Making the difference: integrating structural variation detection tools. - Ke Lin; Sandra Smit; Guusje Bonnema; Gabino Sanchez-Perez; Dick de Ridder (Briefings Bioinform., 2015)

PanTools: representation, storage and exploration of pan-genomic data. - Siavash Sheikhizadeh; M. Eric Schranz; Mehmet Akdel; Dick de Ridder; Sandra Smit (Bioinform., 2016)

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)

Efficient inference of homologs in large eukaryotic pan-proteomes. - Siavash Sheikhizadeh; Dick de Ridder; M. Eric Schranz; Sandra Smit (BMC Bioinform., 2018)

GeneNoteBook, a collaborative notebook for comparative genomics. - Rens Holmer; Robin van Velzen; René Geurts; Ton Bisseling; Dick de Ridder; Sandra Smit (Bioinform., 2019)

Visual Exploration of Genetic Sequence Variants in Pangenomes. - Astrid van den Brandt; Eef M. Jonkheer; Dirk-Jan M. van Workum; Sandra Smit; Anna Vilanova (EuroVis (Posters), 2022)

PanTools v3: functional annotation, classification and phylogenomics. - Eef M. Jonkheer; Dirk-Jan M. van Workum; Siavash Sheikhizadeh Anari; Balázs Brankovics; Jorn R. de Haan; Lidija Berke; Theo A. J. van der Lee; Dick de Ridder; Sandra Smit (Bioinform., 2022)

PanVA: Pangenomic Variant Analysis. - Astrid van den Brandt; Eef M. Jonkheer; Dirk-Jan M. van Workum; Huub van de Wetering; Sandra Smit; Anna Vilanova (IEEE Trans. Vis. Comput. Graph., 2024)

Multipla: Multiscale Pangenomic Locus Analysis. - Astrid van den Brandt; Emilia Ståhlbom; Fredericus Johannes Maria van Workum; Huub van de Wetering; Claes Lundström; Sandra Smit; Anna Vilanova (Comput. Graph. Forum, 2025)