A5093320380- RNA and protein synthesis mechanisms
- RNA modifications and cancer
- SARS-CoV-2 and COVID-19 Research
- Viral gastroenteritis research and epidemiology
- Animal Virus Infections Studies
- RNA Research and Splicing
- Advanced Electron Microscopy Techniques and Applications
- Genomics and Phylogenetic Studies
Stanford University
2023-2024
Howard Hughes Medical Institute
2024
Stanford Medicine
2024
Prediction of RNA structure from sequence remains an unsolved problem, and progress has been slowed by a paucity experimental data. Here, we present Ribonanza, dataset chemical mapping measurements on two million diverse sequences collected through Eterna other crowdsourced initiatives. Ribonanza enabled solicitation, training, prospective evaluation deep neural networks Kaggle challenge, followed distillation into single, self-contained model called RibonanzaNet. When fine tuned auxiliary...
Coronavirus genomes sequester their start codons within stem-loop 5 (SL5), a structured, 5′ genomic RNA element. In most alpha- and betacoronaviruses, the secondary structure of SL5 is predicted to contain four-way junction helical stems, some which are capped with UUYYGU hexaloops. Here, using cryogenic electron microscopy (cryo-EM) computational modeling biochemically determined structures, we present three-dimensional structures from six coronaviruses. The domain betacoronavirus...
RNA-Puzzles is a collective endeavor dedicated to the advancement and improvement of RNA three-dimensional structure prediction. With agreement from structural biologists, structures are predicted by modeling groups before publication experimental structures. We report large-scale set predictions 18 for 23 RNA-Puzzles: 4 elements, 2 Aptamers, Viral 5 Ribozymes 8 Riboswitches. describe automatic assessment protocols comparisons between prediction experiment. Our analyses reveal some critical...
Abstract Myriad families of natural RNAs have been proposed, but not yet experimentally shown, to form biologically important structures. Here we report three-dimensional structures three large ornate bacterial using cryogenic electron microscopy at resolutions 2.9-3.1 Å. Without precedent among previously characterized RNA molecules, Giant, Ornate, Lake- and Lactobacillales-Derived (GOLLD), Rumen-Originating, Large (ROOL), Ornate Extremophilic (OLE) homo-oligomeric complexes whose...
Coronavirus genomes sequester their start codons within stem-loop 5 (SL5), a structured, 5' genomic RNA element. In most alpha- and betacoronaviruses, the secondary structure of SL5 is predicted to contain four-way junction helical stems, some which are capped with UUYYGU hexaloops. Here, using cryogenic electron microscopy (cryo-EM) computational modeling biochemically-determined structures, we present three-dimensional structures from six coronaviruses. The domain betacoronavirus...