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ensembl.org
Join us tomorrow to explore Ensembl resources for pangenomes! Leanne Haggerty is presenting on Ensembl annotation for human, model organism, livestock & crop plant pangenomes.

Free registration: zurl.co/3sSUJ 

Full series:zurl.co/XrVdc
#Pangenomes #Ensembl
November 11, 2025 at 3:20 PM
munkiman.bsky.social
Remembering actor Charles Bronson, born Charles Dennis Buchinsky on November 3, 1921 in Ehrenfeld, Cambria County (the coal region of the Allegheny Mnts north of Johnstown), PA (d. August 30, 2003). Faves: Once Upon a Time in the West, The Great Escape, The Mechanic & so many others. More: alt text
Born Charles Dennis Buchinsky into a poor Lithuanian immigrant family, Bronson worked in the Pennsylvania coal mines before serving during World War II as an aerial gunner on a B-29 bomber. He flew 25 combat missions and received a Purple Heart for wounds sustained in battle. After the war, he studied acting after moving to Hollywood in 1949 and enrolling in acting classes at the Pasadena Playhouse. He pursued acting as a blue-collar job, a means to a better life than the hardship of the coal mines. His long career began with small film roles and guesting on TV shows like "Gunsmoke," "The Twilight Zone," "The Big Valley," and starring as "Mike Kovac" in "Man with a Camera" (1958–1960). He changed his last name to Bronson in 1954 during the McCarthy era, when Slavic names were suspect, and in the '60s had much success with several major ensemble cast films, including The Magnificent Seven (1960), The Great Escape (1963), and The Dirty Dozen (1967). Despite his success in ensemble films, he achieved his status through a string of European-made films, including Once Upon a Time in the West (1968): In his most iconic role, directed by Sergio Leone, Bronson played a mysterious, harmonica-playing gunman simply known as "Harmonica," and Rider on the Rain (1970), a French thriller that was a major success and won a Golden Globe for Best Foreign Language Film. Returning to the U.S. in the '70s, Bronson became a global box-office star in action and revenge films like The Mechanic (1972), starring as "Arthur Bishop," an aging, professional hitman who takes a young apprentice under his wing. Other films include Mr. Majestyk (1974) and, Death Wish (1974), which cemented his superstar status in the U.S, playing an architect who becomes a street vigilante after his family is attacked. Bronson died on August 30, 2003. Sean Penn's The Indian Runner (1991) and several television movies -- Yes, Virginia, there is a Santa Claus and The Sea Wolf -- were his last acting roles.
November 3, 2025 at 10:22 PM
mcsukai.bsky.social
Want good Bioinformatics resources for Phytopathogens?
Plant pathology community at @bspp.bsky.social and @britmycolsoc.org.uk please take the time to complete the Phytopathogen Genomics Resources Survey:-
🔗 zurl.co/gKjC1
Your input is important for FungiDB/@veupathdb.org
& Ensembl @ebi.embl.org.
October 30, 2025 at 4:57 PM
ensembl.org
FungiDB/VEuPathDB + Ensembl are teaming up to enhance fungal & oomycete genome resources — and we need your input!

Complete the survey by Nov 1st, 2025: 
zurl.co/gKjC1

Your feedback will help guide decisions on genome curation, annotation & data integration.
Qualtrics Survey | Qualtrics Experience Management
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zurl.co
October 15, 2025 at 1:49 PM
ensembl.org
Cool update in Ensembl VEP (release 115):
You can now annotate structural variants with @gnomad-project.bsky.social allele frequencies AND ClinVar clinical significance

Perfect for filtering & interpreting SVs!
More info on our blog (zurl.co/3lZjy)
#genomics #bioinformatics
Cool stuff Ensembl VEP can do: annotate structural variants with gnomAD allele frequencies and ClinVar clinical significance – Ensembl Blog
zurl.co
October 10, 2025 at 1:55 PM
michaeltress.bsky.social
So, our definitive paper on the human reference gene set is out this week in Database (Oxford).

We merged and compared @ensembl.org / @gencodegenes.bsky.social , RefSeq and UniProtKB coding genes and investigated the agreements and discrepancies.

Details of what we found in the thread ...
Counts of the merged Ensembl/GENCODE, RefSeq and UniProtKB coding genes with the most likely explanations for the outliers for each gene set. For example, most Ensembl/GENCODE singletons are readthrough genes.
September 30, 2025 at 2:25 PM
hellomailo.bsky.social
Ensemble, faisons grandir Mailo !

Mailo est prêt à franchir une nouvelle étape pour devenir un acteur majeur de l’e-mail en France et en Europe et nous souhaitons la franchir avec vous.

Merci de faire partie de cette belle aventure 💙

blog.mailo.com/blog/ensembl...
#mailo #Email #ViePrivée
Ensemble, faisons grandir Mailo ! - Le blog Mailo
Mailo est prêt à franchir une nouvelle étape pour devenir un acteur majeur de l’e-mail en France et en Europe - et nous souhaitons la franchir avec vous.
blog.mailo.com
September 23, 2025 at 7:50 PM
tommytang.bsky.social
6/ be careful: One ENSEMBL ID can map to multiple gene symbols, and vice versa.
February 7, 2025 at 2:15 PM
tommytang.bsky.social
‘These gold-standard runs typically result in 60%–75% of the 7126 genes in the Ensembl v68 (Flicek et al. 2011) S. cerevisiae annotation being identified as SDE (except for DEGSeq, NOIseq, and PoissonSeq, which call >80% of the genes as SDE’
January 23, 2025 at 1:53 AM
ensembl.org
Did you attend @iscb.bsky.social's #ismbeccb2025 🇬🇧? @ebi.embl.org colleagues (including reps from #Ensembl, @deciphergenomics.bsky.social, @training.ebi.embl.org, @pdbeurope.bsky.social and @expressionatlas.bsky.social) surely did! 🧬

We snapped some pics of @malloryfreeberg.bsky.social in action 🎤
A photograph of a speaker on a stage and a screen projecting presentation slides. A photograph of an EMBL-EBI booth at a conference. A photograph of a speaker on stage with a screen projecting presentation slides and an audience looking towards the stage.
July 23, 2025 at 5:22 PM
jalview.bsky.social
✅ Import genomics VCF files and analyse data like a pro!

Watch Mungo as he outlines how genetic variant data can be imported into and visualised in Jalview using our signature CDS-protein split-screen feature.

Link here: www.youtube.com/watch?v=n_lR...
Jalview CDS-protein split-screen view showing gene and protein products for homogentisate 1,2 dixoygenase (ENSEMBL ID: ENSG00000113924) in 2D and 3D with VCF variants highlighted in red.
August 7, 2025 at 12:30 PM
iansealy.com
Ensembl have confirmed that the human gene name issue will be fixed in Ensembl 115. Yay!
iansealy.com Ian Sealy @iansealy.com · May 17
I've updated this for the recently released Ensembl 114. Things are looking better - there are more genes than ever before annotated to ZFIN IDs, which is great. But there seems to be a major problem still.
iansealy.com Ian Sealy @iansealy.com · Jan 21
Someone on Mastodon recently posted about issues they've seen with #zebrafish annotation in recent #Ensembl versions, so I wrote down some of what I've noticed.

I'll summarise here, but the TL;DR version is that we are just using Ensembl 109's annotation, including for enrichment analyses.
May 19, 2025 at 3:46 PM
ronbeavis.bsky.social
#CanonFolly ENSEMBL canonizes a sequence with 233 aa in 6 exons for human CACFD1:p (calcium channel flower domain containing 1); UNIPROT gets behind one with 172 aa in 5 exons. The #proteomics data favours the shorter assembly.
May 13, 2024 at 11:39 AM
ronbeavis.bsky.social
#CanonFolly ENSEMBL/REFSEQ/MANE/APRIS canonize a sequence with 587 aa in 13 exons for human CKD5RAP1:p (CDK5 regulatory subunit associated protein 1); UNIPROT canonizes one with 601 aa in 14 exons. The #proteomics data shows no observations of the extra exon (red highlight).
June 7, 2024 at 11:42 AM
pastelbio.bsky.social
RT (X) |
twitter.com/ensembl/...

---
#proteomics #prot-RT #prot-other
October 5, 2023 at 2:20 PM
bljog.bsky.social
Having trouble viewing the trees tip labels and homology blocks on @ensembl this morning.
November 25, 2024 at 11:54 AM
sandralaurentino.bsky.social
It's working for me. You can try running it through Ensembl.
March 18, 2025 at 3:42 PM
acstone.bsky.social
Aardvarks have enamel-less teeth & genetic data shows that this is due to inactivating mutations in 3 enamel matrix protein genes (AMEL, AMBN and EDAM) #RIP #2025MMM bmcecolevol.biomedcentral.com/articles/10....
Timetree of edentulous and enamelless amniote taxa for which genomic sequences are available (Ensembl, PreEnsembl, NCBI) with a mapping of inferred inactivating mutations (frameshifts, premature stop codons, splice site mutations) in three EMP genes to particular branches in the tree. Branches with inactivating mutations are marked by vertical bars (pink = ENAM [E], blue = AMBN [B], green = AMEL [A]). Extinct stem taxa with teeth (Odontochelys, Ichthyornis, Eomaia) are also shown. Mutations were mapped to branches by Fitch parsimony with delayed transformation optimization. Teeth with enamel, teeth without enamel, and edentulism are denoted with black, gray, and white-filled circles, respectively, at terminal and internal nodes. In combination with fossil evidence, dN/dS ratios and frameshift mutations in ENAM suggest that enamel was lost independently in the common ancestor of Pilosa (sloths and anteaters) and in multiple armadillo lineages, including Dasypus[2]. Remnants of AMBN and ENAM were not recovered from the Pelodiscus genome. References for divergence dates and fossil ages are provided in Methods.
March 25, 2025 at 2:05 AM
rridrobot.bsky.social
Authors published a paper in Biorxiv, they used Ensembl in the study. Including #RRIDs will make this less ambiguous.

SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #STMpublishing #reproducibility
Accurate sample deconvolution of pooled snRNA-seq using sex-dependent gene expression patterns
www.biorxiv.org
May 8, 2025 at 12:01 PM
tommytang.bsky.social
3/ ENSEMBL ID: A stable identifier assigned by the Ensembl genome browser to genes, transcripts, exons, or proteins. It ensures unambiguous and consistent reference across Ensembl releases
February 7, 2025 at 2:15 PM
dangaurelien.bsky.social
fr.wikipedia.org/wiki/Ensembl...
Ensemble (coalition française) — Wikipédia
fr.wikipedia.org
March 13, 2024 at 1:43 PM
justinwwalley.bsky.social
I havent done anything fun like citrus. Typically use proteome file from whichever group did the genome sequencing and/or annotation (TAIR for arabidizzle, MaizeGDB. Often Ensembl as well).
October 6, 2023 at 1:06 PM
ensembl.org
No worries if you missed our #webinar on 'Introducing the new Ensembl Genome Browser' because the recording is now available on the @training.ebi.embl.org site: www.ebi.ac.uk/training/eve...

Let us know what you think of our new site by clicking on the feedback icon or at helpdesk@ensembl.org 📧
Homepage of the new Ensembl website (https://beta.ensembl.org/)
February 6, 2025 at 1:40 PM
iansealy.com
But it's not just names. Many #zebrafish genes are no longer annotated to #ZFIN genes or to GO terms or to Reactome pathways.
Graph showing the number of genes annotated with ZFIN IDs, GO terms and Reactome pathways for various Ensembl versions. All numbers decrease for Ensembl 112 and 113.
January 21, 2025 at 10:46 PM
ronbeavis.bsky.social
#CanonFolly ENSEMBL/REFSEQ/MANE/APRIS canonize a sequence with 183 aa in 6 exons for human CARD19:p (caspase recruitment domain family member 19); UNIPROT canonizes one with 228 aa in 3 exons. The #proteomics data clearly rejects the 228 aa version in favour of the shorter splice.
June 19, 2024 at 11:40 AM