I am a computational biologist working with Prof. Michael Baym in the Department of Biomedical Informatics at Harvard Medical School and Prof. William Hanage in the Center for Communicable Disease Dynamics at the Harvard T.H. Chan School of Public Health. My research is rooted in computer science and applied mathematics, and applied to biology and epidemiology, with the goal of understanding microbial sequence data, with a particular focus on rapid diagnostics.
Our recent paper introduced Genomic Neighbor Typing, a method for rapid inference of antibiotic resistance of bacteria. When combined with nanopore sequencing, we can diagnose resistance for some species within minutes of sequencing and four hours of sample collection.
My other work includes resource-frugal metagenomic classification (ProPhyle), the concept of simplitigs for efficient representation of de Bruijn graphs, spaced seeds for improving metagenomic classification, k-mer indexing using Burrows-Wheeler Transform (ProPhex), the concept of online consensus and variant calling for faster data analysis (Ococo), a format and toolkit for evaluating read mappers using simulated data (RNFtools), and the concept of dynamic mapping for better read mapping and variant calling. I 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).
Prior to my postdoc, 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 master degree in mathematical computer science at the Czech Technical University in Prague, working with Prof. Edita Pelantová.