Professor @OregonState. #Bioinformatics and #ComputationalBiology #Genomics #RNA #Chronobiology (he/him) https://xitter.cf/t.co/gY1mVezE7g
Corvallis, OR
Joined March 2017
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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 eternagame.org/labs/14660266 by Aug 31, 2026! #RNAworld
Our Replicase pilot results found that the catalytic activity and copyability of the 71-89 polymerase ribozyme can be improved! We have launched a new puzzle for finding a version that excels at both properties simultaneously. Comp methods are encouraged to submit designs!
ALT Puzzle interface displaying both the secondary and tertiary structure of the ribozyme
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.
journals.plos.org/ploscompbiβ¦
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.
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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!!!!
yaelcourtney.com/resources-aβ¦
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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.
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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 β a 25-nt RNA by #cryoEM? predictioncenter.org/casp17/β¦
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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 predictioncenter.org/casp17/
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I would like to thank Beaver Nation on the continental USA and around the world for your love and support. Go Beavs 𦫠β at Mililani Mauka, HI
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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 ππ§¬
#ONT
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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.
What does Paul McCartney say when making the first cut of a pecan pie?
π΅ "Simply halving a wonderful Christmas pie" π΅
Every year @OregonState at the start of Fall quarter, we are greeted by a beautiful Fall Equinox sunset #BeaverHenge
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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.
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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
academic.oup.com/nar/articleβ¦
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
academic.oup.com/nar/articleβ¦
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
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
academic.oup.com/bioinformatβ¦
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
rnajournal.cshlp.org/contentβ¦
