If you find Bgee useful please consider citing:

• Bastian FB, Brandulas Cammarata A, Carsanaro S, Detering H, Huang W-T, Joye S, Niknejad A, Nyamari M, Mendes de Farias T, Moretti S, Tzivanopoulou M, Wollbrett J, Robinson-Rechavi M.
  Bgee in 2024: focus on curated single-cell RNA-seq datasets, and query tools
  in Nucleic Acids Research, 2025, 53:D878-D885.RIS

• Bastian FB, Roux J, Niknejad A, Comte A, Fonseca Costa SS, Mendes de Farias T, Moretti S, Parmentier G, Rech de Laval V, Rosikiewicz M, Wollbrett J, Echchiki A, Escoriza A, Gharib W, Gonzales-Porta M, Jarosz Y, Laurenczy B, Moret P, Person E, Roelli P, Sanjeev K, Seppey M, Robinson-Rechavi M.
  The Bgee suite: integrated curated expression atlas and comparative transcriptomics in animals
  in Nucleic Acids Research, 2021, 49:D831-D847.RIS

or choose the publication that best covers the Bgee aspects or components you used in your work from the list of publications below.

• For the development and life stage ontologies for animals:
  Niknejad A, Mungall CJ, Osumi-Sutherland D, Robinson-Rechavi M, Bastian F.
  Creation and unification of development and life stage ontologies for animals
  inarXiv, 2022.

• For the BgeeDB R package:
  Komljenovic A, Roux J, Wollbrett J, Robinson-Rechavi M, Bastian F.
  BgeeDB, an R package for retrieval of curated expression datasets and for gene list enrichment tests
  inF1000Research, 2018, 5:2748.RIS

• For UBERON:
  Haendel MA, Balhoff JP, Bastian FB, Blackburn DC, Blake JA, Bradford Y, Comte A, Dahdul WM, Dececchi TA, Druzinsky RE, Hayamizu TF, Ibrahim N, Lewis SE, Mabee PM, Niknejad A, Robinson-Rechavi M, Sereno PC, Mungall CJ.
  Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon
  inJ Biomed Semantics, 2014, 5:21.RIS

• Emonet V, Bolleman J, Duvaud D, Mendes de Farias T, Sima AC
  LLM-based SPARQL Query Generation from Natural Language over Federated Knowledge Graphs
  inISWC 2024 Special Session on Harmonising Generative AI and Semantic Web Technologies (HGAIS 2024), 23rd International Semantic Web Conference, 2024, 3953:355

• Bolleman J, Emonet V, Altenhoff A, Bairoch A, Blatter M-C, Bridge A, Duvaud S, Gasteiger E, Kuznetsov D, Moretti S, Michel P-A, Morgat A, Pagni M, Redaschi N, Zahn-Zabal M, Mendes de Farias T, Sima AC
  A large collection of bioinformatics question-query pairs over federated knowledge graphs: methodology and applications
  inGigaScience, 2025, 14:giaf045.

• Rangel JC, Mendes de Farias T, Sima AC, Kobayashi N.
  SPARQL Generation: an analysis on fine-tuning OpenLLaMA for Question Answering over a Life Science Knowledge Graph
  inSemantic Web Applications and Tools for Health Care and Life Sciences, 2024, 3890:36-45.

• Mendes de Farias T, Altenhoff A, Bairoch A, Bastian FB, Crameri K, Dauvillier J, Dessimoz C, Glover N, Gnodtke K, Hayes C, Kriventseva E, Moretti S, Morgat A, Oesterle S, Sima A-C, Szklarczyk D, Topalov O, Toure V, Unni D, von Mering C, Wollbrett J, Zdobnov E, Samarasinghe K, Gehant S, Baratin D, Burdet B, Ibberson M, Redaschi N, Robinson-Rechavi M, Mehl F, Pagni M, Lisacek F, Bolleman J, Michel P-A, Zahn-Zabal M, Bridge AJ, Kuznetsov D, Bansal P.
  The SIB Swiss Institute of Bioinformatics Semantic Web of data
  inNucleic Acids Research, 2024, 52:D44-D51.

• Kushida T, Mendes de Farias T, Sima A-C, Dessimoz C, Chiba H, Bastian FB, Masuya H.
  Federated SPARQL query performance evaluation for exploring disease model mouse: combining gene expression, orthology, and disease knowledge graphs
  inBMC Medical Informatics and Decision Making, 2025, 25:189.

• Sima A-C, Mendes de Farias T.
  On the Potential of Artificial Intelligence Chatbots for Data Exploration of Federated Bioinformatics Knowledge Graphs
  inProceedings of the 6th Workshop on Semantic Web Solutions for Large-Scale Biomedical Data Analytics, 2023, 3466:paper1.

• Mendes de Farias T, Wollbrett J, Robinson-Rechavi M, Bastian F.
  Lessons learned to boost a bioinformatics knowledge base reusability, the Bgee experience
  inGigaScience, 2023, 12:giad058.

• Mendes de Farias T, Kushida T, Sima A-C, Dessimoz C, Chiba H, Bastian F, Masuya H.
  Data in use for Alzheimer disease study: combining gene expression, orthology, bioresource and disease datasets
  inSemantic Web Applications and Tools for Health Care and Life Sciences, 2023, 3415:177–178.

• Dingerdissen HM, Bastian FB, Vijay-Shanker K, Robinson-Rechavi M, Bell A, Gogate N, Gupta S, Holmes E, Kahsay R, Keeney J, Kincaid H, King CH, Liu D, Crichton DJ, Mazumder R.
  OncoMX: A Knowledgebase for Exploring Cancer Biomarkers in the Context of Related Cancer and Healthy Data
  inJCO Clinical Cancer Informatics, 2020, 4:210-220.

• Chen Q, Britto R, Erill I, Jeffery CJ, Liberzon A, Magrane M, Onami J, Robinson-Rechavi M, Sponarova J, Zobel J, Karin Verspoor.
  Quality Matters: Biocuration Experts on the Impact of Duplication and Other Data Quality
  inGenomics, Proteomics & Bioinformatics, 2020, 18:91-103.

• Robinson-Rechavi M, Rech de Laval V, Bastian FB, Wollbrett J, Bgee Team.
  The Expression Comparison Tool in Bgee
  inScornavacca C, Delsuc F, Galtier N. Phylogenetics in the Genomic Era. No commercial publisher | Authors open access book, 2020, pp.4.3:1-4.3:4.

• Sima AC, Mendes de Farias T, Zbinden E, Anisimova M, Gil M, Stockinger H, Stockinger K, Robinson-Rechavi M, Dessimoz C.
  Enabling semantic queries across federated bioinformatics databases
  inDatabase, 2019, 2019:baz106.

• Mendes de Farias T, Stockinger H, Dessimoz C.
  VoIDext: Vocabulary and Patterns for Enhancing Interoperable Datasets with Virtual Links
  inOn the Move to Meaningful Internet Systems: OTM 2019 Conferences. Lecture Notes in Computer Science, 2019, 11877:607–625.

• SIB Swiss Institute of Bioinformatics Members.
  The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases
  inNucleic Acids Research, 2016, 44:D27-D37.

• Bastian FB, Chibucos MC, Gaudet P, Giglio M, Holliday GL, Huang H, Lewis SE, Niknejad A, Orchard S, Poux S, Skunca N, Robinson-Rechavi M.
  The Confidence Information Ontology: a step towards a standard for asserting confidence in annotations
  inDatabase, 2015, 2015:bav043.

• Rosikiewicz M, Robinson-Rechavi M.
  IQRray, a new method for Affymetrix microarray quality control, and the homologous organ conservation score, a new benchmark method for quality control metrics
  inBioinformatics, 2014, 30:1392-1399.

• Niknejad A, Comte A, Parmentier G, Roux J, Bastian FB, Robinson-Rechavi M.
  vHOG, a multispecies vertebrate ontology of homologous organs groups
  inBioinformatics, 2012, 28:1017-1020.

• Roux J, Robinson-Rechavi M.
  An ontology to clarify homology-related concepts
  inTrends Genet, 2010, 26(3):99-102.

• Bastian F, Parmentier G, Robinson-Rechavi M.
  Generating Homology Relationships by Alignment of Anatomical Ontologies
  inNat Prec, 2009.

• Bastian FB, Parmentier G, Roux J, Moretti S, Laudet V, Robinson-Rechavi M.
  Bgee: Integrating and Comparing Heterogeneous Transcriptome Data Among Species
  inDILS: Data Integration in Life Sciences. Lecture Notes in Computer Science, 2008, 5109:124-131.RIS