Reactome: a knowledgebase of biological pathways. - G. Joshi-Tope; Marc Gillespie; Imre Vastrik; Peter D'Eustachio; Esther Schmidt; Bernard de Bono; Bijay Jassal; Gopal R. Gopinath; G. R. Wu; Lisa Matthews; Suzanna Lewis; Ewan Birney; et al. (Nucleic Acids Res., 2005)

Reactome - A Knowledgebase of Biological Pathways. - Esther Schmidt; Ewan Birney; David Croft 001; Bernard de Bono; Peter D'Eustachio; Marc Gillespie; Gopal Gopinath; Bijay Jassal; Suzanna Lewis; Lisa Matthews; Lincoln Stein; Imre Vastrik; et al. (OTM Workshops (1), 2006)

Reactome: An integrated expert model of human molecular processes and access toolkit. - Bernard de Bono; Imre Vastrik; Peter D'Eustachio; Esther Schmidt; Gopal Gopinath; David Croft 001; Marc Gillespie; Bijay Jassal; Suzanna Lewis; Lisa Matthews; Guanming Wu; Ewan Birney; et al. (J. Integr. Bioinform., 2007)

Reactome knowledgebase of human biological pathways and processes. - Lisa Matthews; Gopal Gopinath; Marc Gillespie; Michael Caudy; David Croft 001; Bernard de Bono; Phani V. Garapati; Jill Hemish; Henning Hermjakob; Bijay Jassal; Alexander Kanapin; Suzanna Lewis; et al. (Nucleic Acids Res., 2009)

Achieving Semantic Interoperability between Physiology Models and Clinical Data. - Bernard de Bono; Stephen John Sammut; Pierre Grenon (e-Science Workshops, 2011)

Ontology-Strength Industry Standards: The Case of the Clinical Trial Domain. - Pierre Grenon; Sarala M. Wimalaratne; Bernard de Bono (FOMI, 2011)

Logic-Based Representation of Connectivity Routes in the Immune System. - Pierre Grenon; Bernard de Bono (ICARIS, 2011)

Bridging Multiple Ontologies: Representation of the Liver Immune Response. - Anna Maria Masci; Jeffrey Roach; Bernard de Bono; Pierre Grenon; Lindsay G. Cowell (ICBO, 2011)

Integrating systems biology models and biomedical ontologies. - Robert Hoehndorf; Michel Dumontier; John H. Gennari; Sarala M. Wimalaratne; Bernard de Bono; Daniel L. Cook; Georgios V. Gkoutos (BMC Syst. Biol., 2011)

An infrastructure for ontology-based information systems in biomedicine: RICORDO case study. - Sarala M. Wimalaratne; Pierre Grenon; Robert Hoehndorf; Georgios V. Gkoutos; Bernard de Bono (Bioinform., 2012)

Functional tissue units and their primary tissue motifs in multi-scale physiology. - Bernard de Bono; Pierre Grenon; Richard A. Baldock; Peter Hunter (J. Biomed. Semant., 2013)

HuPSON: the human physiology simulation ontology. - Michaela Gündel; Erfan Younesi; Ashutosh Malhotra; Jiali Wang; Hui Li; Bijun Zhang; Bernard de Bono; Heinz-Theodor Mevissen; Martin Hofmann-Apitius (J. Biomed. Semant., 2013)

Eliciting candidate anatomical routes for protein interactions: a scenario from endocrine physiology. - Pierre Grenon; Bernard de Bono (BMC Bioinform., 2013)

Template-based Treemaps to Preserve Spatial Constraints. - Natallia Kokash; Bernard de Bono; Joost N. Kok (IVAPP, 2014)

Computational horizons in cancer (CHIC): Developing meta- and hyper-multiscale models and repositories for in Silico Oncology - A brief technical outline of the project. - Georgios S. Stamatakos; Dimitra D. Dionysiou; Fay Misichroni; Norbert M. Graf; Stefaan W. Van Gool; Rainer Bohle; Feng Dong 005; Marco Viceconti; Kostas Marias; Vangelis Sakkalis; Nikolaus Forgó; Ravi Radhakrishnan; et al. (IARWISOI, 2014)

ApiNATOMY: Towards Multiscale Views of Human Anatomy. - Bernard de Bono; Pierre Grenon; Michiel Helvensteijn; Joost N. Kok; Natallia Kokash (IDA, 2014)

Automated PDF highlighting to support faster curation of literature for Parkinson's and Alzheimer's disease. - Honghan Wu; Anika Oellrich; Christine Girges; Bernard de Bono; Tim J. P. Hubbard; Richard J. B. Dobson (Database J. Biol. Databases Curation, 2017)

Model annotation and discovery with the Physiome Model Repository. - Dewan M. Sarwar; Reza Kalbasi; John H. Gennari; Brian E. Carlson; Maxwell Lewis Neal; Bernard de Bono; Koray Atalag; Peter J. Hunter; David P. Nickerson (BMC Bioinform., 2019)

Knowledge Representation for Multi-Scale Physiology Route Modeling. - Natallia Kokash; Bernard de Bono (Frontiers Neuroinformatics, 2021)

Data Harmonization through Use of Community Standards in the Common Fund Data Ecosystem. - Michelle G. Giglio; Suvarna Nadendla; Arthur Brady; Amanda Charbonneau; Karl Czajkowski; Jeremy Yang; Tom Gillespie; Philippe Rocca-Serra; Jeffrey S. Grethe; Raja Mazumder; Bernard de Bono; Jonathan C. Silverstein; et al. (ICBO, 2022)

Extending and using anatomical vocabularies in the stimulating peripheral activity to relieve conditions project. - Monique Surles-Zeigler; Troy Sincomb; Thomas H. Gillespie; Bernard de Bono; Jacqueline Bresnahan; Gary M. Mawe; Jeffrey S. Grethe; Susan J. Tappan; Maci L. Heal; Maryann E. Martone (Frontiers Neuroinformatics, 2022)

Layout of anatomical structures and blood vessels based on the foundational model of anatomy. - Niklas Gröne; Benjamin Grüneisen; Karsten Klein 001; Bernard de Bono; Tobias Czauderna; Falk Schreiber (J. Integr. Bioinform., 2024)

Developing a multiscale neural connectivity knowledgebase of the autonomic nervous system. - Fahim T. Imam; Thomas H. Gillespie; Ilias Ziogas; Monique Surles-Zeigler; Susan J. Tappan; Ibrahim Burak Özyurt; Jyl Boline; Bernard de Bono; Jeffrey S. Grethe; Maryann E. Martone (Frontiers Neuroinformatics, 2025)

Ontology- and LLM-based Data Harmonization for Federated Learning in Healthcare. - Natallia Kokash; Lei Wang; Thomas H. Gillespie; Adam Belloum; Paola Grosso; Sara K. Quinney; Lang Li; Bernard de Bono (CoRR, 2025)