Our team

Permanent members

• Bertrand Cosson, scientific director of iPOP-UP since October 2024. He is a professor of molecular biology at Paris Cité University, with expertise focused on gene expression regulation and bioinformatic analysis of high-throughput sequencing data. His research combines molecular biology and bioinformatics to explore post-transcriptional and epigenetic regulation, particularly mRNA stability and translation in various biological contexts. Alongside his research activities, Bertrand Cosson directs the University Diploma in “Creation, Analysis, and Valorization of Omics Biological Data” at the UFR Sciences du Vivant, where he emphasizes the application of bioinformatics tools to address biological issues. He actively contributes to the academic community by developing scientific and educational exchanges with European universities and promoting bioinformatics as a lever for research in biology.
• Emeline Bruyère, bioinformatics Research Engineer at Université Paris Cité since December 2025. She holds a Master’s degree in Bioinformatics and Biostatistics, as well as a dual Bachelor’s degree in Mathematics and Life Sciences from Université Paris-Saclay. Her expertise lies at the interface of computer science, mathematics, and biology. Her skill set includes omics data analysis, the development and optimization of NGS data pipelines, statistical analyses, and database design, with a strong focus on robustness, reproducibility, and FAIR principles. Within iPOP-UP, she supports biologists in using the computing cluster and in adopting best practices in bioinformatics. She also contributes to the development of the platform’s resources, in particular through updates to the website and tutorials, with the aim of facilitating tool adoption by users and enhancing the quality of the services provided.

Steering Committee

The major decisions of iPOP-UP are made by its Steering Committee, which is largely composed of the heads of the founding and supporting Structures.

• Valérie Doye is the Director of the Institut Jacques Monod. A CNRS research director, she also leads the “Non-Conventional Functions of Nuclear Pores” team, studying the role of nucleoporins in intracellular transport, cell division, and gene regulation. After completing her PhD on neuronal differentiation (Université Pierre et Marie Curie, 1991) and a postdoc in Heidelberg, she joined the CNRS in 1994. Recognized for her groundbreaking work, she was awarded the CNRS Silver Medal in 2009. At the Institut Jacques Monod since 2008, she uses models like stem cells and organoids to investigate how nucleoporin anomalies are linked to hereditary diseases.
• Franck Letourneur, a molecular biologist at Université Paris Cité, is a research engineer and manager of the GENOM’IC platform at the Institut Cochin (INSERM U1016). This IBiSA-labeled facility specializes in transcriptome analyses using next-generation sequencing methods, producing and processing data.
• Valérie Mezger is a CNRS research director and head of UMR 7216 “Epigenetics and Cell Fate” at Université Paris Cité. She completed her PhD in 1991 at Université Paris-Sud, focusing on thermal stress response and its effects on gene regulation, followed by a postdoc at Dana-Farber Cancer Institute (Harvard Medical School), where she specialized in the molecular mechanisms of gene expression regulation in response to stress. Since then, her work has focused on epigenetic mechanisms and their role in cellular plasticity, differentiation, and certain human pathologies. As head of UMR 7216, she coordinates multidisciplinary research combining molecular biology, epigenetics, and integrative modeling to better understand how environmental signals influence cellular identity. Under her leadership, the unit has consolidated its international reputation through high-level collaborations and innovative approaches.
• Pierre Tufféry, Director of Research at INSERM, leads the Computational Modeling of Protein-Ligand Interactions team in the Functional and Adaptive Biology unit (BFA). His research focuses on protein-peptide interactions and peptide design. He is also the founder of the RPBS platform, which he directed from 2004 to 2021.
• Bertrand Cosson (see profile above).

Scientific Committee

• Emeline Bruyère (see profile above).
• Nicolas Chevrollier is a research engineer at Inserm, affiliated with the “Computational Modeling of Protein-Ligand Interactions” team within the Functional and Adaptive Biology Unit (BFA) at Université Paris Cité. His work focuses on modeling protein-ligand interactions, contributing to the understanding of key molecular mechanisms in biology. He is also involved in training students in bioinformatics and computational biology, thereby strengthening Université Paris Cité’s scientific expertise in these fields.
• Yves Clément (Institut Jacques Monod, Université Paris Cité) is an assistant professor in the “Stem Cells, Development, and Evolution” team, focusing on comparative genomics and functional genomics to study regeneration variability among animals. He also teaches biostatistics and the analysis of large omics datasets.
• Bertrand Cosson (see profile above).
• Thomas Denecker is a bioinformatician and a representative of the French Institute of Bioinformatics (IFB). An expert in omics data analysis (RNAseq, ChIP-seq, metagenomics) and high-performance computing infrastructure management, he helps develop bioinformatics tools tailored to research needs. Passionate about skills transfer, he assists biologists in their projects by providing technical and methodological support. His commitment also extends to training, with the aim of making bioinformatics accessible to a wide scientific audience.
• Magali Hennion (Université Paris Cité), CNRS research engineer and head of the BiBs platform, supports bioinformatics and biostatistics for the Epigenetics and Cell Fate unit. She specializes in high-throughput sequencing data analysis and develops tools to ensure reproducible and accessible analyses.
• Olivier Kirsh is a lecturer at Université Paris Cité. He teaches various subjects ranging from biostatistics to biology and molecular pathophysiology, as well as functional genomics and bioinformatics. He also teaches continuing education courses (Roscoff School of Bioinformatics and INSERM workshop, Cancéropole Ile de France, University Diploma in Integrative Bioinformatics). Within the “Epigenetics and Cellular Destiny” unit (UMR 7216), he divides his time between P.A. Defossez’s team and the bioinformatics & biostatistics platform (BiB). He develops and optimizes tools and methods for analyzing omics data on high-performance computing clusters, which are necessary for research projects in epigenomics (DNA methylation) and gene expression regulation.
• Nikolaos Konstantinides, head of the “Comparative Developmental Neurobiology” team at the Institut Jacques Monod, investigates neuronal diversity during embryogenesis and its evolution. His work leverages single-cell sequencing and genetic tools in Drosophila to explore neurodevelopmental mechanisms. After studying biology at the University of Athens, he obtained a master’s degree in molecular biology and biomedicine at the University of Crete. He went on to complete a PhD in 2014, focusing on appendage regeneration in the amphipod crustacean Parhyale hawaiensis. He then did a postdoc in Claude Desplan’s lab at New York University, where he studied the mechanisms of neuronal specification in the Drosophila visual system. In 2021, he was appointed to the CNRS and established his own research group at the Institut Jacques Monod. In 2023, he was selected to join the FENS-Kavli Network of Excellence, recognizing his significant contributions to the field of neuroscience.
• Joël Marchand is a research engineer at the CNRS, affiliated with the Institut Jacques Monod (IJM) since 2021. He headed the Mathrice service group for computer scientists within the mathematics laboratories from 2000 to 2006. He contributed to the creation, structuring, and revitalization of this human network of around 100 members. He was awarded the CNRS Crystal Medal in 2002. He has worked in various scientific fields: mathematics, astronomy, multidisciplinary universities, humanities and social sciences, and biology. He has held a variety of positions: technical infrastructure administration, project management, and team supervision. Sensitive to the environmental impact of information technology, he strives to optimize investments and architectures to minimize objects and maximize their use over time.
• Julien Rey is a bioinformatics research engineer at Université Paris Cité, working in the Functional and Adaptive Biology Laboratory (BFA), ERL INSERM 1133, as part of the TPM2PI team – Therapeutic Peptides: Modulation of Protein-Protein Interactions. He is the technical manager of the Parisian Structural Bioinformatics Resource Platform (RPBS), an IBiSA-certified platform and member of the French Institute of Bioinformatics (IFB), which he co-coordinates. In this capacity, he is responsible for the administration of computing resources, the design, development, and deployment of web tools, and the development and deployment of structural bioinformatics and chemoinformatics services. He is also involved in database development and acts as the IFB representative for the platform. Finally, he is also involved in training, teaching bioinformatics and computational biology, as well as organizing and leading training courses within the RPBS platform.
• Benjamin Saintpierre (Université Paris Cité) is a bioinformatician at the GENOM’IC platform at the Institut Cochin. He is responsible for the bioinformatics analysis of the platform’s RNA-Seq and scRNA-Seq projects, from alignment to statistical analysis, including clustering. He also provides bioinformatics support in understanding the latest published techniques and data publication, and supervises several bioinformatics students. He is also responsible for the bioinformatics hub at the Institut Cochin.