Bgee database

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: https://www.bgee.org/search/expression-matrix
@SIB@mstdn.science @marcrr@ecoevo.social @fbastian@ecoevo.social

RE: @xenbase_mod@mastodon.social

Congratulations to Xenbase for 25 years of froggy biocuration!

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@genomic.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.

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.

Learn more here: https://www.linkedin.com/pulse/bgee-global-biodata-coalition-ttyee

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. https://youtube.com/playlist?list=PLbJBK0jNmCGJc3_20tO0P9t86bnaojhgJ&si=PjBm2cOaHS-4yL3w https://bc2.ch/tutorials-workshops @SIB@mstdn.science @marcrr@ecoevo.social @fbastian@ecoevo.social

The SIB course “Gene expression made useful easily: tools and database of Bgee” is now available to view. This course covers the curated and pre-analyzed gene expression data in Bgee, how to detect active genes from bulk or single-cell RNA-Seq, and the various tools available to access Bgee gene expression data. Check it out! https://buff.ly/4j3Zhus
@SIB@mstdn.science @marcrr@ecoevo.social @fbastian@ecoevo.social

The programme for the #bc2basel tutorials & workshops is out! Including our tutorial T10 - The Bgee suite: leveraging standardized and comparable transcriptomics data across animals. https://bc2.ch/tutorials-workshops https://bsky.app/profile/sib.swiss/post/3llofhltjoc2z @SIB@mstdn.science @marcrr@ecoevo.social @fbastian@ecoevo.social

Join us at BioHackathon Europe 2026 to work on Single-cell dataset integration across repositories and species for cell type homology analyses within scFAIR 🧬
https://github.com/elixir-europe/biohackathon-projects-2026/blob/main/23.md
@SIB@mstdn.science @marcrr@ecoevo.social @elixir_europe@mstdn.science #BioHackEU26

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
https://www.sib.swiss/training/course/20260529_BGEEL
@SIB@mstdn.science @marcrr@ecoevo.social @fbastian@ecoevo.social

CAMK1D is "mostly expressed in the central nervous system within mammals" as seen through Bgee's integration and comparison of data in 25 mammals
https://www.bgee.org/analysis/expr-comparison?data=ac253ac417bb5c7292ec1888e230121c4f88653b https://onlinelibrary.wiley.com/doi/10.1002/ctd2.70120 @SIB@mstdn.science @marcrr@ecoevo.social @fbastian@ecoevo.social

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: https://www.sib.swiss/training/course/20260529_BGEEL
#bioinformatics #training #RNAseq #singlecell #GeneExpression #bgee
@SIB@mstdn.science @marcrr@ecoevo.social @fbastian@ecoevo.social

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@mstdn.science
@marcrr@ecoevo.social
@SIB@mstdn.science

Unlike other rhodopsins, fly Rh7 is expressed in many non-retinal neurons. This recent preprint shows why, and Bgee shows where 🤓 🪰
https://www.bgee.org/search/expression-matrix?data_type=RNA_SEQ&data_type=SC_RNA_SEQ&data_type=AFFYMETRIX&data_type=IN_SITU&data_type=EST&data=14c2ebc2adb7a33fe2f7929984d5445f22fe8f85
https://www.biorxiv.org/content/10.1101/2025.07.29.667052v1 @Pingkalai@mastodon.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@ecoevo.social group are offline. We apologize for the inconvenience, and are working to bring them back online. @SIB@mstdn.science @dee_unil@ecoevo.social

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

SWAT4HCLS 2024 conference proceedings are published, including Rangel et al "SPARQL Generation: an analysis on fine-tuning OpenLLaMA for Question Answering over a Life Science Knowledge Graph" which shows how Bgee's open data and integration with Wikidata can be used to train LLMs for complex queries. https://ceur-ws.org/Vol-3890/paper-4.pdf @SIB@mstdn.science @marcrr@ecoevo.social @swat4hcls@genomic.social @fbastian@ecoevo.social