Research teams

Epigenetic Natural Variation

VarEpi 4 members 18 IJPB publications (2006-to date)

PhD project available in the lab - Tomato fruit epigenetics

The PhD project focuses on studying the mechanisms of epigenetic control of fruit ripening in tomatoes. The goal is to better understand the role of DNA methylation in regulating fruit ripening and to improve knowledge on the topic. Tomato is a suitable model for studying DNA methylation due to its large pericentromeric regions and the presence of transposons and repeats in its genome. The PhD project will explore the diversity of methylation patterns in wild and domesticated tomato cultivars and the methylation and RNA landscapes of DNA methylation- or demethylation-deficient tomato plants. The student will obtain methylomes of tomato cultivars at different stages of fruit ripening and analyze the differences using a bioinformatics pipeline developed in the group. This will result in the identification of Differentially Methylated Regions (DMRs) and the student will investigate their genomic distribution and association with genomic features. Additionally, the student will explore the association between tissue-specific epiallelic variants and gene expression, and the involvement of small RNAs in epigenome stability. To further understand the molecular mechanisms, the PhD student will sequence methylomes and transcriptomes of genome-edited and/or RNAi plants with factors involved in DNA methylation. This will include sequencing of Sldml crispr mutants (DNA demethylation), Slddm1 mutants (chromatin remodeling), and other mutants and control lines.

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Ingénieur d'Etude - Saclay Plant Sciences - Position now Open

One position (Ingénieur d’Étude, 18 months) in bioinformatics/biostatistics (M/F)

The Saclay Plant Sciences network (SPS) gathers around 55 research teams specialized in plant sciences belonging to 5 institutes in the Saclay area (south west of Paris) and represents about 700 people. The current research activities of the SPS partners concern the genetic, molecular and cellular mechanisms that control plant physiology and development, as well as their interactions with fluctuating biotic or abiotic environments. These studies extend from the gene to the entire plant, and use the concepts and tools of biochemistry, biophysics, imaging, molecular biology, genetics, cell biology, modelling and bioinformatics. Data analysis and research in bioinformatics and bio-statistics is currently carried out by 25 permanent bio-informaticians and statisticians in the 5 institutes.

SPS is recruiting one bioinformatician “Ingénieur.e de Recherche” to participate and manage the SPS-Bioinformatics Analysis and Research Support (SPS-BARS), a bioinformatics service composed of 3 bioinformaticians (including the IR) that provides support activities to the SPS research community and takes over the increasing requests for the analysis of biological data. The recruited engineer will be allocated for a large part of her/his time to Research Units to work on specific projects. These projects are validated by the SPS bioinformatics committee which is composed of bioinformaticians and biologists from SPS. Teaching missions (academic and/or professional education) may also be requested.

Tasks and responsibilities

The main mission is to provide support to Research Units for the bioinformatics and/or biostatistics analysis of their data. This support includes:
- advising and guiding the implementation of methods and tools for the analysis of biological data,
- maintaining an active bibliographic survey and evaluating published tools and methods,
- developing, when necessary, new analytical methods and tools,
- analyzing data in collaboration with the Units,
- ensuring the transfer of tools and expertise to the Units,
- delivering training courses in bioinformatics and biostatistics,
- maintaining the methods and tools developed by the Units, and ensuring their integration into core software solutions like Snakemake or Nextflow.

The additional mission will be the management of the SPS-BARS through
- the daily interactions and supervision of the other engineers of the service,
- the organization of the SPS bioinformatics calls and training sessions,
- the interactions with the SPS bioinformatics committee.

Job profile

Several needs have been identified and some of the following skills are expected:
- Analysis of HTS data (variant calling, genome assembly, differential expression, epigenomics...),
- Analysis of metabolomic data,
- Analysis of proteomic data,
- Analysis of imaging data,
- Data integration

Duration:
Funds are available for 18 months.

Salary:
The engineer will be recruited by INRAE. Depending on the previous experience, the gross salary will range from 2300€ to 2900€ for the IR position (net salary between 1900€ and 2400€).

Candidate profile and conditions

The candidate is expected to have a PhD or an engineer degree in bioinformatics, statistics, applied mathematics or a related field. Teaching experience in bioinformatics/biostatistics will be appreciated.

SPS is committed to foster gender equality, so female candidates are encouraged to apply.

To apply

Applications (cover letter, detailed CV and 2 reference letters) should be sent to etienne.delannoy[at]inrae.fr and nicolas.bouche[at]inrae.fr.

Leader:

Nicolas Bouché

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