Integrated analysis of DNA copy number and gene expression microarray data using gene sets. - Renée X. de Menezes; Marten Boetzer; Melle Sieswerda; Gert-Jan B. van Ommen; Judith M. Boer (BMC Bioinform., 2009)

Scaffolding pre-assembled contigs using SSPACE. - Marten Boetzer; Christiaan V. Henkel; Hans J. Jansen; Derek Butler; Walter Pirovano (Bioinform., 2011)

SSPACE-LongRead: scaffolding bacterial draft genomes using long read sequence information. - Marten Boetzer; Walter Pirovano (BMC Bioinform., 2014)

NCBI-compliant genome submissions: tips and tricks to save time and money. - Walter Pirovano; Marten Boetzer; Martijn F. L. Derks; Sandra Smit (Briefings Bioinform., 2017)