Context :

The Imagine Institute brings together 28 research teams (24 integrated laboratories and 4 affiliated laboratories) along with 18 technology platforms, 31 national reference centers for rare diseases and 8 clinical units affiliated with the Necker-Enfants Malades, Cochin and HEGP AP-HP hospitals. This unique environment fosters close collaboration between clinicians, researchers, and technical experts, enabling faster progress from patient observation to understanding disease mechanisms, diagnostics and therapeutic development.

Within this ecosystem, the team Pediatric Inflammatory Skin Disorders: Mechanisms and Therapeutic Implications, led by Dr. Elodie Bal, investigates the genetic and pathophysiological study of severe pediatric forms of scleroderma. This rare autoimmune disease causes progressive fibrosis of the skin and internal organs, leading to major disability and reduced life expectancy. It arises from a complex interplay of genetic, epigenetic, and environmental factors. Their goal is to dissect the mechanisms driving fibrosis using cutting-edge multi-omics approaches, with the ambition to uncover novel diagnostic markers and therapeutic targets.

The laboratory of Prof. Bana Jabri focuses on unraveling the mechanisms that drive intestinal inflammation and autoimmunity, using celiac disease as a paradigm. Her team investigates how genetic and environmental factors shape the interplay between epithelial cells, innate lymphoid cells, and adaptive immune responses to trigger loss of tolerance and chronic inflammation. This research extends beyond celiac disease to provide fundamental insights into immune regulation, autoimmunity and inflammatory disorders.

Missions :

The selected candidate will be expected to contribute to several strategic projects for both teams, including:

• Omics data analysis : Bulk RNA-seq and ChIP-seq/CUT&RUN (Cleavage Under Targets & Release Using Nuclease), eventually ATAC-seq (depending on project needs) ;

• Development of new technology-driven projects :

  • Support the development of projects in spatial transcriptomics (e.g. 10x Visium HD or related technologies), with potential single-cell applications depending on patient sample availability (e.g. 10x Xenium) ;

  • Implementation of CRISPR-based functional screens coupled with single-cell transcriptomic profiling (CROP-seq).

• Integration and collaboration :

  • Active involvement in project design, experimental planning, bioinformatics workflows and data interpretation ;

  • Close collaboration with both clinical and experimental scientists across the Jabri and Bal groups.

• Scientific communication :

  • Preparation of analyses and reports, contribution to manuscripts for high-impact journals ;

  • Presentation of results in lab meetings, seminars and international conferences.

Required qualifications :

• PhD in bioinformatics, computational biology, genomics, systems biology or a related field ;

• Hands-on experience with single-cell sequencing data analysis, including use of relevant software/frameworks (e.g. Seurat, Scanpy, ArchR, Signac, Harmony, Liger, etc.) ;

• Strong background in bulk RNA-seq and epigenomic datasets (notably ChIP-seq) ;

• Proficiency in programming languages commonly used in bioinformatics (R, Python), version control (Git) and use of HPC or cloud computing environments ;

• Demonstrated ability to handle large-scale multi-omics datasets ;

• Strong track record of publications in peer-reviewed journals ;

• Strong communication and writing skills in English (French is an advantage but not required).

Desirable skills :

• Experience with spatial transcriptomics analysis and integration with single-cell data ;

• Experience with CRISPR-screen data, particularly CROP-seq or Perturb-seq ;

• Familiarity with multi-modal data integration (transcriptomics, epigenomics) or imaging-based data would be a strong plus ;

• Background knowledge of immunology, inflammatory pathways or mechanisms of fibrosis would be a strong advantage.

Contract :

• Fixed-term contract: 3 years ;

• Starting date: from October 2025 ;

• Salary: on experience.

How to apply :

This is a unique opportunity to work at the interface of computational biology, immunology and translational research, within a highly collaborative and cutting-edge scientific environment.

Interested candidates are invited to submit:

• A CV including a list of publications ;

• Contact details for two referees.