AIMC Topic: Protein Biosynthesis
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Deciphering disordered regions controlling mRNA decay in high-throughput.
Nature
Apr 23, 2025
Intrinsically disordered regions within proteins drive specific molecular functions despite lacking a defined structure. Although disordered regions are integral to controlling mRNA stability and translation, the mechanisms underlying these regulator...
TransRM: Weakly supervised learning of translation-enhancing N6-methyladenosine (mA) in circular RNAs.
International journal of biological macromolecules
Feb 27, 2025
As our understanding of Circular RNAs (circRNAs) continues to expand, accumulating evidence has demonstrated that circRNAs can interact with microRNAs and RNA-binding proteins to modulate gene expression. More importantly, a subset of circRNAs has be...
Deep learning to decode sites of RNA translation in normal and cancerous tissues.
Nature communications
Feb 2, 2025
The biological process of RNA translation is fundamental to cellular life and has wide-ranging implications for human disease. Accurate delineation of RNA translation variation represents a significant challenge due to the complexity of the process a...
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...
Translation as a Biosignature.
Astrobiology
Nov 29, 2024
Life on Earth relies on mechanisms to store heritable information and translate this information into cellular machinery required for biological activity. In all known life, storage, regulation, and translation are provided by DNA, RNA, and ribosomes...
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 ...
Predicting synthetic mRNA stability using massively parallel kinetic measurements, biophysical modeling, and machine learning.
Nature communications
Nov 6, 2024
mRNA degradation is a central process that affects all gene expression levels, though it remains challenging to predict the stability of a mRNA from its sequence, due to the many coupled interactions that control degradation rate. Here, we carried ou...
Predicting photosynthetic bacteria-derived protein synthesis from wastewater using machine learning and causal inference.
Bioresource technology
Oct 15, 2024
Causal inference-assisted machine learning was used to predict photosynthetic bacterial (PSB) protein production capacity and identify key factors. The extreme gradient boosting algorithm effectively predicted protein content, while the gradient boos...
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...
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