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Histopathology has significantly contributed to the understanding of biological phenomena and many diseases. It typically involves visual evaluation of a tissue sample under a light microscope by pathologists to identify structural tissue properties associated with diseases. The emerging use of Whol

Magnetic Resonance Image (MRI) and diffusion MRI in particular have become very useful for assessing brain pathologies and trauma, and for diagnosing neurodegenerative disorders. Although it provides sensitive information pertaining to tissue microstructure and structural connectivity, diffusion MRI

The burden of healthcare-associated infections has increased over the last decades, especially due to the rising prevalence of antimicrobial resistance in opportunistic bacterial pathogens. The treatment of patients infected with antibiotic-resistant bacteria (ARB) is compromised due to the reduced

Helically coiled filaments are ubiquitous in nature. They are observed at different scales, from molecular to multi-cellular structures, giving them great biological and ecological relevance. When confined under constrained physical space, helical filament leads to the formation of non-linear, multi

The need to evolve in response to environmental changes has led living organisms to acquire powerful diversification strategies. Among these, Diversity Generating Retro-elements (DGRs) are natural directed mutagenesis systems capable of efficiently exploring sequence space. DGRs have been identified

This interdisciplinary project aims to develop new methods in mathematics and computer science to stratify patients into homogeneous groups based on biological variables, i.e. biomarkers. The aim is to develop a multi-clustering algorithm based on biological data to discover new clinical interpretat

Most of the life time of an animal consist in exploring and sensing its environment without any specific goal. During this process, the animals encode the statistics of the environmental stimuli that surround them and adapt progressively their neuron responses to these stimuli. This unsupervised lea

IdenTHic will develop a statistical framework to construct tumor evolution history from panel-sequencing and marker data that can be used to monitor patient and identify key genetic features. The project will develop tumor deconvolution model-based methods specific to panel-sequencing from which c

Le cancer est la principale cause de décès dans le monde. Ces derniers temps, les avancées dans le domaine de la médecine de précision ont modifié les normes de traitement du cancer en proposant de nouveaux plans de traitement personnalisés aux résultats prometteurs. Cette spécification du traitemen

At the intersection of cultural and biological heritage, the project develops an interdisciplinary methodology to read and re-interpret two exceptional and massive collections of human biological materials and paper registries in Strasbourg and Geneva amassed over the 20th century. Our radical appro

Phylogenomics aims to analyze genomes in an evolutionary framework to reconstruct their history and understand their functions. This field of research motivates the sequencing of thousands of genomes in all areas of the tree of life. It relies on a series of estimation steps that are costly to run

Angiogenesis is the process by which new blood vessels form from pre-existing vessels. The vascular germination which takes place simultaneously at several points of one or more vessels makes it possible to grow a set of neovessels. These come into contact two by two at their ends to form a bridge o

DNA replication is a fundamental process of the cellular cycle. In metazoan replication starts stochastically at multiple sites called origin of replication. The factors responsible for selecting (i) the location of potential origins by origin licensing in the G1 phase and (ii) which potential origi

The human perception of a complex visual scene requires a cognitive process of visual attention to sequentially direct the gaze towards a visual region of interest to acquire relevant information selectively through foveal vision, that allows maximal acuity and contrast sensitivity in a small region

Recent developments in the field of protein structure prediction, notably those based on AI, showed that protein models can routinely reach unprecedented levels of near-experimental accuracy. In this context, modeling protein interactions in the living cell is becoming more central than ever before.

Alzheimer’s disease (AD) is the most common major neurodegenerative dementia type. Current state-of-the-art diagnostic measures of AD are invasive (cerebro-spinal fluid analysis), expensive (neuroimaging) and time-consuming (neuropsychological assessment). By contrast, AD cognitive fingerprints base

Modularity refers to a pattern of connectivity in which elements are grouped into highly connected subsets, modules or building blocks. It is an important property in biology, as it helps a system to "save its current state" while allowing further evolution. Developmental modules are often represent

When a complex system is studied, it is usually broken down into smaller and simpler subsystems in order to facilitate its analysis. Such a reductionist paradigm is powerful; making the analysis easier, but ignores the interactions and relationships that exist between the parts and scales of the who

Data processing pipelines are at the heart of modern experimental sciences. From data cleaning to statistical analysis they cover the essential steps that transform raw unprocessed data into scientific discoveries. But in practice, researchers face a highly complex pipeline landscape – different mod

Computational protein design (CPD) consists of designing proteins accomplish- ing certain tasks. The case of non-covalent interactions requires designing molecules with a specified binding affinity range. However, this design problem is especially challenging due to the exponential size of the desig

Developing a multiscale model for plants, capable of managing complex plant response to environmental conditions and its underlying genetic diversity, is a major issue in agronomy and biology. The Resource Balance Analysis framework is promising to integrate the finest scales (genes) to the individu

The main objective of the present project is to derive laws governing neuronal integration in networks, through morphological and activity-related changes, and for neurons with both myelinated and unmyelinated axons. The experimental collaborators of the project are the Haas lab, providing data on v

Single-cell sequencing and spatial transcriptomics have the potential to revolutionize our understanding of complex biological systems, but methodological challenges remain before we could exploit their full potential. Standardized methods are indeed required to build spatial signaling networks and

Within the context of tissue engineering and regenerative medicine, organoids, which are simplified miniature organs, can be considered as building blocks for the fabrication of macroscopic tissues (~mm-cm). The main obstacle to this scaling process is the integration of a perfusable vascular networ

Vascular ageing is characterised by the occurrence of alterations in the elastic laminae present in the media of elastic arteries such as the aorta. Imaging of the mouse aorta by very high-resolution X-ray micro-tomography using synchrotron radiation makes it possible to observe these structures in

An explosion in the availability of transcriptomics data, especially in single cells, has produced a surge in methods to infer regulatory networks directly from data, but a systematic comparison with prior knowledge-based models is still lacking. A major question is whether we should consider that s

As the size and complexity of synthetic genetic circuits increase, they progressively become too burdensome for a single cell. Consequently, many toy-model genetic circuits are easily lost to negative selection when the engineered organisms are exposed to less controlled environments. In contrast,

Irradiation with UV light results in bulky DNA lesions that are repaired by Nucleotide Excision Repair (NER) pathway. NER deficiency is linked to Xeroderma Pigmentosum (XP), a human disease characterized by a high rate of skin cancers. Bulky lesion repair in vivo requires chromatin reorganization to

Total hip replacement (THR) is the most common orthopaedic surgery, with around 150,000 patients treated each year in France. Most THR surgeries are performed using the cementless press-fit technique, which consists of ensuring the primary stability of the implant during its insertion thanks to the

Surfactant replacement therapy (SRT) consists of instilling a liquid-surfactant mixture into the trachea of premature newborns, whose high alveolar surface tension makes their lungs stiff and difficult to inflate. Despite indisputable efficacy, the dose and administration method have been primarily

Gaining an understanding of the cellular processes underlying bacterial growth is crucial for fundamental research in biology as well as for applications in biotechnology, health, and environmental technology. Growth laws have been formulated that relate growth rate to the macromolecular composition

Exponentially increasing costs of pharmaceutical development – a phenomenon known as Eroom’s law – is a call for innovation. Here, we propose to integrate scattered genetic information on drug targets to guide their selection. During the past decade, the statistical genetic community discovered and

Neuroimaging offers an unmatched description of the brain’s structure and physiology, which explains its crucial role in the understanding, diagnosis, and treatment of neurological disorders, such as dementia. However, identifying subtle pathological changes simply by looking at images of the brain

The mechanical properties of embryonic cells drive a wide diversity of cell behaviors, ranging from cell division to polarization and cell shape changes. These mechanical properties play a critical role during embryonic development and morphogenesis, as they contribute to the position, shape and fat

RNA is a fundamental molecule of the living, the seat of the genetic material of some viruses and very frequently the conveyer of messages in the cell, for the production and regulation of proteins. Studying RNA reveals functional aspects in cells, as well as fundamental questions about nucleic acid

We propose to develop abstractions of reaction networks to Boolean networks with the most permissive semantics. This is relevant for improving inference of networks from data and the control of networks modeling biological systems. We consider two particular case studies. The first concerns the und

Brain surgery is the usual treatment for most brain tumors. After the craniotomy procedure to access the brain, the high-precision removal of the tumor necessitates an accurate definition of the boundary between the tumor and other vital brain tissues. This assessment is usually done visually by the

AI is used on a large scale on a daily basis to perform various learning and classification tasks. As a result, computing power requirements increase exponentially. It therefore becomes mandatory to explore energy-efficient alternatives. The neuromorphic community tries to get closer to biological e