Publiée 16 juin 2026
Bioinformatics Scientist
Eligo Bioscience
Paris, Île-de-France 75000, France
CDI
- About Eligo -
Eligo Bioscience, backed by top-tier investors from Silicon Valley and Europe, is pioneering next-generation microbiome therapeutics. Co-founded by MIT and Rockefeller University scientists, Eligo is headquartered in Paris, France. Our mission is to address unmet medical needs in inflammatory and infectious diseases, as well as oncology, through groundbreaking gene-editing medicines.
Our first-in-class synthetic biology platform has earned Eligo numerous international awards and recognition, including being named one of the World Economic Forum's "30 Most Innovative Companies" and has been featured in international press Nature, Science, The Economist, BBC, The New York Times, etc.
More recently, two of our works have been published in:
- Nature (In situ targeted base editing of bacteria in the mouse gut)
- Science Translational Medicine (Treatment of Shiga toxin-producing E. coli infection by CRISPR-Cas-targeted cleavage of the Shiga toxin gene in animal models)
- The role -
As a Bioinformatics Scientist in the Bioinformatics team, you will own the computational backbone that turns raw sequencing reads into trustworthy biological answers. You will design, build, and operate the sequencing analysis pipelines that underpin construct validation, strain engineering, and in vivo studies across Eligo's programs, and you will work hand-in-hand with the synthetic biology, the translational pharmacology and the development teams to make sequencing a fast, reliable, and decision-grade tool at Eligo.
- Key Responsibilities -
You will be the technical lead for DNA sequencing analysis at Eligo. Your work will span short-read, long-read, and hybrid sequencing across plasmids, bacterial genomes, phage-derived particles, and microbiome samples. It will include:
- Required qualifications -
Nice to have:
- Applicant profile -
- Perks -
Eligo Bioscience, backed by top-tier investors from Silicon Valley and Europe, is pioneering next-generation microbiome therapeutics. Co-founded by MIT and Rockefeller University scientists, Eligo is headquartered in Paris, France. Our mission is to address unmet medical needs in inflammatory and infectious diseases, as well as oncology, through groundbreaking gene-editing medicines.
Our first-in-class synthetic biology platform has earned Eligo numerous international awards and recognition, including being named one of the World Economic Forum's "30 Most Innovative Companies" and has been featured in international press Nature, Science, The Economist, BBC, The New York Times, etc.
More recently, two of our works have been published in:
- Nature (In situ targeted base editing of bacteria in the mouse gut)
- Science Translational Medicine (Treatment of Shiga toxin-producing E. coli infection by CRISPR-Cas-targeted cleavage of the Shiga toxin gene in animal models)
- The role -
As a Bioinformatics Scientist in the Bioinformatics team, you will own the computational backbone that turns raw sequencing reads into trustworthy biological answers. You will design, build, and operate the sequencing analysis pipelines that underpin construct validation, strain engineering, and in vivo studies across Eligo's programs, and you will work hand-in-hand with the synthetic biology, the translational pharmacology and the development teams to make sequencing a fast, reliable, and decision-grade tool at Eligo.
- Key Responsibilities -
You will be the technical lead for DNA sequencing analysis at Eligo. Your work will span short-read, long-read, and hybrid sequencing across plasmids, bacterial genomes, phage-derived particles, and microbiome samples. It will include:
- Sequencing QC & verification - own the pipelines that take plasmids and bacterial strains from sample to biologist-readable report, covering variant calling and whole-genome/plasmid verification of engineered strains and production runs.
- Metagenomics & comparative genomics - design and interpret metagenomic studies (taxonomic and strain-level profiling, off-target quantification, strain/payload tracking) and build pangenomes that link genomic differences to phenotypes.
- Methylome & defense-system analysis - characterize methylation patterns and bacterial defense systems, feeding findings back into construct design and engineering strains.
- Multi-omics, clinical & statistical analyses - integrate transcriptomic, proteomic, metabolomic, and clinical readouts, and run statistical analyses and custom readouts for quantitative assays and non-standard experimental designs.
- Method development & synthetic biology support - mature next-generation assays and methods, expand the synthetic biology toolkit, and connect dry-lab and wet-lab through automations. Own the evaluation-to-deployment path: define success criteria, run benchmarks, communicate trade-offs, and standardize new methods so they become part of Eligo's routine decision-making.
- Scientific support, visualization & scalable operations - help teams across programs interpret results, build decision-support visualizations, and run reproducible, traceable analyses at scale on the cloud
- Required qualifications -
- MSc or PhD in Bioinformatics, Computational Biology, Genomics, Computer Science, or a closely related field (or equivalent industry experience).
- 3+ years of hands-on experience analyzing DNA sequencing data, with demonstrable expertise on at least two of: long-read (Nanopore/PacBio), short-read (Illumina), Sanger, hybrid assemblies.
- Strong proficiency in Python for pipeline scripting, data wrangling (Pandas, BioPython), and result reporting.
- Production experience with Nextflow (or a comparable workflow manager: Snakemake) and bioinformatics tools: minimap2/BWA, samtools, bcftools, BLAST, MMseqs2, SPAdes/Flye.
- Solid grasp of variant calling for both small variants and structural variants, including the failure modes of each caller and how to reconcile their outputs.
- Comfortable in a Linux/cloud environment: containers (Docker), version control (Git/GitHub), and basic cloud cost/runtime awareness.
- Strong scientific communication in English - able to present results to non-bioinformatician scientists and write clear technical documentation
Nice to have:
- Experience integrating with electronic lab notebooks / LIMS (especially Benchling via its SDK/API).
- Familiarity with the Seqera Platform for pipeline orchestration.
- Experience with methylation analysis (Nanopore, bisulfite pipelines) and/or metagenomics (short-read or long-read).
- Experience with bacterial comparative genomics, pangenome analysis, mobile genetic element / IS-element annotation, or phage genomics.
- Front-end experience for result visualization (Plotly/Dash, JavaScript, JBrowse customization).
- Prior work in a regulated / GxP-adjacent environment (CMC, clinical sequencing data).
- Applicant profile -
- Strong interest in biology, microbiome engineering, and drug development.
- Excellent problem-solving skills and attention to detail; comfortable debugging across the full stack from raw reads to final report.
- Exquisitely organized, strong passion for thorough code documentation and reproducibility.
- Ability to communicate across disciplines and to translate biology into pipelines (and back again).
- General tech-savviness and nerdiness
- Autonomy, initiative, adaptation, and team spirit.
- Perks -
- A team that is passionate, creative, driven, and at the top of their game
- A fast-paced, international, interdisciplinary, inspiring, and collaborative work environment
- An opportunity to apply cutting-edge technologies to solve real-world problems
- A truly unique and fantastic company culture
- Competitive salary, depending on experience
- Commute benefits (100% Navigo refund)
- Ticket Resto (Swile): 8€ per worked day, 50% covered by Eligo
- Office and lab easily accessible via public transit (metro lines 14 and 6, RER C, tram T3a, various bus lines); secure parking for bikes on site
- Brand-new lab and office space in Paris with a rooftop terrace from which we can see the Eiffel Tower sparkle ; 6-minute walk from the river Seine
