Welcome to my home page. I'm a computational biologist working currently at the french Centre National de Recherche en Génomique Humaine (CNRGH, National Center for Human Genomic Research), located in Evry (France). The CNRGH is part of the french Commissariat à l'Énergie Atomique (CEA, Centre for Atomic Energy), and is one of the largest sequencing centres in Europe. It is dedicated to genetic and genomic research on human diseases. I lead the computational genomics (bio-analysis) laboratory. Our activity is focused on the computational analysis of human health related high-throughput genomic data.
Contact: eric-dot-bonnet-at-cnrgh-dot-fr | ORCID | Google Scholar | LinkedIn | GitHub
(*) indicates co-authorship
Bonnet E. (2023). La transcriptomique en cellule unique pour étudier des maladies neurodégénératives. L'Actualité Chimique, numéro 490, Décembre 2023. pdf HAL preprint
Derbois C, Palomares MA, Deleuze JF, Cabannes E, Bonnet E. (2023) Single cell transcriptome sequencing of stimulated and frozen human peripheral blood mononuclear cells. Sci Data, 2023 Jul 6;10(1):433, DOI
M Riquelme-Perez, F Perez-Sanz, JF Deleuze, C Escartin, E Bonnet*, S Brohard*. (2023) DEVEA: an interactive shiny application for Differential Expression analysis, data Visualization and Enrichment Analysis of transcriptomics data. F1000Research, DOI.
Julien Guemri , Morgane Pierre-Jean, Solène Brohard, Nouara Oussada, Caroline Horgues, Eric Bonnet, Florence Mauger and Jean-François Deleuze. (2022) Methylated ccfDNA from plasma biomarkers of Alzheimer's disease using targeted bisulfite sequencing. Epigenomics, vol 14, no 8, DOI.
L. Abjean, L. Ben Haim, M. Riquelme-Perez, P. Gipchtein, C. Derbois, M.A. Palomares, F. Petit, A.S. Hérard, M.C. Gaillard, M. Guillermier, M. Gaudin-Guérif, N. Sagar, N. Dufour, N. Robil, M. Kabani, R. Melki, P. De la Grange, A.P. Bemelmans, G. Bonvento, J.F. Deleuze, P. Hantraye, E. Bonnet, S. Brohard, R. Olaso, E. Brouillet, M.A. Carrillo-de Sauvage, C. Escartin. (2022) The JAK2-STAT3 pathway controls a beneficial proteostasis response of reactive astrocytes in Huntington's disease. Brain, DOI.
Eric Bonnet. (2021) Using convolutional neural networks for the classification of breast cancer images. arXiv DOI.
Vidisha Singh, George D.Kalliolias, Marek Ostaszewski, Maëva Veyssiere, Eleftherios Pilalis, Piotr Gawron, Alexander Mazein, Eric Bonnet, Elisabeth Petit-Teixeira and Anna Niarakis. (2020) RA-map: building a state-of-the-art interactive knowledge base for rheumatoid arthritis. Database, Volume 2020, 2020, baaa017, DOI
Marie-Ange Palomares*, Cyril Dalmasso*, Eric Bonnet*, Céline Derbois, Solène Brohard-Julien, Christophe Ambroise, Christophe Battail, Jean-François Deleuze, Robert Olaso. (2019) Systematic analysis of TruSeq, SMARTer and SMARTer Ultra-Low RNA-seq kits for standard, low and ultra-low quantity samples. Scientific Reports 9 7550 DOI.
Eric Bonnet*, Marie-Laure Moutet*, Céline Baulard*, Delphine Bacq-Daian, Florian Sandron, Lilia Mesrob, Bertrand Fin, Marc Delépine, Marie-Ange Palomares, Claire Jubin, Hélène Blanché, Vincent Meyer, Anne Boland, Robert Olaso, Jean-François Deleuze. (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
Pau Erola, Eric Bonnet, Tom Michoel. Learning differential module networks across multiple experimental conditions. (2018) book chapter, Gene regulatory network inference, Humana Press. Book arXiv preprint
Kernaleguen M., Daviaud C., Shen Y., Bonnet E., Renault V., Deleuze J.F., Mauger F. and Tost J. Whole genome bisulfite sequencing for the analysis of genome-wide DNA methylation and hydroxymethylation patterns at single-nucleotide resolution. (2018) Methods Mol Biol. 1767:311-349. DOI: 10.1007/978-1-4939-7774-1_18.
Fatemeh Seyednasrollah, Devin C. Koestler, Tao Wang, Stephen R. Piccolo, Roberto Vega, Russell Greiner, Christiane Fuchs, Eyal Gofer, Luke Kumar, Russell D. Wolfinger, Kimberly Kanigel Winner, Chris Bare, Elias Chaibub Neto, Thomas Yu, Liji Shen, Kald Abdallah, Thea Norman, Gustavo Stolovitzky, Howard R. Soule, Christopher J. Sweeney, Charles J. Ryan, Howard I. Scher, Oliver Sartor, Laura L. Elo, Fang Liz Zhou, Justin Guinney, James C. Costello, and Prostate Cancer DREAM Challenge Community. A DREAM Challenge to Build Prediction Models for Short-Term Discontinuation of Docetaxel in Metastatic Castration-Resistant Prostate Cancer.(2017) JCO Clinical Cancer Informatics web (as contributing team).
Arnau Montagud, Pauline Traynard, Loredana Martignetti, Eric Bonnet, Emmanuel Barillot, Andrei Zinovyev, Laurence Calzone. Conceptual and computational framework for logical modelling of biological networks deregulated in diseases. (2017) Briefings in Bioinformatics, bbx163. DOI web
Paul Deveau, Emmanuel Barillot, Valentina Boeva, Andrei Zinovyev, Eric Bonnet. Calculating biological module enrichment or depletion and visualizing data on large-scale molecular maps with ACSNMineR and RNaviCell R packages. (2016) The R Journal. The R Journal Vol. 8/2, December 2016, ISSN 2073-4859. pdf bioRxiv
Loredana Martignetti, Laurence Calzone, Eric Bonnet, Emmanuel Barillot, Andrei Zinovyev. ROMA: representation and quantification of module activity from target expression data. Frontiers in genetics 7, 18. DOI
Inna Kuperstein, Eric Bonnet, Hien-Anh Nguyen, David Cohen, Eric Viara, Luca Grieco, Simon Fourquet, Laurence Calzone, Christophe Russo, Maria Kondratova, Marie Dutreix, Emmanuel Barillot and Andrei Zinovyev. Atlas of Cancer Signaling Network: a systems biology resource for integrative analysis of cancer data with Google Maps. (2015) Oncogenesis. 2015 Jul 20;4:e160. DOI: 10.1038/oncsis.2015.19. web
Eric Bonnet, Eric Viara, Inna Kuperstein, Laurence Calzone, David PA Cohen, Emmanuel Barillot, Andrei Zinovyev. NaviCell Web Service for Network-based Data Visualization. (2015) Nucleic Acids Research Web issue, DOI: 10.1093/nar/gkv450. web pdf
Eric Bonnet, Laurence Calzone, Tom Michoel. Integrative multi-omics module network inference with Lemon-Tree. (2015) PLoS Comput Biol 11(2): e1003983. DOI:10.1371/journal.pcbi.1003983 web arXiv
Laurence Calzone, Inna Kuperstein, David Cohen, Luca Grieco, Eric Bonnet, Nicolas Servant, Philippe Hupé, Andrei Zinovyev, Emmanuel Barillot. Modélisation de réseaux biologiques et médecine de précision en oncologie. (2014) Bulletin du Cancer Vol. 101, Issue 1, pp 18-21. pdf
Dagmar Waltemath, Frank T Bergmann, Claudine Chaouiya, Tobias Czauderna, Padraig Gleeson, Carole Goble, Martin Golebiewski, Mickael Hucka, Nick Juty, Olga Krebs, Nicolas Le Novère, Huaiyu Mi, Ion I Moraru, Chris J Myers, David Nickerson, Brett G Olivier, Nicolas Rodriguez, Falk Schreiber, Lucian Smith, Fengkai Zhang, Eric Bonnet. Meeting report from the fourth meeting of the Computational Modeling in Biology Network (COMBINE). (2014) Standards in Genomic Sciences. Vol 9, No 3. web.
Margolin AA, et al. Systematic analysis of challenge-driven improvements in molecular prognostic models for breast cancer. (2013) Sci Transl Med. Apr 17;5(181):181re1. web (as a contributing team with JP Vert).
Vera-Licona, P., Bonnet, E., Barillot, E., Zinovyev, A. (2013) OCSANA: Optimal Combinations of Intervention Strategies for Network Analysis. Bioinformatics. 29 (12), 1571-1573. web pdf
Bonnet, E., Calzone, L., Rovera, D., Stoll, G., Barillot, E., Zinovyev, A. (2013) BiNoM, a Cytoscape plugin for accessing and analyzing pathways using standard systems biology formats, BMC Systems Biology, 7:18. web
Bonnet, E., Calzone, L., Rovera, D., Stoll, G., Barillot, E., Zinovyev, A. (2013) Practical use of BiNoM, a Biological Network Manager software. In In silico Systems Biology: A systems-based approach to understanding biological processes , Humana Press, pp 127-146. pdf
The Ectocarpus genome consortium. The Ectocarpus genome and brown algal genomics. (2012) In Genomic insights gained into the Diversity, Biology and Evolution of Algae, Advances in Botanical Research, Vol. 64, pp 143-174, Elsevier, ISSN 0065-2296. web
Grbić, M., Thomas Van Leeuwen, T., Clark, R.M., Rombauts, S., Rouzé, P., Grbić, V., Osborne, E.J., Dermauw, W., Phuong Cao, T.N., Ortego, F., Hernández-Crespo, P., Diaz, I., Martinez, M., Navajas, M., Sucena, E., Magalhães, S., Nagy, L., Pace, R.M., Djuranović, S., Smagghe, G., Iga, M., Christiaens, O., Veenstra, J.A., Ewer, J., Mancilla Villalobos, R., Hutter, J.L., Hudson, S.D., Velez, M., Yi, S.Y., Zeng, J., Pires-daSilva, A., Roch, F., Cazaux, M., Navarro, M., Zhurov, V., Acevedo, G., Bjelica, A., Fawcett, J.A., Bonnet, E., Martens, C., Baele, G., Wissler, L., Sanchez-Rodriguez, A., Tirry, L., Blais, C., Demeestere, K., Henz, S.R., Gregory, T.R., Mathieu, J., Verdon, L., Farinelli, L., Schmutz, S., Lindquist, E., Feyereisen, R., Van de Peer, Y. The genome of Tetranychus urticae reveals herbivorous pest adaptations. (2011) Nature 479, 487-492 DOI:10.1038/nature10640 pdf web supplementary information
Bonnet, E. Integrating microRNA expression data and other sources in module network reconstruction. (2010) In Proceedings of the 6th workshop on computation of biochemical pathways and genetic networks, Logos Verlag Berlin GmbH. pdf
Bonnet, E., Michoel, T. and Van de Peer, Y. Prediction of a gene regulatory network linked to prostate cancer from gene expression, microRNA and clinical data. (2010) Bioinformatics, 26 (18): i638-i644. pdf web
Michoel, T., Joshi, A., Bonnet, E., Vermeirssen, V. and Van de Peer, Y. Towards system level modeling of functionnal modules and regulatory pathways using genome-scale data. (2010) Proceedings of the Seventh International Workshop on Computational Systems Biology, WCSB.
Bonnet, E., Tatari, M., Joshi, A., Michoel, T., Marchal, K., Beerx, G., Van de Peer, Y. Module network inference from cancer expression dataset identifies microRNAs as high scoring regulators. (2010) PLoS ONE 5(4): e10162.DOI:10.1371/journal.pone.0010162. pdf web
Bonnet, E., He, Y., Billiau, K., Van de Peer, Y. TAPIR, a web server for the prediction of plant microRNA targets, including target mimics. (2010) Bioinformatics, 26(12), 1566-1568. pdf web
Cock, M., Sterck, L., Rouzé, P., Scornet, D., Allen, A., Amoutzias, G., Anthouard, V., Artiguenave, F., Aury, J., Badger, J., Beszteri, B., Billiau, K., Bonnet, E., Bothwell, J., Bowler, C., Boyen, C., Brownlee, C., Carrano, C., Charrier, B., Youn Cho, G., Coelho, A., Colln, J., Corre, E., Da Silva, C., Delage, L., Delaroque, N., Dittami, S., Doulbeau, S., Elias, M., Farnham, G., Gachon, C., Gschloessl, B., Heesch, S., Jabbari, K., Jubin, C., Kawai, H., Kimura, K., Kloareg, B., Kupper, F., Lang, D., Le Bail, A., Leblanc, C., Lerouge, P., Lohr, M., Lopez, P., Martens, C., Maumus, F., Michel, G., Miranda-Saavedra, D., Morales, J., Moreau, H., Motomura, T., Nagasato, C., Napoli, C., Nelson, D., Nyvall-Collén, P., Peters, S., Pommier, C., Potin, P., Poulain, J., Quesneville, H., Read, B., Rensing, S.A., Ritter, A., Rousvoal, S., Samanta, M., Samson, G., Schroeder, D., Sgurens, B., Strittmatter, M., Tonon, T., Tregear, J., Valentin, K., von Dassow, P., Yamagishi, T., Van de Peer, Y., Wincker, P. The Ectocarpus genome and the independent evolution of multicellularity in the brown algae. (2010) Nature, 465, 617-621. pdf web supplementary information
Vermeirssen, V., Joshi, A., Michoel, T., Bonnet, E., Casneuf, T. and Van de Peer, Y. Transcription regulatory networks in Caenorhabditis elegans inferred through reverse-engineering of gene expression profiles constitute biological hypotheses for metazoan development. (2009) Mol. BioSyst., 5, 1817-1830. pdf web
Abeel, T., Saeys, Y., Bonnet, E., Rouzé, P., Van de Peer, Y. Generic eukaryotic core promoter prediction using structural features of DNA. (2008) Genome Research 18, 310-23. pdf web
Van Leene, J., Stals, H., Eeckhout, D., Persiau, G., Van De Slijke, E., Van Isterdael, G., De Clercq, R., Bonnet, E., Laukens, K., Remmerie, N., Hendrickx, K., De Vijlder, T., Abdelkrim, A., Pharazyn, A., Van Onckelen, H., Witters, E., Inzé, D., De Jaeger, G. A Tandem Affinity Purification-based technology platform to study the cell cycle interactome in Arabidopsis thaliana. (2007) Mol. Cel. Prot. 6(7):1226-38. pdf web
Michoel, T., Maere, S., Bonnet, E., Joshi, A., Saeys, Y., Van den Bulcke, T., Van Leemput, K., van Remortel, P., Kuiper, M., Marchal, K., Van de Peer, Y. Validating module networks learning algorithms using simulated data. BMC (2007) Bioinformatics 8, S5. pdf web
Bonnet, E., Van de Peer, Y., Rouzé, P. The small RNA world of plants. (2006) New Phytol. 171, 451-68. (Tansley Review). web pdf
Faes, P., Minnaert, B., Christiaens, M., Bonnet, E., Saeys, Y., Stroobandt, D., Van de Peer, Y. A Scalable Hardware Accelerator for Comparing Protein Sequences. (2006) Proceedings of the First International Conference on Scalable Information Systems. Hong Kong, April 2006, on CD. pdf
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 20, 2911-7. pdf web
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. USA 101, 11511-6. pdf web
Picaud, F., Bonnet, E., Gloaguen, V., Petit, D. Decision Making for Food Choice by Grasshoppers (Orthoptera: Acrididae): Comparison Between a Specialist Species on a Shrubby Legume and Three Graminivorous Species. (2003) Environmental Entomology, 32 (3) 680-688. pdf
Petit, D., Picaud, F. and Bonnet, E. Les peuplements d'Orthoptéroïdes de la lande sur serpentinite de la Flotte et du Cluzeau (Haute-Vienne). (2003) Annales Scientifiques du Limousin, 14, pp 13-28. pdf
Bonnet, E., Van de Peer, Y. zt: a software tool for simple and partial Mantel tests. (2002) J. Stat. Soft. 7, 1-12. web
Bonnet, E. et Petit D. Diversité, densité et biomasse des Orthoptères de la ZNIEFF des Dauges. (1998) Ann. Sc. du Limousin, numéro spécial Dauges, pp 111-120. pdf
Bonnet, E., Chabrol, L. et Petit, D. Mise à jour de l'inventaire des Orthoptères du Limousin. Actes du colloque "Cartographie et Inventaire des Invertébrés comme contribution à la gestion des milleux naturels", série Patrimoine Naturel, Muséum National d'Histoire Naturelle. pdf
Bonnet, E., Vilks, A., Lenain, J.F., Petit D. Temporal and structural analysis of the relationships between orthoptera and vegetation. (1997) Ecologie, 28 (3) 209-216. pdf
Bonnet, E., Chabrol, L. et Petit, D. Catalogue préliminaire des Orthoptères du Limousin (Orthoptera). (1995) Nouv. Revue Ent., T12, fasc. 1, pp 71-83. pdf
Bonnet, E. et Petit, D. A propos de deux espèces d'Orthoptères remarquabkles en Haute-Vienne : Calliptamus italicus et Aiolopus thalassinus . (1994) Annales Scientifiques du Limousin, 10, pp 67-73. pdf