Research Intern – Bioinformatics & Microbial Ecology
UMR 6553 ECOBIO, University of Rennes 1 | February – July 2025
Overview
As part of my M2 in Bioinformatics, I conducted a 6-month research internship at the ECOBIO laboratory in Rennes, working on the DivIDE ANR project.
Research Topic
Division of labor in genetically identical bacterial populations
This project aimed to investigate how genetically identical bacteria (Pseudomonas brassicacearum) can exhibit phenotypic heterogeneity and functional specialization within a population.
Methods & Skills
Technical Skills
Single-cell RNA sequencing (scRNA-seq)
- Data preprocessing and quality control
- Clustering and differential expression analysis
- Gene expression profiling at single-cell resolution
Bioinformatics Tools & Programming
- Python with Scanpy for scRNA-seq analysis
- R with Seurat for complementary analyses
- High-performance computing (HPC) for large-scale data processing
- Workflow development and reproducible analysis pipelines
Data Visualization
- Interactive visualizations for exploratory data analysis
- Publication-ready figures and comprehensive data representations
Professional & Soft Skills
- Analytical Thinking: Applied computational methods to interpret complex biological data and identify meaningful patterns in single-cell gene expression
- Technical Autonomy: Independently developed and optimized bioinformatics workflows for scRNA-seq data analysis
- Problem-Solving: Troubleshot technical challenges in data processing and adapted analytical approaches to address research questions
- Scientific Communication: Prepared comprehensive thesis documentation in English and presented findings to supervisors and research team. Utilized Quarto for professional report formatting and presentation-quality documentation
- Attention to Detail: Maintained rigorous quality control standards throughout data preprocessing and analysis workflows
Supervision
- Philippe Vandenkoornhuyse – Professor, ECOBIO
- Solène Mauger-Franklin – Postdoctoral Researcher, ECOBIO
Outcomes
Reflections on the Internship
Positive Research Experience
This internship was a highly enriching experience that I genuinely enjoyed. I greatly appreciated working with the research team at ECOBIO, who created a collaborative and intellectually stimulating environment.
Technical Challenges and Growth
Working with single-cell RNA sequencing data from bacterial populations (MicroSPLiT technology) presented unique and challenging computational problems. Unlike conventional scRNA-seq applications in eukaryotic systems, analyzing bacterial transcriptomes at single-cell resolution required adapting existing workflows and developing novel analytical approaches. This technical challenge was particularly rewarding, as it pushed me to deepen my understanding of both the biological complexity and the computational methods needed to extract meaningful insights from these datasets.
Exceptional Mentorship
I was fortunate to work with supervisors who provided outstanding mentorship. Their pedagogical approach and constructive feedback created an ideal learning environment. The regular exchanges with my supervisors were particularly valuable—they encouraged critical thinking, offered thoughtful guidance when I encountered difficulties, and gave me the autonomy to explore solutions independently while remaining available for support.
Career Clarity and Self-Discovery
This internship helped me gain important clarity about my professional aspirations and what I seek in a career:
Balance Between Computation and Human Interaction: While I genuinely enjoy programming and machine learning—finding satisfaction in developing analytical pipelines and solving computational problems—I realized that I need more than purely technical work. I don’t envision myself coding around the clock; I need balance and human connection in my professional life.
Missing Human Element: What I valued most during my Master’s program were the interactions with people, particularly during the CoCoBi minor where I worked alongside medical residents. These experiences reminded me of my long-standing interest in medicine and the importance of direct human engagement in my work.
Future Vision: This introspection has crystallized a career goal: I aspire to combine medicine with computational research, potentially as a physician-scientist specializing in AI applications in healthcare. This would allow me to integrate my computational skills with patient-centered work, maintaining the human element that I find essential while applying cutting-edge technology to medical challenges.
Impact on Career Direction
This internship reinforced my technical capabilities in bioinformatics and computational biology while simultaneously clarifying that I seek a career path that balances analytical work with meaningful human interaction. The experience confirmed my interest in pursuing medicine while continuing to develop my expertise in AI and data science, ultimately aiming to bridge these fields in a way that serves both scientific advancement and patient care.