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exploring and/or developing methods for annotating single-cell data based on clustering results from both published and unpublished datasets.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:
- A cover letter describing your interest.
- A CV including academic background and any relevant projects.
- Contact information for at least one academic or professional reference.
Contact Information:
Joseph JOSEPHIDES (bioinformatician): joseph.josephides[ at ]pasteur.fr
Relevant papers linked to the project:
- 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
- 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
- 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.