I am a postdoctoral researcher at Harvard University, working with Michael Baym in the Department of Biomedical Informatics at Harvard Medical School and Bill Hanage in the Center for Communicable Disease Dynamics at the Harvard T.H. Chan School of Public Health. My research lies at the intersection of computer science, applied mathematics, biology and epidemiology. I develop methods for rapid prediction of antibiotic resistance from sequencing data and for epidemiological surveillance. My previous work focused on resource-frugal methods for sequence data analysis.
My research involves software development. I am the lead developer of RASE, ProPhyle, Ococo, RNFtools, SAMsift, ProphAsm, DyMas and Disty McMatrixFace. I also participated in the development of ProPhex, Seed-Kraken, Seed-Jellyfish and NanoSim-H, and occasionally contribute to large projects such as Bioconda or Snakemake. Besides bioinformatics, I also work on methods for automatic generation of tactile maps for blind users.
Prior to joining Harvard, I received my Ph.D. in computer science at Université Paris-Est, while researching also at Institut Curie and Institut Cochin, and a master degree in mathematical computer science at the Czech Technical University in Prague.