Data-Gouv-ML/pcri-informations-sur-les-projets-laureats huggingface dataset:
How viruses switch between glycan and protein receptors and what it means for past and future pandemics (GLYCvsPROT)

Framework: Horizon Europe — Excellent Science
Programme: European Research Council (ERC)
Theme: European research council
Destination: Starting grants
Action type: ERC actions
Panel: Molecules of Life: B iological  Mechanisms , Structures  and Functions
Panel description: For all organisms : Molecular biology , biochemistry, structural biology, molecular biophysics , synthetic and chemical biology, drug design, innovative methods and modelling
Countries involved: United Kingdom
Call: ERC STARTING GRANTS (ERC-2024-STG, 2024)
Start date: 2025-06-01
End date: 2030-05-31
Duration (months): 60.0
Total project cost (EUR): 1492478.0
EU funding (EUR): 1492478.0
Participants: 1
Project status: SIGNED

To enter a host cell a virus needs to bind a receptor on the cell surface. Typically, viruses use specialised glycoproteins to bind to either glycans or proteins as receptors. The specificity and affinity of a virus glycoprotein for cellular receptors is a key determinant for which hosts a virus can infect. Certain enveloped viruses of high pandemic potential, such as influenza A and coronaviruses, have an ability to change their receptor specificity from a glycan to a protein receptor, and in some instances, even bind both with one glycoprotein. These receptor transitions might have contributed to emergence of pandemic viruses, such as SARS-CoV-2, and may underlie future pandemics. Studying the structure and evolution of viral glycoproteins and their receptor complexes can help to understand the mechanisms viruses use to cross the human species barrier. I will build on my recent studies and pilot data on the structure and evolution of viral glycoproteins, and employ the glycoproteins of influenza viruses and coronaviruses which can bind to either or both receptor types to show: - how different receptor types are recognised structurally by very similar viral glycoproteins - how receptor type affects interaction avidity and mechanisms of viral fusion - how receptor transitions may arise during viral evolution and influence its direction This will be achieved by combining structural, biochemical, and biophysical approaches to reveal interactions between viral glycoproteins, influenza haemagglutinins and coronavirus spikes, with glycan and protein receptors. My studies will provide key new insights into the plasticity of viral glycoproteins and the evolutionary pathways associated with changes in receptor specificity, thus shedding light onto emergence of pandemic viruses such as SARS-CoV-2 and pandemic influenza A viruses. Importantly, this will also facilitate monitoring of emerging pathogens and increase our future pandemic preparedness.

Keywords: viral entry,viral receptors,influenza a,coronaviruses,cryoem,crystallography
Medical Image Analysis with Normative Machine Learning (MIA-NORMAL)

Framework: Horizon Europe — Excellent Science
Programme: European Research Council (ERC)
Theme: European research council
Destination: Consolidator grants
Action type: ERC actions
Panel: Computer Science and Informatics
Panel description: Informatics and information systems, computer science, scientific computing, intelligent systems
Countries involved: Germany
Call: ERC CONSOLIDATOR GRANTS (ERC-2022-COG, 2022)
Start date: 2023-09-01
End date: 2028-08-31
Duration (months): 60.0
Total project cost (EUR): 1997841.0
EU funding (EUR): 1997841.0
Participants: 1
Project status: SIGNED

As one of the most important aspects of diagnosis, treatment planning, treatment delivery, and follow-up, medical imaging provides an unmatched ability to identify disease with high accuracy. As a result of its success, referrals for imaging examinations have increased significantly. However, medical imaging depends on interpretation by highly specialised clinical experts and is thus rarely available at the front-line-of-care, for patient triage, or for frequent follow-ups. Very often, excluding certain conditions or confirming physiological normality would be essential at many stages of the patient journey, to streamline referrals and relieve pressure on human experts who have limited capacity. Hence, there is a strong need for increased imaging with automated diagnostic support for clinicians, healthcare professionals, and caregivers. Machine learning is expected to be an algorithmic panacea for diagnostic automation. However, despite significant advances such as Deep Learning with notable impact on real-world applications, robust confirmation of normality is still an unsolved problem, which cannot be addressed with established approaches. Like clinical experts, machines should also be able to verify the absence of pathology by contrasting new images with their knowledge about healthy anatomy and expected physiological variability. Thus, the aim of this proposal is to develop normative representation learning as a new machine learning paradigm for medical imaging, providing patient-specific computational tools for robust confirmation of normality, image quality control, health screening, and prevention of disease before onset. We will do this by developing novel Deep Learning approaches that can learn without manual labels from healthy patient data only, applicable to cross-sectional, sequential, and multi-modal data. Resulting models will be able to extract clinically useful and actionable information as early and frequent as possible during patient journeys.

Keywords: normative machine learning,out of distribution detection,medical imaging,health screening,opportunistic lesion detection,fetal and neonatal care
Decoding and designing biomolecular systems with hybrid DNA:RNA: protein nanotechnology (BIOHYBRITE)

Framework: Horizon Europe — Excellent Science
Programme: Marie Skłodowska-Curie Actions (MSCA)
Theme: Marie Skłodowska-Curie
Destination: Doctoral Networks
Action type: Marie Skłodowska-Curie actions
Panel: Chemistry
Countries involved: Germany,United Kingdom,France,Spain,Italy,Estonia,Belgium
Call: MSCA Doctoral Networks 2024 (HORIZON-MSCA-2024-DN-01, 2024)
Start date: 2026-03-01
End date: 2030-02-28
Duration (months): 48.0
Total project cost (EUR): 4632374.98
EU funding (EUR): 4507972.56
Participants: 18
Project status: SIGNED

In recent years, we have witnessed the emergence of DNA nanotechnology that enables self-assembly of some of the largest and most complex functional molecular systems to date. Simultaneously, RNA plays a pivotal role in nanomedical advancements, notably in the development of Covid-19 vaccines. Moreover, utilising deep learning to address the protein prediction challenge paves the way for de novo protein design in the realm of protein nanotechnology. BioHYBRITE is designed as an innovative and pioneering training network, with the unique vision of developing the next-generation of biomolecular systems based on integrated hybrid DNA:RNA:Protein nanotechnology. BioHYBRITE brings together leading European research groups for combining all sequence-based biomolecules into a unified bottom-up nanobiotechnology. The consortium will collectively build modular platforms with a range of novel functions for molecular sensing, information processing and actuation. Thereby the collaboration synergizes a unique toolset of theoretical and experimental methods for designing and understanding the hybrid systems including state-of-the-art single-molecule and superresolution technology. The outcome will be a new generation of young experts in the development of smart, self-assembling, hybrid nano-devices that detect and act in complex biomolecular systems and will form the basis of a future nanomedicine based on active molecular systems. The doctoral candidates will be trained in all aspects for programmed design of hybrid bottom-up nanostructures, their characterization and use for decoding and interacting with biomolecular systems, thereby fully benefiting from the synergies of the different partners’ competences. The innovative and applied focus is supported by the involvement of pioneering industrial partners providing complementary skills training as well as intersectoral exchange of the doctoral candidates with a potential high impact in future exploitations.

Keywords: dna nanotechnology,protein design,biosensing,rna nanotechnology,biomolecule design,single molecule sensing
When your enemy becomes your friend: Evolution of the interaction between fungi and land plants (FRIENEMIES)

Framework: Horizon Europe — Excellent Science
Programme: European Research Council (ERC)
Theme: European research council
Destination: Starting grants
Action type: ERC actions
Panel: Environmental B iology, Ecology  and E volution
Panel description: For all organisms : Ecology, biodiversity, environmental change , evolutionary biology, behavioural ecology, microbial ecology , marine biology, ecophysiology, theoretical developments and mod elling
Countries involved: Germany
Call: ERC STARTING GRANTS (ERC-2024-STG, 2024)
Start date: 2024-10-01
End date: 2029-09-30
Duration (months): 60.0
Total project cost (EUR): 1499190.0
EU funding (EUR): 1499190.0
Participants: 1
Project status: SIGNED

Plants live in close association with microbes, establishing interactions that range from beneficial to detrimental. Molecular plant-microbe interactions have been extensively studied in flowering plants, whereas research in non-seed plant lineages has been hindered by the lack of pathosystems reflecting natural plant-microbe interactions. My team and I identified the first example of a fungus that establishes opposite interactions with flowering and non-seed plants. We discovered that the fungus Trichoderma, which promotes plant growth, defense, and stress tolerance in flowering plants, is pathogenic for other land plant lineages (non-vascular plants and ferns) indicating unexpected differences in land plant immunity and fungus behavior. The overarching goal of our project FRIENEMIES is to decipher the molecular evolution of plant-microbe interactions from pathogenic to beneficial across land plants. In FRIENEMIES, my team and I will characterize the molecular mechanisms involved in disease in non-seed plants using three genetically tractable non-seed model plants (two bryophytes and the C-fern) and a diversity panel of sequenced Trichoderma strains where we will identify fungal effectors, plant susceptibility and resistance genes and signaling pathways relevant for pathogenic interactions. Combining omics, reverse genetics, natural variation, and phylogenetic analyses we will reveal the conservation of susceptibility/resistance mechanisms in other plant lineages and determine the emergence of mutualistic interactions between Trichoderma and land plants. We envision that FRIENEMIES will describe fundamental differences in immunity across land plants, discover potentially novel and conserved molecular mechanisms mediating plant-microbe interactions, define their evolutionary trajectories, and reveal the key evolutionary switches associated with major innovations in land plants underlying the transition between susceptibility, resistance, and mutualism.

Keywords: evompmi,plant molecular evolution
Veridi: AI-Powered Soil Biodiversity Analysis and Monitoring (VERIDI)

Framework: Horizon Europe — Innovative Europe
Programme: The European Innovation Council (EIC)
Theme: EIC Accelerator
Destination: Other destinations
Action type: EIC actions
Countries involved: Netherlands
Call: EIC Accelerator 2024 - Short application (HORIZON-EIC-2024-ACCELERATOR-01, 2024)
Duration (months): 24.0
Total project cost (EUR): 2500000.0
EU funding (EUR): 2500000.0
Participants: 1
Project status: SIGNED

Soil health and biodiversity are essential for ecosystem functionality and food system resilience, as soil acts as the primary agricultural medium and hosts over 25% of the world's biological diversity. Yet, more than 60% of European soils are degraded due to unsustainable practices, causing significant biodiversity threats and ecosystem service losses, costing Europe over €50B annually. Strategic initiatives like the UN Biodiversity Conference agreement and the EU's Biodiversity Strategy for 2030 support the global importance of soil biodiversity, with substantial investments aimed at combating biodiversity loss. The EU Soil Health Law marks a major advancement toward sustainable soil management. Nematodes, with their diverse ecological roles, serve as excellent bioindicators of soil health. The current market trends in soil research, driven by increasing global awareness and stringent regulatory requirements, present significant growth opportunities, particularly in biodiversity metrics that can enhance agricultural practices and sustainability. Yet, nematodes pose identification challenges with traditional manual methods being labor-intensive and prone to errors. Innovations like DNA sequencing and big data analytics introduce new assessment methods, yet they contend with challenges such as high costs and extended processing times. At Veridi, the development of the Automated Soil Biodiversity Identification system merges nematology with AI, providing a transformative solution for accurately measuring soil biodiversity. This innovation will advance soil research and support sustainable farming and environmental management, driving market growth and opening investment opportunities in the growing field of soil biodiversity. With EIC support, we plan to optimize the hardware and software, expand the database, thoroughly test and validate the system, deploy it end-to-end, conduct customer pilots, and scale up the platform to include fungi and insect analysis.

Keywords: soil biodiversity,nematode analysis,automated identification,artificial intelligence,sustainable agriculture,plant parasitic nematodes
Human genetic determinants of invasive group A streptococcal host-pathogen interactions (HG-iGAS)

Framework: Horizon Europe — Excellent Science
Programme: European Research Council (ERC)
Theme: European research council
Destination: Starting grants
Action type: ERC actions
Panel: Immunity, Infection and I mmunotherapy
Panel description: The immune system , related disorders  and their mechanisms , biology of infectious agents and infection, biological basis of prevention and treatment of infectious diseases , innovative imm unological tools and approaches , including  therapies
Countries involved: Netherlands
Call: ERC STARTING GRANTS (ERC-2024-STG, 2024)
Start date: 2025-01-01
End date: 2029-12-31
Duration (months): 60.0
Total project cost (EUR): 1496978.75
EU funding (EUR): 1496978.75
Participants: 1
Project status: SIGNED

Group A streptococcus (GAS) is a major, human specific, bacterial pathogen. Most people suffer from mild infections, while only a few develop invasive GAS (iGAS) infections. These cases of iGAS infections are unexplained as they strike otherwise healthy people. The human specificity of GAS and the interindividual variability upon infection with GAS are poorly understood. My proposal aims to close both knowledge gaps: I hypothesize that single-gene defects of antistreptococcal immunity increase susceptibility to human-specific GAS virulence factors in some people, thereby underlying their iGAS infections. I propose an innovative framework to unravel iGAS pathophysiology in humans, by applying a strategy to integrate the studies of human genetics and host-pathogen interactions at the molecular level. This project focuses on patients suffering from iGAS infections. Most patients have been enrolled, sampled, and whole exome sequencing (WES) performed. Additional patients will be recruited. The human gene(s) underlying iGAS infections will be identified using complementary WES-based approaches. The discovered inborn error(s) of immunity to GAS and the host-pathogen interactions will be dissected at the molecular, cellular, tissue, and whole-organismal levels, including with patients’ cells and clinical GAS strains. The immediate availability of patients’ genetic data provides a secure starting point for an efficient implementation of this proposal. Preliminary analyses have yielded two promising candidate genes. Access to patients’ specimens and clinical GAS isolates offers an exceptional opportunity to characterize patient-specific host-pathogen interactions. Thus, we are in a unique position to discover the first human genetic determinant(s) of iGAS host-pathogen interactions. This project may uncover the role of genes in human physiology beyond the infectious phenotype and accelerate the development of preventative strategies against GAS infections.

Keywords: host pathogen interactions virulence factors group a streptococcus invasive group a streptococcus infections human genetics of infectious diseases inborn errors of immunity
Cracking the code of amyloid polymorphism: Integrating cryoEM and machine learning to unravel impact of small aggregation modulators on amyloid fibril polymorphism (AMI-CryoML)

Framework: Horizon Europe — Widening Participation and Strengthening the European Research Area
Programme: Widening participation and spreading excellence
Theme: Attracting and mobilising the best talents
Destination: Attracting and mobilising the best talents
Action type: Marie Skłodowska-Curie actions
Panel: Life Sciences
Countries involved: Lithuania
Call: ERA Fellowships (HORIZON-WIDERA-2024-TALENTS-02, 2024)
Start date: 2026-02-01
End date: 2028-01-31
Duration (months): 24.0
Total project cost (EUR): 181136.16
EU funding (EUR): 181136.16
Participants: 1
Project status: SIGNED

Neurodegenerative diseases such as Alzheimer's (AD), Parkinson’s (PD), and prion-related disorders pose major global health challenges due to their progressive nature and lack of effective treatments. Central to these conditions is the misfolding and aggregation of proteins into amyloid structures, which cause severe cellular damage. Despite advances in understanding amyloid aggregation, the role of structural polymorphism in these processes remains underexplored. This proposal aims to address this gap by investigating amyloid aggregation modulators and their effects on aggregation kinetics and polymorphism. The project has five main objectives: 1. Data Collection on agregation modulators: Systematically gather and curate data on known modulators that impact amyloid aggregation, focusing on their chemical properties and mechanisms. 2. Aggregation kinetics studies: Study the impact of selected modulators on the kinetics of amyloid self-aggregation using ThT assays. This includes analyzing how modulators influence different phases of aggregation and testing their efficacy on a range of amyloids, including prions, CsgA, and α-synuclein. 3. Study structural polymorphisms via CryoEM: Utilize Cryo-Electron Microscopy (CryoEM) to resolve and map the structural polymorphs of amyloids under various conditions. Providing insights into impact of modulators on structural polymorphism and aggregation kinetics. 4. AmyloGraph database enhancement: Develop a new module for the AmyloGraph database to store and analyze data on modulators, aggregation kinetics, and structural polymorphisms. 5. Development of ML models: Leverage machine learning to develop predictive and generative models to forecast amyloid aggregation kinetics and modulator effects, incorporating structural polymorphisms, and generate new modulators targeting specific polymorphic forms.

Keywords: amyloid prion polymorphism machine learning cryoem neurodegenerative diseases chronic wasting disease transmission aggregation
Repro-Fiction: Synthesising Literature and Reproductive Healthcare (REPROFIC)

Framework: Horizon Europe — Widening Participation and Strengthening the European Research Area
Programme: Widening participation and spreading excellence
Theme: Attracting and mobilising the best talents
Destination: Attracting and mobilising the best talents
Action type: Marie Skłodowska-Curie actions
Panel: Social Sciences and Humanities
Countries involved: Lithuania,Sweden
Call: ERA Fellowships (HORIZON-WIDERA-2024-TALENTS-02, 2024)
Start date: 2025-09-01
End date: 2027-08-31
Duration (months): 24.0
Total project cost (EUR): 181136.16
EU funding (EUR): 181136.16
Participants: 2
Project status: SIGNED

Elizabeth Grosz has astutely observed that the entire history of Western thought is permeated by “a profound somatophobia” (1994, 1). Female bodies, particularly their reproductive processes, have been viewed within medicine as prone to illness and disorder. They have historically been characterized as impure and polluting, with ‘leaky’ boundaries that disturb social order. Such representations have contributed to the reality that many conditions specific to women, such as endometriosis and dysmenorrhea, lack sufficient research, attention and prioritization, and have not received adequate funding and resources. This project contends that literature is where we should seek to gain oft-overlooked and undervalued insights into women’s healthcare practices across Europe. The project explores representations of the reproductive body as both a contested site and a potent source of knowledge and considers how contemporary writers connect their bodily trauma with the body politic. This project will increase cohesion between literary, medical, and policy discourses and create a template for analyzing and interpreting 'repro-fiction' that can be replicated in other geographical locations to envision a philosophy of reproductive justice where care for the body takes center stage.

Keywords: motherhood,narrative medicine,feminist literature
Monitoring Of Oceanic inteRnal tIdes usiNG fibre optic telecommunication cables (MOORING)

Framework: Horizon Europe — Excellent Science
Programme: Marie Skłodowska-Curie Actions (MSCA)
Theme: Marie Skłodowska-Curie
Destination: Postdoctoral Fellowships
Action type: Marie Skłodowska-Curie actions
Panel: Environment and Geosciences
Countries involved: Spain,United States
Call: MSCA Postdoctoral Fellowships 2021 (HORIZON-MSCA-2021-PF-01, 2021)
Start date: 2022-09-01
End date: 2024-10-31
Duration (months): 26.0
Total project cost (EUR): 165312.96
EU funding (EUR): 165312.96
Participants: 2
Project status: CLOSED

Ocean mixing plays a crucial role in the Earth’s climate as it balances the meridional overturning circulation that buffers global warming. Quantifying mixing is challenging because energy enters the ocean at basin-scale but it dissipates at cm-scale over the vast ocean. One common element in the cascade of energy towards small scales is the transfer of energy to internal waves, which ultimately drive ocean mixing. Energy transfers to the internal wave field are largely enhanced through flow interactions with topography. Observations of wave-topographic interactions are, however, scarce and its mechanistic understanding comes mainly from idealized process ocean studies, which lack a direct benchmark against nature. To fill the observational gap in ocean mixing, the MOORING project will explore wave-topographic interactions at unprecedented spatio-temporal resolution by combining novel submarine cable data with numerical advanced modelling. New data will be gathered using fibre-optic cables by means of a revolutionary technology, which has opened a new door for exploring bottom wave dynamics. The potential of these novel observations to identify ocean-mixing hotspots in the ocean remains, however, unknown. To shed light on this, I will gather conventional oceanographic measurements and integrate them in realistic high-resolution numerical simulations, leveraging my modelling skills. The MOORING project will bridge seismology and oceanography, integrating a variety of approaches, and it will allow me to be trained in observational methods at the hosting institution, while expanding my numerical skills in a secondment institution, fostering a network of national and international collaborators. The proposed approach could eventually be implemented at global scale with the aim to better close energy budgets and improve mixing parametrizations in climate change models for more accurate predictions.

Keywords: ocean mixing,internal tides,continental margins,wave topographic interactions,distributed acoustic sensing,submarine fiber optic cables,ocean turbulence