Researcher (M/F) in Wastewater Epidemiology

Job Description

Missions

The primary responsibility of the successful candidate is to perform bioinformatic analyses of metagenomic sequencing data for viruses present in wastewater (reference-based alignment pipelines, variant detection, and de novo assembly). He or she will design and implement databases dedicated to the storage, annotation, and analysis of viral sequences, ensuring their interoperability with remote systems (secure servers, HPC clusters). Managing remote connections (SSH, APIs, data transfers) and leveraging public or private resources (Santé publique France, GISAID, NCBI, ENA) are essential for enriching the analyses and contextualizing the results. The team's research focuses primarily on priority respiratory pathogens (SARS-CoV-2, influenza, RSV), but it is also possible to analyze available data on other infectious agents (papillomavirus, arboviruses, etc.) with the aim of improving the early detection of concerning epidemiological signals. Cross-referencing environmental data (wastewater) with clinical data (patient sequencing, epidemiological data) will help validate observations and refine predictive models. Automated monitoring tools (scripts, dashboards, alerts) incorporating machine learning algorithms or statistical methods will be implemented to optimize real-time pathogen surveillance and support public health decision-making.

Activity

Bioinformatics analysis of sequencing data (Nanopore)
• Read filtering (quality, barcodes), demultiplexing.
• Assembly/alignment of viral strains (Minimap2, BWA-MEM) and variant detection (iVar, Clair3).
• Sequence characterization and functional annotation via NCBI and GISAID (genes, proteins, resistance motifs).
• Pathogen identification and taxonomic classification (Kraken2, Centrifuge, DIAMOND).
• Storage of FASTQ/FASTA files and metadata in the MEDIANTE system and external repositories (ENA, NCBI SRA, GISAID) in accordance with FAIR principles.
• Version control for pipelines and scripts (Git, GitLab/GitHub).
Development of interactive visualization tools
• Dynamic dashboards (Shiny, Plotly Dash) for visualizing viral abundances by pathogen, time period, or region (curves, heatmaps), and spatialization of detections (Leaflet, Folium) for comparing multiple wastewater treatment plants.
• Analysis of transmission flows (interactive phylogenetic trees, Sankey diagrams).
Report generation and statistical analysis
• Statistical analysis of viral abundances (Wilcoxon, ANOVA), regression models (R, Python: statsmodels, scikit-learn), including predictions of variant emergence.
• Writing articles and preparing figures for scientific journals or technical reports for health authorities (ggplot2, Matplotlib/Seaborn).
Collaboration and Automated Monitoring
• Integration with external data, such as hospital data (clinical sequencing, hospitalization rates), via APIs or shared databases.
• Development or integration with real-time monitoring tools: Nextflow pipelines for variant detection (Pangolin), automatic alerts (viral load thresholds) with updates via dashboards (cron jobs).

Your Profil

Skills

• Proficiency in using Nanopore high-throughput sequencing analysis tools (read preprocessing, demultiplexing, quality control). Knowledge of data formats: FASTQ, FASTA, BAM/SAM, VCF.
• Use of alignment tools (Minimap2, BWA-MEM) and assembly tools (Flye, Canu, SPAdes).
• Variant detection: iVar, Clair3, Pangolin.
• Functional annotation (Prokka, BLAST, NCBI, GISAID), taxonomic classification (Kraken2, Centrifuge, DIAMOND) . Ability to identify pathogens not initially targeted.
• Experience managing large volumes of data from generation through publication. Experience with collaborative version control tools: Git, GitLab, GitHub (including in private mode).
• Expertise in the programming languages R (Shiny, ggplot2, statistical analyses), Python (Plotly Dash, Matplotlib/Seaborn, scikit-learn, statsmodels), and JavaScript (for D3.js, Leaflet, Folium).
• Knowledge of Nextflow or Snakemake bioinformatics pipelines.
• Skills in statistical analysis and modeling
• Ability to work as part of a team in a collaborative setting involving researchers, clinicians, and public health decision-makers, with a strong ability to explain and justify technical findings.
• Cross-functional skills in project management (organizing and monitoring analysis pipelines, data repositories, and tool updates), as well as scientific and technological monitoring: keeping abreast of advances in bioinformatics and molecular epidemiology. Ability to adapt to new tools and methods (e.g., new variant detection algorithms).
• Fluent in French and English.

Your Work Environment

This position is part of the Eukaryotic Genomic Physiology team at the Institute of Molecular and Cellular Pharmacology in Sophia Antipolis, which plays a pioneering role in wastewater sequencing (Rios et al. Monitoring SARS-CoV-2 variant alterations in Nice neighborhoods by wastewater nanopore sequencing. Lancet Reg Health Eur. 2021 PMID: 34423327). As part of national and international networks, the team is involved in the PEPR Sysp&Eau (systemic surveillance of pathogens in water) and WHAOU (emerging pathogen surveillance project) initiatives, as well as the national wastewater-based epidemiological surveillance network Obépine and the IHU Respirera. It draws on the expertise of the UCA Genomix platform, a founding member of the France Génomique national infrastructure for high-throughput sequencing and genomic analysis. This context provides a multidisciplinary and innovative environment, combining expertise in genomics, epidemiology, and bioinformatics, to develop early surveillance approaches and cutting-edge analytical tools.

Constraints and risks

Work in a restricted access area

Compensation and benefits

Compensation

Between €2,991.58 and €4,756.76 (gross)

Annual leave and RTT

44 jours

Remote Working practice and compensation

Pratique et indemnisation du TT

Transport

Prise en charge à 75% du coût et forfait mobilité durable jusqu’à 300€

About the offer

About the CNRS

The CNRS is a major player in fundamental research on a global scale. The CNRS is the only French organization active in all scientific fields. Its unique position as a multi-specialist allows it to bring together different disciplines to address the most important challenges of the contemporary world, in connection with the actors of change.

CNRS

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