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
in arXiv, 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
in F1000Research, 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
in J 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
in arXiv, 2024.
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
in arXiv, 2024.
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
in Semantic 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
in Nucleic Acids Research, 2024, 52:D44-D51.
Kushida T, Mendes de Farias T, Sima A-C, Dessimoz C, Chiba H, Bastian FB, Masuya H.
Exploring Disease Model Mouse Using Knowledge Graphs: Combining Gene Expression, Orthology, and Disease Datasets
in bioXiv, 2023.
Sima A-C, Mendes de Farias T.
On the Potential of Artificial Intelligence Chatbots for Data Exploration of Federated Bioinformatics Knowledge Graphs
in Proceedings 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
in GigaScience, 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
in Semantic 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
in JCO 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
in Genomics, 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
in Scornavacca 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
in Database, 2019, 2019:baz106.
Mendes de Farias T, Stockinger H, Dessimoz C.
VoIDext: Vocabulary and Patterns for Enhancing Interoperable Datasets with Virtual Links
in On 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
in Nucleic 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
in Database, 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
in Bioinformatics, 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
in Bioinformatics, 2012, 28:1017-1020.
Roux J, Robinson-Rechavi M.
An ontology to clarify homology-related concepts
in Trends Genet, 2010, 26(3):99-102.
Bastian F, Parmentier G, Robinson-Rechavi M.
Generating Homology Relationships by Alignment of Anatomical Ontologies
in Nat Prec, 2009.
Bastian FB, Parmentier G, Roux J, Moretti S, Laudet V, Robinson-Rechavi M.
Bgee: Integrating and Comparing Heterogeneous Transcriptome Data Among Species
in DILS: Data Integration in Life Sciences. Lecture Notes in Computer Science, 2008, 5109:124-131. RIS