Mots-Clés

metagenomics metatranscriptomics microbiome virome

Description

Description

We are looking for a highly motivated postdoctoral researcher, specialized in metagenomics and computational analysis of microbiome data. We look for an excellent track record in (meta-)omics data analysis and strong scientific drive.

Projects will focus on:

• bioinformatics/statistics method development for the analysis of the human virome and of its interaction with the host and the microbiota,
• analysis of multi-omics data of the human microbiome (including metabarcoding, metagenomics, metatranscriptomics, and transcriptomics) in different clinical studies as well as in international projects (e.g H2020 HAP2 (https://hap2-project.com/)

Contract: 2 years with possible extension to 3 years.

Profile

• PhD in bioinformatics, computational biology, datamining, biostatistics, population and/or statistical genetics, human microbiota, numerical/microbial ecology or equivalent
• Good programming skills (R, python/perl/java/C++ etc, SQL), proficiency in Unix/Linux and cluster experience 
• A strong track record in omics data analysis (e.g. (meta)genomics, transcriptomics, proteomics, metabolomics, epigenomics, genotyping data) is a plus
• Experience in clinical datamining/machine learning, biomarker detection is a plus

Organization

You will join the GenEPII sequencing platform https://genepii.univ-lyon1.fr located in the Hopital de la Croix Rousse (69004 Lyon) within the Hospices Civils de Lyon. The team includes microbiologists, bioinformaticians, engineers and technicians working on microbiology genomics. The platform is associated with four National Reference Centers (NRC), including the NRC for respiratory viruses and has been heavily involved in SARS-CoV-2 genome sequencing. The lab has on-site robotic sample processing, high-throughput computing resources as well as next-gen sequencing facilities (NextSeq, NovaSeq, oxford nanopore gridion).

How to apply:

Please send an email to Dr Laurence Josset (laurence.josset@chu-lyon.fr) attaching the following documents:

• A cover letter
• A curriculum vitae
• Contact information for 3 references

If you have any questions please contact Dr Laurence Josset (laurence.josset@chu-lyon.fr)

Deadline

Applications will be accepted until October 15th

Recent publications from the lab related to the field

Langevin S, Pichon M, Smith E, […] Josset L « Early Nasopharyngeal Microbial Signature Associated with Severe Influenza in Children: A Retrospective Pilot Study ». The Journal of General Virology 98, no 10 (2017): 2425‑37. https://doi.org/10.1099/jgv.0.000920.

Bal A, Pichon M, Picard C, […] Josset L « Quality Control Implementation for Universal Characterization of DNA and RNA Viruses in Clinical Respiratory Samples Using Single Metagenomic Next-Generation Sequencing Workflow ». BMC Infectious Diseases 18, no 1 (2018): 537. https://doi.org/10.1186/s12879-018-3446-5.

Bal A, Sarkozy C, Josset L, […] Brengel-Pesce K « Metagenomic Next-Generation Sequencing Reveals Individual Composition and Dynamics of Anelloviruses during Autologous Stem Cell Transplant Recipient Management ». Viruses 10, no 11 (2018): E633. https://doi.org/10.3390/v10110633.

Bal A, Oriol G, Josset L, […] Assant S « Metagenomic Investigation of Torque Teno Mini Virus-SH in Hematological Patients ». Frontiers in Microbiology 10 (2019): 1898. https://doi.org/10.3389/fmicb.2019.01898.

Charre C, Ginevra C, Sabatier M, […] L. Josset « Evaluation of NGS-Based Approaches for SARS-CoV-2 Whole Genome Characterisation ». Virus Evolution 6, no 2 (2020): veaa075. https://doi.org/10.1093/ve/veaa075.

Sabatier M, Bal A, Destras G, […] L. Josset « Comparison of Nucleic Acid Extraction Methods for a Viral Metagenomics Analysis of Respiratory Viruses ». Microorganisms 8, no 10 (2020): E1539. https://doi.org/10.3390/microorganisms8101539.

Pérez-Cobas AE, Ginevra C, Rusniok C, Jarraud S, Buchrieser C. «Persistent Legionnaires' Disease and Associated Antibiotic Treatment Engender a Highly Disturbed Pulmonary Microbiome Enriched in Opportunistic Microorganisms». mBio. (2020) May 19;11(3). https://journals.asm.org/doi/10.1128/mBio.00889-20.

Bal A, Destras G, Sabatier M, […] Josset L, Morfin F. «Metagenomic Analysis Reveals High Abundance of TTMV in the Respiratory Tract of Children with Acute Respiratory Illness».Viruses, 2022