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Section: New Results

Sequence annotation

Participants : François Coste, Aymeric Antoine-Lorquin, Catherine Belleannée, Guillaume Collet, Gaëlle Garet, Clovis Galiez, Laurent Miclet, Olivier Quenez, Jacques Nicolas, Valentin Wucher.

Refinement of mi-RNA regulation network thanks to concept analysis MicroRNAs (miRNAs) are small RNA molecules that bind messenger RNAs (mRNAs) to silence their expression. To improve the discrimination between true and false interactions during their prediction, we defined a repair process based on the hypothesis that the true graph is formed by interaction modules represented by formal concepts, i.e. set of miRNAs having the same regulation profile. To validate our hypothesis and method, we have extracted parameters from a biological miRNA/mRNA network and used them to build random networks. Each repaired network can be evaluated with a score balancing the number of edge changes and the conceptual adequacy in the spirit of the minimum description length principle. [J. Nicolas, V. Wucher] [32]

Analogical proportions and the factorization of information in distributive lattices. We have conducted theoretical studies to elucidate whether formal concept lattices can have properties that could be used in further studies. In this direction, analogical proportions are statements involving four entities, of the form 'A is to B as C is to D'. They play an important role in analogical reasoning. They have been formalized in both a propositional logic setting and an algebraic setting. We define and study analogical proportions in the general setting of lattices, and more particularly of distributive lattices. We discussed the decomposition of analogical proportions in canonical proportions as well as the resolution of analogical proportion equations, and illustrate especially on the case of Boolean lattices, which reflects the logical modeling. [L. Miclet] [24] , [29]

Bioinformatics and Artificial Intelligence In this book chapter, we introduce the main objects studied in Bioinformatics at different levels (the macromolecules, their interactions as well as the knowledge formalization or extraction) and present meanwhile a survey of the contribution and influence of Artificial Intelligence to this research field on related key tasks (gene prediction, functional annotation, structure prediction, transcriptomics analysis, network acquisition and analysis, knowledge integration and formalization, information retrieval and extraction from documents, ...). [F. Coste] [33]

Genome studies: fast assembly and SNP identification This work is a follow-up of collaborations with the GenScale team and the GenOuest platform. We reported the first identification of a set of SNPs isolated from the genome of I. ricinus - an important vector of pathogens in Europe, by applying a reduction of genomic complexity, pyrosequencing and new bioinformatics tools[21] [Online publication] . We also contributed to show that the genome assembly program MINIA is successfully able to assemble a 100 Mbp genome on a very low-end, low-power system with 512 MB RAM and a 32 GB flash drive such as a Raspberry Pi. [G. Collet, O. Quenez] [34] [Online publication]