GencodeGenes

Human And Vertebrate Analysis aNd Annotation (HAVANA) team, part of the Ensembl group at the European Bioinformatics Institute.

[GencodeGenes @GencodeGenes]

The HAVANA team @emblebi has multiple open positions to support the GENCODE & PARADIGM projects. We're recruiting annotators (https://t.co/JU3aWoJAIX), an annotation project lead (https://t.co/hhFDTNorKb), & bioinformaticians (https://t.co/ekBDhgzEIu). We’d love to hear from you!

[GencodeGenes @GencodeGenes]

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.

[GencodeGenes @GencodeGenes]

The latest human GENCODE releases for Human (49) and Mouse (M38), have just been released. They're available via https://t.co/Wt6xaPvutm and visible in @ensembl genome browser as part of Ensembl 115 https://t.co/FJ0S5hezcr

[GencodeGenes @GencodeGenes]

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.

[GencodeGenes @GencodeGenes]

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: https://t.co/vwQvqbAEUP and details on how to change the default display settings here: https://t.co/fIsJRTHTvV

[GencodeGenes @GencodeGenes]

The latest human GENCODE releases for Human (48) and Mouse (M37), have just been released. They're available via https://t.co/Wt6xaPvutm and visible in
@ensembl genome browser as part of Ensembl 114 https://t.co/FJ0S5hezcr

[GencodeGenes @GencodeGenes]

We're pleased to share our GENCODE 2025 NAR database paper: https://t.co/W9i478UY9z 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.

[GencodeGenes @GencodeGenes]

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

[GencodeGenes @GencodeGenes]

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

[GencodeGenes @GencodeGenes]

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: https://t.co/U2sySwNky4

[Nature Methods @naturemethods]

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

https://t.co/QxIo92GjUx

[AnaConesa @anaconesa]

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)
https://t.co/xdLwq3LvLU

[EMBL-EBI @emblebi]

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.

https://t.co/mNB5F1s1jh

[GencodeGenes @GencodeGenes]

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: https://t.co/4cJm1N7qYf

[Ensembl @ensembl]

If you are attending #ESHG2024 come and talk to us at 20.063.D in the poster area about our initiative to annotate non-canonical ORFs
@ensembl
#bioinformatics #genomics #berlin

[Dr Aleena M Stolworthy @aleenamolbio]

We had an amazing attendance this morning for the @ensembl workshop at #ESHG2024 #berlin 🎉
@EBItraining @emblebi

[Rory Johnson @_Rory_Johnson_]

🥳👇🧠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

[GencodeGenes @GencodeGenes]

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!!

[🇲🇽 Leonardo Collado-Torres @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!

https://t.co/3H2woEcmmH

#BoG24

[🇲🇽 Leonardo Collado-Torres @lcolladotor]

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

[Rory Johnson @_Rory_Johnson_]

👀👇☀️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!