I’m interested in all bioinformatics problems that have combinatorial and optimization aspects. I try to model these problems with logical constraints and I am a fervent promoter of Answer Set Programming for this purpose, while also having worked in Logic Programming. I am also using graphs and formal concepts in my work.
I am currently focusing on the analysis of long read data generated by the third generation sequencers, especially Nanopore sequencers. It includes three research topics
- Fast and robust identification of bacterial species and strains;
- Haplotype reconstruction from long read data
- Identification of repeated structures (e.g. tandem repeats) from long read data.