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Postdoctoral position to study long noncoding RNAs in eukaryotic marine microorganisms

We are seeking a qualified and highly motivated individual for a postdoctoral position, under the recently funded ANR PRC project DiaLincs, to study long noncoding RNAs in eukaryotic marine microorganisms, at the Institut de Biologie de l’Ecole normale supérieure (IBENS), in central Paris.

The non-protein coding portion of eukaryotic genomes has, in the last decade, been shown to be much more complex than what could have been anticipated. Furthermore, with the advent of deep sequencing it has become clear that genomes are pervasively transcribed and that the noncoding fraction generates huge amounts of transcripts that cannot be accounted for as simple transcriptional noise. The questions that the group led by M.H. Cruz de Carvalho in C. Bowler’s team aims to tackle are the following : How pervasive is the noncoding genome across eukaryotic marine microorganisms ? Can we find sequence conservation between long noncoding RNAs (lncRNAs) from different species/clades ? How does this relate to lncRNAs function conservation ? What are the lncRNAs regions (modules) responsible for the interaction with proteins ? How are these functional modules assembled and how do they work together ? How does this complex assembly result in the regulation of biological processes ?

The group is using state-of-the-art techniques in diatom model systems to study the function of lncRNAs, including loss- and gain-of-function (CRISPR/Cas9, OEX) and global genomics and transcriptomics technologies (RNA-seq, ChIP-seq). Using the MMETSP datasets over 1 million putative lncRNAs from 99 different diatom species have been identified. These will be used to search for sequence conservation across species and eventually across clades. This will provide clues into the occurrence of conserved domain patches that could represent functionally important regions.

Required Experience
The candidate should have experience working with Illumina, PacBio, or Oxford Nanopore sequencing data in both DNAseq and RNAseq contexts, in a UNIX/Linux environment. The candidate should be fluent in one or more programming languages (e.g. C++, Python, Perl, R). Ideally, the candidate should have interest and expertise applying and/or developing tools for multivariate analysis and machine-learning processing of -omics data. Experience on biological experiment design is desired but not required. The candidate should be equally comfortable working independently as well as part of a team.

Skills
Strong oral and written communication skills to present and summarize research results. Ability to manage time and see tasks to completion. General background in biology and bioinformatics. Experience analyzing NGS data

Interested and qualified candidates should submit their CV, cover letter and list of references to Maria Helena Cruz de Carvalho by email : cruz chez biologie.ens.fr. This offer will appear formerly in CNRS Job news at https://emploi.cnrs.fr.