Bgee: Integrating and Comparing Heterogeneous Transcriptome Data Among Species. - Frederic B. Bastian; Gilles Parmentier; Julien Roux; Sébastien Moretti; Vincent Laudet; Marc Robinson-Rechavi (DILS, 2008)

Homolonto: generating homology relationships by pairwise alignment of ontologies and application to vertebrate anatomy. - Gilles Parmentier; Frederic B. Bastian; Marc Robinson-Rechavi (Bioinform., 2010)

Recent advances in biocuration: Meeting Report from the fifth International Biocuration Conference. - Pascale Gaudet; Cecilia N. Arighi; Frederic B. Bastian; Alex Bateman; Judith A. Blake; J. Michael Cherry; Peter D'Eustachio; Robert D. Finn; Michelle G. Giglio; Lynette Hirschman; Renate Kania; William Klimke; et al. (Database J. Biol. Databases Curation, 2012)

vHOG, a multispecies vertebrate ontology of homologous organs groups. - Anne Niknejad; Aurélie Comte; Gilles Parmentier; Julien Roux; Frederic B. Bastian; Marc Robinson-Rechavi (Bioinform., 2012)

Uncovering hidden duplicated content in public transcriptomics data. - Marta Rosikiewicz; Aurélie Comte; Anne Niknejad; Marc Robinson-Rechavi; Frederic B. Bastian (Database J. Biol. Databases Curation, 2013)

Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon. - Melissa A. Haendel; James P. Balhoff; Frederic B. Bastian; David C. Blackburn; Judith A. Blake; Yvonne M. Bradford; Aurélie Comte; Wasila M. Dahdul; Thomas Dececchi; Robert E. Druzinsky; Terry F. Hayamizu; Nizar Ibrahim; et al. (J. Biomed. Semant., 2014)

Fifteen years SIB Swiss Institute of Bioinformatics: life science databases, tools and support. - Heinz Stockinger; Adrian M. Altenhoff; Konstantin Arnold; Amos Bairoch; Frederic B. Bastian; Sven Bergmann; Lydie Bougueleret; Philipp Bucher; Mauro Delorenzi; Lydie Lane; Philippe Le Mercier; Frédérique Lisacek; et al. (Nucleic Acids Res., 2014)

The Confidence Information Ontology: a step towards a standard for asserting confidence in annotations. - Frederic B. Bastian; Marcus C. Chibucos; Pascale Gaudet; Michelle G. Giglio; Gemma L. Holliday; Hong Huang; Suzanna E. Lewis; Anne Niknejad; Sandra E. Orchard; Sylvain Poux; Nives Skunca; Marc Robinson-Rechavi (Database J. Biol. Databases Curation, 2015)

BgeeDB, an R package for retrieval of curated expression datasets and for gene list expression localization enrichment tests. - Andrea Komljenovic; Julien Roux; Marc Robinson-Rechavi; Frederic B. Bastian (F1000Research, 2016)

OncoMX: an Integrated Cancer Mutation and Expression Knowledgebase for Biomarker Evaluation and Discovery. - Amanda Bell; Raja Mazumder; Daniel J. Crichton; Vijay K. Shanker; Frédéric B. Bastian; Hayley Dingerdissen; Samir Gupta; Evan Holmes; Robel Y. Kahsay; Heather L. Kincaid; A. S. M. Ashique Mahmood; Marc Robinson-Rechavi; et al. (AMIA, 2019)

INODE: Building an End-to-End Data Exploration System in Practice [Extended Vision]. - Sihem Amer-Yahia; Georgia Koutrika; Frederic B. Bastian; Theofilos Belmpas; Martin Braschler; Ursin Brunner; Diego Calvanese; Maximilian Fabricius; Orest Gkini; Catherine Kosten; Davide Lanti; Antonis Litke; et al. (CoRR, 2021)

The Bgee suite: integrated curated expression atlas and comparative transcriptomics in animals. - Frederic B. Bastian; Julien Roux; Anne Niknejad; Aurélie Comte; Sara S. Fonseca Costa; Tarcisio Mendes de Farias; Sébastien Moretti; Gilles Parmentier; Valentine Rech de Laval; Marta Rosikiewicz; Julien Wollbrett; Amina Echchiki; et al. (Nucleic Acids Res., 2021)

Data in use for Alzheimer disease study: combining gene expression, orthology, bioresource and disease datasets. - Tarcisio Mendes de Farias; Tatsuya Kushida; Ana Claudia Sima; Christophe Dessimoz; Hirokazu Chiba; Frédéric B. Bastian; Hiroshi Masuya (SWAT4HCLS, 2023)

Boosting interoperability: towards an increasingly reusable bioinformatics knowledge base. - Tarcisio Mendes de Farias; Julien Wollbrett; Marc Robinson-Rechavi; Frederic B. Bastian (CoRR, 2023)

Federated SPARQL query performance evaluation for exploring disease model mouse: combining gene expression, orthology, and disease knowledge graphs. - Tatsuya Kushida; Tarcisio Mendes de Farias; Ana Claudia Sima; Christophe Dessimoz; Hirokazu Chiba; Frederic B. Bastian; Hiroshi Masuya (BMC Medical Informatics Decis. Mak., 2025)