iiinova — where your digital self keeps evolving

Bgee database @bgee.org · 01/09/2026

If you're at #ECCB2026 and have questions about curated bulk and single-cell RNA-seq, members of the Bgee team (Frédéric Bastian, Anne Niknejad, Sébastien Moretti, @marcrr.bsky.social) and other scFAIR (sc-fair.org) participants are here and happy to speak with you. Don't hesitate to reach out!

sc-fair.org

scFAIR

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Marc Robinson-Rechavi @marcrr.bsky.social · 29/06/2026

Do you want easy access to annotated transcriptome data in animals? Where and when genes are expressed? Are you trying to analyse together single-cell datasets of different protocols and species? Come to Frederic Bastian #SMBE2026 talk presenting @bgee.org in S04 Mining the Archive at 16:35!

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Bgee database @bgee.org · 16/06/2026

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...

biorxiv.org

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…

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Ariel Chipman @chipman-lab.bsky.social · 12/06/2026

“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

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Ariel Chipman @chipman-lab.bsky.social · 12/06/2026

#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.

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Bgee database @bgee.org · 11/06/2026

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.

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Bgee database @bgee.org · 09/06/2026

Bgee is down, we are looking into the reasons. We will fix this as rapidly as possible. Thank you for your patience.

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Bgee database @bgee.org · 26/03/2026

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

sib.swiss

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

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FlyBase @flybase.bsky.social · 12/03/2026

FlyBase release FB2026_01 is live! There is news about FlyBase funding. Go to the FlyBase homepage flybase.org for details.

FlyBase Funding Update – March 2026

The NHGRI funding for FlyBase has been restored for US-based FlyBase teams but the foreign subaward that supported the essential curation team at the University of Cambridge UK has been terminated. Therefore, the Cambridge UK team now requests annual contributions from fly labs to support curation of new data into FlyBase and the Alliance of Genome Resources. Without these annual contributions, FlyBase will become frozen in its current state and become progressively less useful.

Please visit the ‘Contribute to FlyBase’ wiki page for details of how to contribute.

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Marc Robinson-Rechavi @marcrr.bsky.social · 02/02/2026

Network Medicine GPT trained on PrimeKG which used @bgee.org expression knowledge: curated data is useful data.

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Bgee database @bgee.org · 02/02/2026

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.org

Bgee Expression Comparison

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Bgee database @bgee.org · 08/01/2026

Congratulations to Xenbase for 25 years of froggy biocuration!

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Bgee database @bgee.org · 16/12/2025

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

sib.swiss

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

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Bgee database @bgee.org · 03/12/2025

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....

bsky.app

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…

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SIB Swiss Institute of Bioinformatics @sib.swiss · 15/09/2025

🧬 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 👇

sib.swiss

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...

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Bgee database @bgee.org · 17/09/2025

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

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Bgee database @bgee.org · 15/09/2025

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

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Bgee database @bgee.org · 14/09/2025

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

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Bgee database @bgee.org · 27/08/2025

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.

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Bgee database @bgee.org · 19/08/2025

The Bgee website has been experiencing some issues, thank you for your patience while we work to solve them.

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Marc Robinson-Rechavi @marcrr.bsky.social · 04/07/2025

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...

zenodo.org

The missing link in FAIR data policy: data resources

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Marc Robinson-Rechavi @marcrr.bsky.social · 04/06/2025

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...

sib.swiss

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

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ELIXIR Europe @elixir-europe.org · 24/06/2025

📣 ELIXIR has published a position paper on the importance of #OpenData infrastructure for 🌍 European competitiveness in life sciences. Read the news 👉 loom.ly/22XW72k #ResearchInfrastructure #Science4EU

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Bgee database @bgee.org · 22/05/2025

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

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Bgee database @bgee.org · 17/04/2025

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

bc2.ch

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…

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Bgee database @bgee.org · 15/04/2025

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

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Bgee database @bgee.org · 07/04/2025

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

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SIB Swiss Institute of Bioinformatics @sib.swiss · 03/04/2025

@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

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albdrg.bsky.social @albdrg.bsky.social · 19/02/2025

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. :)

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Bgee database @bgee.org · 10/02/2025

Bgee has been featured this week by the Global Biodata Coalition! Bgee is a database for retrieval and comparison of gene expression patterns across multiple animal species. Read more here: www.linkedin.com/pulse/bgee-g...

linkedin.com

Bgee

What kind of data does this resource provide? Bgee is a database for retrieval and comparison of gene expression patterns across multiple animal species. It provides an intuitive answer to the questio...

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SIB Swiss Institute of Bioinformatics @sib.swiss · 04/02/2025

The SIB Swiss Institute of #Bioinformatics is on Bluesky! We’re a non-profit organization dedicated to biological & biomedical #dataScience, supporting research & innovation. Follow us for updates on personalized health, biodiversity, pathogens, open science and more. Visit us at sib.swiss

sib.swiss

SIB Swiss Institute of Bioinformatics | Data scientists for life

As a leading organization in biological and biomedical data science, SIB maximizes scientific impact through FAIR data, biodata resources, and innovation.

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Zebrafish Information Network (ZFIN) @zfinmod.bsky.social · 03/02/2025

ZFIN is now on Bluesky!

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Bgee database @bgee.org · 08/01/2025

SWAT4HCLS 2024 conference proceedings are published, including this paper from Rangel et al which shows how Bgee's open data and integration with Wikidata can be used to train LLMs for complex queries. ceur-ws.org/Vol-3890/paper-4.pdf @marcrr.bsky.social @swat4hcls.bsky.social

buff.ly

SPARQL Generation: an analysis on fine-tuningOpenLLaMA for Question Answering over a LifeScience Knowledge Graph

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Bgee database @bgee.org · 07/01/2025

The SIB course “Gene expression made useful easily: tools and database of Bgee” is now available. This course covers the curated gene expression data in Bgee, how to detect active genes from RNA-Seq, and the various tools available to access Bgee gene expression data. buff.ly/4j3Zhus

buff.ly

Bgee Course 2024: Gene Expression made Useful Easily: Tools and Database of Bgee

The 2024 course on Bgee: a curated database of gene expression in animals, including model species such as human, mouse, and drosophila, and others such as l...

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Alliance of Genome Resources @alliancegenome.bsky.social · 14/11/2024

There's a lot of new people here. Welcome! So I'm reposting our starter pack. go.bsky.app/Npxsd7h

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Bgee database @bgee.org · 04/11/2024

Right, phylogeny cartoon showing divergence of paralogs to outgroup, and graph showing higher expression similarity for slower evolving paralogs than for fast evolving ones.

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Bgee database @bgee.org · 04/11/2024

Left, phylogeny cartoon showing divergence between paralogs (symmetric: same branch lengths, asymmetric: different branch lengths for paralogs), and boxplots showing higher expression similarity for symmetric than assymetric paralog pairs.

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Bgee database @bgee.org · 04/11/2024

In this exciting new preprint, Warwick Vesztrocy et al use Bgee to show that "the most diverged orthologues display the greatest change in gene expression, thus suggesting that they have a greater functional divergence" www.biorxiv.org/content/10.1...

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