Reconstructing the Dynamics of HIV Evolution within Hosts from Serial Deep Sequence Data. - Art F. Y. Poon; Luke C. Swenson; Evelien M. Bunnik; Diana Edo-Matas; Hanneke Schuitemaker; Angélique B. van 't Wout; P. Richard Harrigan (PLoS Comput. Biol., 2012)

PuFFIN - a parameter-free method to build nucleosome maps from paired-end reads. - Anton Polishko; Evelien M. Bunnik; Karine G. Le Roch; Stefano Lonardi (BMC Bioinform., 2014)

ThIEF: Finding Genome-wide Trajectories of Epigenetics Marks. - Anton Polishko; Md. Abid Hasan; Weihua Pan; Evelien M. Bunnik; Karine G. Le Roch; Stefano Lonardi (WABI, 2017)