AIMC Topic: DNA

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CacPred: a cascaded convolutional neural network for TF-DNA binding prediction.

BMC genomics Mar 18, 2025
BACKGROUND: Transcription factors (TFs) regulate the genes' expression by binding to DNA sequences. Aligned TFBSs of the same TF are seen as cis-regulatory motifs, and substantial computational efforts have been invested to find motifs. In recent yea...
Software Algorithms Convolutional Neural Networks Neural Networks, Computer DNA Binding Sites Chromatin Immunoprecipitation Sequencing Computational Biology Transcription Factors Protein Binding
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HybProm: An attention-assisted hybrid CNN-BiLSTM model for the interpretable prediction of DNA promoter.

Methods (San Diego, Calif.) Feb 8, 2025
Promoter prediction is essential for analyzing gene structures, understanding regulatory networks, transcription mechanisms, and precisely controlling gene expression. Recently, computational and deep learning methods for promoter prediction have gai...
Humans Neural Networks, Computer Deep Learning Mice Computational Biology Software Animals Escherichia coli Sequence Analysis, DNA Promoter Regions, Genetic DNA
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Deep Learning and Single-Molecule Localization Microscopy Reveal Nanoscopic Dynamics of DNA Entanglement Loci.

ACS nano Feb 4, 2025
Understanding molecular dynamics at the nanoscale remains challenging due to limitations in the temporal resolution of current imaging techniques. Deep learning integrated with Single-Molecule Localization Microscopy (SMLM) offers opportunities to pr...
DNA Fluorescent Dyes Kinetics Deep Learning Microscopy, Fluorescence Single Molecule Imaging Nanotechnology
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Advancing DNA Structural Analysis: A SERS Approach Free from Citrate Interference Combined with Machine Learning.

The journal of physical chemistry letters Jan 23, 2025
Surface-enhanced Raman spectroscopy (SERS) has become an indispensable tool for biomolecular analysis, yet the detection of DNA signals remains hindered by spectral interference from citrate ions, which overlap with key DNA features. This study intro...
Nucleic Acid Conformation Machine Learning Discriminant Analysis Spectrum Analysis, Raman Silver Support Vector Machine DNA Citric Acid Metal Nanoparticles
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Further Development of SAMPDI-3D: A Machine Learning Method for Predicting Binding Free Energy Changes Caused by Mutations in Either Protein or DNA.

Genes Jan 19, 2025
BACKGROUND/OBJECTIVES: Predicting the effects of protein and DNA mutations on the binding free energy of protein-DNA complexes is crucial for understanding how DNA variants impact wild-type cellular function. As many cellular interactions involve pro...
DNA-Binding Proteins Humans Thermodynamics Protein Binding Machine Learning DNA Mutation
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Machine Learning Recognition of Artificial DNA Sequence with Quantum Tunneling Nanogap Junction.

The journal of physical chemistry. B Jan 9, 2025
Artificially synthesized DNA holds significant promise in addressing fundamental biochemical questions and driving advancements in biotechnology, genetics, and DNA digital data storage. Rapid and precise electric identification of these artificial DN...
DNA Quantum Theory Machine Learning
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DNA promoter task-oriented dictionary mining and prediction model based on natural language technology.

Scientific reports Jan 2, 2025
Promoters are essential DNA sequences that initiate transcription and regulate gene expression. Precisely identifying promoter sites is crucial for deciphering gene expression patterns and the roles of gene regulatory networks. Recent advancements in...
Neural Networks, Computer Deep Learning Sequence Analysis, DNA Natural Language Processing Computational Biology Humans Promoter Regions, Genetic DNA Data Mining
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ChromatinHD connects single-cell DNA accessibility and conformation to gene expression through scale-adaptive machine learning.

Nature communications Jan 2, 2025
Gene regulation is inherently multiscale, but scale-adaptive machine learning methods that fully exploit this property in single-nucleus accessibility data are still lacking. Here, we develop ChromatinHD, a pair of scale-adaptive models that uses the...
Regulatory Sequences, Nucleic Acid Chromatin Chromatin Immunoprecipitation Sequencing Gene Expression Regulation Nucleic Acid Conformation Single-Cell Analysis Mice Animals Transcription Factors DNA Computational Biology Humans Machine Learning
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High-Risk Sequence Prediction Model in DNA Storage: The LQSF Method.

IEEE transactions on nanobioscience Jan 2, 2025
Traditional DNA storage technologies rely on passive filtering methods for error correction during synthesis and sequencing, which result in redundancy and inadequate error correction. Addressing this, the Low Quality Sequence Filter (LQSF) was intro...
High-Throughput Nucleotide Sequencing Sequence Analysis, DNA DNA Humans Neural Networks, Computer Deep Learning Computational Biology Algorithms
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A Robust and Efficient Representation-based DNA Storage Architecture by Deep Learning.

Small methods Dec 29, 2024
As one main form of multimedia data, images play a critical role in various applications. In this paper, a representation-based architecture is proposed which takes advantage of the outstanding representation and image-generation abilities of deep le...
Deep Learning Neural Networks, Computer Image Processing, Computer-Assisted Algorithms DNA
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