Human And Vertebrate Analysis aNd Annotation (HAVANA) team, part of the Ensembl group at the European Bioinformatics Institute.
Joined November 2011
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The HAVANA team @emblebi has multiple open positions to support the GENCODE & PARADIGM projects. We're recruiting annotators (bit.ly/4qG28g5), an annotation project lead (bit.ly/4qv05v6), & bioinformaticians (bit.ly/4qevYIY). We’d love to hear from you!
These new transcripts all have a CDS that is based upon the MANE_Select transcript for the gene, but have unique splicing either within their UTRs or between internal coding exons. Each of these unique splice sites has passed our stringent QC filters to ensure their accuracy.
This release sees the addition of >121000 new full-length human protein-coding transcripts based on long-read RNA-seq data that have been integrated into GENCODE using the TAGENE annotation pipeline.
The latest human GENCODE releases for Human (49) and Mouse (M38), have just been released. They're available via gencodegenes.org and visible in @ensembl genome browser as part of Ensembl 115 ensembl.org
The GENCODE Primary dataset is now displayed by default for human and mouse in @ensembl. More information about how this set is created is available here: gencodegenes.org/pages/genco… and details on how to change the default display settings here: ensembl.info/2025/04/29/defa…
The latest human GENCODE releases for Human (48) and Mouse (M37), have just been released. They're available via gencodegenes.org and visible in
@ensembl genome browser as part of Ensembl 114 ensembl.org
We're pleased to share our GENCODE 2025 NAR database paper: tinyurl.com/3etnfw4j Thanks to all our collaborators, friends and users. This is now the main citation for our resource, and hopefully also a good explanation of how and why we do what we do.
3/ How do we interpret immunopeptidomics support in biological terms? How many of these ORFs are bona fide proteins as opposed to unstable peptides or aberrant products? What does this mean for annotation? These are open questions and our work continues... @genenames @uniprot
2/ Relatively few Ribo-seq ORFs have peptide support from tryptic digests, although substantial numbers are supported by immunopeptidomics data. Many thanks to our large number of collaborators @EricWDeutsch @r_l_moritz @johnprensner @s_heesch
1/ GENCODE continue to work on the annotation of non-canonical translations identified by Ribo-seq, and are pleased to support this preprint which examines which ORFs express protein products: biorxiv.org/content/10.1101/…
GencodeGenes retweeted
We are excited to publish our second-ever Registered Report! The #LRGASP Consortium evaluated various methods for transcript identification and quantification using long-read sequencing technologies. @anaconesa @TheSheynkmanLab @TheBrooksLab @calizavi
nature.com/articles/s41592-0…
GencodeGenes retweeted
I´m thrilled to see our #LRGASP paper published in @naturemethods today. This is the work of many to benchmark long-read methods for transcriptomics, and a must-read paper for those using lrRNA-seq. Special thnks to @FJPardoPalacios and @TheBrooksLab (1/6)
rdcu.be/dJ9ev
GencodeGenes retweeted
DNA and RNA sequencing methods are rapidly evolving, each with its own benefits and challenges.
Find out how the Long-read RNA-Seq Genome Annotation Assessment Project (LRGASP) can help you choose the right long-read sequencing method for your research.
nature.com/articles/s41592-0…
Out today: the Long-read RNA-Seq Genome Annotation Assessment Project (LRGASP) paper, featuring contributions from many GENCODE members, a systematic evaluation of methods for long-read transcript detection and quantification: nature.com/articles/s41592-0…
GencodeGenes retweeted
We had an amazing attendance this morning for the @ensembl workshop at #ESHG2024 #berlin 🎉
@EBItraining @emblebi
GencodeGenes retweeted
🥳👇🧠Calling all RN-Aficionados! The deadline for #ncRNA2024 has been extended to 11 June. Remaining places are filling fast so be sure to submit your Abstract ASAP.
@RNASociety
@jrRNAscientists
@NCCR_RNADisease
@GencodeGenes
@NCCR_RNADisease
@RNASociety #RNA #ncRNA #lncRNA
📢Following great interest and numerous requests, the submission deadline for #ncRNA2024 has been extended to 11 June!🧬
📅Submit your abstract now to claim our Early Bird offer 🐦bit.ly/3vXOwGl
🌟Don’t miss this last chance to showcase your research to the best and brightest in the ncRNA community!✨
That might be a gin&tonic in my hand, but it still holds true that #recount3 is a wonderful resource and super useful in our annotation efforts! Great to meet you @lcolladotor!!
Thank you Toby Hunt from @emblebi for agreeing to record this shoutout from @GencodeGenes to #recount3
Not every day do you get to hear praise from users! This is a hugely motivating!
doi.org/10.1186/s13059-021-0…
#BoG24
GencodeGenes retweeted
You might know someone but you will definitely come across people whom you do not know that are somehow connected to you
It’s a pleasure to discover these connecting 🧵s #BoG24
Known: #PEC2 data harmonization
Me ↔️ @julcollado ↔️ @GuigoLab
Unknown: #recount3 ➡️ @GencodeGenes
GencodeGenes retweeted
👀👇☀️Dear Colleagues, there are 2 weeks left to submit an abstract at our October conference #ncRNA2024! Why come?
-Brilliant international speakers
-fantastic city
-loads of networking + social time
-high probability of selected talks. So come join us!
⚠️Two weeks left to submit your abstracts for #ncRNA2024!⚠️
👥Don't miss out on the opportunity to meet with leading experts in the field and catch up on their latest research and breakthroughs