Bioinformatics Scientist

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)

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.

• →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
  

• 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).

• 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.