AJ Sethi

@arjunrajlab scaling up throughput doesn't increase signal to noise ratio. there is a huge need to improve signal across most targeted assays.

The bitter lesson of genomics: If you find yourself optimizing a targeted method, don't—betting against increased throughput is generally a bad idea.

@NikoMcCarty super cool! i tried to give it a nucleus: #cell-0" target="_blank" rel="nofollow noopener">observablehq.com/d/fd4f924efd5f…

I built an interactive visualization of the Central Dogma. You can speed it up or slow it down. You can set the length of genes, the initiation rates of ribosomes, protein decay rates, and more.

@_AJSethi That’s awesome but it’s not on the list 🤣😂

I’d say most PhD students don’t even have ONE of these !

@sonohoor PhD years 3-5

hey sorry i can’t come out tonight i need to research an incredibly specific and random topic alone and in silence for hours on end for no reason at all

SWARM (Single-molecule Workflow for Analysing RNA Modifications) detects pseudouridine, m6A, and m5C on individual molecules from direct RNA nanopore signals (in both chemistries RNA002 and RNA004) github.com/comprna/SWARM see more on poster P2-396 at #rna2025 #RNA25 #RNAmods

Thanks to all co-authors, without whom this work would be impossible. @GuarnacciMarco @starstuffkarthi @pol2rna @TominAustralia @RippeiH and others.

dFORCE is directly applicable to mammalian tissue samples, and produces results consistent with cell culture, unlocking analysis of mRNA synthesis kinetics in vivo:

We describe the temporal organisation of central pre-mRNA processing events, including splicing, m6A modification and 3' end formation, during mRNA synthesis. Check out the preprint here!

New work reveals the impact of anxiety & depression on PhD students. "Anxiety and depression can have a substantially detrimental impact on graduate students’ experiences [..] and likely also contribute to increased time to degree and student attrition." nature.com/articles/s4158…

it gets me fr

R2Dtool github.com/comprna/R2Dtool for handling, integrating, and viualising isoform-resolved RNA feature data - led by @_AJSethi #bioinformatics #RNA #isoforms academic.oup.com/bioinformatics…

@ribonucleicacid The spliced AS transcripts could also be RT artefacts. I don't see almost any antisense mRNA reads in cerevisiae nanopore RNA libraries.

@_AJSethi That's very weird. Yes, I would agree with you that these are unlikely to arise from genomic transcription, and more likely from RNA-dependant transcription of processed mRNAs.

I don't know what to make of this paper. The evidence in vertebrate cells is that double stranded regions inhibit mRNA nuclear export. Why would it be the opposite in yeast? nature.com/articles/s4158…

@ribonucleicacid And a little further down at RPS18B:

@ribonucleicacid I'm seeing splicing of sense introns on the antisense transcripts, which isn't possible if these transcripts arise from genomic transcription. Could the AS transcripts come from RNA-dependant RNA polymerase transcription of processed mRNA? RPS17A in SRR27483326 shown:

Now online! Capturing totipotency in human cells through spliceosomal repression dlvr.it/T7tnPv

It's finally published. This one took a long time to get through reviewers: Prediction of m6A and m5C at single-molecule resolution reveals a transcriptome-wide co-occurrence of RNA modifications link.springer.com/article/10.103…

@mitchguttman @Nature @_prashantbhat super cool work!!

What are the functional roles of 3D genome organization? Our paper in @Nature led by @_prashantbhat demonstrates how dynamic 3D genome organization around nuclear speckles plays a crucial role in regulating mRNA splicing efficiency. rdcu.be/dHkez