AIMC Topic: DNA
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Deep learning deciphers the related role of master regulators and G-quadruplexes in tissue specification.
Scientific reports
Jul 2, 2025
G-quadruplexes (GQs) are non-canonical DNA structures encoded by G-flipons with potential roles in gene regulation and chromatin structure. Here, we explore the role of G-flipons in tissue specification. We present a deep learning-based framework for...
Predict the degree of secondary structures of the encoding sequences in DNA storage by deep learning model.
Scientific reports
Jul 1, 2025
DNA storage has been widely considered as a promising alternative for exponentially growing data. However, the inherent complex secondary structures severely compromise the processes of synthesis, PCR amplification, and sequencing, interfering with r...
Quantifying complexity in DNA structures with high resolution Atomic Force Microscopy.
Nature communications
Jul 1, 2025
DNA topology is essential for regulating cellular processes and maintaining genome stability, yet it is challenging to quantify due to the size and complexity of topologically constrained DNA molecules. By combining high-resolution Atomic Force Micro...
Data-driven protease engineering by DNA-recording and epistasis-aware machine learning.
Nature communications
Jul 1, 2025
Protein engineering has recently seen tremendous transformation due to machine learning (ML) tools that predict structure from sequence at unprecedented precision. Predicting catalytic activity, however, remains challenging, restricting our capabilit...
Coordinated Residue Motions at the Enzyme-Substrate Interface Promote DNA Translocation in Polymerases.
Journal of the American Chemical Society
Jun 17, 2025
The translocation of DNA in polymerase (Pol) enzymes is a critical step for Pol-mediated nucleic acid polymerization, essential for storing and transmitting genetic information in all living organisms. During this process, the newly elongated double-...
Split DNA Tetrahedron-Mediated Spatiotemporal-Hierarchy CRISPR Cascade Integrated with Au@Pt Nanolabels and Artificial Intelligence for a Cervical Cancer MicroRNA Bioassay.
ACS nano
Jun 11, 2025
The screening and monitoring of microRNAs as cancer molecular biomarkers is clinically significant, but traditional methods lack sufficient sensitivity, accuracy, and convenience. The CRISPR-colorimetric lateral flow assay (CLFA) integration offers a...
Shining Light on DNA Mutations through Machine Learning-Augmented Vibrational Spectroscopy.
Analytical chemistry
Jun 4, 2025
A method to directly predict the number of nucleic acid bases in a single-stranded DNA (ssDNA) or a genomic DNA has been proposed with a combination of Raman spectroscopy and an Artificial Neural Network (ANN) algorithm. In this work, the algorithm w...
Melting Profile of DNA in Crowded Solution: Model-Based Study.
International journal of molecular sciences
May 31, 2025
Recent advances in molecular dynamics (MD) simulations and the introduction of artificial intelligence (AI) have resulted in a significant increase in accuracy for structure prediction. However, the cell is a highly crowded environment consisting of ...
Exon-intron boundary detection made easy by physicochemical properties of DNA.
Molecular omics
May 15, 2025
Genome architecture in eukaryotes exhibits a high degree of complexity. Amidst the numerous intricacies, the existence of genes as non-continuous stretches composed of exons and introns has garnered significant attention and curiosity among researche...
iEnhancer-DS: Attention-based improved densenet for identifying enhancers and their strength.
Computational biology and chemistry
May 5, 2025
Enhancers are short DNA fragments that enhance gene expression by binding to transcription factors. Accurately identifying enhancers and their strength is crucial for understanding gene regulation mechanisms. However, traditional enhancer sequencing ...
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