Daniel Cerdán Vélez

So, still a lot of work to be done to get down a final agreed set of coding genes. One big step would be to eliminate all readthrough genes. Let's see ...

And that winds up our work in @gencodegenes.bsky.social

It has been fun.

Work carried out by Miguel Maquedano and @danielcerdan.bsky.social

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.

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 ...

FlyBase needs your help!

Because of recent changes to government funding, the NIH grant that supported FlyBase has been "terminated." flybase.org

We have updated APPRIS to @gencodegenes.bsky.social v48/ @ensembl.bsky.social v114. New principal isoforms for human, mouse, rat, cow and fruit fly ( @flybase.bsky.social ).

Principal isoforms for a total of 73 human genes have been updated manually.

¡Abierta la preinscripción del Máster en Bioinformática y Ciencias de Datos en Medicina Personalizada de Precisión y Salud 2025/26!
📍Organizan: @saludisciii.bsky.social @cniostopcancer.bsky.social @bsc-cns.bsky.social
🤝 Colaboran: SEBiot,Instituto Roche
📅 Plazas limitadas
🔗 masterbioinformatica.com

APPRIS web page screenshot showing the new Principal:M annotation for the gene DCD

Users of APPRIS may have noticed that there is a new category of principal isoforms, Principal:M.

These principal isoforms are exclusive to the human gene set and are principal isoforms that have been manually corrected. In GENCODE v47 there were 45 genes with Principal:M isoforms.

Here is DCD:

@vigalondo.bsky.social mil gracias por compartir un rato con nosotras tras Carretera Perdida, por formarnos los libros y por hablarnos de la maquina de café gratuita ✨ El segundo chocolate caliente lo tiré al suelo y acabamos comiendo tarta de cereza en la Estupenda

Our paper analysing the protein coding genes added as part of the new T2T-CHM13 assembly of the human genome was officially published over the holidays.

In particular it shows that what was previously thought to be the human WASH1C gene is actually a pseudogene.

bsky.app/profile/mich...

The rapid degradation of translated upstream regions points to an inefficient translation initiation process Large-scale experimental analyses find ever more abundant evidence of translation from start codons upstream of the canonical start site. This translation either generates entirely new proteins (from ...

So, this week's paper is about signal peptides and what they reveal about the function of N-terminally extended protein isoforms and other upstream translation such as uORFs.

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

Por aquí necesitan ayuda 👇🏻

Una estantería con nueve cómics diferentes de Doctor Who.

¡SORTEÓN WHOVIAN!
¡Para celebrar que hoy es el Doctor Who Day
sorteamos una colección completa de los cómics que hemos publicado del Doctor, es decir, 11 TEBEOS!
👉 Síguenos
👉 Comparte este maripost. Retuitea este skeet. Ya sabes lo que quiero
👉 ¡El sorteo termina a las 23:59 del 25/11!
¡¡SUERTE!!

A deep audit of the PeptideAtlas database uncovers evidence for unannotated coding genes and aberrant translation The human genome has been the subject of intense scrutiny by experimental and manual curation projects for more than two decades. Novel coding genes have been proposed from large-scale RNASeq, ribosom...

So, we have posted a new paper at BioRxiv. We carried out a deep manual curation of the human peptides identified in PeptideAtlas. This allowed to fill in some of the blanks in the @gencodegenes.bsky.social human gene set, including 16 novel protein coding genes.
www.biorxiv.org/content/10.1...

A deep audit of the PeptideAtlas database uncovers evidence for unannotated coding genes and aberrant translation https://www.biorxiv.org/content/10.1101/2024.11.14.623419v1 The human genome has been the subject of intense scrutiny by experimental and manual curation projec

A deep audit of the PeptideAtlas database uncovers evidence for unannotated coding genes and aberrant translation https://www.biorxiv.org/content/10.1101/2024.11.14.623419v1

APPRIS has new annotations for GENCODE human v46 and mouse M35. The human reference set now has 16,483 genes with Principal:P1 isoforms and mouse has 18,782 genes.

Agreement with MANE Select transcripts in human (no MANE Select in mouse) has risen slightly to 17,661 genes.

appris.bioinfo.cnio.es#/

Evidence for widespread translation of 5′ untranslated regions Abstract. Ribosome profiling experiments support the translation of a range of novel human open reading frames. By contrast, most peptides from large-scale

We have just published a paper in which we take an in depth look at translation of 5' UTR regions.

The key takeaways are that it is common and that most translation from 5' UTR is in-frame, so the effect at the protein level is to extend the N-terminal.

academic.oup.com/nar/advance-...

APPRIS has annotated principal and alternative isoforms and TRIFID functional isoform scores for Ensembl Bos taurus version e111: appris.bioinfo.cnio.es#/

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