CyClus3D: a Cytoscape plugin for clustering network motifs in integrated networks. - Pieter Audenaert; Thomas Van Parys; Florian Brondel; Mario Pickavet; Piet Demeester; Yves Van de Peer; Tom Michoel (Bioinform., 2011)

U-Compare bio-event meta-service: compatible BioNLP event extraction services. - Yoshinobu Kano; Jari Björne; Filip Ginter; Tapio Salakoski; Ekaterina Buyko; Udo Hahn; K. Bretonnel Cohen; Karin Verspoor; Christophe Roeder; Lawrence E. Hunter; Halil Kilicoglu; Sabine Bergler; et al. (BMC Bioinform., 2011)

Diffany: an ontology-driven framework to infer, visualise and analyse differential molecular networks. - Sofie Van Landeghem; Thomas Van Parys; Marieke Dubois; Dirk Inzé; Yves Van de Peer (BMC Bioinform., 2016)

Top 10 metrics for life science software good practices. - Haydee Artaza; Neil P. Chue Hong; Manuel Corpas; Angel Corpuz; Rob W. W. Hooft; Rafael C. Jiménez; Brane Leskosek; Brett G. Olivier; Jan Stourac; Radka Svobodová Vareková; Thomas Van Parys; Daniel Vaughan (F1000Research, 2016)

A Cytoscape app for motif enumeration with ISMAGS. - Thomas Van Parys; Ine Melckenbeeck; Maarten Houbraken; Pieter Audenaert; Didier Colle; Mario Pickavet; Piet Demeester; Yves Van de Peer (Bioinform., 2017)

Optimising orbit counting of arbitrary order by equation selection. - Ine Melckenbeeck; Pieter Audenaert; Thomas Van Parys; Yves Van de Peer; Didier Colle; Mario Pickavet (BMC Bioinform., 2019)