AIMC Topic: DNA

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CryoREAD: de novo structure modeling for nucleic acids in cryo-EM maps using deep learning.

Nature methods Oct 2, 2023
DNA and RNA play fundamental roles in various cellular processes, where their three-dimensional structures provide information critical to understanding the molecular mechanisms of their functions. Although an increasing number of nucleic acid struct...
DNA Models, Molecular Deep Learning Protein Conformation Cryoelectron Microscopy RNA Nucleic Acids
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SNN6mA: Improved DNA N6-methyladenine site prediction using Siamese network-based feature embedding.

Computers in biology and medicine Sep 27, 2023
DNA N6-methyladenine (6mA) is one of the most common and abundant modifications, which plays essential roles in various biological processes and cellular functions. Therefore, the accurate identification of DNA 6mA sites is of great importance for a ...
DNA Adenine DNA Methylation Humans Neural Networks, Computer Animals Computational Biology
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DeepCAC: a deep learning approach on DNA transcription factors classification based on multi-head self-attention and concatenate convolutional neural network.

BMC bioinformatics Sep 18, 2023
Understanding gene expression processes necessitates the accurate classification and identification of transcription factors, which is supported by high-throughput sequencing technologies. However, these techniques suffer from inherent limitations su...
Computational Biology Transcription Factors Neural Networks, Computer Deep Learning DNA
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Accelerating the characterization of dynamic DNA origami devices with deep neural networks.

Scientific reports Sep 14, 2023
Mechanical characterization of dynamic DNA nanodevices is essential to facilitate their use in applications like molecular diagnostics, force sensing, and nanorobotics that rely on device reconfiguration and interactions with other materials. A commo...
Neural Networks, Computer DNA
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TidyTron: Reducing lab waste using validated wash-and-reuse protocols for common plasticware in Opentrons OT-2 lab robots.

SLAS technology Sep 9, 2023
Every year biotechnology labs generate a combined total of ∼5.5 million tons of plastic waste. As the global bioeconomy expands, biofoundries will inevitably increase plastic consumption in-step with synthetic biology scaling. Decontamination and reu...
Saccharomyces cerevisiae Escherichia coli Robotics DNA Decontamination
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DeepSATA: A Deep Learning-Based Sequence Analyzer Incorporating the Transcription Factor Binding Affinity to Dissect the Effects of Non-Coding Genetic Variants.

International journal of molecular sciences Jul 27, 2023
Utilizing large-scale epigenomics data, deep learning tools can predict the regulatory activity of genomic sequences, annotate non-coding genetic variants, and uncover mechanisms behind complex traits. However, these tools primarily rely on human or ...
Animals Chromatin Swine Humans Mice Deep Learning Transcription Factors Chickens Cattle DNA
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Mechanistic Task Groupings Enhance Multitask Deep Learning of Strain-Specific Ames Mutagenicity.

Chemical research in toxicology Jul 21, 2023
The Ames test is a gold standard mutagenicity assay that utilizes various strains with and without S9 fraction to provide insights into the mechanisms by which a chemical can mutate DNA. Multitask deep learning is an ideal framework for developing Q...
Neural Networks, Computer Mutagenesis Deep Learning Mutagenicity Tests DNA Mutagens
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Gradient-mixing LEGO robots for purifying DNA origami nanostructures of multiple components by rate-zonal centrifugation.

PloS one Jul 19, 2023
DNA origami purification is essential for many fields, including biophysics, molecular engineering, and therapeutics. The increasing interest in DNA origami has led to the development of rate-zonal centrifugation (RZC) as a scalable, high yield, and ...
Nanotechnology DNA Robotics Centrifugation, Zonal Nucleic Acid Conformation Nanostructures
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DNA protein binding recognition based on lifelong learning.

Computers in biology and medicine Jun 16, 2023
In recent years, research in the field of bioinformatics has focused on predicting the raw sequences of proteins, and some scholars consider DNA-binding protein prediction as a classification task. Many statistical and machine learning-based methods ...
DNA-Binding Proteins Machine Learning Protein Binding Computational Biology DNA
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A light-operated integrated DNA walker-origami system beyond bridge burning.

Nanoscale horizons May 30, 2023
Integrating rationally designed DNA molecular walkers and DNA origami platforms is a promising route towards advanced nano-robotics of diverse functions. Unleashing the full potential in this direction requires DNA walker-origami systems beyond the p...
Fluorescent Dyes Robotics Motion DNA Nanotechnology
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