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Our Latest Review on Advances in Metabolism Modelling for Plant-Microbe Interactions

Our latest review explores advances in metabolic modeling for plant-microbe interactions, highlighting key collaborations.

Our Latest Review on Advances in Metabolism Modelling for Plant-Microbe Interactions We are pleased to announce a new review on the latest advances in metabolic modelling to unravel the complexity of plant-microbe interactions, written in collaboration with Feth El Zahar Haichar from INSA Lyon. Indeed, It marks a significant milestone for our talented PhD student, […]

Jean-Clément Gallardo holds a Bachelor’s degree in Life Sciences and graduated in 2020 from the University of Bordeaux with a Master’s degree in Bioinformatics and Computational Biology. He has strong expertise in data visualisation and analysis, and full stack development applied to biological systems and metabolomics.

From 2021 to 2025, Jean-Clément worked as a bioinformatics engineer at INRAE ToxAlim, where he focused on the development of a web solutions serving as a comprehensive platform for metabolomics research, providing a workflow of tools designed as a step-by-step analysis process.

During this period, he was a key contributor to the development, maintenance, and project management of MetExploreViz 3, a JavaScript library for metabolic network visualisation, which is also part of the ecosystem of MetExplore, a web server dedicated to metabolic network analysis. He also led the development of graph based data visualisation web components, core base of the new version of MetExploreViz 4, and initiated projects for the automated drawing of metabolic networks.

Alongside his main activities, Jean-Clément developed for the eMetaToul group, a community website for bioinformaticians, and contributed to guided reconstruction tools and desktop versions of MetExploreViz.

Jean-Clément joined iMEAN in January 2026 as a full stack developer, bringing strong expertise in biomodelling, data visualisation, and web-based analytical platforms to support the development of innovative predictive tools.

Susie holds a Master’s degree in Bioinformatics from the University of Bordeaux and a Bachelor’s degree in Health Sciences from Université Picardie Jules Vernes. Passionate about software engineering, web development, and biological data processing, she brings a strong interdisciplinary expertise at the interface of biology and computation.

In 2024, she joined the Molecular Networks team at EMBL-EBI in Hinxton, UK, where she developed Java-based tools for high-throughput molecular interaction data formatting and visualization, integrating them with Cytoscape, IntAct and Complex Portal.
Her work has been presented at HUPO conferences in 2025 and contributes to publications in Nucleic Acids Research.

In addition to her research experience, Susie has completed international projects, including an Erasmus exchange in Slovakia, where she combined microbiology analysis with cross-cultural collaboration.
She also designs and implements robotics and web projects, demonstrating her versatility across software, data analysis, and applied biological research.

Susie’s broad range of skills for tackling complex biological problems, combined with her strong background in programming will bring significant added value to iMEAN’s expanding activities.

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Laura is pursuing a Master’s degree in Life Sciences Engineering at EPFL, with a focus on computational methods in biomedicine. Her academic training is interdisciplinary, spanning biology, chemistry, mathematics, physics, and computer science. During her Bachelor’s project, she worked on molecular modelling, where she estimated ligand-protein binding energies, an experience that sparked her interest in computational approaches to biomedical research.

Miquel is a student in the Bioinformatics, Modelling, and Statistics (BIMS) Master’s program at the University of Rouen Normandy. He previously completed a Master 1 internship at UMR 1331 TOXALIM, focusing on metabolic network modelling to study the role of the p53 regulatory gene in cancer cell metabolism, in collaboration with the Institut de Cancérologie de Montpellier. His academic background combines cellular biology, physiology, and bioinformatics, giving him a strong foundation for systems biology and modelling.

Edmond Berne is currently pursuing an Engineering degree in Bioinformatics from Polytech Nice Sophia, where he is developing expertise in biological systems, web development, and computational tools.
He recently completed a four-month internship at the University of Copenhagen, focusing on the sequencing of amplicons from the wheat microbiome. His research involved studying microbial diversity and profiling NRPS (Non-Ribosomal Proteins) molecules in the rhizosphere and rhizoplane of wheat, using bioinformatics tools and programming languages such as Java and Python.
In 2023, Edmond conducted a research internship at the CNRS in Orléans, studying a severe asthma model caused by Aspergillus fumigatus. Previously, in 2022, he assisted in drug candidate research as a Laboratory Technician at CNRS.
Through these experiences, Edmond has developed strong analytical skills in bioinformatics, microbiome research, and programming, positioning himself at the intersection of biology and computational biology.
He will apply and further strengthen these skills during his internship at iMEAN as part of our bioinformatics and developer’s team.

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    Jeanne Burdin is in her final year at INSA Toulouse, specializing in Computational Biology within the Biological Engineering department. She gained significant experience in modeling during her work with the iGEM competition, where she developed models for anticancer drug production in liposomes, and through a six-month internship on the double-haploidization of maize.
    At iMEAN, Jeanne will focus on applying her skills in biostatistics, bioinformatics, and biomodeling to plant biology projects, further advancing her expertise in this exciting field.

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    Amandine Paulay completed her PhD at INRAE and Biomathematica, focusing on microbial systems biology and metabolic modeling. Her doctoral research involved modeling protein degradation by the human gut symbiont Bacteroides caccae, where she developed a proteolytic module for enhanced metabolic simulations and analyzed protease distribution across multiple Bacteroides species.
    Amandine holds a Bachelor’s degree in Biochemistry, Molecular and Cellular Biology, and Genetics and a Master’s degree in Genomics and Environment. She has previously conducted bioinformatics analyses on various microbial genomes and worked on metabolic models related to human gut microbiota.
    By joining iMEAN, Amandine will continue to apply her skills in biomodeling, bioinformatics, and microbiology to further advance our research.

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    Amélie graduated from a master’s degree in modelling and computational biology bioinformatics at Grenoble university. During her university course, she built her expertise through various experiences on biochemistry, virology with the development of malaria vaccines, and on the modelling of Escherichia coli.

    Amélie first joined iMEAN in 2022 as an intern, during which she worked on the  bacterial modelling of microbiota. Amélie will carry on her work as an doctoral student for the dynamic modelling of microbiota and its impact on the plant project, and thus reinforce iMEAN’s modelling platform.

    She’s a brilliant student with an already strong expertise in building dozens of genome-scale  metabolic models.

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    After graduating with a Bachelor’s degree in Cellular Biology, Genetics, Microbiology and Animal Physiology from the University of Rennes 1, Anastasia pursued a Master’s degree in Pathophysiology at the Paul Sabatier University in Toulouse.
    During her PhD at the RESTORE institute, she combined in vivo and in silico approaches to study tissue regeneration and developed significant expertise in bioinformatics, machine learning, and agent-based mathematical modelling.

    By joining iMEAN’s modelling team, she’ll bring in her expertise in Physiology and will also apply and gain more experience in Biostatics, Bioinformatics and Biomodelling.

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    Pablo earned a Mathematical Engineering degree from the Universidad de Chile and has a PhD in Microbiology and Biotechnology at the University of Montpellier in France.
    During his academic journey, he conducted research at reputable institutions and gained a broad spectrum of skills.

    Take a look at Pablo’s academic and professional journey:

    2010 – 2017: Mathematical Engineering and a Master thesis on Optimization models with a focus on sustainable development

    2017 – 2020: Ph.D in Microbiology and Biotechnology with a focus on mathematical models of microbial community dynamics in continuous reactors and embraced the concept of environmental biorefinery

    2021 – 2023: Postdoctoral fellowship on Statistical learning for coupling metabolic modelling to a spatial model of gut microbiota and metabolic networks analysis at Centre INRIA of the Université de Bordeaux

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    Luana earned her Bachelor’s degree in Biological Science, followed by a Master’s degree in Molecular Biology, and then a PhD in Genetics Microbiology. During her academic journey, she conducted research at reputable institutions and gained a broad spectrum of skills.

    Here’s a glimpse of Luana’s academic and professional journey:

    2010: Conducted her Bachelor thesis at DB-LEMM Lab. of Microbial and Molecular Evolution in Italy.

    2013: Completed her Master Thesis in the UK at the Bioinformatics and Molecular Evolution Unit.

    2014: Commenced her PhD in Italy at COMBO Computational Biology Group.

    2017: Undertook a PhD Internship in Sweden at SYS2BIO Systems and Synthetic Biology Group.

    2018: Engaged in a Post-doctoral research position in Luxembourg at the Systems Biology Group.

    Since 2022: Worked remotely as a consultant, showcasing her expertise in coding, biology, and computer science.

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    Nolwenn is an engineer in Biochemical Engineering, graduated from INSA Toulouse, specialized in Plant Biosciences research. She obtained a PhD in microalgae lipid metabolism at the CEA of Grenoble and has a 2-year experience at the INRAE of Auzeville working on seed defense in Arabidopsis Thaliana.

    It’s at the beginning of the year 2023 that Nolwenn joined iMEAN to strengthen its modelling team.

    Nolwenn is a skilled scientist, and through her triple degree and extensive knowledge on lipid metabolism and microalgae, she will boost iMEAN’s capability to design bioprocesses.

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    After concluding his internship as a Developer in Systems Biology at iMEAN, Mohamed graduated top of his class for his master’s degree in Bioinformatics Software Development and Data Analysis at University of Aix-Marseille.

    He also has an engineering degree in Industrial Biology from the National Institute of Applied Sciences and Technologies in Tunis (Tunisia), with several professional internships in Industry, research laboratories (Institut Pasteur de Tunis) and analysis laboratories.

    Thanks to his background, Mohamed strongly contributed to the acceleration of iMEAN’s bioinformatics tools and he’ll continue to help speed up its model reconstruction process.

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    Raphaël is an engineer in bioinformatics. He obtained a PhD in computational biology at the INSA Lyon, during which he modelled the transcriptional regulation by DNA supercoiling in bacteria. He published various articles in the field of microbiology and bioinformatics using different modelling approaches like thermodynamic, deterministic and stochastic modelling approaches.

    Raphaël joined iMEAN in 2022 to develop new models and methods from fine description of molecular interactions toward genome-scale networks.

    Raphaël is a rigorous modeller with a strong multidisciplinary background, the perfect combination  to ride off-road modelling approaches.

    Margit is a Doctor in Biophysics, & Biochemistry from Humboldt University (Germany) specialised in systems biology and mitochondria models.

    She published more than 15 outstanding scientific publications in the field of energy metabolism and human genetics, and built very accurate kinetics models of oxidative phosphorylation able to reveal mechanisms behind diseases.

    It’s in 2021 that Margit joined iMEAN to reinforce our modelling team. She developed the modelling module predicting subcellular concentration of metabolites from application on a whole organism which enleaches the capacity to screen biostimulants effect using iMEAN’s models. She is also involved in modelling microbial communities in their complex ecological niches.

    Margit is a rock solid biophysicist and modeller who easily builds highly sophisticated models.

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    Marine graduated from a master’s degree in bioinformatics at Bordeaux university.

    Marine joined iMEAN in 2021, and thanks to her rigorous developer skills, she set up a rock-solid algorithm that ensured the industrialisation of iMEAN’s genome-scale models reconstruction pipeline. She’s in charge of setting up and maintaining iMEAN’s computer tools for both our modellers and our customers.

    Marine is a talented bioinformatician who propels any projects she is involved in to the top.

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    Vincent studied plant biology at Paul Sabatier University of Toulouse (France) and got a PhD in plant regulatory networks involved in seed development and plant-microbe interactions at INRAE.

    Vincent started working at iMEAN as a Plant Modeller in 2019, and is currently supervising the reconstruction of genome-scale mathematical models of crops and other plants. Among others, Vincent developed metabolic, regulatory and multi-scale models of plants, and to our knowledge, the most advanced model of Arabidopsis thaliana.

    Vincent excels in translating his wide knowledge in plant physiology into complex in silico regulatory and metabolic networks.

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    Jonathan is a Doctor in biotechnology and molecular engineering from University Provence-Marseille. Jonathan has a 15 years tremendous experience in metabolic engineering and genetic engineering for many biotechnology projects at the interface of academia, industry and start-up environments. He engineered a broad kind of microorganisms like Yeast, filamentous fungi, or Cyanobacteria, to produce various chemicals and polymers.

    Jonathan joined iMEAN in 2019 and uses his in-depth expertise in metabolic microorganism to build accurate models mimicking physiological behaviour of the cells, and to design the next generation of industrial microbes in silico.

    Jonathan is a talented scientist with a broad vision about the biotech industry and the smart strategies to boost industrial processes.

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    Damien holds a PhD in Food Microbiology & Bioprocessing from the University of Burgundy in France, building upon his educational background in biology and Biotechnology.

    After that, Damien starts his career path as a scientific project manager within the framework of the EURL Listeria mandate at ANSES (French Agency for Food, Environmental, and Occupational Health & Safety). After this great experience, he co-founded a start-up in the Agri-Environment sector, where he applied his expertise to address pressing challenges in sustainable agriculture.

    Drawing from his multifaceted experience, Damien now thrives in assisting companies—ranging from start-ups and SMEs to large corporations—in their R&D endeavors, particularly in helping them in the development of their innovative biotechnology projects. His three-year tenure as a Start-up Partnership Manager at TWB honed his ability to forge impactful collaborations and translate customer needs into concrete solutions.

    With a breadth of knowledge spanning various domains such as Food, Environment, Agri-Agro, Industrial Biotech, and Health, Damien excels in navigating the complexities of biotechnology to drive meaningful outcomes. His recent role as a Business Developer at iMEAN underscores his commitment to fostering the growth and development of iMEAN.

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    Yasmine got a master’s degree in biology at Paul Sabatier University in France, and completed a specialised master’s degree in sales and marketing for the health sector at Toulouse Business School.

    Various experiences as an assistant researcher in public (Inserm, Pasteur Institute of Tunisia) and private laboratories (Pierre Fabre), provided her with an extensive knowledge in immunology. Yasmine was an R&D Project Manager at the competitive cluster Eurobiomed, giving her insight on the process of R&D projects along with management and communication skills.

    Yasmine joined iMEAN as a Business Developer in July 2022. She is in charge of the development of the sales and the marketing of the company.

    Yasmine has a wide knowledge of the biotechnology sector to mount perfect modelling projects for our customers.

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    Lucas studied bioinformatics, and got his PhD in systems biology & plants regulatory networks at Université Paul Sabatier – Toulouse III. This provided him with a strong expertise in the development of innovative algorithms to analyse the complex molecular networks of living organisms.

    After getting some industrial experience in software and web interface development, Lucas founded iMEAN with Rémi Peyraud in 2018.

    Lucas designed the optimization algorithm used by iMEAN, “the tracker”, dedicated to de novo design of synthetic organisms. Lucas also set up the entire modelling platform, allowing iMEAN to build high-quality models at an unprecedented speed.

    Lucas is an outstanding developer with an amazing capacity to quickly transform ideas into concrete and efficient applications.

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    Rémi studied biochemistry and got his PhD at ETH Zurich in Switzerland in systems biology and microbiology.

    Rémi has a world-renowned expertise in modelling of living organisms and he conducted pioneer research on systems biology of plant pathogens. He published more than 20 scientific publications in outstanding journals and applied his cutting-edge modelling expertise in many sectors such as environmental microbiology, plant pathogens, industrial biotech, and human health.

    In 2018, in partnership with Lucas Marmiesse, Rémi founded the company iMEAN, based on a modelling technology they developed during 10 years of research at INRAE.

    Rémi provides his unique vision to the company to lead its business and scientific development.

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    Rémi studied biochemistry and got his PhD at ETH Zurich in Switzerland in systems biology and microbiology.

    Rémi has a world-renowned expertise in modelling of living organisms and he conducted pioneer research on systems biology of plant pathogens. He published more than 20 scientific publications in outstanding journals and applied his cutting-edge modelling expertise in many sectors such as environmental microbiology, plant pathogens, industrial biotech, and human health.

    In 2018, in partnership with Lucas Marmiesse, Rémi founded the company iMEAN, based on a modelling technology they developed during 10 years of research at INRAE.

    Rémi provides his unique vision to the company to lead its business and scientific development.

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    List of publications