Eric Bonnet
Welcome to my home page. I'm a computational biologist working at the CEA and more precisely at the Centre National de Recherche en Génomique Humaine (CNRGH, National Center for Human Genomic Research), located in Evry (France). The CNRGH is one of the largest sequencing centres in Europe. It is dedicated to genomic research on human health and diseases.
I am leading the computational genomics laboratory. We focus on the computational analysis of high-throughput genomic data related to human health and disease.
ORCID | Google Scholar | LinkedIn | GitHub
Professional experience
2016 - now CEA Research Director at the Centre National de Recherche en Génomique Humaine (CNRGH, National Center for Human Genomic Research) in Evry (France). .
2010 - 2015 Research Engineer at the Institut Curie (Paris), in the Team Computational Systems Biology of Cancer.
2001 - 2010 Research Engineer at the VIB Department of Plant Systems Biology, Gent University (Belgium), in the Team Bioinformatics and Evolutionary Genomics.
1997 - 2001 Junior consultant and developer for computer science companies in Paris, France.
Education
2021 HDR (Habilitation à Diriger les Recherches). University of Evry Val d'Essone (UEVE, Paris-Saclay).
1994 - 1996 PhD in computational ecology "Phylogeny and resource sharing in Orthoptera Acrididae". University of Limoges (France), supervisor prof. Daniel Petit (summa cum laude).
1989 - 1994 Master's degree in Biology & Neurosciences, University of Poitiers & Toulouse (France).
1987 - 1989 Undergraduate studies in Biology, University of Limoges (France).
Selected Publications
50+ articles in peer-reviewed journals and book chapters.
Poulot-Becq-Giraudon, Y., Guillemaud, O., Degl’Innocenti, E., Letenneur, V., Bascarane, K., Barbay, T., Møller Clausen, M., Derbois, C., Guillermier, M., Juricek, L., Riquelme-Perez, M., Lakomy, T., Benhaim, L., Dufour, N., Gipchtein, P., Petit, F., Siron, L., Aurégan, G., Dechamps, N., Gaillard, M.C., Bemelmans, A.P., Bos, R., Carrillo-de Sauvage, M.A., Milior, G., Rouach, N., Brohard, S., Muret, K., Bonnet, E. & C Escartin, C. (2026) Signaling cascades shape functional subpopulations of cortical astrocytes in male wild-type mice and APP/PS1dE9 Alzheimer’s disease model. (2026) Nature Communications. DOI.
Derbois, C., Palomares, M.A., Deleuze, J.F., Cabannes, E., Bonnet E. (2023) Single cell transcriptome sequencing of stimulated and frozen human peripheral blood mononuclear cells. Sci Data, 6, 10(1):433. DOI.
Abjean, L., Ben Haim, L., Riquelme-Perez, M., Gipchtein, P., Derbois, C., Palomares, F., Petit, Hérard, A.S., Gaillard, MC., Guillermier, M., Gaudin-Guérif, M., Sagar, N., Dufour, N., Robil, N., Kabani, M., Melki, R., De la Grange, P., Bemelmans, A.P., Bonvento, G., Deleuze, J.F., Hantraye, P., Bonnet, E., Brohard, S., Olaso, R., Brouillet, E., Carrillo-de Sauvage, M.A., Escartin, C. (2022) The JAK2-STAT3 pathway controls a beneficial proteostasis response of reactive astrocytes in Huntington's disease. Brain. DOI.
Bonnet, E.*, Moutet, M.L.*, Baulard, C.*, Bacq-Daian, D., Sandron, F., Mesrob, L., Fin, B., Delépine, M., Palomares, M.A., Jubin, C., Blanché, H., Meyer, V., Boland, A., Olaso, R., Deleuze, J.F. (2018) Performance comparison of three DNA extraction kits on human whole-exome data from formalin-fixed paraffin-embedded normal and tumor samples. PLOS One. DOI.
Palomares, M.A.*, Dalmasso, C.*, Bonnet, E.*, Derbois, C., Brohard-Julien, S., Ambroise, C., Battail, C., Deleuze, JF., Olaso, R. (2019) Systematic analysis of TruSeq, SMARTer and SMARTer Ultra-Low RNA-seq kits for standard, low and ultra-low quantity samples. Scientific Reports. DOI.
Cock, M., et al. The Ectocarpus genome and the independent evolution of multicellularity in the brown algae. (2010) Nature. DOI.Bonnet, E., Wuyts, J., Rouzé, P., Van de Peer, Y. Evidence that microRNA precursors, unlike other non-coding RNAs, have lower folding free energies than random sequences. (2004) Bioinformatics. DOI.
Bonnet, E.*, Wuyts, J.*, Rouzé, P., Van de Peer, Y. Detection of 91 potential conserved plant microRNAs in Arabidopsis thaliana and Oryza sativa identifies important new target genes. (2004) Proc. Natl. Acad. Sci. DOI.
Recent Grants & Projects
2023 Association France Alzheimer & maladies apparentées. Project PrimAstro, "Uncovering the role of astrocytes in Alzheimer pathology in a non-human primate". Project PI, collaboration with Dr Marc Dhenain (CEA MIRCen), Dr Carole Escartin (CEA MIRCen) and Dr H. Hirbec (IGF Montpellier).
2023 University Paris-Saclay Life Sciences and Health. Funding for the project "Age and Alzheimer's disease-related transcriptomic changes in astrocytes". Project PI, collaboration with with Dr Marc Dhenain (CEA MIRCen).
2019 CEA grant for PhD project "Glial cells and elimination of toxic aggregates in Huntington disease". Project partner & co-writer with Dr Carole Escartin (CEA MIRCen).
2019 Fondation Maladie Rares - Transcriptomics for the study of the role of Astrocytes and Glial Cells in Huntington's disease. Partner & co-writer with Dr Carole Escartin (CEA MIRCen).
Other activities
Supervision of 15+ master & PhD students.
Examiner and jury member for 12+ PhD, HDR & CSI committees.
Main author & maintainer for 12+ software packages and models on GitHub.
Oral communications at 20+ seminars, workshops & international conferences.
Referee for numerous peer-reviewed scientific journals & grant agencies (ANR, Canadian FCI, french ANR, belgian FWO & IWT, european ERC, US NSF, US USDA).
Teaching & seminars for students.