𝙳𝚊𝚟𝚒𝚍 𝙰 𝙷𝚎𝚗𝚍𝚛𝚒𝚡

Professor @OregonState. #Bioinformatics and #ComputationalBiology #Genomics #RNA #Chronobiology (he/him)

[𝙳𝚊𝚟𝚒𝚍 𝙰 𝙷𝚎𝚗𝚍𝚛𝚒𝚡 @profhendrix]

@KEZI9 and Corvallis. At 2am.

[𝙳𝚊𝚟𝚒𝚍 𝙰 𝙷𝚎𝚗𝚍𝚛𝚒𝚡 @profhendrix]

@MarvinBeaverman In three years, it will be 10,000 ! Go Beavs!

[𝙳𝚊𝚟𝚒𝚍 𝙰 𝙷𝚎𝚗𝚍𝚛𝚒𝚡 @profhendrix]

@BarakRotblat @PLOSCompBiol Thank you!

[𝙳𝚊𝚟𝚒𝚍 𝙰 𝙷𝚎𝚗𝚍𝚛𝚒𝚡 @profhendrix]

We are pleased to share our paper in @PLOSCompBiol where we reveal patterns of position-dependent codon usage that we call "POSCO". POSCO is a score that describes biases in codon occurrence relative to the start codon. High POSCO is associated with increased translational efficiency and changes in ribosomal occupancy.
https://t.co/1GsI54qwPt

[Das Lab @RDasLab]

We and @eternagame are joining the quest to find a molecule that can sustainably replicate itself. Pilot results on first 1000 designs are posted, next up will be million-design-scale expts. Come design at https://t.co/dDCM1KVNe0 by Aug 31, 2026! #RNAworld

[𝙳𝚊𝚟𝚒𝚍 𝙰 𝙷𝚎𝚗𝚍𝚛𝚒𝚡 @profhendrix]

This paper is the work of former undergraduate honor student Kaavya Subramanian, MS student Nathan Waugh, and former undergraduate student Cole Shanks

[𝙳𝚊𝚟𝚒𝚍 𝙰 𝙷𝚎𝚗𝚍𝚛𝚒𝚡 @profhendrix]

Transcripts with high POSCO scores are related to developmental biology, immune response, and response to stimulus -- genes that need rapid activation, while low POSCO is associated with adaptive immunity and metabolic processes.

[𝙳𝚊𝚟𝚒𝚍 𝙰 𝙷𝚎𝚗𝚍𝚛𝚒𝚡 @profhendrix]

@benbfly @anshulkundaje Cool to see two people I know from different times and places talking online! Interesting discussion. I think interpreting AI models with domain knowledge to uncover new patterns in data is key. Also a big thing for us is understanding the data so it can be simulated/augmented

[Ya'el Courtney, PhD @ScienceYael]

HHMI released the official 2027 Gilliam Fellowship details, and a lot changed. Deadline's earlier this cycle: Oct 27. Int'l & MD-PhD students now eligible. Stipend up to 50K. New postdoc pathway adds up to 7 yrs of support. No Journal names!!!!

https://t.co/fi5rPJHLEA

[𝙳𝚊𝚟𝚒𝚍 𝙰 𝙷𝚎𝚗𝚍𝚛𝚒𝚡 @profhendrix]

@CoryMSimon See any in Oregon?

[𝙳𝚊𝚟𝚒𝚍 𝙰 𝙷𝚎𝚗𝚍𝚛𝚒𝚡 @profhendrix]

@mbeisen Situations like that make me wonder if there is a newer AI element in the past years. Like someone missed a turn and Maps "learned" that it might be a better route

[Das Lab @RDasLab]

Third (& last?) intense week of #RNA server-only targets on #CASP17: small molecule binding ribozymes and aptamers & more group II introns in multiple states. Strange mix of natural and non-natural RNA and compounds and proteins. Looking forward to less crazy pace in next weeks.

[𝙳𝚊𝚟𝚒𝚍 𝙰 𝙷𝚎𝚗𝚍𝚛𝚒𝚡 @profhendrix]

@silvirouskin @grok I saw today that you can buy a flat-screen TV for as much as 8 jars of almond butter. Life is strange

[Das Lab @RDasLab]

Latest #CASP17 #RNA targets are a tiny aptamer for tryptophan selected by Yarus lab @cuboulder, a miniTTR by RNAmake @JosephYesselman, and two singlet glycine riboswitches discovered by @ronbreaker Strobel. Note that first one — a 25-nt RNA by #cryoEM? https://t.co/r9IAvhN28g

[Das Lab @RDasLab]

The 17th Critical Assessment of Structure Prediction #CASP17 begins tomorrow. 2 #RNA targets per day for next few weeks! >60 servers registered already, including @kaggle teams. Join the fun at https://t.co/wbMGUMryza

[The Legend of BEAVERMAN @MarvinBeaverman]

I would like to thank Beaver Nation on the continental USA and around the world for your love and support. Go Beavs 🦫

[Samuel Talbot @SamCTalbot]

A Nanopore ultralong run we just did for Hop! Nearly 110Gb off a single flow cell with the true N50 probably >70Kb. Very excited for this one 🚀🧬

#ONT

[Sushmita Roy @sroyyors.bsky.social,genomic.social @sroyyors]

somebody said in this age of agentic AI its become easier to write papers.. I don't think it's true (for me). It's become harder... maybe I am doing it wrong. I am seriously worried about AI slop and halucinations.

[𝙳𝚊𝚟𝚒𝚍 𝙰 𝙷𝚎𝚗𝚍𝚛𝚒𝚡 @profhendrix]

@silvirouskin I could host the data for you if needed on the bpRNA website!

[𝙳𝚊𝚟𝚒𝚍 𝙰 𝙷𝚎𝚗𝚍𝚛𝚒𝚡 @profhendrix]

What does Paul McCartney say when making the first cut of a pecan pie?

🎵 "Simply halving a wonderful Christmas pie" 🎵