AIMC Topic: DNA

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ResidualBind: Uncovering Sequence-Structure Preferences of RNA-Binding Proteins with Deep Neural Networks.

Methods in molecular biology (Clifton, N.J.) Jan 1, 2023
Deep neural networks have demonstrated improved performance at predicting sequence specificities of DNA- and RNA-binding proteins. However, it remains unclear why they perform better than previous methods that rely on k-mers and position weight matri...
Neural Networks, Computer Protein Binding RNA Position-Specific Scoring Matrices RNA-Binding Proteins DNA
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Deep learning-assisted genome-wide characterization of massively parallel reporter assays.

Nucleic acids research Nov 11, 2022
Massively parallel reporter assay (MPRA) is a high-throughput method that enables the study of the regulatory activities of tens of thousands of DNA oligonucleotides in a single experiment. While MPRA experiments have grown in popularity, their small...
Genome, Human Humans Regulatory Sequences, Nucleic Acid Deep Learning Sequence Analysis, DNA DNA
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A deep learning-based method for the prediction of DNA interacting residues in a protein.

Briefings in bioinformatics Sep 20, 2022
DNA-protein interaction is one of the most crucial interactions in the biological system, which decides the fate of many processes such as transcription, regulation and splicing of genes. In this study, we trained our models on a training dataset of ...
Databases, Protein DNA Deep Learning DNA-Binding Proteins Position-Specific Scoring Matrices
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DNAffinity: a machine-learning approach to predict DNA binding affinities of transcription factors.

Nucleic acids research Sep 9, 2022
We present a physics-based machine learning approach to predict in vitro transcription factor binding affinities from structural and mechanical DNA properties directly derived from atomistic molecular dynamics simulations. The method is able to predi...
Binding Sites Algorithms Protein Binding Transcription Factors DNA Machine Learning
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Identifying modifications on DNA-bound histones with joint deep learning of multiple binding sites in DNA sequence.

Bioinformatics (Oxford, England) Sep 2, 2022
MOTIVATION: Histone modifications are epigenetic markers that impact gene expression by altering the chromatin structure or recruiting histone modifiers. Their accurate identification is key to unraveling the mechanisms by which they regulate gene ex...
Deep Learning Transcription Factors Histones DNA Binding Sites Base Sequence
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Provenance of life: Chemical autonomous agents surviving through associative learning.

Physical review. E Sep 1, 2022
We present a benchmark study of autonomous, chemical agents exhibiting associative learning of an environmental feature. Associative learning systems have been widely studied in cognitive science and artificial intelligence but are most commonly impl...
DNA Animals Neural Networks, Computer Artificial Intelligence Learning
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Nonlinear manipulation and analysis of large DNA datasets.

Nucleic acids research Aug 26, 2022
Information processing functions are essential for organisms to perceive and react to their complex environment, and for humans to analyze and rationalize them. While our brain is extraordinary at processing complex information, winner-take-all, as a...
Humans Computers, Molecular DNA Neurons Neural Networks, Computer Brain
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Intelligent dynamic data perturbation OCDM encryption scheme based on cellular neural network and biological genetic encoding.

Optics express Jun 20, 2022
In this paper, an intelligent dynamic perturbation orthogonal chirp division multiplexing (OCDM) encryption scheme based on cellular neural network and biological genetic encoding for seven-core optical fiber is proposed for the first time to our kno...
DNA Equipment Design Signal Processing, Computer-Assisted Neural Networks, Computer
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A tool for feature extraction from biological sequences.

Briefings in bioinformatics May 13, 2022
With the advances in sequencing technologies, a huge amount of biological data is extracted nowadays. Analyzing this amount of data is beyond the ability of human beings, creating a splendid opportunity for machine learning methods to grow. The metho...
Proteins DNA Humans Sequence Analysis Machine Learning RNA
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DNAcycP: a deep learning tool for DNA cyclizability prediction.

Nucleic acids research Apr 8, 2022
DNA mechanical properties play a critical role in every aspect of DNA-dependent biological processes. Recently a high throughput assay named loop-seq has been developed to quantify the intrinsic bendability of a massive number of DNA fragments simult...
Nucleosomes Cyclization Animals Mice Binding Sites Software Deep Learning Chromatin DNA Mammals Saccharomyces cerevisiae
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