Department of Computational Biology

We live at a time when biology is producing vast reams of data, which can only be deciphered using mathematical modeling, statistics and computing, providing answers to a wide variety of biological and medical questions. The Department of Computational Biology was set up to analyze and model these data, and develop new analytical methods tailored to new data acquisition technologies (sequencing, bioimaging, etc.) and massive increases in available data volumes.

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Nowadays, biology is a computational science with multiple applications, notably in healthcare. The Department of Computational Biology processes Institut Pasteur campus data on a large scale, while also providing its expertise to the international scientific community. This research department stems from a joint unit with the CNRS (USR 3756) formerly known as the Center for Bioinformatics, Biostatistics and Integrative Biology (C3BI), which was set up in 2015 and became one of the largest bioinformatics centers in France.

The Department of Computational Biology is located in the Omics buildings inaugurated in September 2018 – so named because mainly “omics” data are analyzed here (genomics, transcriptomics, proteomics, etc.). The department is inherently multidisciplinary and cross-cutting. It facilitates cooperation and dialog on bioinformatics issues at the Institut Pasteur. It develops methodological research in computer science, statistics and modeling, offers support to experimental research units, and works in conjunction with the Institut Pasteur International Network. The department maintains partnerships with major digital operators in France and other countries.

Interdisciplinary research teams

The Department of Computational Biology brings together teams of scientists from various fields (computer science, statistics, mathematics, physics, biology, medicine), who work closely with other Institut Pasteur departments involved in a wide variety of research areas:

  • algorithms for biological sequences, statistical genetics, systems biology, human evolutionary genetics, microbial evolutionary genomics, spatial regulation of genomes (Department of Genomes and Genetics);
  • structural bioinformatics and dynamics (Department of Structural Biology & Chemistry);
  • human genetics and cognitive functions, neuronal imaging and dynamics, neural circuits, decision and Bayesian computation (Department of Neuroscience);
  • evolutionary bioinformatics, mathematical epidemiology (Department of Global Health);
  • bioimaging: analysis and modeling (Department of Cell Biology & Infection).

The teams apply new methods and models to help scientists understand and make use of the profusion of data generated by experimental biology, public health, and clinical research. As such, the Department of Computational Biology has been given responsibility for a very ambitious research project entitled INCEPTION (INstitut Convergence: Emergence of Pathology Through Individuals and Populations), selected by the French National Research Agency (ANR) in 2016 for the Investing in the Future program. INCEPTION is aimed at understanding and monitoring the emergence of diseases in populations (epidemic control, etc.) and individuals (precision medicine, etc.) through multidisciplinary approaches including data science and social sciences.

A bioinformatics platform

"I need you to analyze the data that we've collected." The Department of Computational Biology handles such requests issued by Institut Pasteur teams and the international network. It performs these analyses through the “Bioinformatics and Biostatistics Hub”, which responds to any questions related to this field. With around fifty research engineers, large-scale data analyses are performed routinely. The Hub and the department in general form a flagship bioinformatics platform, which is a member of the ELIXIR European network and the French Institute of Bioinformatics.

Training opportunities

The Department of Computational Biology offers a wide variety of training opportunities for biologists, mathematicians, computer scientists, statisticians and other professionals, either as part of PhD training programs or continuing training for working scientists. For example, training courses on high-throughput sequencing data analysis have been held at institutes in the Institut Pasteur International Network (in Montevideo, Dakar, São Paulo, Hong Kong, etc.) and on the Paris campus.

 

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Olivier Gascuel - Institut Pasteur
 

Olivier Gascuel, Director of the Department of Computational Biology

Until the late 1990s, biology was a discipline that was carried out using test tubes and Petri dishes. Nowadays, biologists are just as likely to be sat at a computer as they are working in a lab, and that applies to all areas of biology." The Institut Pasteur has approached this new field with a great deal of energy and commitment in recent years. We are now reaping the benefits of this work with numerous partnerships and publications in a wide variety of fields."

 

 

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