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PomBase: The S. pombe knowledgebase

@pombase.bsky.social
535 followers 181 following 54 posts

www.pombase.org Knowledgebase for Schizosaccharomyces pombe (a fission yeast). Supporting scientific discovery for cell-level processes; #OpenScience, #FAIR data #CommunityCuration; Monitoring #UnknownProteins; Elixir and GBC Core Data Resource.

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Reposted by PomBase: The S. pombe knowledgebase
Neil Hall @neilhall.bsky.social · 20/08/2026
Biological Databases are critical infrastructure - not projects. As so much effort is put into harnessing AI to solve all our problems, we are allowing the foundational data resources crumble. Treat biological databases as infrastructure, not projects www.nature.com/articles/d41...
nature.com
Treat biological databases as infrastructure, not projects
Letter to the Editor
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Reposted by PomBase: The S. pombe knowledgebase
Yeast Journal @yeast-journal.bsky.social · 19/08/2026
In this review, Chieh-Ping Lin, Alberto Geroldi, Nelly Selem @litinice.bsky.social and @ishengtsai.bsky.social analyse #yeasts in fungal #metabarcoding samples from the GlobalFungi database, revealing distinct patterns of distribution across environments 🍄 👇 onlinelibrary.wiley.com/doi/10.1002/...
onlinelibrary.wiley.com
A Global Synthesis of Yeast in Microbiomes
Yeasts are widespread members of microbial communities across terrestrial, aquatic, and host-associated environments, yet they remain underrepresented in microbiome studies due to low abundance and m....
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Reposted by PomBase: The S. pombe knowledgebase
Yeast Journal @yeast-journal.bsky.social · 19/08/2026
New review article out in #Yeast: Stefania Francesconi and team developed a new protocol to investigate the mutational patterns of #quiescent #Schizosaccharomyces #pombe cells, revealing a mutational spectrum distinct from that observed during proliferation. onlinelibrary.wiley.com/doi/10.1002/...
onlinelibrary.wiley.com
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PomBase: The S. pombe knowledgebase @pombase.bsky.social · 20/08/2026
Treat biological databases as infrastructure, not projects www.nature.com/articles/d41... We're quietly defunding the infrastructure modern biology runs on. PomBase, FlyBase, HGNC. have faced, or facing, existential funding crises since 2024. Curation expertise, once lost, is difficult to rebuild.
nature.com
Treat biological databases as infrastructure, not projects
Letter to the Editor
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Reposted by PomBase: The S. pombe knowledgebase
Kilchert lab @kilchertlab.bsky.social · 09/07/2026
Our scientific program ranged from chalk talks and "odds & ends" to brainstorming future research and improving lab onboarding & mentoring. A real highlight: the hands-on workshop on curating papers for @pombase.bsky.social , led by the one & only Valerie Wood. Huge thank you for joining us, Val!
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Shiv Grewal @grewalsh.bsky.social · 09/07/2026
Thank you, @Pombase.bsky.social, for your kind words about our work! This study would not have been possible without the incredible support and resources provided by PomBase. We truly appreciate everything you do for the S. pombe community!
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Reposted by PomBase: The S. pombe knowledgebase
Marc Robinson-Rechavi @marcrr.ecoevo.social.ap.brid.gy · 09/07/2026
There are often legitimate complaints about the fun photos illustrating news articles on climate change and heat waves, so here's @TheGuardian doing it well.
Title "Climate crisis
Western Europe records hottest-ever June as heatwaves intensify"
Illustrated by photo of miserable looking cows among dried vegetation.
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PomBase: The S. pombe knowledgebase @pombase.bsky.social · 09/07/2026
Another game changer from @grewalsh.bsky.social lab. We look forward to integrating this data and pathways @pombase.bsky.social
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PomBase: The S. pombe knowledgebase @pombase.bsky.social · 18/06/2026
Congratulations Pascal. Really well deserved.
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Reposted by PomBase: The S. pombe knowledgebase
Paul Gardner @ppgardne.bsky.social · 26/04/2026
Is it time to blacklist authors identified as papermill users? They clearly have integrity problems which raise concerns about the rest of their work.
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PomBase: The S. pombe knowledgebase @pombase.bsky.social · 27/04/2026
@Pombase links to SOGs from every gene page. See the ortholog section.
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Reposted by PomBase: The S. pombe knowledgebase
Genetics Society of America @genetics-gsa.bsky.social · 09/04/2026
Updates from: Caenorhabditis Genetics Center CartograPlant, @treegenes.bsky.social CottonGen Genome Database for Vaccinium GrainGenes Legume Information System @maizegdb.bsky.social Mondo PeanutBase @pombase.bsky.social @sorghumbase.bsky.social SoyBase @tairnews.bsky.social @xenbase.bsky.social 2/2🧵
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PomBase: The S. pombe knowledgebase @pombase.bsky.social · 02/04/2026
2 more Proteins from the PomBase Exploration of the proxiOME of large subunit ribosomal proteins reveals Acl1 and Bcl1 as cooperating dedicated chaperones of Rpl1 url: academic.oup.com/nar/article/...
academic.oup.com
Exploration of the proxiOME of large subunit ribosomal proteins reveals Acl1 and Bcl1 as cooperating dedicated chaperones of Rpl1
Abstract. In eukaryotes, most newly synthesized ribosomal proteins (r-proteins) need to rapidly and safely get into the nucleus to reach their assembly sit
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PomBase: The S. pombe knowledgebase @pombase.bsky.social · 02/04/2026
#UnknownProtein #NewGeneCharacterization 2 more proteins from the @pombase #Unknome Exploration of the proxiOME of large subunit ribosomal proteins reveals Acl1 and Bcl1 as cooperating dedicated chaperones of Rpl1 url: academic.oup.com/nar/article/...
academic.oup.com
Exploration of the proxiOME of large subunit ribosomal proteins reveals Acl1 and Bcl1 as cooperating dedicated chaperones of Rpl1
Abstract. In eukaryotes, most newly synthesized ribosomal proteins (r-proteins) need to rapidly and safely get into the nucleus to reach their assembly sit
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Reposted by PomBase: The S. pombe knowledgebase
Kelly Nguyen @kellythd-nguyen.bsky.social · 26/03/2026
Proud to share the yeast telomerase structure, led by the talented @hongmiaohu.bsky.social in collaboration with the Wellinger and Chartrand labs. Discovered 37 years ago and took us nearly 7 years but totally worth the wait 😍. www.science.org/doi/10.1126/... www.youtube.com/watch?v=gFE4...
youtube.com
Cryo-EM structure of yeast telomerase
YouTube video by MRC Laboratory of Molecular Biology
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Reposted by PomBase: The S. pombe knowledgebase
Manuel Lera-Ramirez @handle.invalid · 25/03/2026
🧬 Phage recombinases just landed in hashtag#OpenCloning Simulate site-specific recombination defining your own recognition sites. 🎥 See it in action below 👇 Links in the comments 🔗
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PomBase: The S. pombe knowledgebase @pombase.bsky.social · 26/03/2026
Corrections: Note that we have detailed gene function annotations for over 80% of proteins (not 20%). The 20% (should be 25%) is the number now linked into the GO-CAM pathway models! The community makes a HUGE amount to our curation, but these models were made by PomBase curators.
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Reposted by PomBase: The S. pombe knowledgebase
Omaya Dudin 𓂆 ¦🍉¦🦠¦🔬¦ @dudinlab.bsky.social · 06/03/2026
I can only recommend...
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Nature @nature.com · 21/02/2026
These scientists and medical experts are taking to social media to counter climate denialism, vaccine scepticism and wellness pseudoscience go.nature.com/4tFXSjb
go.nature.com
The science influencers going viral on TikTok to fight misinformation
Nature - Scientists and medical experts are countering climate denialism, vaccine scepticism and wellness pseudoscience on social media.
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valwood.bsky.social @valwood.bsky.social · 16/02/2026
Empowering biological knowledgebases: advances in human-in-the-loop AI-driven literature curation url: academic.oup.com/bioinformati... @elixiruknode.org @biocurator.bsky.social
academic.oup.com
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
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Chris Mungall @cmungall.bsky.social · 12/02/2026
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!
zenodo.org
Staying in the Loop: A Biocurator's Guide to Agentic AI Developments
Staying in the Loop: A Biocurator’s Guide to Agentic AI Developments Large language models have rapidly become part of everyday scientific workflows, yet most biocurators still interact with AI primar...
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Reposted by PomBase: The S. pombe knowledgebase
Manuel Lera-Ramirez @handle.invalid · 11/02/2026
🚀 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
Pombase gene page with an arrow pointing at the link to OpenCloning
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Reposted by PomBase: The S. pombe knowledgebase
Chris Mungall @cmungall.bsky.social · 12/02/2026
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.🧵
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PomBase: The S. pombe knowledgebase @pombase.bsky.social · 31/01/2026
Amazing work, Congrats!
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Sophie G Martin @sophiemartinlab.bsky.social · 30/01/2026
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 👇
biorxiv.org
PAK-family kinases promote cell fusion irreversibility by preventing cell wall repair
Cell-cell fusion is critical for the sexual life cycle, as it drives the unidirectional transition between haploid and diploid phases. In eukaryotes where fusion occurs between partners with cell wall, fusion requires not only plasma membrane merging but also local removal of the intervening cell wall. However, the integrity of the cell wall, which resists the strong internal turgor pressure and is essential for survival, is normally monitored by signaling pathways that promote repair upon damage. How cell wall integrity pathways allow localized cell wall degradation is not known. In the fission yeast Schizosaccharomyces pombe, we previously identified pak2 deletion mutants that exhibit transient fusion: cells briefly fuse and exchange cytoplasmic contents that signal meiosis but then reseal their fusion pore. This reversal of fusion directionality induces meiosis in haploid cells, with catastrophic consequences. Here, we show that PAK activity is essential for cell-cell fusion, with major contribution for Pak2 and a more minor role for the essential Pak1. Pak2 accumulates at the fusion site, where its kinase activity is controlled to promote both fusion pore opening and expansion, thereby preventing post-fusion pore closure. Strikingly, osmotic stabilization largely suppresses all PAK-associated fusion defects, pointing to a role in cell-wall remodeling rather than plasma-membrane merging. Indeed, correlative light and cryo-soft-X-ray tomography reveals that resealed pores in PAK mutants rebuilt an intact cell wall. Thus, PAKs enforce fusion directionality by antagonizing cell-wall repair mechanisms that otherwise restore separation between mating partners. ### Competing Interest Statement The authors have declared no competing interest. Swiss National Science Foundation, https://ror.org/00yjd3n13, 310030_207909 European Research Council, https://ror.org/0472cxd90, SexYeast; 101019630 European Molecular Biology Organization, ALTF 351-2021
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Rhea knowledgebase @rhea-db.bsky.social · 30/01/2026
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.
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The Braun Lab @thebraunlab.bsky.social · 30/01/2026
📣 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
mdpi.com
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PomBase: The S. pombe knowledgebase @pombase.bsky.social · 30/01/2026
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)
pombase.org
PomBase, the S. pombe genome database
PomBase is a comprehensive database for the fission yeast Schizosaccharomyces pombe, providing structural and functional annotation, literature curation and access to large-scale data sets
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Saccharomyces Genome Database @yeastgenome.bsky.social · 29/01/2026
🧬 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...
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Juan S. Bonifacino @juanbonifacino.bsky.social · 29/01/2026
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
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InterPro @interprodb.bsky.social · 30/01/2026
🚀 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/
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Savage-Dunn lab @cswormlab.bsky.social · 28/10/2025
Micropublication @micropub7n.bsky.social is peer reviewed and PubMed indexed. A great way to get the data out in uncertain times 👇🏼
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Gene Ontology @geneontology.bsky.social · 19/12/2025
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/...
doi.org
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
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David Tomkins 🦋 @davidctomkins.bsky.social · 20/12/2025
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...
lyrebirddreaming.com
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...
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PomBase: The S. pombe knowledgebase @pombase.bsky.social · 03/12/2025
Truly amazing knowledge synthesis. I will use this to demonstrate why biocuration is so difficult 😃
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Manuel Lera-Ramirez @handle.invalid · 24/11/2025
#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
A cloning strategy as depicted in the OpenCloning website
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PomBase: The S. pombe knowledgebase @pombase.bsky.social · 14/11/2025
@flybase.bsky.social @alliancegenome.bsky.social
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PomBase: The S. pombe knowledgebase @pombase.bsky.social · 08/11/2025
Congrats!
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Theresa Zeisner @theresazeisner.bsky.social · 12/11/2025
🧬 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.
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Gautam Dey @gautamdey.bsky.social · 07/11/2025
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 🤩
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Armando Rubio Ramos @bioarm.bsky.social · 07/11/2025
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
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PomBase: The S. pombe knowledgebase @pombase.bsky.social · 08/11/2025
Congrats!
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Yeast Journal @yeast-journal.bsky.social · 05/11/2025
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...
onlinelibrary.wiley.com
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.
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PomBase: The S. pombe knowledgebase @pombase.bsky.social · 08/11/2025
More great work on mitochondrial dynamics from ‪@leeba.bsky.social‬ et al!
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The Braun Lab @thebraunlab.bsky.social · 07/11/2025
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
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Hiten Madhani @hitenmadhani.bsky.social · 29/10/2025
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...
cell.com
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...
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Snezhka Oliferenko @alebenoit.bsky.social · 29/10/2025
Minimal CDK continues delivering 💥 www.biorxiv.org/content/10.1...
biorxiv.org
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...
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PomBase: The S. pombe knowledgebase @pombase.bsky.social · 30/10/2025
If you use PomBase, please help us to demonstrate our value, and make improvements by completing our user survey www.surveymonkey.com/r/7GXJL6X
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PLOS Biology @plosbiology.org · 28/10/2025
How is #cytokinesis coordinated to ensure successful #CellDivision? Jian-Qiu Wu @sophiemartinlab.bsky.social &co show that the Ync13-Rga7-Rng10 module coordinates selective tethering & fusion of vesicles containing glucan synthases at the division site @plosbiology.org 🧪 plos.io/43zJ35Z
Working model for the major pathways of plasma membrane deposition and septum formation during cytokinesis. The septum is illustrated asymmetrically intentionally. The top half septum shows septum formation and digestion of the primary septum; the bottom half shows septum formation. (1) F-BAR protein Cdc15 (and others) anchor the contractile ring to the plasma membrane, which recruits the β(1,3)-glucan synthase Bgs1 and its adaptor Sbg1 for primary septum formation. (2) Association of the F-BAR protein Rga7 and coiled-coil protein Rng10 with the Munc13/UNC-13 protein Ync13 recruits the TRAPP-II complex along the cleavage furrow, which tethers vesicles and primes the SM protein Sec1 and its binding partner Mso1 for the SNARE complex assembly to trigger vesicle fusion with the plasma membrane. This pathway maintains normal levels and distribution of gluacan synthases Bgs4/Smi1 and Ags1 for secondary septum formation. (3) The anillin Mid2 and septin rings restrict most of the exocyst complex to the rim of cleavage furrow to tether secretory vesicles loaded with the glucanases Eng1 and Agn1 and other cargos for digestion of primary septum to trigger daughter-cell separation.
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PomBase: The S. pombe knowledgebase @pombase.bsky.social · 27/10/2025
Every funder and policy-maker should take note, as we burn through our scientific capital, "the incandescent lamp did not emerge from the continuous improvement of candles”.
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