AIMC Topic: 5' Untranslated Regions
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Identification of potential riboswitch elements in Homo sapiens mRNA 5'UTR sequences using positive-unlabeled machine learning.
PloS one
Apr 24, 2025
Riboswitches are a class of noncoding RNA structures that interact with target ligands to cause a conformational change that can then execute some regulatory purpose within the cell. Riboswitches are ubiquitous and well characterized in bacteria and ...
UTR-Insight: integrating deep learning for efficient 5' UTR discovery and design.
BMC genomics
Feb 4, 2025
The 5' UTR is critical for mRNA stability and translation efficiency in therapeutics. We developed UTR-Insight, a model integrating a pretrained language model with a CNN-Transformer architecture, explaining 89.1% of the mean ribosome load (MRL) vari...
The regulatory landscape of 5' UTRs in translational control during zebrafish embryogenesis.
Developmental cell
Jan 15, 2025
The 5' UTRs of mRNAs are critical for translation regulation during development, but their in vivo regulatory features are poorly characterized. Here, we report the regulatory landscape of 5' UTRs during early zebrafish embryogenesis using a massivel...
Interpreting deep neural networks for the prediction of translation rates.
BMC genomics
Nov 9, 2024
BACKGROUND: The 5' untranslated region of mRNA strongly impacts the rate of translation initiation. A recent convolutional neural network (CNN) model accurately quantifies the relationship between massively parallel synthetic 5' untranslated regions ...
Current limitations in predicting mRNA translation with deep learning models.
Genome biology
Aug 20, 2024
BACKGROUND: The design of nucleotide sequences with defined properties is a long-standing problem in bioengineering. An important application is protein expression, be it in the context of research or the production of mRNA vaccines. The rate of prot...
Optimizing 5'UTRs for mRNA-delivered gene editing using deep learning.
Nature communications
Jun 20, 2024
mRNA therapeutics are revolutionizing the pharmaceutical industry, but methods to optimize the primary sequence for increased expression are still lacking. Here, we design 5'UTRs for efficient mRNA translation using deep learning. We perform polysome...
Predicting mean ribosome load for 5'UTR of any length using deep learning.
PLoS computational biology
May 10, 2021
The 5' untranslated region plays a key role in regulating mRNA translation and consequently protein abundance. Therefore, accurate modeling of 5'UTR regulatory sequences shall provide insights into translational control mechanisms and help interpret ...
Transfer learning for cross-context prediction of protein expression from 5'UTR sequence.
Nucleic acids research
Jul 22, 2024
Model-guided DNA sequence design can accelerate the reprogramming of living cells. It allows us to engineer more complex biological systems by removing the need to physically assemble and test each potential design. While mechanistic models of gene e...
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