Bgee, a gene expression database

Global Biodata Coalition features our resource Bgee, a gene expression database as its Global Core Biodata Resource of the week ??. Read their concise and informative article about the resource's wide-ranging impacts, which includes a study to identify specific brain regions associated with disrupted biological processes in Autism Spectrum Disorder for example. Marc Robinson-Rechavi Frederic Bastian

We are very pleased to be featured this week by the Global Biodata Coalition!

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://buff.ly/4h5HHnZ SIB Swiss Institute of Bioinformatics SWAT4LS

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 Swiss Institute of Bioinformatics

Bgee in 2024! Single-cell integrated with bulk RNAseq and other technologies, 52 species, and new programmatic and web access. https://buff.ly/3BzV9Bn SIB Swiss Institute of Bioinformatics

It's great when PubPeer allows dialogue with researchers to improve single-cell annotation ?? https://lnkd.in/eGTekrQ2 The PubPeer Foundation SIB Swiss Institute of Bioinformatics

We enjoyed our time at #BioHackEU24, connecting with great people and working on interesting projects. We look forward to next year!

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" https://lnkd.in/eqxfyAAq SIB Swiss Institute of Bioinformatics 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. Right, phylogeny cartoon showing divergence of paralogs to outgroup, and graph showing higher expression similarity for slower evolving paralogs than for fast evolving ones.

Delighted to represent SIB Swiss Institute of Bioinformatics at the AI-Bioscience Collaborative Summit in Washington DC, organized by the U.S. Department of State & others. Great to see a growing recognition of curated biodata’s critical role in AI breakthroughs, exemplified by resources like PDB and UniProt enabling AlphaFold. Now, let’s focus on securing sustainable funding for these invaluable resources to continue advancing AI and bioscience innovation.

Bgee is proud to contribute open gene expression data to Wikidata. Happy birthday Wikidata! You can leverage this data directly through Wikidata, or find it under RNA expression pattern in the info box of every gene page in Wikipedia. https://lnkd.in/eJ3RVZQ2 SIB Swiss Institute of Bioinformatics