Jack Tierney

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

A large consortium of researchers introduces the term 'translon' to denote any transcriptome region that is decoded by ribosomes. nature.com/articles/s4159…

Translon: a single term for translated regions. #Translation @naturemethods nature.com/articles/s4159…

@ewjwallace @guo_lab Transcript leader is definitely my preferred term for TSS -> CDS region. But any leader of decent length more often than not will contain translons so there is need for more fundamental units if we want to characterise the translation of these RNAs properly

I find it a strange claim that something is understudied because it lacks a proper name 🤷

@guo_lab If you wish haha but I would be interested in hearing a good definition of a 5' untranslated region as the classic definition of region between TSS and CDS is more often a misnomer than not. We played with the idea of a scantron for the scanned rather than translated regions 5'

@JackATierney So 5'-untranslon?

@guo_lab The necessity for such a unit of translation became clear during my PhD when we were developing the Ribosome Decision Graph concept pubmed.ncbi.nlm.nih.gov/38719470/

@guo_lab No problem. But like in “exon” vs “expressed region” the -on suffix is the mark of a fundamental unit across science and we want to conceptually establish a unit to allow us to describe what is translated and the relationships between these regions

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/s4159…

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

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

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

@Pharma_Pro @princetongb @JackScannell13 Box not Bayes, I believe.

@princetongb @JackScannell13 AI in it's forms are mathematical models. AI certainly cannot "solve all diseases". However, to quote Bayes "No models are true, however, some are quite useful".

AI can't "solve" all diseases for the simple reason that all diseases were solved by computational chemistry in 1985, by high throughput screening in 1995, by genomics in 2000, by RNAi in 2004, by stem cells and nanotechnology in 2005, before being solved by CRISPR in 2015. @DShaywitz

Ribosome profiling helps to reveal the first example of human mRNA translated in all three reading frames simultaneously: researchsquare.com/article/rs-539…

@SendoelLab Very exciting! Congratulations to everyone involved. Will the code and data be made available upon publication? Apologies if I missed a statement on this somewhere

How does aging alter the translational landscape of stem cells and how do these changes impact their regenerative capacity? Here we developed an in vivo single-cell ribosome profiling strategy to monitor translational landscapes of the mouse skin. 1/6 biorxiv.org/content/10.110…

@HHorkan Congratulations Helen! Save travels

May or may not do a little Xplainer next week, but tomorrow I’m darting across the world to my new lab in Kansas City

My first little first author publication, out now in GBE. We expanded on our previous work which looked at the evolution of apoptosis across metazoa. This time we took a deep dive into the understudied group, lophotrocozoans. academic.oup.com/gbe/advance-ar…

@greally Do we know what happened in the case of GMI? I had a quick look but nothing clear jumped out.

Sad for friends working there, but the company looks to be done. What happens with all the genotypes when a genomics company fails? The same happened in Ireland with the implosion of Genomics Medicine Ireland.

@BroshRan @johnprensner That annotated translated regions can be loaded as a custom track from BigBed. gencodegenes.org/pages/riboseq_… Have a look on our UCSC clone for looking at ribo-seq data, GWIPS-viz: gwips.ucc.ie/cgi-bin/hgTrac…

@johnprensner Interesting! will this dataset be available as public tracks on the UCSC genome browser?

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!

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!

@gavreilly While not actually representing Ireland, Irishman John Flanagan of near Kilmallock, Co. Limerick won gold at 3 separate Olympiads! Adding to further add to these great Pat O'Callaghan anecdotes, Pat was reportedly trained by John Flanagan en.wikipedia.org/wiki/John_Flan…