Ontologies Put More Meaning into Meaningful Use. - Tomasz Adamusiak; Naoki Shimoyama; Alexandra Fuiks; Mary Shimoyama (SWAT4LS, 2012)

Next generation ontology browser. - Tomasz Adamusiak; Naoki Shimoyama; Marek Tutaj; Mary Shimoyama (ICBO, 2013)

PhenoGeneRanker: A Tool for Gene Prioritization Using Complete Multiplex Heterogeneous Networks. - Cagatay Dursun; Naoki Shimoyama; Mary Shimoyama; Michael Schläppi; Serdar Bozdag (BCB, 2019)