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Medical imaging provides a wide spectrum of modalities giving access to data of various physical natures and dimensions. Each imaging modality provides valuable information for the diagnosis and monitoring of patients. Nevertheless, the linking of these information is made complex by the heterogenei

The objective of this project is to develop rigorous and explainable artificial intelligence (AI) models for the prediction of etiological diagnosis of cardiac diseases from heterogeneous inputs. For this purpose, we will create a cohort composed of 1000 patients with 4 distinct pathologies that req

Epithelia have a viscoelastic behaviour: they respond as solids over short times and as fluids over large times. This fluidity plays an essential role in morphogenesis and tissue deformation. At the cellular scale, fluidity is achieved by the remodelling of junctions between cells due to their inter

Neurophysiologists are nowadays able to record from a large number of extracellular electrodes and to extract, from the raw data, the sequences of action potentials or spikes generated by many neurons. Unfortunately these "many neurons" still represent only a tiny fraction of the neuronal population

Functional annotation is often performed by phylogenomics approaches or machine learning approaches. On the one hand, phylogenomics approaches rely on quantifying sequence similarity and genomic context between the protein of interest and proteins for which functional annotation is available. Partic

ANDES aims at developing and experimentally validating new computational methods for nanobody design, with a large spectrum of applications (therapies, diagnosis…) in order to have efficient technological solutions, ready to react very quickly and to face the emergence of new viruses. Our ambition l

With the increase in life expectancy in most countries, understanding the mechanisms of tissue decline has become a major public health priority for our society. Decline of tissue functions is correlated with a loss of its architecture. The emergence of this architecture and subsequent maintenance

Cardiovascular diseases are the leading cause of premature death in developed countries. Among them, abdominal aortic aneurysm (AAA) has become a significant health public challenge worldwide, with extremely high rates of mortality in case of rupture. The only curative treatment relies on surgery an

Virtual screening and docking-scoring methods are essential in preselecting hit molecules for pharmacological targets among millions of compounds. Structure-based methods aim to select the best potential hits for in vitro assays. Docking and scoring remain currently a major challenge in retrieving t

High-throughput sequencing of genomes of one or many species living in distinct habitats has opened extraordinary perspectives for predicting species responses to climate change. The objective of this research project is to develop statistical methods for predictive ecological genomics (PEG) based o

Non-coding RNA molecules make up for more than 90% of the genome of higher organisms and are known to be key elements in gene expression regulation in viruses. Targeting RNA with drugs would open to a whole new class of possible therapies, now mainly limited to proteins. However, the flexible and dy

Finding how regulatory DNA sequence operates to control genome expression (i.e. characterizing a DNA cis-regulatory code) is an intense field of research as this information is key to clinically interpret genetic variations and foster genomic medicine. Bioinformatics and machine learning approaches

Cancers are heterogeneous diseases. Variations in tumor composition, gene expression, and response to environmental changes are key factors in cancer progression, while hampering scientific efforts to understand and treat the disease. Current knowledge of cancer biology and corresponding therapeutic

One of the core challenges in biology is to understand how behavior at the scale of populations and ecosystems emerges from biochemical processes inside single cells. Central to this problem is that intracellular processes are inherently stochastic and create variability in isogenic microbial popula

Pulmonary embolism (the blockage of a pulmonary artery by a blood clot) is the third cause of cardiovascular death in Europe. Upon diagnosis confirmation, clinicians evaluate the patient prognosis based on risk stratification models. The management of patient, thus its outcome, highly depend on this

Female reproductive function is supported by a massive production of specialised germ cells, the oocytes. In women, as in most mammals, the stock of oocytes is established in the peri-natal period and it keeps decreasing all along life, leading to its exhaustion at menopause and to reproductive func

I-VESSEG aims to close the gap hindering the use of 3D vessel segmentation tools to assist clinicians in angiographic clinical routines. The project will build on learning-based techniques and will address their limitations regarding the need for large, fully annotated training sets and their poor g

Up to now, protein structure prediction and design problems have been mostly formulated assuming that proteins fold into a well-defined three-dimensional form. Nevertheless, there is an increasing corpus of work showing that Intrinsically Disordered Proteins/Regions (IDPs/IDRs) perform highly releva

The heart is an electrically activated mechanical pump. Its proper functioning is facilitated by interaction between electrical and mechanical systems across spatial scales and physics. Scar is associated with an increased propensity for arrhythmia in the ventricles. Functionally, it alters act

Autism spectrum disorder (ASD) is a frequent neurodevelopmental disease, whose diagnosis is based exclusively on behavioral criteria: i) social interaction deficits and ii) restricted, repetitive and stereotyped patterns of behavior, interests and activities. The etiology of ASD is multifactorial an

In Nuclear Magnetic Resonance (NMR), radiofrequency (RF) pulses are used to modify the magnetization state of the system. The amplitude and energy of the pulses must comply with both harware limitations (amplifier, coil), and clinical regulation (Specific Absorption Rate). When the desired pulse fai

InSync is a research project at the interface of mathematics, computation, and biology, with the objective to decipher intercellular synchronization mechanisms responsible for generating robust circadian rhythms in peripheral tissues. Correctly phased oscillations of cellular circadian clocks ensure

Cell migration guidance allows cells to reach their target and appropriate location as is the case during embryogenesis. We showed in vitro that curved surfaces guide cell migration locally, with cells always migrating to concave areas and this is independently of gravity. In vivo, the curvature of

Implants are widely used in oral surgery. However, there remain risks of failure, which are difficult to anticipate. The main determinant of the implant surgical success is the implant stability at insertion and healing stages. The causes for implant failures, which depend on the biomechanical prope

Recently, we studied optical interferometry imaging methods and in particularly the interference patterns originating from the interaction of light waves with an eye. These interference patterns are inherently complex, containing information about the organization of cell structures at sub-micron sc

In the innovative connectomics field, only diffusion magnetic resonance imaging (dMRI) tractography allows building a complete structural connectome non-invasively. However, dMRI tractography results are still controversial compared to the ground truth white matter (WM) anatomy. DMRI tractography al

For people with ventricular tachycardia, the electrical wave traveling through the heart is chaotic and this affects the heart's pumping function. One of the major treatments of this arrhythmia is catheter ablation which consists in destroying small areas of heart tissue to isolate or destroy the ca

The pathological processes leading to Alzheimer’s (AD) and Parkinson’s (PD) diseases start decades before the onset of the typical clinical symptoms. However, current diagnosis comes quite late in the course of the disease, while evidence underlines the multiple benefits that would be associated wit

Water uptake by the roots of land plants is a key process for plant survival (and, indirectly, for our survival as well). In the actual context of climate change, water scarcity and water usage conflicts put pressure on farming conditions. A better understanding of water transport from outside of th

Functional Magnetic Resonance Imaging (fMRI) is the dedicated modality for studying functional brain connectivity (FC). The analysis of fMRI data (3D + time) allows the identification of brain regions whose temporal activity, also called timecourse, is strongly correlated: these regions form what ar

High-throughput RNA sequencing (RNA-seq) is a unique tool for the discovery of medical biomarkers and drug targets. However, while nearly one million human RNA-seq libraries are publicly available, this treasure trove of medical information cannot realize its full potential because it is impossible

Microtubules are semi-flexible and dynamic filaments that play major roles in vivo. During mitosis, they appear highly curved compared to in vitro. It suggests that microtubule bending rigidity may play a role and be regulated. While it is established that microtubule dynamics contribute to cell div

The size of the instances that current experimental settings can solve by DNA assembly is very limitted (typically < 10). This is due to two limiting factors: an important error rate (~1/10.000), and the difficulty to generate enough significantly different strands for the reaction to be selective

Cancer deaths occur in the vast majority of cases in patients with metastatic disease. Currently, although the prognosis depends on the number and type of organs affected, on the degree of invasion and the survival can range from weeks to years, patients with metastatic disease are all grouped into