AIMC Topic: RNA

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SequenceCraft: machine learning-based resource for exploratory analysis of RNA-cleaving deoxyribozymes.

BMC bioinformatics Jan 6, 2025
BACKGROUND: Deoxyribozymes or DNAzymes represent artificial short DNA sequences bearing many catalytic properties. In particular, DNAzymes able to cleave RNA sequences have a huge potential in gene therapy and sequence-specific analytic detection of ...
Computational Biology RNA DNA, Catalytic Machine Learning
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Trans-m5C: A transformer-based model for predicting 5-methylcytosine (m5C) sites.

Methods (San Diego, Calif.) Dec 30, 2024
5-Methylcytosine (m5C) plays a pivotal role in various RNA metabolic processes, including RNA localization, stability, and translation. Current high-throughput sequencing technologies for m5C site identification are resource-intensive in terms of cos...
Deep Learning Mice Computational Biology Neural Networks, Computer Animals 5-Methylcytosine RNA High-Throughput Nucleotide Sequencing Humans
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Systematic benchmarking of deep-learning methods for tertiary RNA structure prediction.

PLoS computational biology Dec 30, 2024
The 3D structure of RNA critically influences its functionality, and understanding this structure is vital for deciphering RNA biology. Experimental methods for determining RNA structures are labour-intensive, expensive, and time-consuming. Computati...
Benchmarking RNA Sequence Alignment Nucleic Acid Conformation Computational Biology Sequence Analysis, RNA Deep Learning
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Predicting RNA structure and dynamics with deep learning and solution scattering.

Biophysical journal Dec 25, 2024
Advanced deep learning and statistical methods can predict structural models for RNA molecules. However, RNAs are flexible, and it remains difficult to describe their macromolecular conformations in solutions where varying conditions can induce confo...
Deep Learning Models, Molecular X-Ray Diffraction Magnesium Solutions RNA Nucleic Acid Conformation Scattering, Small Angle
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Determining structures of RNA conformers using AFM and deep neural networks.

Nature Dec 18, 2024
Much of the human genome is transcribed into RNAs, many of which contain structural elements that are important for their function. Such RNA molecules-including those that are structured and well-folded-are conformationally heterogeneous and flexible...
RNA Microscopy, Atomic Force Neural Networks, Computer Signal-To-Noise Ratio Unsupervised Machine Learning Deep Learning Nucleic Acid Conformation Humans Models, Molecular
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GenoM7GNet: An Efficient N-Methylguanosine Site Prediction Approach Based on a Nucleotide Language Model.

IEEE/ACM transactions on computational biology and bioinformatics Dec 10, 2024
N-methylguanosine (m7G), one of the mainstream post-transcriptional RNA modifications, occupies an exceedingly significant place in medical treatments. However, classic approaches for identifying m7G sites are costly both in time and equipment. Meanw...
Guanosine Algorithms Deep Learning Sequence Analysis, RNA Humans Computational Biology RNA Neural Networks, Computer
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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...
Ribosomes RNA Machine Learning Exobiology Nanopores Protein Biosynthesis DNA
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Accurate RNA 3D structure prediction using a language model-based deep learning approach.

Nature methods Nov 21, 2024
Accurate prediction of RNA three-dimensional (3D) structures remains an unsolved challenge. Determining RNA 3D structures is crucial for understanding their functions and informing RNA-targeting drug development and synthetic biology design. The stru...
Models, Molecular RNA Humans Nucleic Acid Conformation Deep Learning Software Computational Biology
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Deciphering Cas9 specificity: Role of domain dynamics and RNA:DNA hybrid interactions revealed through machine learning and accelerated molecular simulations.

International journal of biological macromolecules Nov 19, 2024
CRISPR/Cas9 technology is widely used for gene editing, but off-targeting still remains a major concern in therapeutic applications. Although Cas9 variants with better mismatch discrimination have been developed, they have significantly lower rates o...
CRISPR-Cas Systems Francisella Bacterial Proteins Substrate Specificity Machine Learning Molecular Dynamics Simulation CRISPR-Associated Protein 9 Protein Domains DNA RNA
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Deep-m5U: a deep learning-based approach for RNA 5-methyluridine modification prediction using optimized feature integration.

BMC bioinformatics Nov 19, 2024
BACKGROUND: RNA 5-methyluridine (m5U) modifications play a crucial role in biological processes, making their accurate identification a key focus in computational biology. This paper introduces Deep-m5U, a robust predictor designed to enhance the pre...
Neural Networks, Computer Deep Learning Computational Biology Algorithms Uridine RNA, Messenger RNA
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