I am a computational biologist at Harvard University, 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 lies at the intersection of computer science, applied mathematics, biology and epidemiology. I develop methods for rapid diagnostics of antibiotic resistance and epidemiological surveillance. My previous work focused on resource-frugal methods for DNA 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 computational biology, 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.