Bgee database
@bgee.org
Bgee is a database at SIB and UNIL to retrieve and compare gene expression patterns in multiple animal species. bgee.org
New preprint, where we present scFAIR, a consortium of single-cell data resources that has developed a unified metadata schema and common curation framework to improve the FAIRness of scRNA-seq data. www.biorxiv.org/content/10.6...
scFAIR Consortium: a decentralized hub for single-cell RNA-Seq data standardization and unification
The rapid accumulation of single-cell RNA-Seq (scRNA-seq) data across multiple repositories presents major challenges for data accessibility, integration, and reproducibility. While primary…
biorxiv.org
“If your data is not easy to find we will publicly shame you”. “It is polite to cite us, but we won’t sue you if you don‘t. It is all openly available”. The data are mapped to different ontologies. The aim is to increase the number of species up to 1K species. www.bgee.org @bgee.org
bgee.org
#EED2026 @marcrr.bsky.social talking about the Bgee database for curated animal gene expression patterns. The database is manually curated, freely available. Collects data from published papers.
Our website is back online, although we are still working on restoring full functionality to the BgeeDB R package. Thank you for your patience. We've had to add filtering of bots, we apologize for the bother of proving you're human.
Bgee is down, we are looking into the reasons. We will fix this as rapidly as possible. Thank you for your patience.
Join us at BioHackathon Europe 2026 to work on Single-cell dataset integration across repositories and species for cell type homology analyses within scFAIR 🧬 github.com/elixir-europ... @sib.swiss #BioHackEU26
biohackathon-projects-2026/23.md at main · elixir-europe/biohackathon-projects-2026
Project descriptions for BioHackathon Europe 2026. Contribute to elixir-europe/biohackathon-projects-2026 development by creating an account on GitHub.
github.com
Registration is open for the training course on Bgee 🧬 Gene Expression made Useful Easily: Tools and Database of Bgee Friday 29 May 2026 The course is online, starting at 16:00 CEST / 10:00 EDT / 7:00 PDT www.sib.swiss/training/cou... @sib.swiss @marcrr.bsky.social
Gene Expression made Useful Easily: Tools and Database of Bgee
Attendance is free of charge; however, registration is mandatory. Overview Bgee is a curated database of gene expression in animals, including model s
sib.swiss
FlyBase release FB2026_01 is live! There is news about FlyBase funding. Go to the FlyBase homepage flybase.org for details.
Network Medicine GPT trained on PrimeKG which used @bgee.org expression knowledge: curated data is useful data.
Marc Robinson-Rechavi@marcrr.ecoevo.social.ap.brid.gy · 6mo agoFirst talk of "Al in Biology & Medicine" #LGD2026 session: Jan Baumbach "Network Medicine GPT -A knowledge-graphs based foundation model for drug repurposing" https://www.biorxiv.org/content/10.64898/2026.01.04.697552v1.full I see with pleasure that the knowledge graph they trained on, PrimeKG ( […]
CAMK1D is "mostly expressed in the central nervous system within mammals" as seen through Bgee's integration and comparison of data in 25 mammals www.bgee.org/analysis/exp... onlinelibrary.wiley.com/doi/10.1002/... @sib.swiss @marcrr.bsky.social
Bgee Expression Comparison
bgee.org
🎉 Congratulations to Bgee and the two complementary SwissOrthology knowledgebases, OMA and OrthoDB, for being selected as ELIXIR Core Data Resources! See more👇 @bgee.org @marcrr.bsky.social @dessimoz.bsky.social @elixir-europe.org
Three further SIB knowledgebases gain prestigious European recognition
A total of eight expertly curated knowledgebases developed by SIB scientists are now designated as ELIXIR Core Data Resources (CDRs) – with the three new additions representing half of those sel...
sib.swiss
We are excited to announce a new training course on Bgee 🧬 Course: Gene Expression made Useful Easily: Tools and Database of Bgee Date: Friday 29 May 2026 Taught by: the Bgee team (Frédéric Bastian and Marc Robinson-Rechavi) Learn more: www.sib.swiss/training/cou... #bgee @marcrr.bsky.social
Gene Expression made Useful Easily: Tools and Database of Bgee
Overview This is a course on bioinformatics resources taught by the developers of the resources. Bgee is a curated database of gene expression in anim
sib.swiss
All of the Bgee team shares the shock and sadness of the community. Amos's support was instrumental in guiding Bgee towards high quality curation and a focus on being useful to the community. He will be deeply missed. @sib.swiss @marcrr.bsky.social bsky.app/profile/sib....
SIB Swiss Institute of Bioinformatics (@sib.swiss)
We are deeply saddened to share the passing of Amos Bairoch, pioneer of bioinformatics and co-founder of SIB. His lifelong commitment for high-quality, open data transformed global research. We…
bsky.app
🧬 US genomics expert Paul Thomas joins SIB as Swiss-Prot co-director, with @alanbridge.bsky.social 🔍 Leader in gene function research; among the world’s most-cited scientists 📊 His arrival strengthens SIB’s role in generating trustworthy, AI-ready biological knowledge #UniProt #GeneOntology More 👇
US genomics pioneer Paul Thomas joins SIB as Swiss-Prot co-director
Paul Thomas joins Alan Bridge in leading SIB’s largest group, based in Geneva. As a pioneer in computational biology for genomics, principal investigator of a globally important resource on gene...
sib.swiss
Unlike other rhodopsins, fly Rh7 is expressed in many non-retinal neurons. This recent preprint shows why, and Bgee shows where 🤓 🪰 www.bgee.org/search/expre... www.biorxiv.org/content/10.1... @pingkalai.bsky.social @v-kirsch.bsky.social
We are back online! Thank you to all teams @unil.bsky.social for their help in securing our infrastructure. @sib.swiss @dee-unil.bsky.social @marcrr.bsky.social
Bgee database@bgee.org · 11mo agoFollowing water dammage in the building which hosts our servers, electricity had to be turned off. Thus Bgee and all other databases from the @marcrr.bsky.social group are offline. We apologize for the inconvenience, and are working to bring them back online. @sib.swiss @dee-unil.bsky.social
Following water dammage in the building which hosts our servers, electricity had to be turned off. Thus Bgee and all other databases from the @marcrr.bsky.social group are offline. We apologize for the inconvenience, and are working to bring them back online. @sib.swiss @dee-unil.bsky.social
We have improved the situation with the website and thank you for your patience. We are continuing to make changes to prevent this from happening in the future.
The Bgee website has been experiencing some issues, thank you for your patience while we work to solve them.
Very nice preprint on the importance of #FAIR data resources in the life sciences, for AI and generally for science, by a great @sib.swiss team led by @dessimoz.bsky.social. With @bgee.org inside ;) zenodo.org/records/1572...
The missing link in FAIR data policy: data resources
zenodo.org
Registration is open for our @sib.swiss course Biodiversity bioinformatics: from large-scale phylogenomics to gene families and functions! Orthologs, paralogs, non model animal genomes, comparison of gene expression and of function, and more! www.sib.swiss/training/cou...
Biodiversity bioinformatics: from large-scale phylogenomics to gene families and functions
Overview The aims of this biodiversity bioinformatics course are to (i) explore key evolutionary concepts, (ii) examine different methodological appro
sib.swiss
📣 ELIXIR has published a position paper on the importance of #OpenData infrastructure for 🌍 European competitiveness in life sciences. Read the news 👉 https://loom.ly/22XW72k #ResearchInfrastructure #Science4EU
The SIB course "Gene expression made useful easily: tools and database of Bgee" is now available. I you want hands-on experience with Bgee check out our tutorial "The Bgee suite: leveraging standardized and comparable transcriptomics data across animals" at #BC2. buff.ly/IQc9uGD buff.ly/BI5jySb
The programme for the #bc2basel tutorials & workshops is out! Including our tutorial T10 - The Bgee suite: leveraging standardized and comparable transcriptomics data across animals. bc2.ch/tutorials-wo... bsky.app/profile/sib.... @sib.swiss @marcrr.bsky.social
Tutorials & workshops
The [BC]2 Basel Computational Biology Conference is Switzerland's main event in the domain of Computational Biology and one of the major events of its kind in Europe. The conference unites scientists…
bc2.ch
We are excited to release our gene expression heatmap visualization tool. Add genes and identify which organs or cell types the genes are highly or lowly expressed in. Try it out here: www.bgee.org/search/expre... @sib.swiss @marcrr.bsky.social
We had a great time at our workshop on FAIRification of single-cell RNA-Seq data and sharing the goals of #scFAIR at #biocuration2025 @biocurator.bsky.social
@bgee.org was used to design stem-cell based vaccines 💉against cancer in mouse models, opening a door to potential application with humans. 🔎 This is an example of the impact that bioinformatics databases and tools developed by SIB groups have. 👉 www.sib.swiss/services/ope... #SIBResourceImpacts
This looks great. I plan to use Bgee open data to further annotate genomic on the fly. I'm already using Wikidata and Uniprot. All this sounds exciting. :)