Workshops
For the 2026 edition, 29 workshops are offered by engineers and researchers from the core facilities of Biogenouest network. The workshops are divided into 6 sessions over the 2 days, and cover the 6 areas of Biogenouest: Genomics, Proteomics, Functional Exploration, Bio-imaging, Structural Analysis and Metabolomics, and Bioinformatics.
In addition to the workshops run by the Biogenouest core facilities, 3 workshops are dedicated to projects supported by the Vegepolys Valley and Valorial competitiveness clusters, partners of Gen2Bio2026, and another dedicated to the GO-EV federative project.
Each workshop lasts 30 minutes.
Session 1
Thursday, March 12: 10:50-11:20
Use of Low Pass data in the construction of a polygenic risk score in the context of intracranial aneurysms (Marine CORNEC, GenoA & Kinnie LE ROY, Thorax Institute)
Genotyping by sequencing, or low-pass sequencing, is an emerging method that is establishing itself as an alternative to DNA microarrays, enabling interoperability and data reuse. The GenoA core facility recently implemented this low-coverage sequencing technique and is currently developing automated library preparation.
And then, what to do with this data? In the context of intracranial aneurysms, the bioinformatics methods and tools deployed will be presented.
Organ-on-Chip: an alternative in vitro organ model for the functional exploration of human pathologies (Vincent SAUZEAU and Morgane ROUSSEL, The Thorax Institute)
To identify new therapeutic targets, a better understanding of the molecular mechanisms leading to the pathology is essential. Developing an animal model is often necessary to validate the identified target(s). This step remains crucial, although our research activities should strive to reduce the use of animals. Alternative in vitro models exist, such as 3D models of human cell cultures, known as organoids, which replicate tissue architecture and cell behavior. However, this innovative technology is performed in a static environment, which limits the cells' ability to differentiate.
For this workshop, the Therassay core facility will present a new technology called "organ-on-chip," which integrates 3D cell culture with microfluidics technology. The main objective of this workshop is to present this "organ-on-chip" technology from Emulate®, which has been available on the core facility since September.
As an example, we will describe the contributions of this solution to the culture of smooth muscle cells for the implementation of vessels-on-chip or lung-on-chip.
Comparative study of different methods of catching common carp (Philippe HULIN, soon-to-be retired MicroPICell employee)
The transition to carp fishing, far from being a simple pastime, represents an active lifestyle engineering strategy aimed at optimizing the bio-psycho-social parameters of the retiree, promoting neurochemical balance and maintaining cognitive and motor abilities.
This study aims to quantify and compare the relative impact of a series of biotic, abiotic and methodological variables on the capture of Common Carp.
Discover VEGEPOLYS VALLEY, the plant-based competitiveness cluster, and its project opportunities through the PARSADA TRANS'THRIPS project (Cécile ABALAIN, Vegepolys Valley & Fabrice FOUCHER, IRHS)
VEGEPOLYS VALLEY, a plant-based competitiveness cluster, brings together 650 members. It stimulates and supports the co-design of innovations in plant production and the development of food and non-food uses for plants. With a focus on partnerships with academic institutions, it offers a dedicated range of services, which will be presented. This will be illustrated by the PARSADA TRANS'THRIPS project, whose Action 1.3 was supported by the cluster. This action aims to determine the genetic, molecular, biochemical, and physical basis of the rose-thrips interaction.
Seed phenotyping: what's new? (Didier DEMILLY, PHENOTIC)
The workshop presented here will showcase the methodological and applied advances in seed phenotyping deployed on the PHENOTIC core facility at GEVES. This high-throughput phenotyping imaging equipment characterizes dry seeds and the imbibition, germination, and growth kinetics of young heterotrophic seedlings under controlled conditions.
Session 2
Thursday, March 12: 11:40-12:20
Optimization of genome editing in human induced pluripotent stem cells (Sarah TESSIER, iPSC)
The CRISPR/Cas9 genome editing technology is used to correct pathogenic mutations in patient-derived iPS cells, or conversely to introduce specific mutations into healthy donor iPS cells.
This workshop will cover the design principles of CRISPR components, nucleofection optimization, and subcloning. Essential quality controls at each stage of the process will also be addressed.
Protein localization by electron microscopy (Nina SOLER, MRic-TEM)
Microscopy Rennes Imaging Center (MRic) is a joint light and electron microscopy core facility that brings together in one location the instruments and expertise necessary for cellular observation by imaging. After a brief presentation of the two MRic core facilities, the presentation will focus on aspects related to the study of protein localization by TEM using two different methods: immuno-EM and correlative optical and electron microscopy.
Characterization of plant response to water stress by NMR and MRI of leaf tissues (Pierre-Nicolas BOULC'H, IGEPP & Maja MUSSE, PRISM/OPAALE)
This workshop will illustrate the combined application of relaxometry, diffusometry, and NMR imaging approaches to characterize water distribution and dynamics within the mesophyll of rapeseed leaves at different scales. The objective is to better understand the regulation of water relations in response to drought experienced by the plant.
How to access the plant volatolome: agroecological applications to the study of plant/insect interactions (Léo ANDRUSZKOW, CORSAIRE-P2M2)
The workshop will focus on deploying key techniques, particularly those available on our core facilities, for analyzing volatile organic compounds emitted by plants, and more specifically the fraction of volatolome mobilized in beneficial or detrimental interactions with insects. Applied to cultivated plants and phytophagous insects, these approaches aim to establish the mechanistic basis of these interactions and identify new agroecological solutions to replace chemical insecticides.
Best practices for machine learning and artificial intelligence models in bioinformatics (Pauline LE CORRE, GenOuest)
Machine learning and artificial intelligence models are increasingly used in bioinformatics for various applications such as sequence and image analysis. Some well-known models are widely used, such as AlphaFold for predicting the 3D structure of a protein from its sequence. However, many models are also being developed in laboratories to address more specific problems.
To support this evolution in bioinformatics, practices are emerging to use these technologies while respecting the FAIR principles (Findable, Accessible, Interoperable, Reusable). However, these methods are still not widely adopted, which hinders the quality and commercial viability of the models produced.
Building on the experience gained in data or software management in recent years (management plans, metadata, reference warehouses, software packaging, etc.), GenOuest initiated the GOIA project aimed at promoting the adoption of these best practices within the community, through training modules, the implementation of services, and the application of these methods to practical cases.
Session 3
Thursday, March 12: 15:20-15:50
Unicellular and spatial proteomics without prior knowledge accessible in Angers (François GUILLONNEAU & Benjamin BARRE, Prot'ICO)
The need for analysis of ultra-low quantities of proteins is becoming increasingly evident, particularly in the field of biology (cell interactions, tissue organization, communication, transduction) and especially in the field of health (cancer, biopsy, drug).
Building on 20 years of involvement with the ICO, Angers is deploying new ultrasensitive and high-throughput analysis tools, at the single-cell level and without prior knowledge (neither labeling nor targeted antibodies).
During this workshop we will present the new possibilities offered and their applications in the various accessible research fields.
When real-time imaging combined with high-throughput flow cytometry enables cell sorting: presentation of the Cell-View™ technology (Laurence DELBOS, Lucile GUENO & Cécile DAUSSY-ABES, Cytocell)
The arrival on the market in the early 2010s of equipment combining flow cytometry and imaging, such as ImageStream® (originally developed by Luminex, now by Cytek), made it possible to visualize elements in flow, thus enabling multiparametric analysis of a sample from a large number of images. This approach allows, for example, for a more precise definition than with conventional flow cytometry of protein localization or colocalization compartments, the identification of cell-cell interactions, and so on.
In 2022, Schraivogel's team reached a new milestone by developing a cell sorter combining imaging and high-speed flow cytometry. Presented that same year in the journal Science, this sorter has since been marketed by BD Biosciences under the name FACSDiscover™ S8.
This equipment and its "analyzer" version (BD FACSDiscover™ A8) were added to the Cytocell core facility's inventory in 2025. In addition to spectral technology that facilitates the use of high-dimensional panels, both devices benefit from Cell-View™ technology developed by Schraivogel et al. This technology enables real-time visualization of elements in flux and the generation of additional information about them through imaging. It is now possible to select and sort elements based on imaging parameters.
This workshop will aim to present Cell-View™ technology, methods and points of vigilance for setting up panels with this option as well as several applications developed on the Cytocell core facility illustrating the contribution of imaging in cell sorting.
Combining FRET and super resolution microscopy to monitor protein kinase biochemical activity (Xavier PINSON, MRic & Pierre-Jean DESMAISON, IGDR)
The MRic Photonics facility aims to give access to high resolution imaging technologies allowing for assessing the dynamics of biological processes.
Here we present a collaboration between the IGDR Cyclonchondria Team and the MRic facility to introduce BioSenSRRF.
BioSenSRRF is a versatile approach that combines conventional genetically-encoded FRET biosensors to monitor protein kinases activity, with Super-Resolution Radial Fluctuations (SRRF) microscopy.
The combination of these two techniques allowed us to image protein kinase AURKA activation at mitochondria and monitor its biochemical activity in regulating mitochondrial ATP levels at the nanoscale.
Our pipeline can be easily implemented using standard microscopy setups, and is supported by a publicly available ImageJ framework to streamline image processing and data analysis.
We thus believe that this strategy opens new avenues for dissecting the subcellular organization of protein complexes and their contribution to physiology and disease states.
GO-EV: a network to discover to understand the challenges, opportunities and advances in extracellular vesicle research (Julie GAVARD, CRCI²NA/GO-EV Network)
The GO-EV network is based on pooling research capacity and close collaboration between disciplines, laboratories, and core facilities within Biogenouest. This dynamic allows for the structuring of a robust scientific space around extracellular vesicles in Bretagne and the Pays de la Loire region, leveraging complementary expertise and regional technological potential. The sharing of skills, reflection on the standardization of methods, and the training of the next generation of scientists have already laid the foundations for innovations with strong diagnostic and therapeutic potential. This workshop will present several success stories illustrating how this collaborative approach, conducted in close collaboration with the core facilities, can lead to advances in the development of knowledge and technologies, as well as industrial and clinical applications.
Session 4
Thursday, March 12: 16:10-16:40
Long read and RNA sequencing: application for the study of translation during early sea urchin development (Claire DAGUIN-THIEBAUT, Genomer & Maïwenn PETIT, LBI2M)
The Genomer core facility has been offering applications related to long read sequencing since 2018, integrating efficient high molecular weight nucleic acid extraction methods adapted to heterogeneous samples, and library construction protocols prior to long read sequencing. It supports Oxford Nanopore sequencing projects, using DNA and RNA libraries, including a direct mRNA sequencing project during early sea urchin development to better understand the role of cis elements (polyA tails and methylations) in translational regulation at fertilization.
Authors: Maïwenn Petit, Lucie Caradec, Gwenn Tanguy, Sandrine Boulben, Oliver Godfroy, Julia Morales (UMR 8227 LBI2M), Claire Daguin-Thiébaut (Genomer).
Fine-tuning of gene expression by CRISPRai: from the iPS cell model to the rat animal model (Vanessa QUILLAUD-CHENOUARD, CR2TI & Séverine REMY, TRIP)
Genome editing has transformed molecular biology by enabling the generation of a wide variety of experimental models. However, classical approaches based on the insertion of a DNA sequence (knock-in) or the creation of a premature stop codon (knock-out) are irreversible, thus limiting their flexibility. Furthermore, the need to introduce double-strand breaks into genomic DNA carries risks of chromosomal instability and makes it difficult to implement complex combinations of gene perturbations.
In this context, the development of technologies that allow for reversible, targeted modulation of gene expression without permanent alteration of the genome represents a major advance. CRISPR-based interference (CRISPRi) or activation (CRISPRa) systems offer the possibility of specifically inhibiting or activating a gene of interest while preserving genome integrity. This approach paves the way for more refined and dynamic functional screening strategies, enabling the exploration of transcriptional regulation and gene interactions with previously unattainable precision and reversibility.
With this in mind, the TRIP core facility has developed a dual CRISPRai system, simultaneously integrating gene activation and inhibition functions within a single experimental model. This device enables the bidirectional and coordinated modulation of multiple genes, thus providing a powerful tool for studying complex functional interactions. The core facility demonstrates the application of this system in two complementary models: induced pluripotent stem cells (iPSCs), allowing for cellular-level studies, and the rat, providing a relevant in vivo model.
Identification of identity markers of asexual and sexual germ cells during pea aphid embryogenesis by a laser microdissection approach coupled with Bulk RNAseq (Eglantine SOUCAT, IGEPP & Gevorg GHUKASYAN, H2P2)
Aphids exhibit reproductive polyphenism, a particular case of phenotypic plasticity that allows them to alternate between asexual and sexual reproduction. During their annual life cycle, asexual females reproduce by cloning in spring and summer, and then sexually in autumn and winter. At the beginning of autumn, asexual females are able to perceive and integrate the decrease in day length, which induces the production of female and male sexual morphs. To date, no specific markers for asexual or sexual females during embryonic stages have been identified. This project aims to identify cellular markers specific to the two types of embryos that will become asexual and sexual females, and to understand the cellular mechanisms involved in their differentiation. We implemented a novel approach to screening candidate genes using laser capture microdissection (LCM) to collect tissue samples from the abdomens of asexual and sexual embryos and extract ultra-low quantities of mRNA (< 10 ng). RNA sequencing was performed on these samples, allowing the identification of differentially expressed genes (DEGs) between asexual and sexual embryos. These putative markers will be validated by in situ hybridization. The preliminary results, which should provide a good starting point for characterizing embryonic development in asexual and sexual ovaries, will be presented.
Discover VEGEPOLYS VALLEY, the plant-based competitiveness cluster, and its project opportunities through the EVAGRAIN project (Cécile ABALAIN, Vegepolys Valley & Luc SAULNIER, BIA)
VEGEPOLYS VALLEY, a plant-based competitiveness cluster, brings together 650 members. It stimulates and supports the co-design of innovations in plant production and the development of food and non-food uses for plants. With a focus on partnerships with academic institutions, it offers a dedicated range of services, which will be presented. This will be illustrated by the ANR PRCE EVAGRAIN project, which the cluster supported from its inception to the final presentation symposium. The project aimed to develop smart tools for the agile use of wheat.
TEM2C: Cryo-electron microscopy at the service of structural biology (Aurélien DUPONT, TEM2C)
TEM2C, the only core facility dedicated to cryo-electron microscopy in Western France, offers a comprehensive suite of imaging techniques for observing biological samples under cryogenic conditions, i.e., in their native hydrated state. The core facility provides several cryofixation methods, including high-pressure freezing for cells and tissues, as well as thin-film vitrification for isolated macromolecular complexes in suspension.
These approaches enable the analysis of numerous biological objects, such as extracellular vesicles, viruses, and liposomes, without chemical fixation artifacts or heavy metals. TEM2C also allows for the three-dimensional reconstruction of complex samples using cryo-electron tomography. Finally, the installation of a new, state-of-the-art microscope in 2025 will now allow for very high-resolution studies, down to the near-atomic scale.
Session 5
Friday March 13: 10 a.m.-25 p.m.
Generative molecular design using autoencoders for the discovery of new therapeutic compounds and SAR optimization (Mike MAILLASSON, Imp@ct/CRCI²NA)
In the search for new bioactive molecules, deep learning and chemoinformatics converge to accelerate hit discovery and lead optimization. We present a molecular design tool based on a generative autoencoder, integrated with an automated virtual docking pipeline. This approach allows exploration of chemical space by encoding molecular structures as latent vectors, generating new compounds through slight perturbations, and then evaluating them via docking simulations against a predefined biological target. The system iteratively refines the generated molecules based on docking scores, enabling de novo design with enhanced bioactive potential. Furthermore, the Imp@ct core facility facilitates structure-activity relationship (SAR) analysis, thus contributing to the optimization of promising hits. This AI-assisted algorithm provides valuable insights for drug discovery and chemical optimization, offering a scalable solution for ligand design.
Model of deep skin burn and healing (Stéphanie BERNARDET, LGA & Ugo LANCIEN, CHU Nantes)
Deep second-degree burns (DVBs) cause major trauma to the skin, leading to an increased risk of infection and scarring. Because pig skin is similar to human skin, we developed a preclinical porcine model of DVBs to study epithelialization, scar formation and contraction, and to test the efficacy of wound-healing treatments. We evaluated an innovative composite treatment on wound healing, re-epithelialization, and neocollagenesis over 28 days.
Presentation of the Plant Molecular Cytogenetics core facility: Oligos-FISH and Immunostaining for detailed analysis of plant genome structure (Olivier CORITON, PCV)
Contribution of Plant Molecular Cytogenetics – Molecular cytogenetics, whose main tool is Fluorescence In Situ Hybridization (FISH) on chromosome preparations, has revolutionized the approach to traditional cytogenetics. Its high resolution allows for genome studies through detailed analysis of chromosome structure during meiosis and mitosis. This workshop will present the various tools available on the core facility. The value of this technology will be illustrated through examples developed on the core facility focusing on understanding the structure of Brassica genomes using Oligos-FISH and Immunostaining.
Sharing and harmonization in imaging (the "Image Analysis" Working Group & Emmanuel CARUYER, Neurinfo)
The "Image Analysis" working group of Biogenouest is an inter-regional and inter-axis thematic network focused on image analysis, which organizes thematic workshops and webinars. During this workshop, Emmanuel Caruyer (Neurinfo) will present a tool for harmonizing practices and sharing imaging data.
Accelerating agri-food innovation: Opportunities and strategic role of R&D partners in European projects and feedback from the Biotech4Food project (Adrienne GENTIL, Valorial & Alexis MEHAIGNERIE, Abyss Ingredients)
The program includes a review of the experience gained from Biotech4Food, a key European project for biotechnology applied to food, with the participation of Abyss Ingredients. The discussion will then broaden to other European funding opportunities beyond the traditional Horizon Europe R&I programs (AI, RIA). The workshop will offer a practical overview of these funding mechanisms, illustrated by several initiatives led by Valorial, to guide companies wishing to engage in diverse and strategic European collaborations.
Session 6
Friday March 13: 11 a.m.-15 p.m.
GIP Arronax Radiobiology core facility: Presentation and Initial Experimental Results in External Beam Radiotherapy (Charbel KOUMEIR, Arronax)
Multidisciplinary exploration of the effects of ionizing radiation on living organisms: illustration of collaborations in innovative external beam radiotherapy (Ultra High Dose Rate UHDD, Spatially Fractionated SFRT), applied to biological models, cells, fish egg embryos and mice, and bringing together nuclear and medical physicists as well as radiochemists and radiobiologists.
MRI with very high magnetic field gradients: new perspectives for clinical imaging research (Emmanuel CARUYER, Neurinfo)
Magnetic resonance imaging (MRI) is a non-invasive medical examination that has revolutionized patient management for a wide range of conditions. While ultra-high field MRI (7T and above) is often highlighted for its improved spatial resolution, another, complementary technological approach relies on the use of very powerful field gradients (200 mT/m and above). These gradients play a key role in image formation and microstructural imaging, enabling the detection of tissue changes on the order of micrometers. In this presentation, we will explore the advances and opportunities offered by such systems, particularly in the context of studying neurological diseases.
Spectral confocal microscopy, a method adapted to the analysis of multi-labels but also interesting for exploiting the autofluorescence of agri-food products (Laurence DUBREIL, APEX & Gabriel LE FLEM, GEPEA)
The APEX core facility is equipped with a spectral confocal microscope that can collect fluorescence from samples ranging from 405 nm to 900 nm. The capabilities of this new microscope will be presented during the workshop. This equipment is suitable for analyzing multilabels, particularly for imaging OPAL fluorescent probes used on paraffin-embedded tissue sections. We will see that spectral confocal microscopy is also a very interesting technology for exploiting the different autofluorescence spectra of samples. Gabriel Le Flem, an APEX core facility user, will demonstrate how this non-destructive, label-free technique has been used to characterize the biodistribution of an ingredient in a food matrix. Image analysis tools used to characterize products will also be presented during the workshop.
Let's use Phenobean! (Etienne BELIN, Tristan BOUREAU, Rémi GARDET, PHENOTIC)
The workshop presented here will showcase the methodological and applied advancements of the Phenobean phenotyping robots deployed on the PHENOTIC core facility. These robots are dedicated to high-throughput phenotyping through imaging of plant growth kinetics and interactions with pathogens, as well as robotic management of environmental conditions (irrigation, light, humidity).
HUMESS: A tool to integrate quantitative transcriptomic and metabolic network modeling to unveil context specific gene signatures (Louis PARE, LS2N/BiRD)
Transcriptomic analysis is a powerful tool for elucidating gene expression patterns associated with specific biological conditions, offering invaluable insights into cellular responses and regulatory mechanisms. However, one major challenge in transcriptomic analysis is the need for external knowledge to interpret gene expression changes in a meaningful biological context, which can be time-consuming and prone to biases. Consequently, many gene expression signatures derived from transcriptomic data remain quite superficial and lack the depth necessary for true mechanistic understanding. In another hand, multi-omics data allows the reconstruction of genome-scale metabolic networks which represent all biochemical reactions involved in a given organism and how these reactions interplay. These networks are model of phenotypic metabolism which can have many applications such as the identification of potential therapeutic targets. Nethertheless, these genome-scale metabolic model are difficult to obtain due to the tedious steps of manual curation required to obtain good quality models. Here we introduce HUMESS (HUman Metabolis Specific Signature), a tool that seeks to bridge the gap between both approaches. Using a snakemake implementation, HUMESS integrates quantitative transcriptomic data with metabolic network modeling by (i) identifying significantly expressed genes from quantitative 3'seq-RNA Profiling (3'SRP) sequencing data, and (ii) uses a modified version of CarveMe top-down approach for metabolic model reconstruction from a universal human metabolic model – for building a metabolic model specific to the differentially expressed gene. The metabolic model is then (iii) extensively analyzed for identifying reactions essential to sustain the human metabolic phenotype. In order to facilitate the analysis of the results, an online Rshiny interface has been developed allowing an in depth exploration of the results.
Reference paper: https://doi.org/10.1093/bioinformatics/btaf448