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Jay Hesselberth @jayhesselberth.bsky.social · Jun 20

I have been trying to onboard the 2A peptide pHMM models into Pfam to no avail. If anyone has a contact there, I would appreciate an introduction for a discussion.

github.com/rnabioco/2a-...

GitHub - rnabioco/2a-peptide-search: HMM models of the 2A peptide and DB search results

HMM models of the 2A peptide and DB search results - rnabioco/2a-peptide-search

github.com

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Jay Hesselberth @jayhesselberth.bsky.social · Jun 20

This entire project would not have been possible with out HMMER.

bsky.app/profile/cryp...

Sean Eddy @cryptogenomicon.bsky.social · May 22

NIH funding supporting the HMMER and Infernal software projects has been terminated. NIH states that our work, as well as all other federally funded research at Harvard, is of no benefit to the US.

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Jay Hesselberth @jayhesselberth.bsky.social · Jun 20

Excited to see this collaborative work with Olivia Rissland's lab finally out. We found lots of 2A peptides and an entirely new 2A class.

www.cell.com/cell-reports...

Systematic identification and characterization of eukaryotic and viral 2A peptide-bond-skipping sequences

Rao et al. identified thousands of previously unknown 2A peptides across both viruses and eukaryotes using an HMMER analysis. The authors further identified a unique class of 2A peptides, class B, who...

www.cell.com

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Jay Hesselberth @jayhesselberth.bsky.social · Mar 11

Any word on whether these are all NIAID grants? Or do they include neoepitope mRNA vaccine studies funded by NCI, etc?

Jay Hesselberth @jayhesselberth.bsky.social · Feb 20

In my experience REPORTER is not updated in real-time. Not sure it's a reliable measure of the effect.

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Jay Hesselberth @jayhesselberth.bsky.social · Feb 13

I just updated this R data package for NIH EXPORTER data. Can you file an issue with your approach for calculating ICR?

github.com/rnabioco/nih...

GitHub - rnabioco/nihexporter: An R data package for NIH EXPORTER data

An R data package for NIH EXPORTER data. Contribute to rnabioco/nihexporter development by creating an account on GitHub.

github.com

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Jay Hesselberth @jayhesselberth.bsky.social · Feb 9

Just released an update of an R data package for NIH funding data from 1985-2024.

github.com/rnabioco/nih...

GitHub - rnabioco/nihexporter: An R data package for NIH EXPORTER data

An R data package for NIH EXPORTER data. Contribute to rnabioco/nihexporter development by creating an account on GitHub.

github.com

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Jay Hesselberth @jayhesselberth.bsky.social · Feb 9

I maintain an R data package of NIH EXPORTER data. Updated last week.

github.com/rnabioco/nih...

GitHub - rnabioco/nihexporter: An R data package for NIH EXPORTER data

An R data package for NIH EXPORTER data. Contribute to rnabioco/nihexporter development by creating an account on GitHub.

github.com

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Jay Hesselberth @jayhesselberth.bsky.social · Feb 8

And I forgot the default REPORTER search only lists active grants. This list is pretty long.

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Jay Hesselberth @jayhesselberth.bsky.social · Feb 8

Technically speaking, your last point is incorrect.

(but the NIH REPORTER link doesn't go anywhere useful to confirm this is the same person; I inferred it from the abstract)

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Jay Hesselberth @jayhesselberth.bsky.social · Nov 19

This is on a (very long) to-do list.

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Jay Hesselberth @jayhesselberth.bsky.social · Nov 19

Also crossing "publish with your scientific grandfather" off my bucket list.

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Jay Hesselberth @jayhesselberth.bsky.social · Nov 19

Here for my first post. Our new approach to study tRNA aminoacylation by nanopore sequencing. Started as a napkin sketch ~1 year ago! This was a fun one, congrats to @laurakwhite.bsky.social and Aleks.

www.biorxiv.org/content/10.1...

Nanopore sequencing of intact aminoacylated tRNAs

Transfer RNAs (tRNA) are decorated during biogenesis with a variety of modifications that modulate their stability, aminoacylation, and decoding potential during translation. The complex landscape of ...

www.biorxiv.org

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