AIMC Topic: DNA

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DNA Origami Nanostructure Detection and Yield Estimation Using Deep Learning.

ACS synthetic biology Jan 25, 2023
DNA origami is a milestone in DNA nanotechnology. It is robust and efficient in constructing arbitrary two- and three-dimensional nanostructures. The shape and size of origami structures vary. To characterize them, an atomic force microscope, a trans...
DNA Nanostructures Deep Learning Nanotechnology Nucleic Acid Conformation
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MultiScale-CNN-4mCPred: a multi-scale CNN and adaptive embedding-based method for mouse genome DNA N4-methylcytosine prediction.

BMC bioinformatics Jan 18, 2023
N4-methylcytosine (4mC) is an important epigenetic mechanism, which regulates many cellular processes such as cell differentiation and gene expression. The knowledge about the 4mC sites is a key foundation to exploring its roles. Due to the limitatio...
Neural Networks, Computer Software DNA Genome Animals Mice Epigenesis, Genetic
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Fused deep learning paradigm for the prediction of o6-methylguanine-DNA methyltransferase genotype in glioblastoma patients: A neuro-oncological investigation.

Computers in biology and medicine Jan 4, 2023
BACKGROUND: The O6-methylguanine-DNA methyltransferase (MGMT) is a deoxyribonucleic acid (DNA) repairing enzyme that has been established as an essential clinical brain tumor biomarker for Glioblastoma Multiforme (GBM). Knowing the status of MGMT met...
Magnetic Resonance Imaging DNA Methylation Brain Neoplasms Deep Learning DNA Modification Methylases Methyltransferases Glioblastoma DNA Humans Biomarkers
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Prediction of designer-recombinases for DNA editing with generative deep learning.

Nature communications Dec 27, 2022
Site-specific tyrosine-type recombinases are effective tools for genome engineering, with the first engineered variants having demonstrated therapeutic potential. So far, adaptation to new DNA target site selectivity of designer-recombinases has been...
Directed Molecular Evolution Recombinases DNA Deep Learning
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Mechano-fluorescence actuation in single synaptic vesicles with a DNA framework nanomachine.

Science robotics Dec 21, 2022
Biomimetic machines that can convert mechanical actuation to adaptive coloration in a manner analogous to cephalopods have found widespread applications at various length scales. At the nanoscale, a transmutable nanomachine with adaptive colors that ...
Robotics DNA Exocytosis Synaptic Vesicles
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Protein-DNA Binding Residue Prediction via Bagging Strategy and Sequence-Based Cube-Format Feature.

IEEE/ACM transactions on computational biology and bioinformatics Dec 8, 2022
Protein-DNA interactions play an important role in diverse biological processes. Accurately identifying protein-DNA binding residues is a critical but challenging task for protein function annotations and drug design. Although wet-lab experimental me...
Protein Structure, Secondary Neural Networks, Computer Proteins Protein Binding DNA
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CNN-Pred: Prediction of single-stranded and double-stranded DNA-binding protein using convolutional neural networks.

Gene Nov 26, 2022
DNA-binding proteins play a vital role in biological activity including DNA replication, DNA packing, and DNA reparation. DNA-binding proteins can be classified into single-stranded DNA-binding proteins (SSBs) or double-stranded DNA-binding proteins ...
DNA Replication DNA DNA-Binding Proteins Software Neural Networks, Computer
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iEnhancer-DCLA: using the original sequence to identify enhancers and their strength based on a deep learning framework.

BMC bioinformatics Nov 14, 2022
Enhancers are small regions of DNA that bind to proteins, which enhance the transcription of genes. The enhancer may be located upstream or downstream of the gene. It is not necessarily close to the gene to be acted on, because the entanglement struc...
Enhancer Elements, Genetic Chromatin Deep Learning Neural Networks, Computer DNA
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Current understanding of biological interactions and processing of DNA origami nanostructures: Role of machine learning and implications in drug delivery.

Biotechnology advances Oct 25, 2022
DNA origami has emerged as an exciting avenue that provides a versatile two and three-dimensional DNA-based platform for nanomedicine and drug delivery applications. Their incredible programmability, custom synthesis, efficiency, biocompatibility, an...
Nanostructures Machine Learning Nanomedicine Artificial Intelligence Nanotechnology DNA
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Nonlinear decision-making with enzymatic neural networks.

Nature Oct 19, 2022
Artificial neural networks have revolutionized electronic computing. Similarly, molecular networks with neuromorphic architectures may enable molecular decision-making on a level comparable to gene regulatory networks. Non-enzymatic networks could in...
DNA Electronics MicroRNAs Computers, Molecular Miniaturization Neural Networks, Computer Logic
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