Objective
Tissues are multicellular systems organized into niches, highly specialized communities of spatially co-localized cells (spatial neighborhood) that interact with one another (intercellular signaling), shaping their coordinated functions (intracellular states). Advances in single-cell sequencing and spatially resolved technologies now enable the reconstruction of whole-tissue spatial atlases spanning millions of cells and thousands of molecular features (e.g. transcriptomics, epigenomics). However, identifying functional niches from these data remains challenging due to the complexity and multidimensionality of biological processes, as well as the scale of modern datasets. INSPiRe project proposes a novel graph deep learning–based computational framework that integrates single-cell multi-omics with spatial transcriptomics to systematically identify and characterize cellular niches. Unlike existing approaches, our method jointly encodes three complementary dimensions of tissue organization: (i) cellular neighborhood and proximity, (ii) intercellular communication via ligand–receptor interactions, and (iii) intracellular, pathway-specific signaling activity, a combination not addressed by current tools. Leveraging adversarial learning and efficient graph representations, the framework generates interpretable and scalable cell embeddings from large multi-tissue datasets, quantitatively capturing niche structure and providing a functional understanding of how cellular niches emerge within tissue microenvironments. This is a timely and innovative project that will advance our understanding of tissue biology and disease mechanisms, with applications across healthy, developmental, and diseased tissues. Moreover, the project will provide the newly-formed researcher hands-on experience in advanced computational methods, gaining in-depth knowledge of modeling complex systems, while also developing project management and leadership skills, through a structured training plan.
Fields of science (EuroSciVoc)
CORDIS classifies projects with EuroSciVoc, a multilingual taxonomy of fields of science, through a semi-automatic process based on NLP techniques. See: The European Science Vocabulary.
CORDIS classifies projects with EuroSciVoc, a multilingual taxonomy of fields of science, through a semi-automatic process based on NLP techniques. See: The European Science Vocabulary.
- natural sciences computer and information sciences computational science
- natural sciences computer and information sciences artificial intelligence machine learning deep learning
- natural sciences biological sciences histology
- natural sciences biological sciences genetics epigenetics
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Keywords
Project’s keywords as indicated by the project coordinator. Not to be confused with the EuroSciVoc taxonomy (Fields of science)
Project’s keywords as indicated by the project coordinator. Not to be confused with the EuroSciVoc taxonomy (Fields of science)
Programme(s)
Multi-annual funding programmes that define the EU’s priorities for research and innovation.
Multi-annual funding programmes that define the EU’s priorities for research and innovation.
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HORIZON.1.2 - Marie Skłodowska-Curie Actions (MSCA)
MAIN PROGRAMME
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Topic(s)
Calls for proposals are divided into topics. A topic defines a specific subject or area for which applicants can submit proposals. The description of a topic comprises its specific scope and the expected impact of the funded project.
Calls for proposals are divided into topics. A topic defines a specific subject or area for which applicants can submit proposals. The description of a topic comprises its specific scope and the expected impact of the funded project.
Funding Scheme
Funding scheme (or “Type of Action”) inside a programme with common features. It specifies: the scope of what is funded; the reimbursement rate; specific evaluation criteria to qualify for funding; and the use of simplified forms of costs like lump sums.
Funding scheme (or “Type of Action”) inside a programme with common features. It specifies: the scope of what is funded; the reimbursement rate; specific evaluation criteria to qualify for funding; and the use of simplified forms of costs like lump sums.
HORIZON-TMA-MSCA-PF-EF - HORIZON TMA MSCA Postdoctoral Fellowships - European Fellowships
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Call for proposal
Procedure for inviting applicants to submit project proposals, with the aim of receiving EU funding.
Procedure for inviting applicants to submit project proposals, with the aim of receiving EU funding.
(opens in new window) HORIZON-MSCA-2025-PF
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Net EU financial contribution. The sum of money that the participant receives, deducted by the EU contribution to its linked third party. It considers the distribution of the EU financial contribution between direct beneficiaries of the project and other types of participants, like third-party participants.
52074 Aachen
Germany
The total costs incurred by this organisation to participate in the project, including direct and indirect costs. This amount is a subset of the overall project budget.