PomBase: The S. pombe knowledgebase

Empowering biological knowledgebases: advances in human-in-the-loop AI-driven literature curation Abstract. Biological knowledgebases facilitate discovery across the life sciences by structuring experimental findings into human-readable and computable f

Empowering biological knowledgebases: advances in human-in-the-loop AI-driven literature curation url: academic.oup.com/bioinformati... @elixiruknode.org @biocurator.bsky.social

Key challenges ahead: picking the right tasks, generating reliable benchmarks, staying accurate as knowledge evolves, and fostering shared standards.

Key challenges ahead: picking the right tasks, generating reliable benchmarks, staying accurate as knowledge evolves, and fostering shared standards.

This week I participated in the excellent @biocurator.bsky.social virtual AI workshop. I presented some general tips for learning about agents. zenodo.org/records/1861... A lot of the advice comes down to: find time to learn+don't wait for the perfect curation tool, start using existing agent tools!

Pombase gene page with an arrow pointing at the link to OpenCloning

🚀 Update from @pombase.bsky.social!

Gene pages now link to OpenCloning. Load the gene region instantly and design primers + cloning strategies in one click 🧬🧪✨

To get started with OpenCloning, check the docs: docs.opencloning.org

Over the last few months I've been helping organize various tutorials and workshops on agentic AI, aimed mostly at biocurators, ontology developers, and PIs of knowledge bases / data resources. Some of this might be generally useful to folks who don't identify as a 'technical' or an 'AI' person.🧵

Amazing work, Congrats!

Very excited about this new preprint, in which @juliacoronasserna.bsky.social shows how cells ensure that fusion with another cell is irreversible!

www.biorxiv.org/content/10.6...

@biology-unige.bsky.social

👇

The first release of 2026 of the Rhea database is out! Release 140 (2026-01-28) contains 18,343 unique reactions and 15,125 unique reaction participants, with 25M protein sequence entries annotated with Rhea reactions in UniProtKB.

📣 NuQuest consortium update: Our first joint publication is out!
Review on quiescence—A milestone for our initiative laying out the scientific groundwork & collaborative vision for our MSCA-DN application coordinated by @jlugiessen.bsky.social 1/n
www.mdpi.com/3700996
#NuQuest #MSCA #DoctoralNetwork

Another removal from the #UnknownProteins inventory!
This is pombe SPAC630.06c and human 'Custos' ortholog
-There are still plenty of broadly conserved eukaryotic proteins to study: www.pombase.org/status/prote... 144 in our high priority list (well 143 tomorrow)

🧬 Meet Sni445, a newly discovered #Yeast ribosome assembly factor! Ynl050c/Sni445 recruits specialized snoRNPs (snR4 & snR45) that guide precise rRNA acetylation during ribosome synthesis. Another piece of the puzzle solved!

🧪 #YeastResearch #SGD

www.yeastgenome.org/reference/S1...

Structure of the adaptor protein 4 (AP-4) complex revealed! AP-4 exists in a dynamic equilibrium between closed and open conformations in solution. ARF1 does not shift this equilibrium but is required—together with cargo—for membrane recruitment. rdcu.be/e1ozM

🚀 InterPro 108.0 is live!
✨ Updated to Pfam 38.1 and NCBIFam 18.0
✨ 1,911 InterPro entries
Explore the latest annotations and discover new protein insights.
Explore it now: www.ebi.ac.uk/interpro/

Micropublication @micropub7n.bsky.social is peer reviewed and PubMed indexed. A great way to get the data out in uncertain times
👇🏼

The Gene Ontology knowledgebase in 2026 Abstract. The Gene Ontology (GO) knowledgebase (https://geneontology.org) is a comprehensive resource describing the functions of genes. The GO knowledgeba

As a final nod to 2025, #GeneOntology announces our latest paper in @narjournal.bsky.social! Updates include expanded #Ontology & annotations in #Metabolism, multi-org interactions, #chromatin remodeling, & more.

Also ft. #Functionome v2 and 1500+ GO-CAM pathway models! 🧬🧪

doi.org/10.1093/nar/...

Two Years to 1.7°C: the “Prediction Game” We Can’t Afford to Lose Australia’s sweltering through another early-summer heatwave, and I’m trying to decide whether to write about the weather outside my window - or the bigger climate system we’re reengineering on this p...

This week, Professor James Hansen and colleagues published projections that the global temperature record could reach +1.7°C by 2027.
And if that number lands in your gut the way it landed in mine, good. It should.
#climatecrisis #auspol www.lyrebirddreaming.com/post/two-yea...

Truly amazing knowledge synthesis. I will use this to demonstrate why biocuration is so difficult 😃

A cloning strategy as depicted in the OpenCloning website

#OpenCloning is a an Open Source alternative to SnapGene/Benchling that supports automation and integration with other software

✅ Free
🔓 Open Source
🧬 More cloning methods than SnapGene
🤖 Can be automated with python
👨‍🔬 Built by a researcher — for researchers!

👉 Check it out at opencloning.org

@flybase.bsky.social @alliancegenome.bsky.social

Congrats!

🧬 PomBase needs you! 🧬
If you PomBase on a regular basis, now it’s the time to show your support to the team behind this incredibly useful resource (and help them secure funding to keep up the amazing work). Fill out their short user survey, which they will use to support their grant application.

And just when you thought things were settling down, the enigmatic Asgard archaea have another surprise in store! Cell cycle/life cycle stage-specific internal compartments with almost no eukaryote-derived clues as to how they might function.

Beautiful tomography and microscopy - congrats all 🤩

This is a glimpse of the cytoskeletal structures we found doing U-ExM in more than 200 species, now in Cell🤩: shorturl.at/6oHvi
Amazing collaboration between @centriolelab.bsky.social , @dudinlab.bsky.social and @gautamdey.bsky.social labs.
I believe last one is a 🕷️
#FluorescenceFriday
#Microscopy

Congrats!

Happy 40th birthday Yeast: Yeast: Vol 42, No 11 Yeast is a microbiology journal for research in the rapidly moving field of yeast biology. We publish the most significant developments in unicellular fungi.

The new issue of #Yeast of 2025 (Volume 42, Issue 11, November 2025) is out! It includes papers about new yeast genomes, the biodiversity of yeasts in dough, polyphosphate accumulation and even a new #FantasticYeasts species 😃

You can browse it at this link:

onlinelibrary.wiley.com/toc/10970061...

More great work on mitochondrial dynamics from ‪@leeba.bsky.social‬
et al!

Enjoyed three days at #EMBOMobileGenome —fantastic talks and inspiring discussions on TE regulation across diverse model systems, great community! Excited to share our recent work on solo LTR silencing in S. pombe via talk and poster by @vishnuss.bsky.social. @pombase.bsky.social @embo.org

The Piwi-piRNA complex initiates transposon silencing via transcription termination factors PNUTS and Senataxin Wu et al. reveal that the SFiNX complex triggers transposon silencing through the association of Sov with two transcription termination factors, PNUTS and Senataxin, leading to RNA Pol II stalling. Th...

Interesting to see new papers connecting Pol II stalling to heterochromatin formation.

www.cell.com/molecular-ce...

Reminiscent of our work in S. pombe:
pmc.ncbi.nlm.nih.gov/articles/PMC...

Regulation of cell proliferation by a novel feedback system on Cdk function The proliferation of eukaryotic cells is regulated by a complex network of regulatory systems that promotes efficient cell cycle progression and ensures proper responses to the environment. Despite th...

Minimal CDK continues delivering 💥

www.biorxiv.org/content/10.1...