<div dir="ltr"><div>Dear SocBiN community,</div><div><br></div><div>I am offering a Master's internship in bioinformatics at IRD, Montpellier, France (<a href="https://en.ird.fr">https://en.ird.fr</a>). The project focuses on developing a Nextflow pipeline for RNA editing analysis.</div><div><br></div><div>Details about the internship and application process are provided below. Please feel free to share with interested students!</div><div><br></div><div>Best regards,</div><div><br></div><div>Jacques Dainat Ph.D.</div><div><span style="color:rgb(0,0,0);font-family:Helvetica;font-size:12px">Research engineer in Bioinformatics at IRD</span><br style="color:rgb(0,0,0);font-family:Helvetica;font-size:12px"><span style="color:rgb(0,0,0);font-family:Helvetica;font-size:12px">UMR (IRD 224-CNRS 5290-UM) MIVEGEC </span><br></div><div><span style="color:rgb(0,0,0);font-family:Helvetica;font-size:12px"><br></span></div><div>----------------------------------</div><div><br></div><div><u>In Brief</u></div><div><b>What: </b>Internship</div><div><b>How long</b>: >= 6 Month</div><div><b>When</b>: Beginning of 2025</div><div><b>Where</b>: IRD Montpellier France</div><div><b>Gratification</b>: ~600 euro/month</div><div><br></div><div><span style="color:rgb(47,84,150);font-family:"Calibri Light",sans-serif">Subject</span></div><div><p class="MsoNormal" style="margin:0cm;font-family:Calibri,sans-serif;color:rgb(0,0,0);line-height:21.6px"><span lang="EN-US" style="line-height:27px;font-family:"System Font";color:rgb(14,14,14)"><b>Development of a Pipeline for the Analysis of Epitranscriptomic Modifications</b></span></p><p class="MsoNormal" style="margin:0cm;font-family:Calibri,sans-serif;color:rgb(0,0,0);line-height:21.6px"><span style="color:rgb(47,84,150);font-family:"Calibri Light",sans-serif"><br></span></p><p class="MsoNormal" style="margin:0cm;font-family:Calibri,sans-serif;color:rgb(0,0,0);line-height:21.6px"><span style="color:rgb(47,84,150);font-family:"Calibri Light",sans-serif">Context</span></p><p class="MsoNormal" style="margin:0cm;font-family:Calibri,sans-serif;color:rgb(0,0,0);text-align:justify;line-height:21.6px"><span lang="EN-US" style="line-height:25.200001px;font-family:"System Font";color:rgb(14,14,14)">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).</span></p><p class="MsoNormal" style="margin:0cm;font-family:Calibri,sans-serif;color:rgb(0,0,0);text-align:justify;line-height:21.6px"><span lang="EN-US" style="line-height:25.200001px;font-family:"System Font";color:rgb(14,14,14)"> </span></p><p class="MsoNormal" style="margin:0cm;font-family:Calibri,sans-serif;color:rgb(0,0,0);text-align:justify;line-height:21.6px"><span lang="EN-US" style="line-height:25.200001px;font-family:"System Font";color:rgb(14,14,14)">In this context, we propose an internship aimed at developing a bioinformatics pipeline using<span class="gmail-Apple-converted-space"> </span>Nextflow, to integrate and automate the use of various existing relevant tools and to combine their outputs into a “meta-editome.”</span></p><h1 style="margin:12pt 0cm 0cm;break-after:avoid;font-family:"Calibri Light",sans-serif;color:rgb(47,84,150)"><span lang="EN-US" style="font-weight:normal"><font size="2">Objective of the Internship</font></span></h1><p class="MsoNormal" style="margin:0cm;font-family:Calibri,sans-serif;color:rgb(0,0,0);text-align:justify;line-height:21.6px"><span lang="EN-US" style="line-height:25.200001px;font-family:"System Font";color:rgb(14,14,14)">The main goal of this internship is to develop a complete pipeline in<span class="gmail-Apple-converted-space"> </span>Nextflow<span class="gmail-Apple-converted-space"> </span>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:</span></p><p class="gmail-MsoListParagraphCxSpFirst" style="margin:0cm 0cm 0cm 56.35pt;text-align:justify;line-height:135%;font-family:Calibri,sans-serif"><span lang="EN-US" style="line-height:135%;font-family:"System Font";color:rgb(14,14,14)">•<span style="font-stretch:normal;line-height:normal;font-family:"Times New Roman";font-size-adjust:none;font-kerning:auto;font-variant-alternates:normal;font-variant-ligatures:normal;font-variant-numeric:normal;font-variant-east-asian:normal;font-feature-settings:normal">     <span class="gmail-Apple-converted-space"> </span></span></span><span lang="EN-US" style="line-height:25.200001px;font-family:"System Font";color:rgb(14,14,14)">Preparation and quality control of RNA sequencing data.</span></p><p class="gmail-MsoListParagraphCxSpMiddle" style="margin:0cm 0cm 0cm 56.35pt;text-align:justify;line-height:135%;font-family:Calibri,sans-serif"><span lang="EN-US" style="line-height:135%;font-family:"System Font";color:rgb(14,14,14)">•<span style="font-stretch:normal;line-height:normal;font-family:"Times New Roman";font-size-adjust:none;font-kerning:auto;font-variant-alternates:normal;font-variant-ligatures:normal;font-variant-numeric:normal;font-variant-east-asian:normal;font-feature-settings:normal">     <span class="gmail-Apple-converted-space"> </span></span></span><span lang="EN-US" style="line-height:25.200001px;font-family:"System Font";color:rgb(14,14,14)">Alignment of RNA reads to the reference genome.</span></p><p class="gmail-MsoListParagraphCxSpMiddle" style="margin:0cm 0cm 0cm 56.35pt;text-align:justify;line-height:135%;font-family:Calibri,sans-serif"><span lang="EN-US" style="line-height:135%;font-family:"System Font";color:rgb(14,14,14)">•<span style="font-stretch:normal;line-height:normal;font-family:"Times New Roman";font-size-adjust:none;font-kerning:auto;font-variant-alternates:normal;font-variant-ligatures:normal;font-variant-numeric:normal;font-variant-east-asian:normal;font-feature-settings:normal">     <span class="gmail-Apple-converted-space"> </span></span></span><span lang="EN-US" style="line-height:25.200001px;font-family:"System Font";color:rgb(14,14,14)">Identification of editing sites from RNA-seq data.</span></p><p class="gmail-MsoListParagraphCxSpMiddle" style="margin:0cm 0cm 0cm 56.35pt;text-align:justify;line-height:135%;font-family:Calibri,sans-serif"><span lang="EN-US" style="line-height:135%;font-family:"System Font";color:rgb(14,14,14)">•<span style="font-stretch:normal;line-height:normal;font-family:"Times New Roman";font-size-adjust:none;font-kerning:auto;font-variant-alternates:normal;font-variant-ligatures:normal;font-variant-numeric:normal;font-variant-east-asian:normal;font-feature-settings:normal">     <span class="gmail-Apple-converted-space"> </span></span></span><span lang="EN-US" style="line-height:25.200001px;font-family:"System Font";color:rgb(14,14,14)">Annotation and interpretation of identified editing sites, with options for cross-species and cross-condition comparisons.</span></p><p class="gmail-MsoListParagraphCxSpMiddle" style="margin:0cm 0cm 0cm 56.35pt;text-align:justify;line-height:135%;font-family:Calibri,sans-serif"><span lang="EN-US" style="line-height:135%;font-family:"System Font";color:rgb(14,14,14)">•<span style="font-stretch:normal;line-height:normal;font-family:"Times New Roman";font-size-adjust:none;font-kerning:auto;font-variant-alternates:normal;font-variant-ligatures:normal;font-variant-numeric:normal;font-variant-east-asian:normal;font-feature-settings:normal">     <span class="gmail-Apple-converted-space"> </span></span></span><span lang="EN-US" style="line-height:25.200001px;font-family:"System Font";color:rgb(14,14,14)">Testing and validating the pipeline on public datasets.</span></p><p class="gmail-MsoListParagraphCxSpLast" style="margin:0cm 0cm 0cm 56.35pt;text-align:justify;line-height:135%;font-family:Calibri,sans-serif"><span lang="EN-US" style="line-height:135%;font-family:"System Font";color:rgb(14,14,14)">•<span style="font-stretch:normal;line-height:normal;font-family:"Times New Roman";font-size-adjust:none;font-kerning:auto;font-variant-alternates:normal;font-variant-ligatures:normal;font-variant-numeric:normal;font-variant-east-asian:normal;font-feature-settings:normal">     <span class="gmail-Apple-converted-space"> </span></span></span><span lang="EN-US" style="line-height:25.200001px;font-family:"System Font";color:rgb(14,14,14)">Documenting the pipeline, including configuration, workflow steps, and execution instructions.</span></p><h1 style="margin:12pt 0cm 0cm;break-after:avoid;font-family:"Calibri Light",sans-serif;color:rgb(47,84,150)"><span lang="EN-US" style="font-weight:normal"><font size="2">Candidate Profile</font></span></h1><p class="gmail-MsoListParagraphCxSpFirst" style="margin:0cm 0cm 0cm 56.35pt;text-align:justify;line-height:135%;font-family:Calibri,sans-serif"><span lang="EN-US" style="line-height:135%;font-family:"System Font";color:rgb(14,14,14)">•<span style="font-stretch:normal;line-height:normal;font-family:"Times New Roman";font-size-adjust:none;font-kerning:auto;font-variant-alternates:normal;font-variant-ligatures:normal;font-variant-numeric:normal;font-variant-east-asian:normal;font-feature-settings:normal">     <span class="gmail-Apple-converted-space"> </span></span></span><span lang="EN-US" style="line-height:25.200001px;font-family:"System Font";color:rgb(14,14,14)">Master’s student in their second year (bioinformatics, computational biology, or related field).</span></p><p class="gmail-MsoListParagraphCxSpMiddle" style="margin:0cm 0cm 0cm 56.35pt;text-align:justify;line-height:135%;font-family:Calibri,sans-serif"><span lang="EN-US" style="line-height:135%;font-family:"System Font";color:rgb(14,14,14)">•<span style="font-stretch:normal;line-height:normal;font-family:"Times New Roman";font-size-adjust:none;font-kerning:auto;font-variant-alternates:normal;font-variant-ligatures:normal;font-variant-numeric:normal;font-variant-east-asian:normal;font-feature-settings:normal">     <span class="gmail-Apple-converted-space"> </span></span></span><span lang="EN-US" style="line-height:25.200001px;font-family:"System Font";color:rgb(14,14,14)">Skills in bioinformatics, especially in RNA sequencing data analysis.</span></p><p class="gmail-MsoListParagraphCxSpMiddle" style="margin:0cm 0cm 0cm 56.35pt;text-align:justify;line-height:135%;font-family:Calibri,sans-serif"><span lang="EN-US" style="line-height:135%;font-family:"System Font";color:rgb(14,14,14)">•<span style="font-stretch:normal;line-height:normal;font-family:"Times New Roman";font-size-adjust:none;font-kerning:auto;font-variant-alternates:normal;font-variant-ligatures:normal;font-variant-numeric:normal;font-variant-east-asian:normal;font-feature-settings:normal">     <span class="gmail-Apple-converted-space"> </span></span></span><span lang="EN-US" style="line-height:25.200001px;font-family:"System Font";color:rgb(14,14,14)">Prior experience with bioinformatics workflows (e.g., Nextflow, Snakemake) is a plus.</span></p><p class="gmail-MsoListParagraphCxSpMiddle" style="margin:0cm 0cm 0cm 56.35pt;text-align:justify;line-height:135%;font-family:Calibri,sans-serif"><span lang="EN-US" style="line-height:135%;font-family:"System Font";color:rgb(14,14,14)">•<span style="font-stretch:normal;line-height:normal;font-family:"Times New Roman";font-size-adjust:none;font-kerning:auto;font-variant-alternates:normal;font-variant-ligatures:normal;font-variant-numeric:normal;font-variant-east-asian:normal;font-feature-settings:normal">     <span class="gmail-Apple-converted-space"> </span></span></span><span lang="EN-US" style="line-height:25.200001px;font-family:"System Font";color:rgb(14,14,14)">Good proficiency in one or more scripting languages (e.g., Bash, Python, Perl, R).</span></p><p class="gmail-MsoListParagraphCxSpLast" style="margin:0cm 0cm 0cm 56.35pt;text-align:justify;line-height:135%;font-family:Calibri,sans-serif"><span lang="EN-US" style="line-height:135%;font-family:"System Font";color:rgb(14,14,14)">•<span style="font-stretch:normal;line-height:normal;font-family:"Times New Roman";font-size-adjust:none;font-kerning:auto;font-variant-alternates:normal;font-variant-ligatures:normal;font-variant-numeric:normal;font-variant-east-asian:normal;font-feature-settings:normal">     <span class="gmail-Apple-converted-space"> </span></span></span><span lang="EN-US" style="line-height:25.200001px;font-family:"System Font";color:rgb(14,14,14)">Familiarity with RNA-seq analysis tools and biological databases.</span></p><h1 style="margin:12pt 0cm 0cm;break-after:avoid;font-family:"Calibri Light",sans-serif;color:rgb(47,84,150)"><span lang="EN-US" style="font-weight:normal"><font size="2">Supervision</font></span></h1><p class="MsoNormal" style="margin:0cm;font-family:Calibri,sans-serif;color:rgb(0,0,0);text-align:justify;line-height:21.6px"><span lang="EN-US" style="line-height:25.200001px;font-family:"System Font";color:rgb(14,14,14)">Jacques Dainat, Ph.D. - Research Engineer in Bioinformatics</span></p><h1 style="margin:12pt 0cm 0cm;break-after:avoid;font-family:"Calibri Light",sans-serif;color:rgb(47,84,150)"><span lang="EN-US" style="font-weight:normal"><font size="2">Location</font></span></h1><p class="MsoNormal" style="margin:0cm;font-family:Calibri,sans-serif;color:rgb(0,0,0);text-align:justify;line-height:21.6px"><span lang="EN-US" style="line-height:25.200001px;font-family:"System Font";color:rgb(14,14,14)">French National Research Institute for Sustainable Development (IRD), MiVEGEC Laboratory, Montpellier.</span></p><h1 style="margin:12pt 0cm 0cm;break-after:avoid;font-family:"Calibri Light",sans-serif;color:rgb(47,84,150)"><span lang="EN-US" style="font-weight:normal"><font size="2">Duration</font></span></h1><p class="MsoNormal" style="margin:0cm;font-family:Calibri,sans-serif;color:rgb(0,0,0);text-align:justify;line-height:21.6px"><span lang="EN-US" style="line-height:25.200001px;font-family:"System Font";color:rgb(14,14,14)">Six-month internship starting in January, with potential for extension.</span></p><h1 style="margin:12pt 0cm 0cm;break-after:avoid;font-family:"Calibri Light",sans-serif;color:rgb(47,84,150)"><span lang="EN-US" style="font-weight:normal"><font size="2">Application</font></span></h1><span lang="EN-US" style="font-family:"System Font";color:rgb(14,14,14)">Please send your CV, cover letter, transcript of records, and names of referees to<span class="gmail-Apple-converted-space"> </span></span><span style="color:rgb(0,0,0);font-family:Calibri,sans-serif"><a href="mailto:jacques.dainat@ird.fr" style="color:rgb(149,79,114)"><span lang="EN-US" style="font-family:"System Font"">jacques.dainat@ird.fr</span></a></span><span style="color:rgb(0,0,0);font-family:-webkit-standard"></span><br></div><div><br></div></div>