Illustration DIGIT-BIO



Axis 1: Deciphering the functions of living

This line of research addresses the understanding of biological processes, their regulation and the way in which these processes interact or cooperate. It concerns all levels of organisation of living organisms up to the organism and the population.

The aim is to describe, understand and model biological systems and to establish causal links within and between biological scales, integrating systemic effects such as stochasticity or retroactions as determinants of system dynamics and evolution. Beyond the study of processes under standardised conditions, it will also be necessary to characterise them in a diversity of environments (biotic, abiotic, contaminant) and contexts.

These challenges call for mathematical and computer modelling of dynamic systems, digital calculation, knowledge extraction and integration of heterogeneous data to calibrate and evaluate the quality of models. The integration of data from different sources requires progress on knowledge representation methods using ontologies, controlled vocabularies and networks, as well as on spatialization methods. Learning methods are also used.

Research themes

  • Characterisation of the principles of organisation, functioning and evolution of genomes, cells, organs and organisms;
  • The construction of molecular networks underlying biological functions, and in particular multi-scale or multi-species metabolic networks;
  • The links between gene(s) and form(s) by integrating geometric and physical constraints and associated retroaction;
  • The mechanisms underlying the adaptive responses of organisms and populations and the spatial and temporal scales of evolution of these responses.

Methodological challenges

  • Extract and represent knowledge in forms that allow the formalisation of hypotheses and integration into models;
  • Search for causal relationships using statistical and automatic learning methods on large-scale data;
  • Develop multi-scale modelling, rule inference on systems and simulation studies of complex dynamic systems describing living organisms;
  • Optimise the modelling and coupling of different models;
  • Identify "meta-mechanisms" as an alternative to coupling models between successive levels of organisation.

In this folder

Understanding the genetic determinism of a trait, i.e. the set of genes involved in the development and expression of this trait, is a major challenge for better understanding biological processes and supporting genetic improvement programmes.
The IFM2A2 consortium proposes to bring together in a sustainable manner the different scientific communities that are currently working separately on simulating the functioning of apical meristems at different scales, operating in different INRAE departments (BAP, MAthNum and AgroEoSystem) in close interaction with INRIA.
In biology, as in other scientific fields, the integration of multi-source data is more relevant than ever. Indeed, the data collected are increasingly complex and their volume is growing, due to the development of analytical platforms, imaging techniques, the rise of omics data, etc
Integrative biology is based on the study of complex biological networks. Understanding the plasticity of biological interaction networks due to phenotypic, environmental or interventional variability is an important challenge in fields as diverse as genomics or human nutrition. Such studies often include comparisons between contrasting groups, including variables of various natures (continuous, counts, binary, etc.). These so-called "mixed-type" data can be difficult to analyse in a unified way. While multivariate probabilistic models provide a robust framework for inferring interrelationships among continuous variables, an analogous model for mixed-type data has yet to be defined.
The prion paradigm unifies a number of age-related, devastating neurodegenerative pathologies. The PrionDif project seeks to develop a multi-scale mechanistic model accounting for the spatiotemporal dynamic of prion spreading within the brain. This approach will allow the identification of key processes to enable therapeutic advances and promote early diagnosis.
In the natural environment as well as in fish farming, the process of formation and maturation of female gametes (oogenesis) is essential for reproductive success.
Illustration adn
in the nucleus of a cell, the three-dimensional conformation of the genome has a major impact on how it functions. A better understanding of the links between the 3D structure of the genome and its functioning represents a methodological challenge and requires dialogue between different disciplines
Sclerotinia sclerotiorum sur une tige de coco
Understanding how plants defend themselves against pathogens is a major challenge for moving towards an agriculture that uses fewer pesticides.

Modification date: 26 September 2023 | Publication date: 10 January 2022 | By: Com