A Feature Selection Algorithm for Detecting Subtype Specific Functional Sites from Protein Sequences for Smad Receptor Binding. - Elena Marchiori; Walter Pirovano; Jaap Heringa; K. Anton Feenstra (ICMLA, 2006)

Sequence harmony: detecting functional specificity from alignments. - K. Anton Feenstra; Walter Pirovano; Klaas Krab; Jaap Heringa (Nucleic Acids Res., 2007)

Correlated substitution analysis and the prediction of amino acid structural contacts. - David Stephen Horner; Walter Pirovano; Graziano Pesole (Briefings Bioinform., 2008)

PRALINETM: a strategy for improved multiple alignment of transmembrane proteins. - Walter Pirovano; K. Anton Feenstra; Jaap Heringa (Bioinform., 2008)

The meaning of alignment: lessons from structural diversity. - Walter Pirovano; K. Anton Feenstra; Jaap Heringa (BMC Bioinform., 2008)

Structure and function analysis of flexible alignment regions in proteins. - Walter Pirovano; Anneke van der Reijden; K. Anton Feenstra; Jaap Heringa (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)