Expert Engineer - Coordination of the "Production and Resequencing" Hub M/F

RESPONSIBILITIES:

The bioinformatics platform of the Institut Imagine / SFR Necker ensures the analysis, interpretation, and management of data from high-throughput sequencing technologies for the research teams and translational projects of the Campus Necker. Within the Production and Resequencing hub, the candidate contributes to the coordination of activities in connection with sequencing platforms, research teams, clinicians & engineers. Participates in the smooth running of production activities, the scientific enhancement of generated data, and the evolution of analysis methods. In a context of continuous increase in the volume of produced data (genomes, exomes, transcriptomes, long-read and single-cell data) and diversification of collaborative projects, this position contributes to ensuring the continuity of production activities, maintaining the quality of analyses, and supporting platform users. Main Missions - Coordinate the scientific, technical, and organizational activities of the Production and Resequencing hub

• Organize high-throughput sequencing data analysis activities
• Lead a team of three engineers and contribute to the distribution of activities
• Ensure the quality, reproducibility, and traceability of the analyses performed
• Ensure the follow-up of sequencing projects in connection with research teams and technological platforms
• Participate in the development & evolution of methods, tools, and infrastructures dedicated to genomic data analysis

Activities - Organize and coordinate the platform's sequencing data analysis activities

• Contribute to production monitoring & ensure the quality of results delivered to research teams and translational projects
• Develop and evolve genomic data analysis pipelines and tools
• Ensure the follow-up of sequencing data & projects
• Provide methodological expertise to researchers for data analysis and interpretation
• Coordinate the activities of a team of 3 engineers
• Participate in user training and the dissemination of best practices
• Contribute to collaborative scientific projects & the technological evolution of the platform
• Participate in meetings, training, conferences, and working groups
• Ensure scientific and technological monitoring

REQUIRED PROFILE:

Knowledge - Genomics, human genetics, and molecular biology

• High-throughput sequencing technologies (Illumina, PacBio, Oxford Nanopore)
• NGS data analysis: panels, exomes, genomes, transcriptomics, single-cell, and long-read
• Management and structuring of large-scale biological data
• High-performance computing (HPC) environments
• Good software development practices and analysis reproducibility
• Scripting languages (Bash) and relational databases
• Classic bioinformatics tools applied to sequencing
• Scientific and technical English

Operational Skills - Mastery of high-throughput sequencing technologies (NGS) and their applications

• Mastery of analysis methods for panel, exome, genome, transcriptomics (RNA-seq), single-cell, and long-read data
• Knowledge of the main genomic and transcriptomic analysis tools
• Good understanding of human genetics, genomics, and molecular biology
• Mastery of biological data formats (FASTQ, BAM/CRAM, VCF, GTF...) and associated quality standards

IT and Data Management - Mastery of Linux/Unix environments

• Knowledge of scripting languages (Bash, Python, Perl or equivalent)
• Knowledge of relational database management systems (MySQL, PostgreSQL or equivalent)
• Use of version control tools (Git) and software development best practices
• Knowledge of high-performance computing (HPC) infrastructures and job schedulers
• Knowledge of principles for management, security & traceability of scientific data

Soft-skills - Organizational skills

• Scientific and methodological rigor
• Analytical skills and synthesis ability
• Ability to coordinate and work in a team
• Autonomy, ability to take initiative
• Interpersonal & pedagogical skills
• Reactivity to priority requests
• Ability to evolve in a multidisciplinary environment

Desired Degree Level Engineering degree or Master's in bioinformatics, genomics, computational biology, or an equivalent discipline Special Working Conditions - Participation in the follow-up of projects requiring adherence to tight deadlines, particularly within the framework of priority or translational projects Contract - Fixed-term contract...