Project description
Predicting the structure and function of RNA molecules
Recent years have witnessed an explosion in the discovery of RNA molecules, namely microRNAs, small nucleolar RNAs, piRNAs and others, generating the need for robust methods capable of predicting their structure and function. To address this need, the EU-funded RNA-RAPSODY project proposes a mathematical framework that can integrate multiple biological and structural parameters of RNA molecules and generate meaningful biological results. Implementation of such an approach in science will provide important information about RNA molecules implicated in molecular and genetic processes of medical and pharmaceutical significance.
Objective
The proposed bioinformatics project has strong ties to even several diverse disciplines, namely computer science, molecular biology, genetics, mathematics and statistics. RNA Biology plays a central role in bioinformatics research such that numerous model-driven algorithms and methods are developed to predict and calculate structures and functions or compare sequences of RNA molecules that are essential in molecular and genetic processes and thus for medical and pharmaceutical applications.
Many of these problems can be cleanly phrased as optimization problems with 'optimal substructure' and thus solved exactly and efficiently by dynamic programming (for arbitrary parametrization of the objective function). This project will systematically explore the impact of parameter changes on the quality of results of DP optimization methods, such as predictions of molecule structures or comparison of sequences. Our approach strongly relies on algebraic dynamic programming (ADP), which decouples the decomposition of the search space from the algebra used to compute a final result. Thus, the ADP framework provides a unified setting and a generic implementation to quickly test working hypotheses. Here, it enables naturally implementing the suggested parametric optimization by developing novel algebras. Those include the polytope algebra, which allows to segment the parameter space based on its impact of the final prediction, and a formal derivative algebra, which allows to compute the derivative of ensemble predictions with respect to a given parameter. Conversely, those methods can be used to learn the optimal parameter sets based on a reference set of instances. This will result in deeper insights into robustness of the algorithms to changes of parameters or input data and hence, results can be assessed based on robustness measures and leads to the calculation of biologically more meaningful results.
The overall methodology will be applied to problems in RNA Bioinformatics.
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.
- engineering and technology industrial biotechnology biomaterials bioplastics polylactic acid
- natural sciences mathematics pure mathematics algebra
- natural sciences biological sciences genetics RNA
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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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H2020-EU.1.3. - EXCELLENT SCIENCE - Marie Skłodowska-Curie Actions
MAIN PROGRAMME
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H2020-EU.1.3.2. - Nurturing excellence by means of cross-border and cross-sector mobility
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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.
MSCA-IF - Marie Skłodowska-Curie Individual Fellowships (IF)
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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) H2020-MSCA-IF-2020
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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.
91128 PALAISEAU CEDEX
France
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.