VIRUSBreakend: Viral Integration Recognition Using Single Breakends. - Cameron, Daniel; Jacobs, Nina; Roepman, Paul; Priestley, Peter; Cuppen, Edwin; Papenfuss, Anthony T. (Bioinform., 2021)

Sambamba: fast processing of NGS alignment formats. - Tarasov, Artem; Vilella, Albert J.; Cuppen, Edwin; Nijman, Isaac J.; Prins, Pjotr (Bioinform., 2015)

Comparing genome-wide chromatin profiles using ChIP-chip or ChIP-seq. - Johannes, Frank; Wardenaar, René; Colomé-Tatché, Maria; Mousson, Florence; Graaf, Petra de; Mokry, Michal; Guryev, Victor; Timmers, H. Th. Marc; Cuppen, Edwin; Jansen, Ritsert C. (Bioinform., 2010)

CONREAL web server: identification and visualization of conserved transcription factor binding sites. - Berezikov, Eugene; Guryev, Victor; Cuppen, Edwin (Nucleic Acids Res., 2005)

GENOTRACE: cDNA-based local GENOme assembly from TRACE archives. - Berezikov, Eugene; Plasterk, Ronald H. A.; Cuppen, Edwin (Bioinform., 2002)