Detecting patterns of co-variation in deep-sequenced virus populations. - Susana Posada-Céspedes; David Seifert; Niko Beerenwinkel (ICCABS, 2016)

V-pipe: a computational pipeline for assessing viral genetic diversity from high-throughput data. - Susana Posada-Céspedes; David Seifert; Ivan Topolsky; Kim Philipp Jablonski; Karin J. Metzner; Niko Beerenwinkel (Bioinform., 2021)

Comparing mutational pathways to lopinavir resistance in HIV-1 subtypes B versus C. - Susana Posada-Céspedes; Gert van Zyl; Hesam Montazeri; Jack Kuipers; Soo-Yon Rhee; Roger D. Kouyos; Huldrych F. Günthard; Niko Beerenwinkel (PLoS Comput. Biol., 2021)