Open PhD positions

Open PhD Position — Microbiome Data Science

We are seeking a motivated PhD candidate to join us and investigate the causal role of the gut microbiome in autoimmune disease. This position sits at the intersection of computational biology, biostatistics, and biomedicine, and offers a unique opportunity to contribute to one of the most rapidly evolving areas of human disease research.

Project overview

Dysregulation of the gut microbiome has been increasingly implicated in the onset and progression of autoimmune conditions, including rheumatoid arthritis and systemic lupus erythematosus. While robust microbial associations with disease have been established, translating these findings into causal understanding and clinical application remains a central open challenge. This PhD project will address that gap by leveraging large-scale microbiome datasets — including 16S rRNA amplicon and shotgun metagenomic data — alongside host multi-omics layers (transcriptomics, metabolomics) to identify and causally characterize microbial features associated with disease susceptibility, progression, and treatment response.

The work will combine bioinformatics pipelines with rigorous statistical and causal inference frameworks, including mediation analysis and longitudinal multi-omics modeling.

Profile of the candidate

We welcome applications from candidates with a Master's degree (or equivalent) in molecular biology, biotechnology, bioinformatics, computational biology, biostatistics, data science, or a related quantitative field. Programming skills in R and/or Python are essential. Experience with microbiome data analysis, compositional statistics, causal inference methods, or machine learning applied to biological data is a significant asset. Familiarity with multi-omics integration frameworks and longitudinal study designs is a plus. A genuine interest in immunology and human disease, intellectual curiosity, and the ability to work both independently and collaboratively in an interdisciplinary environment are equally important.

You will benefit from strong methodological mentorship in both bioinformatics and statistics, an active network of clinical and computational collaborators at an international level, and a stimulating scientific environment.

Interested?

Please send your CV and a brief motivation describing your research interests to eliana.ibrahimi@fshn.edu.al