In silico exploration of the Bacterial Divisome

Type de poste
Dates
Durée du poste
Contrat renouvelable
Contrat non renouvelable
Date de prise de fonction
Date de fin de validité de l'annonce
Localisation
Adresse

<p>Modeling Biological Macromolecules (MOBI)</p><p>IBCP-BMSSI, UMR 5086</p><p>7 passage du Vercors</p><p>69367 LYON, France</p><p>Phone: +33(0)4 37 65 29 36</p><p>Fax: +33(0)4 72 72 26 04</p>
LYON
France

Contacts
Guillaume Launay
Email du/des contacts
guillaume.launay@ibcp.fr
Description

<div title="Page 1"><p class="p1"><span class="s1">Our team needs a M2 student internship, proficient in python programming to work on the following structural bioinformatics project.</span></p><p class="p1">&nbsp;</p><p class="p1"><span class="s1"><b>Keywords:</b></span></p><p>Protein interaction network construction</p><p>Object-oriented Python programming</p><p>Structural Bioinformatics</p><p>Data mining</p><div>Protein complex modeling</div><p>Team work</p><p class="p1">&nbsp;</p><p class="p1"><span class="s1"><b>Tools</b></span></p><p class="p1"><span class="s1">Python, Jupyter, scipy/networkX, bash, slurm.</span></p><p class="p1"><span class="s1"><b>Description</b></span></p><p class="p1">The objective of this internship is to identify the protein interaction network responsible for the division process of a bacterial human pathogen (aka divisome), Streptococcus pneumonia.</p><p class="p1"><span style="-webkit-text-stroke-width: initial;">The MOBI team has made recent progress in the in silico modeling of the protein interaction network of the pneumococcus divisome. This advance was made possible by the set up a new bioinformatics method which allows for the screening of the entire pneumococcus proteome against all databases of protein-protein interactions. The corresponding, current, in silico network of the divisome is built around a core set of 73 proteins communicated by the partner team. All core proteins are experimentally known as related to the division process.</span></p><p class="p1">The candidate will improve and analyze the structural bioinformatics network of the pathogen protein-protein interaction to identify key proteins responsible for the division of the pathogen.</p><p class="p1">&nbsp;</p><p class="p1"><span class="s1"><b>Tasks</b></span></p><ul class="ul1"><li class="li2"><span class="s1">Use the latest versions of the protein interaction database to build the up-to-date in silico interaction network of the pneumococcus divisome</span></li><li class="li2"><span class="s1">Refine the parameters used by the network construction method</span></li><li class="li2"><span class="s1">Use the&nbsp;available protein complex structures to enrich the network</span></li><li class="li2"><span class="s1">Perform the analysis of the network topology.</span></li></ul><p class="p1">&nbsp;</p><p class="p1"><span class="s1"><b>Outcomes</b></span></p><ul class="ul1"><li class="li3">I<span class="s1">dentify yet unknown protein involved in the division process of pneumococcus</span></li><li class="li3"><span class="s1">Identify groups of proteins not directly involved in the division process but connected to the divisome. Such groups of proteins are likely to carry metabolic function essential to the division process.</span></li><li class="li3"><span class="s1">All identified proteins will be communicated to the team &laquo; Bacterial Pathogens and Protein Phosphorylation&raquo; for knockouts and possible functional study.</span></li></ul><p class="p1"><span class="s1">This internship is an essential part of an ongoing collaboration between microbiologist and bioinformaticians of our institute. The candidate will benefit from a friendly and multidisciplinary work environment.</span></p><p class="p1">&nbsp;</p><p class="p1">&nbsp;</p><p class="p1">&nbsp;</p><p class="p1"><br /><br />&nbsp;</p><p>
<style type="text/css">
p.p1 {margin: 0.0px 0.0px 16.0px 0.0px; line-height: 19.0px; font: 16.0px Verdana; color: #ffffff; -webkit-text-stroke: #ffffff}
li.li2 {margin: 0.0px 0.0px 2.4px 0.0px; line-height: 19.0px; font: 16.0px Verdana; color: #ffffff; -webkit-text-stroke: #ffffff}
li.li3 {margin: 0.0px 0.0px 2.4px 0.0px; line-height: 16.0px; font: 13.3px Verdana; color: #ffffff; -webkit-text-stroke: #ffffff}
span.s1 {font-kerning: none}
span.s2 {font: 16.0px Verdana; font-kerning: none}
ul.ul1 {list-style-type: disc}</style>
</p></div><p>&nbsp;</p><br/>
Laboratoire: Laboratoire MMSB, Equipe de Modélisation des Macromolécules Biologiques (MOBI)