Bioinformatics Postdoctoral position

Organization
INRA (French National Institute for Agricultural Research)
Job Location
Nancy, France
France
Job Description

Genomics and metagenomics of forest symbiotic interactions TITLE Exploration of forest symbiotic fungi genomes and functional analysis of metatranscriptome data. RESEARCH CONTEXT Under its researches in biology and ecology of the forest interactions, the UMR IaM contribute to the functional annotation of fungi and tree (meta)genomic sequences. A series of research programs are developed within it based (1) on comparative analysis of fungal genomes and transcriptomes and (2) on the study of metagenomes and metatranscriptomes of forest soils (JGI projects: CSP #305 ‘Exploring the Genome Diversity of Mycorrhizal Fungi to Understand the Evolution and Functioning of Symbiosis in Woody Shrubs and Trees’, CSP#978 ‘Mycorrhizal Genomics Initiative: Exploring the Symbiotic Transcriptomes’ et CSP#570 ‘Metatranscriptomics of Forest Soil Ecosystems’). RESEARCH PROJECT The research project is part of the comparative genomics and metagenomics programs developed in the UMR IaM Ecogenomics of interactions team. Its aim is to identify and characterize genetic determinants involved in symbiotic interactions between the mycorrhizal fungi and the forest trees using comparative analysis of genome, transcriptome and metatranscriptome data. Over the last few years, UMR IaM and JGI (Joint Genome Institute) joint efforts have allowed the assembly and the annotation of about thirty symbiotic fungi genomes. Bioinformatics analysis, carried in this project, will be focused particularly on lignocellulose degradation enzymes (CAZymes and FOLymes) of the fungal genomes to build a reference database and to better understand their regulation. These data will also help in the annotation and joint analysis of environmental eukaryotic metatranscripts sequences. The in silico analysis of metatranscriptomic expression data will require the development of informatics processes dedicated to massive datasets, and the transposition of transcriptome analysis tools and programs to metatranscriptome data. METHODOLOGICAL APPROACHES - Comparative (meta)genomics of genes repertoires. - In silico analysis of 454 and Illumina (HiSeq et MiSeq) sequencing data. - Quantification of fungal genes expression (trimming, mapping, normalization) - Differential gene expression and gene co-expression network - Graphical visualization of data and basic statistical analysis. POSITION - Short-term contract of 15 months (renewable one year) - The position is at INRA in Champenoux (France).

Requirements

- PhD in Biology, Informatics or equivalent - Experience in Perl and Python programing, object oriented development, database management (MySQL, PostgreSQL) - Good knowledge of UNIX environment - Fundamentals in biology and biostatistics for data valorization. - Good interpersonal skills, team spirit and autonomy.

How to Apply

UMR 1136, Interactions Arbres/Microorganismes (IaM), http://mycor.nancy.inra.fr/IAM Annegret KOHLER, kohler@nancy.inra.fr - Marc BUEE, buee@nancy.inra.fr - Tél : +33 (0)3 83 39 40 72. Francis MARTIN, fmartin@nancy.inra.fr. Emmanuelle MORIN, emmanuelle.morin@nancy.inra.fr - Tél : +33 (0)3 83 39 41 33

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