Bioinformatics scientist
Genomines
Paris, France
Posted on Thursday, December 21, 2023
Who we are
Genomines is a young biotechnology company based in Paris and Saclay, specialized in the sustainable extraction of Nickel from plants. The mission of Genomines is to usher in a new era of sustainable mining by using genetically enhanced plants to extract metals from soil (agromining). Through synthetic biology and cutting-edge technology, we harness the power of nature to create bioengineered plants that can extract metals while decontaminating soils and creating cleaner lands for agriculture. Our ultimate goal is to become the world's first carbon-neutral mining group, using sustainable and environmentally friendly methods to extract the precious resources our society needs.
What We're Looking For
(we are not looking for people outside the plant domain)
Education & Background
- PhD degree in molecular biology, bioinformatics, or a related field
- Fluent in English (both written and spoken); additional language skills are advantageous
-Understand best practices in reproducible science, including tool version control and crafting quality reports, along with developing data management plans
- Experienced in plant genetic engineering techniques such as CRISPR and bacterium-mediated transformation, with a focus on optimization
Bioinformatics
- Demonstrated experience in assembling non-bacterial and non-fungal genomes, preferably plant or animal genomes
- Skilled in RNAseq analysis, annotation, and database management
IT Competencies
- Proficient with IT tools for independent process management, including familiarity with software licensing and usage rights
- Proficient in Linux
- Skilled in Programming Tools and Languages (Competent with GitHub/GitLab for code versioning and Proficient in programming languages like Python and Shell/Bash)
- Knowledgeable in short reads/long reads sequencing technologies
- Familiar with computing and storage systems, including experience with computing clusters and data storage and backup solutions like OVH
Personal Qualities
- Collaborative team player with effective communication skills
- Demonstrates scientific rigor and meticulous attention to detail
- Shows adaptability and a commitment to continuous learning
- Possesses humility and openness to growth
Principal Responsibilities
Genome Assembly
- Conduct complex genome assemblies, focusing on non-bacterial and non-fungal organisms, with a preference for plant or animal genomes
- Capable of performing comprehensive plant genome assemblies
- Execute relevant quality control measures
Genomic Annotation and Analysis
- Perform structural and functional annotation of transposable elements
- Critically analyze automated processing workflows
Transcriptome Analysis
- Assemble transcriptomes to explore differences between mutants and original organisms
RNAseq and Data Processing
- Apply RNAseq techniques
- Lead transcriptomic analyses across one or multiple factors, with or without a reference genome
- Establish and conduct quality control procedures
Bioinformatics Pipeline and Development Environment Management
- Utilize pipeline managers like Snakemake or Nextflow
- Configure and manage isolated development environments, such as coding environments, modules, or Python virtual environments
Data and IT Process Management
- Ensure effective genomic data traceability and associated IT process backups
- Documentation and Reporting: Keep accurate documentation and produce research reports
- Technical Support: Assist in preparing data for analysis and managing databases
(On-site position in Paris-Saclay, 91400)