Bioinformatician @ EMBL-EBI - Using Ribo-Seq for genome annotation
Joined October 2012
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Ribo-Seq has unearthed thousands of fascinating cases of translation complexity over the last decade. Through the exploration of Ribo-Seq datasets it became clear that a more accurate representation is required to help us better understand this complexity. #Translation #RiboSeq
Ribosome Decision Graphs for the Representation of Eukaryotic RNA Translation Complexity biorxiv.org/cgi/content/shor… #biorxiv_genomic
Jack Tierney retweeted
A large consortium of researchers introduces the term 'translon' to denote any transcriptome region that is decoded by ribosomes.
nature.com/articles/s41592-0…
Jack Tierney retweeted
Translon: a single term for translated regions. #Translation @naturemethods
nature.com/articles/s41592-0…
Jack Tierney retweeted
There is a lack of general terminology for translated regions that does not depend on the properties of their products or their sequence. Spearheaded by Pavel (Pasha) Baranov, this primer provides a unifying nomenclature for translation units: *Translon*
nature.com/articles/s41592-0…
Many transcriptome regions are translated but not known to encode proteins. They remain poorly annotated and thus under studied, partly due to the lack of terminology for these features.
In @naturemethods we propose using "Translon" for any region decoded by the ribosome
Just as Walter Gilbert's exon/intron terminology ('Why genes in pieces?', Nature 1978) gave us language to discuss and understand gene structure, 'Translon' aims to provide vocabulary to better conceptualise the pervasive, largely still enigmatic, translation revealed by Ribo-Seq
Writing this short correspondence sparked great semantic discussions with leaders of a diverse set of fields and particularly among the primary instigators of this initiative (myself, Michał Świrski, Eivind Valen (@eviledv) and Pasha Baranov)
Full Text:
rdcu.be/eDnOj
Jack Tierney retweeted
Ribosome profiling helps to reveal the first example of human mRNA translated in all three reading frames simultaneously: researchsquare.com/article/r…
Jack Tierney retweeted
A big congratulations to @JackATierney who passed his viva today 👏👏👏. Jack's PhD research project was on "Graph based data structures for the representation of protein coding loci" under the supervision of Pasha Baranov @bioucc . Fantastic work Jack and well deserved!
Jack Tierney retweeted
We are delighted to introduce Dr. Sebastiaan Van Heesch, Princess Máxima Center for Paediatric Oncology & Oncode Institute, Utrecht-our first research seminar of the academic year next Wednesday- Details below - all welcome!
Jack Tierney retweeted
Outstanding scientists elected to EMBO Membership: in EMBO’s 60th anniversary year, 100 new members and 20 associate members join the community
embo.org/press-releases/outs…
Delighted to see Ribosome Decision Graphs, our novel concept for the representation of translation complexity, published in Genome Research earlier this week.
genome.cshlp.org/content/ear…
Ribo-Seq has unearthed thousands of fascinating cases of translation complexity over the last decade. Through the exploration of Ribo-Seq datasets it became clear that a more accurate representation is required to help us better understand this complexity. #Translation #RiboSeq
Jack Tierney retweeted
Pipeline release! nf-core/riboseq v1.0.0 - nf-core/riboseq v1.0.0 - Altruistic Aventurine!
Please see the changelog: github.com/nf-core/riboseq/r…
Jack Tierney retweeted
the Rise of the Translons!
A novel concept for representation of multiple translated regions in RNA: doi.org/10.1101/2023.11.10.5…
Jack Tierney retweeted
Ribosome Decision Graphs for the Representation of Eukaryotic RNA Translation Complexity biorxiv.org/cgi/content/shor… #biorxiv_genomic
Ribosome Decision Graphs are then the graph based representation of a set of Ribosome Paths for a given RNA.
In this manuscript we explore how RDGs can be applied to Annotation, Differential Expression and Variant Effect Prediction although we do not exhaust the possibilities.
