Mots-Clés
X chromosome
epigenetics
single-cell
bioinformatics
Description
Host Laboratories: Institut Curie - Centre de Recherche / Institut Imagine.
An internship position in bioinformatics is available between the bioinformatics core facility of Institut Curie (INSERM U1331) and the Epigenetics and sex differences team (Institut Imagine).
Context:
X chromosome inactivation (XCI) is a fundamental epigenetic process that ensures dosage compensation between XX females and XY males by silencing one of the two X chromosomes. Despite extensive research, many aspects of XCI establishment, maintenance, and variability at the single-cell level remain poorly understood. Recent advances in single-cell sequencing technologies provide unprecedented opportunities to investigate XCI dynamics at cellular resolution. However, extracting allele-specific information from single-cell datasets remains challenging due to sparse coverage, technical noise, and limitations in variant detection.
Project Description:
The goal of this internship is to assess the depth and resolution at which allele-specific analyses can be performed using single-cell sequencing data generated from mouse models. The project will combine computational method development, data analysis, and biological interpretation to characterize X chromosome inactivation patterns across individual cells.
This internship represents a collaborative effort between the team of Nicolas Servant at Institut Curie, which specializes in computational genomics and bioinformatics, and the laboratory of Agnese Loda at Institut Imagine, an expert in X chromosome biology and mouse models. The student will work at the interface between computational and experimental biology and benefit from complementary expertise from both groups.
Objectives:
The main objectives of the project are:
• Process and quality-control single-cell sequencing datasets generated from mouse models.
• Develop and evaluate workflows for allele-specific mapping and quantification.
• Characterize the level of allelic information that can be reliably extracted from different single-cell modalities.
• Investigate cell-to-cell variability in X chromosome inactivation.
• Identify technical and biological limitations affecting allele-specific analyses in single-cell data.
• Contribute to the development of robust bioinformatics pipelines for future large-scale studies of XCI.
Methods and Tools:
The intern will be trained in and utilize:
• Single-cell data analysis (scRNA-seq and potentially other single-cell modalities)
• Allele-specific expression analysis
• Genomic variant processing and haplotype-aware mapping strategies
• Statistical analysis and data visualization
• Linux and high-performance computing environments
• Bioinformatics tools and workflows management (Nextflow)
Expected Profile:
We are looking for a highly motivated Master’s student (M2) or engineering student with:
• An interest in genomics, epigenetics, and single-cell biology
• Basic knowledge of bioinformatics and/or computational biology
• Experience with programming (R, Python, or similar)
• Familiarity with Linux environments
• Strong analytical and communication skills
• Good technical english level
Prior experience with next-generation sequencing data is a plus.
Duration : 6 months
Location : Paris 5e