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Integrated Project - Genomes

Coordinators : Fabio Pardi and Gilles Didier

The Integrated Project (IP) Genomes (created in 2014) concerns the design of novel mathematical and biophysical models to understand genetic and epigenetic processes, and algorithms for the treatment and analysis of the huge amounts of DNA data available today in all life science domains. The areas where the “Genomes” community is particularly active are comparative and functional genomics, evolutionary biology, including population genetics, theoretical biological physics of DNA and chromosomes, and the analysis of Next Generation Sequencing data (NGS). An example of research project funded by NUMEV and led by Dr Olivier Gascuel (awarded in 2018 by the Grand Prize INRIA-Académie des Sciences), was about a research work on the bioinformatics of HIV, concerning the transmission of resistance mutations in the UK population[1],[2]. Another major result obtained, in a collaboration with the Banyuls oceanological observatory and the Joint Genome Institute in the USA, is about the genome of the smallest known alga, O. tauri[3] recently led to important discoveries on the biology of these pico-algae, showing their sexual reproduction and an intriguing link between genome structure and viral immunity[4]. Very recent results also reveal that a non-linear physics approach leads to a coherent description of the dynamics of DNA (partition complex) segregation and stable positioning before cell division in bacteria, a mechanism that has until now resisted full understanding[5].

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[1]F. Chevenet, M. Jung, M. Peeters, T. De Oliveira, O. Gascuel (2013) Searching for Virus Phylotypes. Bioinformatics, 29 (5), pp. 561-570

[2]R. Mourad, F. Chevennet, D. T. Dunn, E. Fearnhill, V. Delpech, D. Asboe, O. Gascuel, S. Hue. (2015) A phylotype-based analysis highlights the role of drug-naive HIV-positive individuals in the transmission of antiretroviral resistance in the UK. AIDS, vol. 29(15), pp.1917-25, doi: 10.1097/QAD.0000000000000768.

[3]R. Blanc-Mathieu, B. Verhelst, E. Derelle, S. Rombauts, F-Y. Bouget, I. Carré, A. Château, A. Eyre-Walker, N. Grimsley, H. Moreau, B. Piégu, É. Rivals, W. Schackwitz, Y. van de Peer, G. Piganeau (2014) An improved genome of the model marine alga Ostreococcus tauri unfolds by assessing Illumina de novo assemblies. BMC Genomics. Vol. 15 (1103), doi: 10.1186/1471-2164-15-1103 2014

[4]R. Blanc-Mathieu, M. Krasovec, M. Hebrard, S. Yau, E. Desgranges, J. Martin, W. Schackwitz, A. Kuo, G. Salin, C. Donnadieu, Y. Desdevises (2017). Population genomics of picophytoplankton unveils novel chromosome hypervariability. Science Advances 1;3(7):e1700239.

[5]J.C. Walter, J. Dorignac, V. Lorman, J. Rech, J.Y. Bouet, M. Nollmann, J. Palmeri, A. Parmeggiani, F. Geniet (2017). Surfing on protein waves: proteophoresis as a mechanism for bacterial genome partitioning.Physical Review Letters, 119(2), 028101