Daniel Cerdán-Vélez
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View article: An audit of the PeptideAtlas database uncovers evidence for repurposed pseudogenes and co-opted retroviral ORFs
An audit of the PeptideAtlas database uncovers evidence for repurposed pseudogenes and co-opted retroviral ORFs Open
View article: The state of the human coding gene catalogues
The state of the human coding gene catalogues Open
In 2018, we analysed the three main repositories for the human proteome: Ensembl/GENCODE, RefSeq, and UniProtKB. At that time the three gene sets disagreed on the coding status of one of every eight annotated coding genes, and our results …
View article: More than 2,500 coding genes in the human reference gene set still have unsettled status
More than 2,500 coding genes in the human reference gene set still have unsettled status Open
In 2018 we analysed the three main repositories for the human proteome, Ensembl/GENCODE, RefSeq and UniProtKB. They disagreed on the coding status of one of every eight annotated coding genes. The analysis inspired bilateral collaborations…
View article: GENCODE 2025: reference gene annotation for human and mouse
GENCODE 2025: reference gene annotation for human and mouse Open
GENCODE produces comprehensive reference gene annotation for human and mouse. Entering its twentieth year, the project remains highly active as new technologies and methodologies allow us to catalog the genome at ever-increasing granularit…
View article: A deep audit of the PeptideAtlas database uncovers evidence for unannotated coding genes and aberrant translation
A deep audit of the PeptideAtlas database uncovers evidence for unannotated coding genes and aberrant translation Open
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, ribosome profiling and proteomics experiments.…
View article: GENCODE: massively expanding the lncRNA catalog through capture long-read RNA sequencing
GENCODE: massively expanding the lncRNA catalog through capture long-read RNA sequencing Open
Accurate and complete gene annotations are indispensable for understanding how genome sequences encode biological functions. For twenty years, the GENCODE consortium has developed reference annotations for the human and mouse genomes, beco…
View article: Evidence for widespread translation of 5′ untranslated regions
Evidence for widespread translation of 5′ untranslated regions Open
Ribosome profiling experiments support the translation of a range of novel human open reading frames. By contrast, most peptides from large-scale proteomics experiments derive from just one source, 5′ untranslated regions. Across the human…
View article: The T2T-CHM13 reference assembly uncovers essential WASH1 and GPRIN2 paralogues
The T2T-CHM13 reference assembly uncovers essential WASH1 and GPRIN2 paralogues Open
Summary The recently published T2T-CHM13 reference assembly completed the annotation of the final 8% of the human genome. It introduced 1956 genes, close to 100 of which are predicted to be coding because they have a protein coding parent …
View article: Lost in the WASH. The functional human WASH complex 1 gene is on chromosome 20
Lost in the WASH. The functional human WASH complex 1 gene is on chromosome 20 Open
The WASH1 gene produces a protein that forms part of the developmentally important WASH complex. The WASH complex activates the Arp2/3 complex to initiate branched actin networks at the surface of endosomes. As a curiosity, the human refer…
View article: GENCODE: reference annotation for the human and mouse genomes in 2023
GENCODE: reference annotation for the human and mouse genomes in 2023 Open
GENCODE produces high quality gene and transcript annotation for the human and mouse genomes. All GENCODE annotation is supported by experimental data and serves as a reference for genome biology and clinical genomics. The GENCODE consorti…
View article: Origins and Evolution of Human Tandem Duplicated Exon Substitution Events
Origins and Evolution of Human Tandem Duplicated Exon Substitution Events Open
The mutually exclusive splicing of tandem duplicated exons produces protein isoforms that are identical save for a homologous region that allows for the fine tuning of protein function. Tandem duplicated exon substitution events are rare, …
View article: APPRIS: selecting functionally important isoforms
APPRIS: selecting functionally important isoforms Open
APPRIS (https://appris.bioinfo.cnio.es) is a well-established database housing annotations for protein isoforms for a range of species. APPRIS selects principal isoforms based on protein structure and function features and on cross-species…