CONTACT  |  SITE MAP  |  ABOUT US  |  TEAM   
Go to GnpIS Go to WheatIS Go to faidare Go to repet tool Go to RepetDB

About us

You are here : Home / Home URGI / About us / Publications

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)
 14 Feb 2025 [hal-04947937] The Brachypodium distachyon Pangenome Highlights Transposable Element Dynamics in the Species
Individuals of the same species independently undergo transposable elements (TEs) insertions, causing inter-individual genetic variability. This variability is the basis of the natural selection that leads to an increased adaptation of individuals to their environment. A way to search for the potential role of TEs in host adaptation is through a pangenomic approach. The advent of long-read sequencing technologies makes now possible to approach this question better using several whole-genome de novo assembled of the same species to avoid the bias introduced by a single reference genome. We developed a new pipeline, called panREPET, to handle this data. It compares TE copies between each pair of individuals then identifies TE copies shared by a group of individuals. As we work on assembled genomes, we access to exact genomic contexts of TE copies and their exact sequences. We described the shared TEs insertions among 54 Brachypodium distachyon genomes. panREPET allows to improve TE families evolutionary history description and to date insertion events more precisely thanks to shared TE insertions. We dated two major TE bursts corresponding to major climate events: around 22 kya during the Last Glacial Maximum and 10 kya during the Holocene. We searched for factors affecting TE families evolutionary dynamics, we found that climate is a factor that may explain certain TE dynamics.
et al.
In ProdINRA
...
COM (communication)
 06 Feb 2025 [hal-04932327] URGI services to support FAIR research data management
The Unit of Resources for Genomic-Info (URGI) of the French National Research Institute for Agriculture, Food and Environment (INRAE) supplies services dedicated to the FAIR management of research data on plants of interest for agriculture and forestry. The services address various stages of the data cycle (https://rdmkit.elixir-europe.org/data_life_cycle). They support other research infrastructures as well as major research projects with their data management plans. URGI develops project-specific data management guidelines, aligned on ELIXIR plant science community’s guidelines (https://rdmkit.elixir-europe.org/plant_sciences), which are then applied by the partners of projects (https://doi.org/10.5281/zenodo.12625360). These guidelines precise in particular how the data will be stored and reused all along the project. URGI services also support the data collection stage, by providing reference data (identifiers, genetic resources) and by defining a template for sample metadata collection. This template is aligned on existing standards such as MIAPPE and MCPD and was developped with the ELIXIR plant science community (https://faircookbook.elixir-europe.org/content/recipes/reusability/miappe.html). During the data processing phase, URGI provides a space for sharing and curating metadata (FAIRDOM-SEEK). If data is not suitable for storage in FAIRDOM-SEEK, a tool has been developed to deploy a standard folder and file structure for projects. URGI also performs metadata curation and enrichment. As part of data preservation, URGI supplies scripts for submitting data to international archives such as BioSamples and ENA. In addition it offers guidance on submitting genetic resources and phenotyping data to the INRAE information system GnpIS (https://doi.org/10.25504/FAIRsharing.dw22y3) as well as to the French national catalog of research data, Recherche Data Gouv, for data not covered by GnpIS, or by the EBI's European archives. It participates significantly in the reuse stage of the data cycle by developing and maintaining metadata standards and ontologies for plant phenotyping data (including forests).
et al.
In ProdINRA
...
COM (communication)
 03 Feb 2025 [hal-04927258] Forest Tree data in FAIDARE, a plant data discovery portal
Forest adaptation to climate change is at the heart of forestry research, as forests are directly affected by these disruptions that are likely to diminished their ecosystems as they loses diversity. Moreover, a significant portion of forest data holds precious heritage nature, as it is impossible to reproduce them due to the singular subject of study: trees, which have a particularly long life cycle. Plant research requires the integration of heterogeneous and dispersed datasets. However, these datasets are often structured in different formats that are not standardised and stored in various databases across the world. This makes it difficult to discover and integrate them in a way that allows them to be analysed and reused. To tackle this issue, FAIDARE has been designed. It simplify this work and maximise the visibility and reuse of forest research data, in accordance with the FAIR principles (Findable, Accessible, Interoperable, Reusable). FAIDARE is a data discovery portal developed for the european plant science community (ELIXIR). It allows the search of public data on plant biology from a federation of more than forty established data repositories over the world. It eases the findability and access of relevant datasets of most plant research data types, including genotyping, phenotyping and germplasms, via an easy-to-use web interface. It also provides a standard interface that can be accessed programmatically via web services conform to the Breeding API standard. Forest data from various sources are already accessible through FAIDARE. These data include the genetic resources conserved and distributed by the French forest Biological Resource Center ARTEMIS and their phenotypic and genotypic characterisation (currently 1,252 accessions from 3 species but more to come).The portal also hosts phenotypic data from the French network of comparative plantations and arboretums, GEN4X (1,232 trials genotype x environment and 8 arboretums observed over 60 years). Furthermore, FAIDARE includes project data of H2020 GenTree project, data from the French collection of forest genetic resources with in-situ and ex-situ conservation units and the sequencing and annotations of the oak and poplar genomes.
et al.
In ProdINRA
...
COM (communication)
 06 Dec 2024 [hal-04822964] PHENET-EMPHASIS Data Management Training
Training overview PHENET and EMPHASIS-GO communities share converging data management issues and needs. To this end, we organized a data management training course in Paris on 04, 05 and 06 December, open to the PHENET-EMPHASIS community. Pedagogical objectives At the end of this course, participants will have acquired theoretical and practical knowledge of : * the management of plant phenotyping data in accordance with FAIR principles * the use of plant community (meta)data standards. They will also have standardised a dataset in MIAPPE format and identified ways of improving the management of their data. This training was organised by PHENET and EMPHASIS with support from URGI. Link to the Training Website: https://moodle.france-bioinformatique.fr/course/view.php?id=31& et al.
In ProdINRA
...
COM (communication)
 06 Dec 2024 [hal-04822902] AGENT Guidelines for dataflow
The AGENT project aims at integrating data from different sources (genebanks, research institutes, international archives) and types (passport, phenotypic, genomic data). These guidelines have been developed to explain the data flow within the AGENT project and should be useful for other projects.
et al.
In ProdINRA
...
COM (communication)
 25 Oct 2024 [hal-04739711] Atelier « L'IA en pratique: de la perception à l'application »
[...]
et al.
In ProdINRA
...
« Previous 1 2 3 4 5 6 7 8 9 10 ... 16 Next  »
Update: 19 Nov 2010
Creation date: 01 Dec 2009



Loading...