Société Française de Bioinformatique

Mots-Clés

Genomics Machine Learning Single-Cell

Description

Bioinformatics Internship Opportunity: Single-Cell Annotation Methods with AI

Location: Institut Pasteur, Paris, France

Duration: 6 months

Start Date: Early 2025

Overview:

The Deczkowska lab studies how immune cells and signals shape brain development, activity and aging. We are offering a 6-month internship opportunity for a motivated intern to contribute to cutting-edge research in single-cell RNA sequencing. This internship will focus on exploring and/or developing methods for annotating single-cell data based on clustering results from both published and unpublished datasets. The intern will work closely with our team in neuroimmunology and bioinformatics, gaining hands-on experience in the rapidly evolving field of single-cell genomics.

Responsibilities:

• Develop and implement novel single-cell annotation methods.
• Analyse clustering results from scRNA-seq datasets to identify and annotate cell types.
• Evaluate the performance and accuracy of developed methods against existing annotation tools.
• Present results at lab meetings.

Requirements:

• Currently enrolled in a master’s program in Bioinformatics, Genomics, Machine Learning or a related field.
• Strong programming skills in Python and Bash (R would be an advantage).
• Understanding of machine learning (experience with deep learning would be an advantage).
• Interest in single-cell RNA sequencing data.
• Experience with clustering algorithms is highly desirable.
• Problem-solving skills and the ability to work independently as well as part of a team.
• Proficiency in English.

How to Apply:

Interested candidates should send the following documents:

1. A cover letter describing your interest.
2. A CV including academic background and any relevant projects.
3. Contact information for at least one academic or professional reference.

Contact Information:

Joseph JOSEPHIDES: joseph.josephides[ at ]pasteur.fr

Relevant papers linked to the project:

1. Deczkowska, A., Keren-Shaul, H., Weiner, A., Colonna, M., Schwartz, M., & Amit, I. (2018). Disease-associated microglia: a universal immune sensor of neurodegeneration. Cell, 173(5), 1073-1081 https://doi.org/10.1016/j.cell.2018.05.003
2. Cui, H., Wang, C., Maan, H., Pang, K., Luo, F., Duan, N., & Wang, B. (2024). scGPT: toward building a foundation model for single-cell multi-omics using generative AI. Nature Methods, 1-11. https://doi.org/10.1038/s41592-024-02201-0
3. Shao, X., Liao, J., Lu, X., Xue, R., Ai, N., & Fan, X. (2020). scCATCH: automatic annotation on cell types of clusters from single-cell RNA sequencing data. Iscience, 23(3). https://doi.org/10.1016/j.isci.2020.100882

The selection process will take place in September-October.