AIMC Topic: Protein Biosynthesis

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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...
Deep Learning Escherichia coli Protein Biosynthesis 5' Untranslated Regions
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Predicting functional consequences of SNPs on mRNA translation via machine learning.

Nucleic acids research Aug 25, 2023
The functional impact of single nucleotide polymorphisms (SNPs) on translation has yet to be considered when prioritizing disease-causing SNPs from genome-wide association studies (GWAS). Here we apply machine learning models to genome-wide ribosome ...
Machine Learning Genome-Wide Association Study Polymorphism, Single Nucleotide RNA, Messenger Protein Biosynthesis Codon, Terminator
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Revealing determinants of translation efficiency via whole-gene codon randomization and machine learning.

Nucleic acids research Mar 21, 2023
It has been known for decades that codon usage contributes to translation efficiency and hence to protein production levels. However, its role in protein synthesis is still only partly understood. This lack of understanding hampers the design of synt...
Machine Learning RNA, Messenger Escherichia coli Random Allocation Codon Protein Biosynthesis
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Predicting protein condensate formation using machine learning.

Cell reports Feb 2, 2021
Membraneless organelles are liquid condensates, which form through liquid-liquid phase separation. Recent advances show that phase separation is essential for cellular homeostasis by regulating basic cellular processes, including transcription and si...
Humans Machine Learning Protein Biosynthesis Biomolecular Condensates
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A deep recurrent neural network discovers complex biological rules to decipher RNA protein-coding potential.

Nucleic acids research Sep 19, 2018
The current deluge of newly identified RNA transcripts presents a singular opportunity for improved assessment of coding potential, a cornerstone of genome annotation, and for machine-driven discovery of biological knowledge. While traditional, featu...
Humans Neural Networks, Computer Machine Learning Reproducibility of Results Computational Biology RNA, Messenger Sequence Analysis, RNA RNA, Long Noncoding Base Sequence Protein Biosynthesis Open Reading Frames
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