Transcriptomics and data mining

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


Nicolas de Lamballerie Claire
Rosa-Calatrava Manuel
Email du/des contacts

<p class="p1">[Flexible starting date]</p><p class="p1">&nbsp;</p><p class="p1"><u>Project overview :</u></p><p class="p1">In the frame of high throughput transcriptomics sequencing, RNAseq data from patients was obtained. The first step of the project is to process these RNAseq data. A classic pipeline with tools such as FastQC or Trimmomatic will be used. Cloud computing would be a solution for processing.<span class="Apple-converted-space">&nbsp;</span></p><p class="p1">These data will then be compared with data from multiple databases in the second project phase, focusing on metadata exploration and data homogenization.</p><p class="p1">According to the advancement of the project, the student will be asked to build a database containing the results of the precedent analysis for future query operations.</p><p class="p2">&nbsp;</p><p class="p1"><u>Candidate profile :</u></p><p class="p1">The candidate should ideally have an experience in programming (data analysis in bash, python and R) and be familiar with high throughput sequencing analysis and genomics.<span class="Apple-converted-space">&nbsp;</span></p><p class="p1">A good knowledge in database (SQL - MariaDB etc) would be a plus.<span class="Apple-converted-space">&nbsp;</span></p><p class="p1">Autonomy is absolutely essential, as well good communication and teamwork skills!</p><p class="p2">&nbsp;</p><p class="p1"><u>Context :</u></p><p class="p1"><strong>CIRI :<span class="Apple-converted-space">&nbsp;</span></strong></p><p class="p1">&ldquo;Decoding fundamental host-microbe interactions to better control infectious diseases !&rdquo;&nbsp;is the motto of the International Center for Infectiology Research, the CIRI!</p><p class="p1">CIRI was created on 1st January 2013 by the Inserm, CNRS, ENS Lyon and University Claude Bernard Lyon 1. Along with these trustees and with its other partners, i.e., the Institut Pasteur, the FondationMérieux and the Hospices Civils de Lyon, the CIRI comprises over 20 teams behind one goal: the fight against infectious diseases, the second cause of death worldwide. Through a multidisciplinary approach combining microbiology (bacteriology and virology), immunology, cell biology, clinical research and epidemiology, plus a strong interface with the industry, the CIRI intends to be a research center opened to therapeutic innovation and to act a major player in the areas of medical prevention and treatment of infectious diseases.</p><p class="p3"><strong><span class="s1">The VirPath Lab :</span></strong></p><p class="p3"><span class="s1">Emerging influenza viruses offer considerable threat to the overall global health of people and their economies, as evidenced by serial emergence of antigenically unique and highly pathogenic influenza strains over the past two decades. Importantly, respiratory viruses have considerable potential to spread rapidly across the globe, dictating an urgent need for new and rapid response strategies for effective containment and control.</span></p><p class="p3"><span class="s1">The Virpath team proposes an integrative approach on a broad range of influenza virus facets from surveillance to control. We are organized in two interplaying groups (B Lina/PI and M Rosa-Calatrava/Co-PI) and work on different aspects of influenza virus biology, from the deciphering of the mechanisms leading to virus emergence and pathogenesis, to the analysis of viral interplays with cells and host factors during virus infection. We focus on (i) the understanding the role of the packaging signals harbored by viral gene segments during genetic reassortments, (ii) the importance of the functional balance between the two surface glycoproteins for infection and pathogenesis, (iii) and the virus-induced modification of specific cellular signaling pathways.</span></p><p class="p3"><span class="s1">From a more translational point of view, we are also interested in the mechanisms of antiviral resistance, as well as the discovery innovative antiviral strategies targeting the host and optimization of vaccine quality as new means to control influenza infections. To that end, in addition to the long-standing basic skills to study influenza viruses, our laboratory has implemented new technical skills including Reverse Genetics, transcriptomic analysis of clinical specimens and a fully functional vaccine-antigen production and characterization platform. In addition, VirPath has strong connections with the National Influenza Reference Centre and the clinical research activities hosted by the Hospices Civils de Lyon. Importantly, a Technology Research Platform (VirNext) has been developed in order to enhance translational research and stimulate partnerships and transfer of technology towards the industry. Such connections resulted into a substantial portfolio of patents, the implementation of clinical trials and the founding of two companies (VirHealth and Signia Therapeutics).</span></p><p class="p2">&nbsp;</p><p class="p2">&nbsp;</p><p class="p1">More info about the laboratory :</p><p class="p1"><a href=""></a></p><p class="p1"><a href=""></a></p><p>&nbsp;</p><br/…;
Lieu: <p style="margin-top: 0px; margin-bottom: 0px; color: rgb(24, 56, 119); font-family: &quot;Open Sans Condensed&quot;, sans-serif, google; font-size: 20px;"><span style="font-size: 16px;">Faculté de médecine RTH Laennec</span></p><p style="margin-top: 0px; margin-bottom: 0px; color: rgb(24, 56, 119); font-family: &quot;Open Sans Condensed&quot;, sans-serif, google; font-size: 20px;"><span style="font-size: 16px;">7-11 rue Guillaume Paradin</span></p><p style="margin-top: 0px; margin-bottom: 0px; color: rgb(24, 56, 119); font-family: &quot;Open Sans Condensed&quot;, sans-serif, google; font-size: 20px;"><span style="font-size: 16px;">69372 Lyon cedex 08</span></p>
Laboratoire: Laboratoire de Virologie et Pathologies humaines - VirPath