𝙳𝚊𝚟𝚒𝚍 𝙰 𝙷𝚎𝚗𝚍𝚛𝚒𝚡

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

[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

[Marvin @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" 🎵

[𝙳𝚊𝚟𝚒𝚍 𝙰 𝙷𝚎𝚗𝚍𝚛𝚒𝚡 @profhendrix]

@wachitas @ABC From what I can tell, it was "traditional Mexican cuisine" that was recognized in 2010, but for Italy it was "entire national cuisine". So Italy was the first for entire national cuisine.
https://t.co/lidHhSooI6

[𝙳𝚊𝚟𝚒𝚍 𝙰 𝙷𝚎𝚗𝚍𝚛𝚒𝚡 @profhendrix]

@mbeisen @HistoryBoomer Not sure what this is about, but gotta go with the mint ice cream with no chocolate chips.

[𝙳𝚊𝚟𝚒𝚍 𝙰 𝙷𝚎𝚗𝚍𝚛𝚒𝚡 @profhendrix]

Every year @OregonState at the start of Fall quarter, we are greeted by a beautiful Fall Equinox sunset #BeaverHenge

[𝙳𝚊𝚟𝚒𝚍 𝙰 𝙷𝚎𝚗𝚍𝚛𝚒𝚡 @profhendrix]

@pastramimachine Yes! Give me big physical buttons and knobs. There is nothing cool about cranking the volume on the radio on a Friday afternoon with a touchscreen

[Jason H. Moore, PhD @moorejh]

Received two reviews on a paper I am a co-author on that was submitted the @NaturePortfolio Scientific Reports. Both reviews were written by ChatGPT & clearly not edited with hallucinations. Shame on the editors for letting this unethical AI slop out the door.

[𝙳𝚊𝚟𝚒𝚍 𝙰 𝙷𝚎𝚗𝚍𝚛𝚒𝚡 @profhendrix]

We are excited to share a new publication w/ @JosephYesselman in @NAR_Open. RNA secondary structure prediction and design typically minimize the global free energy. We show that *local* stability compensation is a powerful RNA design approach 1/4
https://t.co/tZMbPeLozY

[𝙳𝚊𝚟𝚒𝚍 𝙰 𝙷𝚎𝚗𝚍𝚛𝚒𝚡 @profhendrix]

Local Stability Compensation presents a bottom-up approach to RNA design, focusing on local interactions, compared to the top-down approach of global free energy minimization. Check out the paper for more! 4/4

[𝙳𝚊𝚟𝚒𝚍 𝙰 𝙷𝚎𝚗𝚍𝚛𝚒𝚡 @profhendrix]

We are excited to share a new publication w/ @JosephYesselman in @NAR_Open. RNA secondary structure prediction and design typically minimize the global free energy. We show that *local* stability compensation is a powerful RNA design approach 1/4
https://t.co/tZMbPeLozY

[𝙳𝚊𝚟𝚒𝚍 𝙰 𝙷𝚎𝚗𝚍𝚛𝚒𝚡 @profhendrix]

Our large design libraries demonstrate that local stability compensation (net free energy of local substructure) correlates with folding accuracy through a Hill equation relationship. 3/4

[𝙳𝚊𝚟𝚒𝚍 𝙰 𝙷𝚎𝚗𝚍𝚛𝚒𝚡 @profhendrix]

We hope to apply these methods to identify novel structures and to improve our RNA secondary structure meta-database, stay tuned for bpRNA-hub.

[𝙳𝚊𝚟𝚒𝚍 𝙰 𝙷𝚎𝚗𝚍𝚛𝚒𝚡 @profhendrix]

We are excited to share our latest publication, bpRNA-CosMoS, a k-mer based measure of #RNA structural similarity. This method allows us to perform millions of structural comparisons for clustering in a short amount of time. #OpenAccess in #Bioinformatics
https://t.co/xtzsqJW2ow

[𝙳𝚊𝚟𝚒𝚍 𝙰 𝙷𝚎𝚗𝚍𝚛𝚒𝚡 @profhendrix]

Although it isn't as accurate as our other alignment-based method bpRNA-align, (Published in RNA) it allows us to perform an initial clustering of 100s of thousands of structures, which we can refine, reducing the overall number of calculations
https://t.co/7CjaD73WUa