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

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

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

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

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