder when I decided to turn my attention to this field. Even though we have never worked together - as the problems we deal with are quite different - we have regularly rubbed shoulders, particularly within the French National Committee for Scientific Research, where he presided over an interdisciplinary commission focusing on themes relating to biology. Over the course of our meetings, I have on numerous occasions had the opportunity to see just how Olivier Gascuel is a researcher of great scientific precision, combined with undeniable human qualities. This Inria Grand Prize is certainly well-deserved! "

Antoine Danchin, honorary professor at the School of Biomedical Sciences at the Li Ka Shing Faculty of Medicine (University of Hong Kong), honorary professor at the Beijing Genome Institute, scientific director of AMABiotics

“Thirty years ago, nobody thought that we would be able to decipher any genomes. I had conceived reversing the order of living cell exploration by starting from genes as a group and not one-by-one. In order to do this computer exploration -in silico- was essential. Artificial intelligence was - already - in fashion. That is how I met Olivier Gascuel, who was a specialist in expert systems at the time. In order to understand the text of the proteins coded by the genomes, he designed a grammatical approach to decipher their addressing code to the nanomachine that exports them outside the cell. This work, used by industry, has enabled the effective synthesis of human proteins by Escherichia coli. Whilst it convinced me that genome exploration was becoming a possibility, it led Olivier Gascuel to discover a major interest in their evolution, a theme that today has won him worldwide recognition.”

Bio express

1981 : Olivier Gascuel defends his PhD on informatics
1983 : Joins the CNRS.
1987 : Joins the LIRMM;
1990 : Obtains Research Director accreditation (HdR)
2000 : Becomes a Research Director
2009 : Receives the CNRS Silver Medal
2015 : Becomes Director of the Institut Pasteur’s Center of Bioinformatics, Biostatistics and Integrative Biology