Category Archives: ribosome profiling

Our group participates in ECCB 2022

We had a great time at the European Conference in Computational Biology celebrated in Sitges in September 2022. Mar gave a keynote talk on The emerging small proteome, and we presented research on cancer (mutations, neoantigens, immunotherapy, lncRNAs..) and transcriptomics … Continue reading

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Filed under lncRNA, ribosome profiling, transcriptomics, yeast

ERC Advanced Grant NovoGenePop

Our ERC Advanced Grant NovoGenePop has just started! This means we can already recruits scientists and start to gather data. The project will investigate how new genes arise in closely related species and populations. This will involve the development of … Continue reading

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Filed under de novo gene evolution, ribosome profiling, RNA-Seq, transcriptomics, yeast

mRNA molecules one at a time

Fascinated by the potential of long read technologies to make a difference in our knowldege of the transcriptome, two years ago we started generating Nanopore dRNA data for different yeast species, including the yeast S. pombe. This organism is ideal … Continue reading

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Filed under ribosome profiling, transcriptomics, yeast

Large scale annotation of small proteins by ribosome profiling

We participate in a a new world-wide initiative for the large-scale annotation of small ORF translation events detected by ribosome profiling in the human genome. The initiative, led by researchers at Ensembl, Max Delbrück Center and Broad Institute, among others, … Continue reading

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Filed under de novo gene evolution, lncRNA, micropeptide, ribosome profiling

Protein translation from uORFs: roles in stress

The current view of an mRNA is that of a central coding sequence (CDS) flanked by 5′ and 3′ untranslated regions (UTRs). But often UTRs contain open reading frames which, as revealed by ribosome profiling, can also be translated. The … Continue reading

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Thousands of small ORFs are translated, what are they doing?

The high throughput sequencing of ribosome-protected RNA fragments, or ribosome profiling (Ribo-Seq), has uncovered the translation of thousands of novel small ORFs (< 100 amino acids) that were not annotated. These ORFs had remained hidden from annotation pipelines because of … Continue reading

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Filed under de novo gene evolution, proteomics, ribosome profiling, science

Using ribosome profiling to improve our understanding of gene regulation

To measure changes in the expression of the genes we normally compare mRNA abundances using high throughput RNA sequencing data (RNA-Seq), as a proxy for the changes in the encoded proteins. However, it is well known that the correlation between … Continue reading

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Filed under differential gene expression, proteomics, ribosome profiling, transcriptomics, yeast