AIMC Topic: DNA

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Developing a method for predicting DNA nucleosomal sequences using deep learning.

Technology and health care : official journal of the European Society for Engineering and Medicine Nov 20, 2024
BackgroundDeep learning excels at processing raw data because it automatically extracts and classifies high-level features. Despite biology's low popularity in data analysis, incorporating computer technology can improve biological research.Objective...
Sequence Analysis, DNA DNA Algorithms Humans Neural Networks, Computer Deep Learning Nucleosomes
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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...
Francisella CRISPR-Cas Systems Substrate Specificity Bacterial Proteins CRISPR-Associated Protein 9 Molecular Dynamics Simulation Machine Learning Protein Domains RNA DNA
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Predicting cell type-specific epigenomic profiles accounting for distal genetic effects.

Nature communications Nov 16, 2024
Understanding how genetic variants affect the epigenome is key to interpreting GWAS, yet profiling these effects across the non-coding genome remains challenging due to experimental scalability. This necessitates accurate computational models. Existi...
Humans Genome-Wide Association Study Polymorphism, Single Nucleotide Deep Learning Epigenome Quantitative Trait Loci Chromatin Models, Genetic DNA Epigenesis, Genetic Epigenomics
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Visualization Methods for DNA Sequences: A Review and Prospects.

Biomolecules Nov 14, 2024
The efficient analysis and interpretation of biological sequence data remain major challenges in bioinformatics. Graphical representation, as an emerging and effective visualization technique, offers a more intuitive method for analyzing DNA sequence...
Sequence Analysis, DNA DNA Machine Learning Computational Biology Humans Neural Networks, Computer
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Deep learning enables the use of ultra-high-density array in DNBSEQ.

Scientific reports Nov 13, 2024
DNBSEQ employs a patterned array to facilitate massively parallel sequencing of DNA nanoballs (DNBs), leading to a considerable boost in throughput. By employing the ultra-high-density (UHD) array with an increased density of DNB binding sites, the t...
High-Throughput Nucleotide Sequencing Sequence Analysis, DNA DNA Deep Learning Image Processing, Computer-Assisted
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Challenges and Prospects of DNA-Encoded Library Data Interpretation.

Chemical reviews Nov 7, 2024
DNA-encoded library (DEL) technology is a powerful platform for the efficient identification of novel chemical matter in the early drug discovery process enabled by parallel screening of vast libraries of encoded small molecules through affinity sele...
Machine Learning Drug Discovery Small Molecule Libraries Gene Library DNA Humans
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Effect of graphene electrode functionalization on machine learning-aided single nucleotide classification.

Nanoscale Nov 7, 2024
Solid-state nanogap-based DNA sequencing with a quantum tunneling approach has emerged as a promising avenue due to its potential to deliver swift and precise sequencing outcomes. Nevertheless, despite significant progress, experimentally achieving s...
DNA Nucleotides Machine Learning Graphite Electrodes Sequence Analysis, DNA
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A General DNA-Like Hybrid Symbiosis Framework: An EEG Cognitive Recognition Method.

IEEE journal of biomedical and health informatics Nov 6, 2024
In electroencephalogram (EEG) cognitive recognition research, the combined use of artificial neural networks (ANNs) and spiking neural networks (SNNs) plays an important role to realize different categories of recognition tasks. However, most of the ...
Electroencephalography Signal Processing, Computer-Assisted Pattern Recognition, Automated Cognition DNA Neural Networks, Computer Algorithms Humans
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GeoNet enables the accurate prediction of protein-ligand binding sites through interpretable geometric deep learning.

Structure (London, England : 1993) Nov 1, 2024
The identification of protein binding residues is essential for understanding their functions in vivo. However, it remains a computational challenge to accurately identify binding sites due to the lack of known residue binding patterns. Local residue...
Computational Biology Proteins Deep Learning Protein Binding RNA Ligands Binding Sites DNA Models, Molecular
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An Integrated Multi-Model Framework Utilizing Convolutional Neural Networks Coupled with Feature Extraction for Identification of 4mC Sites in DNA Sequences.

Computers in biology and medicine Oct 28, 2024
N4-methylcytosine (4mC) is a chemical modification that occurs on one of the four nucleotide bases in DNA and plays a vital role in DNA expression, repair, and replication. It also actively participates in the regulation of cell differentiation and g...
Sequence Analysis, DNA DNA Cytosine Humans Neural Networks, Computer
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