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.

PhD Students

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