Cellenion is a fast-growing biotech company, specialized in automated single-cell isolation and liquid handling, developing breakthrough technology in the field of single cell Omics. In 2020, Cellenion joined BICO for an even more exciting journey.

BICO is a corporate structure focusing on the intersection of technology and biology, pioneering the bio convergence revolution, and paving the way for the future of health.

With a thriving international customer portfolio, Cellenion is committed to the development of single-cell next-generation sequencing (scNGS) solutions, from laboratory solutions development to data analysis and interpretation.

We are looking for a dynamic Bioinformatician to join our Applications Development team. You have an extensive knowledge of genomics and epigenetics/epigenomics dataset handling applied to any type of biology? You are eager to imagine valuable and straightforward bioinformatics solutions? You enjoy helping end-users implementing those solutions to answer their questions? Join us!

Your goal will be to manage the scNGS data flow and analyses internally as well as developing customers ready to use solution for data analysis with the help of a multidisciplinary team of molecular, cell and microbial biologists as well as engineers.

Tasks & Responsibilities:

  • Take responsibility for all bioinformatic related topics in Cellenion.
  • Manage collaborators and students’ part of or joining the team.
  • Maintain and improve existing single cell NGS analysis pipelines developed in house
  • Develop, test, deploy and maintain new NGS data analysis pipelines (sc or bulk; RNA, DNA, epigenomics), with a focus on single cell analysis pipelines, by following the best practices.
  • Develop biologist-friendly, intelligible, yet customizable, applications for end-users, supporting scNGS data processing and interpretation, from out-of-sequencer data to graphical analysis and statistics.
  • Document and annotate codes and pipelines.
  • Do bibliographic research and benchmarking to find optimal tools for each pipeline
  • Track changes and trends in NGS data analysis practices and tools.
  • Interact and discuss with wet lab scientists to support them in designing relevant experiments for data analyses and statistical studies.
  • Work with Product managers, sales manager, and engineers to define customer’s needs for new and improved products and services offered by the company.
  • Proceed to single cell analysis for customer and participate to customer support.
  • Setup/maintain infrastructure (Cloud and/or servers) required to analyze NGS data internally and as service offer for customers.
  • Create and maintain Cellenion data flow system.
  • Write manuals for internal and customer use (in English).
  • Prepare and deliver technical presentations at customer sites and tradeshows.
  • Travel to customer sites (national and international) or scientific congress.

Required skills and qualifications:

  • Extensive knowledge of Illumina dataset: formats, QC, and metrics.
  • Advanced computational skills, in several scripting languages (R, Python, Bash).
  • Proven experience in genomics (WGS, comparative genomics…) and epigenetics/epigenomics (RNA-seq, ATAC-seq, ChIP-seq…) NGS data analysis.
  • Excellent knowledge/understanding of commonly used software for NGS and scNGS data exploration and analysis (e.g., Bowtie2, MACS 2, SAMtools, HOMER, Schnapps/Bioconductor/Seurat R packages, etc.).
  • Taste for highly collaborative and interdisciplinary teamwork.
  • Ability to independently identify and prioritize requirements, research axes and challenges.
  • Excellent oral and written communication for interactions with co-workers, collaborators, and customers.
  • Proficient in English (everyday language of work).

Optional skills:

  • Computational skills in programming languages (C/CC++, JavaScript, Java)
  • Knowledge in pipeline development using snakemake or nextflow
  • Knowledge in webApp development using Dash, flask, or Django

Added-value skills:

  • Experience/knowledge of single-cell -omics data analysis.
  • Experience/knowledge of microbial genome assemblage/annotation.
  • Experience/knowledge of (microbial) evolution reconstruction, (microbial) molecular phylogeny.
  • Experience/knowledge of multi-omics approaches data analysis.
  • Experience/knowledge of long reads data handling.
  • Experience/knowledge of methodology and good practices in (software) development.

To join us you will definitely:

  • Demonstrate that you can work independently in a fast-paced environment with rapidly changing priorities.
  • Be proactive and continuously develop processes and routines.
  • Show excellent documenting and time-management skills.
  • Have excellent interpersonal skills and be highly collaborative.
  • Have eagerness to learn quickly in new areas.
  • Be able to work daily in French and English. German is a plus but not mandatory.


The position is based in Lyon – France, starting as soon as possible.

If you want to join our team:

Please send your CV, cover letter and salary expectations to [email protected]  with as object the reference “Bioinformatic scientist”.