- Microbiome: bioinformatics, machine learning. Metagenomic and metatranscriptomic method development. Collaborations with experimentalists and applications on publicly available data.
- Immune-microbiome interactions. Focus on gut mucus layer.
- Theory of microbial ecology and engineered microbial communities – with applications for agriculture, waste treatment, etc.
- Quantitative immunology methods development – specifically flow cytometry analysis methods.