Apr 2021: Paper on the simplitig representation published in Genome Biology
    Feb 2021: Talk at DSB 2021 (All microbes on a flash drive)
    Oct 2020: Invited talk at the BAARN symposium (Rapid inference of antibiotic resistance and susceptibility)
    Feb 2020: Paper on rapid inference of antibiotic resistance published in Nature Microbiology

I am a postdoctoral researcher in the Baym lab in the Department of Biomedical Informatics at Harvard Medical School. The fundamental goal of my research is achieving rapid, robust and affordable diagnostics and real-time surveillance of infectious diseases at points of care. To do so, I develop novel algorithms, data representations, software and databases for computational genomics, which are then provided to the scientific community as building blocks for larger efforts. I am particularly interested in the problem of search across all existing sequence data, as well as unlocking the full potential of portable genomic technologies, such as nanopore sequencing and CRISPR-Dx.

Genomic Neighbor TypingMy recent work includes Genomic Neighbor Typing, a method that can identify antibiotic resistance within 10 minutes of nanopore sequencing (and 4 hours of sample collection from metagenomic sputum samples); by similarity genome search across data from epidemiological surveillance, it can rapidly infer the likely resistance profile of a sample from its closest known relatives. Genomic Neighbor Typing built on my contributions to computational genomics, including simplitigs as an efficient and scalable representation of de Bruijn graphs (and ProphAsm for their computation), the ProPhyle metagenomic classifier, and ProphEx for k-mer indexing using the Burrows-Wheeler Transform.

My other work includes spaced seeds for metagenomic classification, online consensus and variant calling for a rapid analysis of streamed NGS data (Ococo), a format and a toolkit for evaluating read mappers (RNFtools), and the concept of dynamic mapping for better read mapping and variant calling. I also occasionally contribute to large projects such as Bioconda or Snakemake and develop methods for automatic generation of tactile maps for blind users (Blind Friendly Maps).

I received my Ph.D. in computer science at Université Paris-Est, while researching also at Institut Curie and Institut Cochin, being supervised by Prof. Gregory Kucherov and Prof. Valentina Boeva. Prior to that, I received a bachelor and masters degree in mathematical computer science at the Czech Technical University in Prague, working with Prof. Edita Pelantová and Prof. Karel Klouda.

Selected publications