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THE CNRGH LABORATORIES

Bioanalysis (LBA)

​ Bio-analyse 

Published on 28 October 2025

​Team leader​ : Eric Bonnet, PhD, HDR, DR CEA
E-mail​: eric.bonnet​at​cnrgh.fr

The Computational Genomics Laboratory of the CNRGH conducts research projects in NGS data analysis (short reads & long reads) on human genomics, in collaboration with experimental biologists or on the laboratory's own research topics. The genomic data analysed are bulk transcriptomic, single cell transcriptomic, variants, chromatin accessibility or 3D genome architecture. We work on various human pathologies such as neurodegenerative diseases (Huntington, Alzheimer) or certain dermatological diseases. The data comes from patient cohorts, animal models, or simple or 3D cell cultures (organoïds). The laboratory also has expertise in tools and methods for inference and analysis of biological networks.


Team members

Solène Brohard, PhD, ingénieur-chercheur CEA

Kévin Muret, PhD, ingénieur-chercheur CEA

Nouara Oussada, ingénieur-chercheur CEA (50% avec l'Institut François Jacob CEA)

A​ltynbek Zhubanchaliyev, PhD Student (Co-supervision with L. Martignetti, Institut Curie)

Julie Le Borgne​, PhD, CEA post-doc (joined the lab in Apr. 2025)​

Alum​ni

Lilia Mesrob ​, ingénieur de recherche INSERM (2018 – 2020)
Jeanne Cherruaud, étudiante en médecine et Master 1 sciences et santé, Université de Nantes (Mai – Juin 2022)
Alexandre Hubert, stagiaire Master 1 bioinformatique, Université de Rennes (Avril – Juillet 2022)
Seydi Thimbo, stagiaire Master 2 bioinformatique, Université de Montpellier (Février – Juillet 2022)
Sara Bencheikh, stagiaire Master 2 (contrat d'apprentissage), Université de Rouen (2021 - 2023)
Miriam Riquelme-Pérez, PhD student (2019 - 2023)
Camille Lemercier, stagiaire M2 Bioinformatique, Université d'Evry (Février - Juin 2023) 
Naëla Gourri, stagiaire M1 Bioinformatique, Université d'Evry (Mai - Juillet 2023) 
Clara Cherruaud, stagiaire école d'ingénieur ISEN Brest (Juin - Septembre 2023)​
Vincent Le Goff, CDD Ingénieur-Chercheur CEA (Avril-Septembre 2023)
​​Clémence Su, stagiaire M2 Bioinformatique, Université Clermont Auvergne​
Audrey Chathuant, stagiaire M2 Bioinformatique, Université Aix-Marseille
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Collaborations 

  • Laboratoire Astrocytes réactifs dans les maladies neurodégénératives (Dr Carole Escartin, MIRCen, CEA Fontenay-aux-Roses)
  • Laboratoire Imagerie Multimodale Intégrative des Maladies Neurodégénératives et Thérapies (Dr Marc Dhenain, MIRCen, CEA Fontenay-aux-Roses)
  • Hôpital Henri Mondor à Créteil (Pr Sophie Hüe PUPH)
  • Laboratoire de Bioinformatique, CNRGH, Evry (Dr Vincent Meyer)
  • Equipe Maths et Statistiques, CNRGH, Evry (Dr Edith Le Floch)
  • Equipe Chromatine et organisation 3D du génome, CNRGH, Evry (Dr Sophie Chantalat)
  • Equipe de recherche biomarqueurs circulant, CNRGH, Evry (Dr Florence Mauger)
  • Laboratoire Epigénétique et environnement, CNRGH, Evry (Dr Jörg Tost)
  • Computational Biology Unit, Department of bioinformatics, Bergen (Pr Tom Michoel)

Publications

AS Devonshire, J Morata, C Jubin, RPA Pereira, L Hernandez-Hernandez, D Yener, E Cabannes, S McGinn, M Delepine, C Fund, R Tonda, S Heath, M Dabad, J Gutierrez-Cuesta, I Sanchez Escudero, M Cristina Frias-Lopez, S Cowen, A Whale, Thorsten Voss, JF Deleuze, I Gut, M Gut & CA Foy.  (2025) Interlaboratory evaluation of high molecular weight DNA extraction methods for long-read sequencing and structural variant analysis. BMC Genomics volume 26, Article number: 698. https://doi.org/10.1186/s12864-025-11792-7.

M Mziou-Sallami, P Roger, A Gloaguen, C Dandine-Roulland, T Jiogho Ngaho, S Brohard, K Muret, F Sandron, E Bonnet, JF Deleuze, E Le Floch, V Meyer. (2025) GNNenrich: a novel method for pathway enrichment analysis based on Graph Neural Network. Bioinformatics, Volume 41, Issue 9, September 2025, btaf478. https://doi.org/10.1093/bioinformatics/btaf478.

C Rodilla, G Núñez-Moreno, Y Benitez, M Rodríguez de Alba, F Blanco-Kelly, A López-Alcojor, L Fernández-Caballero, I Perea-Romero, M Del Pozo-Valero, G García-García, M Balanzá, C Villaverde, O Zurita, C Jubin, C Fund, M Delepine, A Leduc, JF Deleuze, J M. Millán, P Minguez, M Corton and C Ayuso. (2025) Long-Read Whole-Genome Sequencing as a Tool for Variant Detection in Inherited Retinal Dystrophies. IJMS, https://doi.org/10.3390/ijms26083825.

A Onfroy, F Jean-Louis, P Le Corvoisier, F Coulpier, K Muret, E Bonnet, R Arrouasse, C Boucle, S Abid, E Sbidian, C Bergqvist, P Wolkenstein, V Godot, JF Deleuze, Y Lévy, P Topilko, E Audureau, S Hüe. (2025) Hair follicle stem cell fate supports distinct clinical endotypes in Hidradenitis Suppurativa. Journal of the European Academy of Dermatology and Venereology. https://hal.science/hal-05134707v1/file/Onfroy_Hue_HidraSupp_2025.pdf

K Muret, V Le Goff, C Dandine-Roulland, C Hotz, F Jean-Louis, B Boisson, L Mesrob, F Sandron, D Daian, R Olaso, E Le Floch, V Meyer, P Wolkenstein, JLCasanova, Y Lévy, E Bonnet, JF Deleuze* and S Hue*. (2024) Comprehensive Catalog of Variants Potentially Associated with Hidradenitis Suppurativa, Including Newly Identified Variants from a Cohort of 100 Patients. Int. J. Mol. Sci., 25, 10374. https://doi.org/10.3390/ijms251910374.

J Sanceau, L Poupel, C Joubel, I Lagoutte, S Caruso, S Pinto, C Desbois-Mouthon, C Godard, A Hamimi, E Montmory, C Dulary, S Chantalat, A Roehrig, K Muret, B Saint-Pierre, JF Deleuze, S Mouillet-Richard, T Forné, C Grosset, J Zucman-Rossi, S Colnot and A Gougelet. (2024) DLK1/DIO3  locus upregulation by a β-catenin-dependent enhancer drives cell proliferation and liver tumorigenesis. Molecular Therapy. https://doi.org/10.1016/j.ymthe.2024.01.036.

D Derbala, A Garnier, E Bonnet, JF Deleuze & J Tost. (2024) Whole-Genome Bisulfite Sequencing Protocol for the Analysis of Genome-Wide DNA Methylation and Hydroxymethylation Patterns at Single-Nucleotide Resolution,  In: Jeltsch, A., Rots, M.G. (eds) Epigenome Editing. Methods in Molecular Biology, https://doi.org/10.1007/978-1-0716-4051-7_18.

L Abjean, L Ben Haim, M  Riquelme-Perez, P Gipchtein, C Derbois, MA Palomares, F Petit, AS Herard, MC Gaillard, M Guillermier, M Gaudin-Guerif, G Auregan, N Sagar, C Hery, N Dufour, N Robil, M Kabani, R Melki, P De la Grange, AP Bemelmans, G Bonvento, JF Deleuze, P Hantraye, J Flament, E Bonnet, S Brohard, R Olaso, E Brouillet, MA Carrillo-de Sauvage and C Escartin. (2023) Reactive astrocytes promote proteostasis in Huntington's disease through the JAK2-STAT3 pathway. Brain, https://doi.org/10.1093/brain/awac068.

Bonnet E. (2023) La transcriptomique en cellule unique pour étudier des maladies neurodégénératives. L'Actualité Chimique, https://cea.hal.science/cea-04394836.

C Derbois, MA Palomares, JF Deleuze, E Cabannes and E Bonnet. (2023) Single cell transcriptome sequencing of stimulated and frozen human peripheral blood mononuclear cells. Scientific Data, https://doi.org/10.1038/s41597-023-02348-z.

A Damián, G Núñez-Moreno, C Jubin, A Tamayo, MR de Alba, C Villaverde, C Fund, M Delépine, A Leduc, JF Deleuze, P Mínguez, C Ayuso, M Corton. (2023) Long-read genome sequencing identifies cryptic structural variants in congenital aniridia cases. Human Genomics, https://doi.org/10.1186/s40246-023-00490-8.

M Riquelme-Pérez, F Perez-Sanz, JF Deleuze, C Escartin, E Bonnet*, S Brohard*. (2022) DEVEA: an interactive shiny application for Differential Expression analysis, data Visualization and Enrichment Analysis of transcriptomics data. F1000Research. https://doi.org/10.12688/f1000research.122949.2.

J Guemri, M Pierre-Jean, S Brohard, N Oussada, C Horgues, E Bonnet, F Mauger, JF Deleuze. (2022) Methylated ccfDNA from plasma biomarkers of Alzheimer's disease using targeted bisulfite sequencing. Epigenomics, https://doi.org/10.2217/epi-2021-0491.

S Brohard-Julien, V Frouin, V Meyer, S Chalabi, JF Deleuze, E Le Floch, C Battail. (2021) Region-specific expression of young small-scale duplications in the human central nervous system.BMC Ecology & Evolution, https://doi.org/10.1186/s12862-021-01794-w.

F Mauger, C Horgues, M Pierre-Jean, N Oussada, L Mesrob, JF Deleuze. (2020) Comparison of commercially available whole-genome sequencing kits for variant detection in circulating cell-free DNA. Scientific Reports, https://doi.org/10.1038/s41598-020-63102-8.

MA Palomares*, C Dalmasso*, E Bonnet*, C Derbois, S Brohard-Julien, C Ambroise, C Battail, JF Deleuze, R Olaso. (2019) Systematic analysis of TruSeq, SMARTer and SMARTer Ultra-Low RNA-seq kits for standard, low and ultra-low quantity samples. Scientific Reports,  https://doi.org/10.1038/s41598-019-43983-0.

E Bonnet*, ML Moutet*, C Baulard*, D Bacq-Daian, F Sandron, L Mesrob, B Fin, M Delépine, MA Palomares, C Jubin, H Blanché, V Meyer, A Boland, R Olaso, JF 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, https://doi.org/10.1371/journal.pone.0195471.