Publications by authors named "Fernando U Montoya"
The degree to which translational control is specified by mRNA sequence is poorly understood in mammalian cells. Here, we constructed and leveraged a compendium of 3,819 ribosomal profiling datasets, distilling them into a transcriptome-wide atlas of translation efficiency (TE) measurements encompassing >140 human and mouse cell types. We subsequently developed RiboNN, a multitask deep convolutional neural network, and classic machine learning models to predict TEs in hundreds of cell types from sequence-encoded mRNA features, achieving state-of-the-art performance (r=0.
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- mRNA-based vaccines and therapeutics are increasingly used, and optimizing the mRNA sequence is critical for their effectiveness.
- CodonBERT, a large language model designed specifically for mRNAs, uses codons to improve understanding and predictions regarding mRNA properties.
- Trained on over 10 million mRNA sequences from various organisms, CodonBERT outperforms previous prediction methods, including in the context of a new flu vaccine data set.
Article Synopsis
- Lipid nanoparticles (LNPs) are key for mRNA vaccine delivery, and optimizing their lipid composition can enhance effectiveness by improving properties such as biodegradability and transfection efficiency.
- The study presents a novel method that utilizes Simplified Molecular-Input Line-Entry System (SMILES) to virtually screen LNPs, using large language models for better prediction of lipid properties.
- Results demonstrate this approach can increase transfection efficiency while saving time and costs in testing, with resources available online for further implementation.
In this paper, we considered different methods to test the interaction between treatment and a potentially large number (p) of covariates in randomized clinical trials. The simplest approach was to fit univariate (marginal) models and to combine the univariate statistics or p-values (e.g.
View Article and Find Full Text PDFIn order to facilitate production and secretion of a soluble form of a small, single-chain antibody ScFv (32 kDa) in tobacco cell suspension culture, several modifications were made simultaneously to the antibody cDNA that included elements that have been shown to regulate the expression of proteins in plants. The scFv cDNA was initially ligated into a binary vector under the control of the CaMV 35S promoter and the T7 terminator for expression in tobacco suspension culture. Subsequently, modifications were engineered into the cDNA for enhancement of scFv production.
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