A5015816584- RNA modifications and cancer
- RNA and protein synthesis mechanisms
- COVID-19 Clinical Research Studies
- Long-Term Effects of COVID-19
- SARS-CoV-2 and COVID-19 Research
- RNA Research and Splicing
- Intensive Care Unit Cognitive Disorders
- Diet and metabolism studies
- Bacterial Genetics and Biotechnology
- CRISPR and Genetic Engineering
- Bariatric Surgery and Outcomes
- Respiratory Support and Mechanisms
- Pneumonia and Respiratory Infections
- Advanced biosensing and bioanalysis techniques
- Diabetes Treatment and Management
- SARS-CoV-2 detection and testing
- RNA Interference and Gene Delivery
- Venous Thromboembolism Diagnosis and Management
- Heparin-Induced Thrombocytopenia and Thrombosis
- Obesity and Health Practices
- Bacteriophages and microbial interactions
- Viral Infections and Immunology Research
Eterna Massive Open Laboratory
2020-2024
Southmead Hospital
2022
Stanford University
2020
The rapid spread of COVID-19 is motivating development antivirals targeting conserved SARS-CoV-2 molecular machinery. genome includes RNA elements that offer potential small-molecule drug targets, but most their 3D structures have not been experimentally characterized. Here, we provide a compilation chemical mapping data from our and other labs, secondary structure models, model ensembles based on Rosetta's FARFAR2 algorithm for regions including the individual stems SL1-8 in extended 5'...
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...
Abstract Functional design of ribosomes with mutant ribosomal RNA (rRNA) can expand opportunities for understanding molecular translation, building cells from the bottom-up, and engineering altered capabilities. However, such efforts are hampered by cell viability constraints, an enormous combinatorial sequence space, limitations on large-scale, 3D structures functions. To address these challenges, we develop integrated community science experimental screening approach rational ribosomes....
Abstract The rapid spread of COVID-19 is motivating development antivirals targeting conserved SARS-CoV-2 molecular machinery. genome includes RNA elements that offer potential small-molecule drug targets, but most their 3D structures have not been experimentally characterized. Here, we provide a compilation chemical mapping data from our and other labs, secondary structure models, model ensembles based on Rosetta’s FARFAR2 algorithm for regions including the individual stems SL1-8 in...
Abstract The ribosome is a ribonucleoprotein complex found in all domains of life. Its role to catalyze protein synthesis, the messenger RNA (mRNA)-templated formation amide bonds between α-amino acid monomers. Amide bond occurs within highly conserved region large ribosomal subunit known as peptidyl transferase center (PTC). Here we describe step-wise design and characterization mini-PTC 1.1, 284-nucleotide that recapitulates many essential features Escherichia coli PTC. Mini-PTC 1.1 folds...
Introduction Bariatric surgery is an effective method of controlling glycaemia in patients with type 2 diabetes mellitus (T2DM) and obesity. Long-term studies suggest that although glycaemic control remains good, only 20%–40% will maintain remission according to the American Diabetes Association criteria. Purpose This trial aims examine safety efficacy combining Roux-en-Y gastric bypass or sleeve gastrectomy goal-directed medical therapy improve long-term T2DM. Methods analysis prospective,...
Homopolymeric adenosine RNA plays numerous roles in both cells and noncellular genetic material. We report herein an unusual poly(A) signature chemical mapping data generated by the Eterna Massive Open Laboratory. Poly(A) sequences of length seven or more show unexpected results selective 2′-hydroxyl acylation read out primer extension (SHAPE) dimethyl sulfate (DMS) probing. This first appears grows to its maximum strength at ∼10. In a long sequence, substitution single A any other...
ABSTRACT Functional design of ribosomes with mutant ribosomal RNA (rRNA) could expand opportunities for understanding molecular translation, building cells from the bottom-up, and engineering altered capabilities. However, such efforts have been hampered by cell viability constraints, an enormous combinatorial sequence space, limitations on large-scale, 3D structures functions. To address these challenges, we developed integrated community science experimental screening approach rational...
ABSTRACT Splice-modulating antisense oligonucleotides (ASOs) are precision RNA-based drugs that becoming an established modality to treat human disease. Previously, we reported the discovery of ASOs target a novel, putative intronic RNA structure rescue splicing multiple pathogenic variants F8 exon 16 cause hemophilia A. However, conventional approach discovering splice-modulating is both laborious and expensive. Here, describe alternative paradigm integrates data-driven prediction community...
ABSTRACT The ribosome is a ribonucleoprotein complex found in all domains of life. Its role to catalyze protein synthesis, the messenger RNA (mRNA)-templated formation amide bonds between α-amino acid monomers. Amide bond occurs within highly conserved region large ribosomal subunit known as peptidyl transferase center (PTC). Here we describe stepwise design and characterization mini-PTC 1.1, 284-nucleotide that recapitulates many essential features Escherichia coli PTC. Mini-PTC 1.1 folds...