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Publications

URGI members are underlined in authors list. In the talks sections, names in bold are the speakers.

There are different types of publications, Papers with reading comittee (ACL), Papers in books (ACT), Invited talks (INV), Talks (COM), Posters (COM), Specialised Media and Press (SMP) and Thesis.

Other
COM (communication)
04 Sep 2023 [hal-04195707] PlantBioinfoPF (URGI) et son offre de service d'annotation des éléments transposables dans les génomes
Les outils d'annotation des éléments transposables (ET) sont de plus en plus accessibles au grand public mais peuvent rester complexes dans le traitement de génomes de grandes tailles ou en trop grand nombre pour des non initiés. La plateforme PlantBioinfoPF hebergée par l'URGI propose l'accès à des ressources de calculs adaptées et un service d'annotation des ET dans les génomes. Illustration au travers de 2 projets et présentation de l'offre de service.
et al.
In ProdINRA
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COM (communication)
30 Aug 2023 [hal-04191716] Development of a knowledge graph framework to ease and empower translational approaches in plant research: a use-case on grain legumes
While the continuing decline in genotyping and sequencing costs has largely benefited plant research, some key species for meeting the challenges of agriculture remain mostly understudied. As a result, heterogeneous datasets for di erent traits are available for a significant number of these species. As gene structures and functions are to some extent conserved through evolution, comparative genomics can be used to transfer available knowledge from one species to another. However, such a translational research approach is complex due to the multiplicity of data sources and the non-harmonized description of the data. Here, we provide two pipelines, referred to as structural and functional pipelines, to create a framework for a NoSQL graph-database (Neo j) to integrate and query heterogeneous data from multiple species. We call this framework Orthology-driven knowledge base framework for translational research (Ortho_KB). The structural pipeline builds bridges across species based on orthology. The functional pipeline integrates biological information, including QTL, and RNA-sequencing datasets, and uses the backbone from the structural pipeline to connect orthologs in the database. Queries can be written using the Neo j Cypher language and can, for instance, lead to identify genes controlling a common trait across species. To explore the possibilities o ered by such a framework, we populated Ortho_KB to obtain OrthoLegKB, an instance dedicated to legumes. The proposed model was evaluated by studying the conservation of a flowering-promoting gene. Through a series of queries, we have demonstrated that our knowledge graph base provides an intuitive and powerful platform to support research and development programmes.
et al.
In ProdINRA
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COM (communication)
25 Jul 2023 [hal-04169996] REPET evolutions: faster and easier
The detection and annotation of transposable elements (TEs) are now considered mandatory to any genome sequencing project. To this aim, the REPET package integrates bioinformatics pipelines dedicated to detect, annotate and analyse TEs in genomic sequences. The two main pipelines are (i) TEdenovo, that search for interspersed repeats, build consensus sequences and classify them according to TE features and (ii) TEannot, which mines a genome with a library of TE sequences, for instance the one produced by the TEdenovo pipeline, to provide TE annotations. The REPET package is in continuous improvement. Several implementations and algorithms to reduce the time required for analysing large genome have been tested. With our new speed improvements and tuned annotation strategies, REPET is now able to annotate and analyse easily large genomes up to 3 Gb. Now, we chain all required steps through a process called "Repet-Factory". This process uses parameters optimized for specificity and computing time. It is capable of successively annotate several genomes in batches with all the traceability required for reproducibility. We also simplified the distribution of REPET by developing a Docker image of REPET
et al.
In ProdINRA
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COM (communication)
11 Jul 2023 [hal-04158902] Characterization of Transposable Elements in Pangenomes
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et al.
In ProdINRA
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COM (communication)
11 Jul 2023 [hal-04158362] Characterization of Transposable Elements in Pangenomes
[...]
et al.
In ProdINRA
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COM (communication)
07 Jul 2023 [hal-04156193] REPET novelties : a versatile and modular package
The detection and annotation of transposable elements (TEs) are now considered mandatory to any genome sequencing project. To this aim, the REPET package integrates bioinformatics pipelines dedicated to detect, annotate and analyse TEs in genomic sequences. The two main pipelines are (i) TEdenovo, that search for interspersed repeats, build consensus sequences and classify them according to TE features and (ii) TEannot, which mines a genome with a library of TE sequences, for instance the one produced by the TEdenovo pipeline, to provide TE annotations. The REPET package is in continuous improvement. Several implementations and algorithms to reduce the time required for analysing large genome have been tested. With our new speed improvements and tuned annotation strategies, REPET is now able to annotate and analyse easily large genomes up to 3 Gb. Now, we chain all required steps through a process called ”Repet-Factory”. This process uses parameters optimized for specificity and computing time. It is capable of successively annotate several genomes in batches with all the traceability required for reproducibility. We also simplified the distribution of REPET by developing a Docker image of REPET. And for an HPC usage, REPET is currently developped in SnakeMake with dependencies in Apptainer.
et al.
In ProdINRA
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Update: 19 Nov 2010
Creation date: 01 Dec 2009