Notre recherche vise à décrypter les déterminants moléculaires du cancer et à rendre ces connaissances disponibles pour améliorer la prise en charge des patients. Elle est basée sur des analyses de profils tumoraux omiques multi-niveaux et de haute dimension, et sur des approches sophistiquées d'apprentissage automatique combinées à la modélisation de réseaux biologiques.

Dans le cadre de notre recherche, nous développons des logiciels qui sont disponibles publiquement sur le repertoire GitHub de notre équipe:


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Vie de l'équipe
EMBO Workshop
- 26 novembre 2023
Computational models of life: From molecular biology to digital twins

Single-cell and spatial omics have increased the data granularity available for understanding biological mechanisms as well as exponentially increasing the amount of biomedical data available. Modelling has helped biomedical projects by uncovering mechanisms behind drug synergies and personalizing drug treatments while allowing for the study of all scales, from molecules to cells to tissues to organs and even to whole bodies. High-Performance Computing (HPC) environments have enabled the scaling up of scientific computing allowing it to reach an unprecedented scope. HPC has become an essential tool in many fields due to its ability to power up data analysis, storage and large-scale processing.

This in-person 5-day EMBO Workshop will gather early-career researchers and field leaders at the crossroads of single-cell omics, modelling and HPC to pave the way for realistic, scalable human digital twins of cells, tissues and organs. Presentations and discussions around these rapidly-evolving topics will push the field forward by training researchers with techniques from neighbouring fields and allowing them to tackle problems using combined approaches.

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bc2 2023
Workshop at BC2 conference in Basel
- 11 septembre 2023
Mechanistic and AI digital twins in personalized medicine - two sides of the same coin

Digital twins are an emergent concept in Computational Systems Biology and personalized medicine. Many initiatives manifest an interest of creating computational models of increasing complexity that could be used to represent virtual patients and help in the decision-making regarding the appropriate treatment. Having robust and reliable computational models spanning all biological layers such as gene expression, signalling and metabolism to name a few, could revolutionize the way we treat Big Data for the benefit of precision medicine and improved medical care - tailored to the needs of each patient. As the number of computational models rapidly increases, the production of data is ever growing and the approaches, both mechanistic and AI-based, are rapidly developing, discussions about challenges and best practices are needed more than ever.

The purpose of the workshop is to bring together researchers working in the field of digital twins in computational systems biology who use various formalisms to address challenges of data integration and model personalization. The focus will be on presenting the state of the art in the field and how mechanistic computational modelling can upscale benefiting from AI-based methodological advances.

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permedcoe logo
From pathway modelling tools to cell-level simulations
- 25 juin 2023
PerMedCoE Summer School 2023

The PerMedCoE summer school will take place on the 25 – 30 June 2023 at the Hotel Montanyà in Seva, less than an hour away from Barcelona.

The course will combine lectures and hands-on exercises to:

- Introduce attendees to key practicalities of working with high-performance computing (HPC) clusters

- Build first-hand experience in using PerMedCoE modelling tools (CellNOpt, CARNIVAL, COBREXA, MaBoSS, PhysiCell and PhysiBoSS)

- Develop a practical appreciation of using workflow managers and containerised PerMedCoE modelling tools to execute biomedical workflows


You can access the material we presented there on our sysbio GitHub:

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