Player-dev at citizen science game Eterna where players around the world help researchers learn more about RNA structure and design
https://eternagame.org/about
https://eternagame.org/challenges
https://eternagame.org/publications
| ORCID | 0000-0001-8528-2227 |
Will Kagglers be able to crack the #RNA structure code? Kaggle's Ribonanza competition will attempt to predict reactivity patterns in one million RNA of varying lengths. https://www.kaggle.com/competitions/stanford-ribonanza-rna-folding/overview
Eterna players spent the spring/summer submitting 683,000 diverse sequences scanned from viruses, bacterial genomes, human genes, and extensive mutation series of known pseudoknots.
New paper published in Nature Communications describing how Eterna players redesigned the E. coli #ribosome to produce 42% more protein in iSAT experiments.
https://www.nature.com/articles/s41467-023-35827-3
I sure would like to have this arcade game in my basement! @amw_stanford
While the ribosome has been harnessed for synthetic biology, designing ribosomes has remained challenging. Here, the authors demonstrate a community science approach for rational design of ribosomes with beneficial properties.
Eterna soon will be launching a new antisense oligonucleotide project in collaboration with the University of California, Santa Cruz exploring how short pieces of #RNA can remediate aberrant #splicing caused by genetic mutations.
New #citsci players can try our Oligo Training puzzles to get familiar with the game interface: https://eternagame.org/collections/11431896.
Eterna's collaboration with #Kaggle has been published in Nature Machine Intelligence! The pandemic was awful but it did lead us to develop new models of #RNA degradation. @dosoon
Predicting RNA degradation is a fundamental task in designing RNA-based therapeutics. Two crowdsourcing platforms, Kaggle and Eterna, united to develop accurate deep learning models for RNA degradation on a timescale of 6 months.
Have any antisense oligonucleotide #ASO experts made it onto mastodon?
I'm trying to find evidence on how much of a role #intron secondary structure remediation plays in splice-switching ASO design. A presentation by an ASO researcher from a biotech stated that the #spliceosome recognizes intron #secstruct, particularly the intron 5' structure, but haven't found published evidence or hypothesis.
#introduction
Hi, I’m Jill and I collaborate with researchers to develop #RNA modeling puzzles for the science game Eterna.
Our current project asks players around the world to submit sequences up to 90 nt that may fold into a #pseudoknot. The structure will be verified by SHAPE testing at the Das Lab (Stanford). We hope to generate a large dataset containing thousands of pseudoknot and tertiary structures that researchers can use to train new #RNAmodeling algorithms.
