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Computational approaches with the objective to explore intra and cross-species interactions and their role in all domains of life

Grant number: 19/22845-9
Support type:Regular Research Grants
Duration: March 01, 2020 - February 28, 2022
Field of knowledge:Physical Sciences and Mathematics - Computer Science - Computational Mathematics
Cooperation agreement: INRIA
Mobility Program: SPRINT - Projetos de pesquisa - Mobilidade
Principal Investigator:André Fujita
Grantee:André Fujita
Principal investigator abroad: Marie-France Sagot
Institution abroad: Institut National de Recherche en Informatique et en Automatique, France
Home Institution: Instituto de Matemática e Estatística (IME). Universidade de São Paulo (USP). São Paulo , SP, Brazil
Assoc. researchers:Ariel Mariano Silber ; Carlos Alberto Moreira Filho ; Carlos Eduardo Ferreira ; Cristina Gomes Fernandes
Associated research grant:18/21934-5 - Network statistics: theory, methods, and applications, AP.TEM

Abstract

The CAPOEIRA project will cover theoretical computer science (essentially graph theory), mathematics (combinatorics, statistics, and probability), and the development of algorithms to address various biological questions, in particular, the intra and cross-species interactions, which have implications in all aspects of life sciences, including health, ecology, and environment. Two main general topics will be addressed, namely evolution/co-evolution, and biological network (graph/hypergraph) analysis and comparison. Both have already been explored by the partners (see Section 11.1 on the Joint publications of the partners). Some of the specific questions to be treated within each problem will thus represent a continuation of previous works. Each problem however also contains entirely new questions. Furthermore, the interaction with biologists within the project at both the modelling and validation steps is entirely new in the context of the past collaboration between the two partners. The first topic concerns better understanding and characterising the moment of speciation leading to new species on one hand, and on the other, how one set of species may influence the evolution of another. The second topic concerns metabolism on one hand, and (post-)transcriptional regulation on the other, with the post-transcriptional level involving also inference "from scratch" of the main actors, namely the non-coding RNAs and their targets, and the regulatory network they form. In the first two cases (of metabolism and transcriptional regulation), we will assume that the networks are already inferred albeit with possibly numerous missing and incorrect data. Finally, in the case of regulation, we will also consider the problem of inferring variants, notably related to alternative splicing, from a set of RNA-seq data using a de Bruijn graph approach.Overseeing these two main topics are the issues of knowledge representation and model revision that will also be addressed. These are crucial in the life sciences, and notably in the context of post-transcriptional regulation by non-coding RNAs, for which the different actors, features, and overall mechanisms are constantly being questioned and revised. (AU)