[SocBiN] Internship Opportunity: Pipeline Development for Epitranscriptomics

[Jacques Dainat]

Dear SocBiN community,

I am offering a Master's internship in bioinformatics at IRD, Montpellier,
France (https://en.ird.fr). The project focuses on developing a Nextflow
pipeline for RNA editing analysis.

Details about the internship and application process are provided below.
Please feel free to share with interested students!

Best regards,

Jacques Dainat Ph.D.
Research engineer in Bioinformatics at IRD
UMR (IRD 224-CNRS 5290-UM) MIVEGEC

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*In Brief*
*What: *Internship
*How long*: >= 6 Month
*When*: Beginning of 2025
*Where*: IRD Montpellier France
*Gratification*: ~600 euro/month

Subject

*Development of a Pipeline for the Analysis of Epitranscriptomic
Modifications*


Context

RNA editing is a key post-transcriptional mechanism that modifies the
genetic information carried by the RNA molecule and influences the
diversity of the transcriptional signal. In more concrete cases, this
process leads to nonsynonymous mutations at the codon level, which can
affect protein function. In most cases, these mutations occur outside of
translated regions but can still impact the regulation of gene expression.
Despite the importance of this phenomenon, it remains understudied due to
the challenges associated with using existing tools (portability,
reproducibility, parallelization).



In this context, we propose an internship aimed at developing a
bioinformatics pipeline using Nextflow, to integrate and automate the use
of various existing relevant tools and to combine their outputs into a
“meta-editome.”
Objective of the Internship

The main goal of this internship is to develop a complete pipeline in
Nextflow that will facilitate the analysis of RNA sequencing data to detect
RNA editing events. This pipeline must be reproducible, portable, and easy
to execute on various computing platforms (local or HPC). It will integrate
commonly used bioinformatics tools for:

•      Preparation and quality control of RNA sequencing data.

•      Alignment of RNA reads to the reference genome.

•      Identification of editing sites from RNA-seq data.

•      Annotation and interpretation of identified editing sites, with
options for cross-species and cross-condition comparisons.

•      Testing and validating the pipeline on public datasets.

•      Documenting the pipeline, including configuration, workflow steps,
and execution instructions.
Candidate Profile

•      Master’s student in their second year (bioinformatics, computational
biology, or related field).

•      Skills in bioinformatics, especially in RNA sequencing data analysis.

•      Prior experience with bioinformatics workflows (e.g., Nextflow,
Snakemake) is a plus.

•      Good proficiency in one or more scripting languages (e.g., Bash,
Python, Perl, R).

•      Familiarity with RNA-seq analysis tools and biological databases.
Supervision

Jacques Dainat, Ph.D. - Research Engineer in Bioinformatics
Location

French National Research Institute for Sustainable Development (IRD),
MiVEGEC Laboratory, Montpellier.
Duration

Six-month internship starting in January, with potential for extension.
ApplicationPlease send your CV, cover letter, transcript of records, and
names of referees to jacques.dainat at ird.fr
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