AIMC Topic: DNA
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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...
Loop Nucleotide Chemical Shifts as a Tool to Characterize DNA G-Quadruplexes.
Chemphyschem : a European journal of chemical physics and physical chemistry
May 7, 2025
DNA G-quadruplexes are known to play myriad functional roles in the cellular context and their structural diversity has diverse applications in various fields of science. Solution-state NMR spectroscopy has been instrumental in characterization of DN...
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 ...
Neural Network Circuits for Bionic Associative Memory and Temporal Order Memory Based on DNA Strand Displacement.
IEEE transactions on neural networks and learning systems
May 2, 2025
Pavlovian associative memory plays an important role in our daily life and work. The realization of Pavlovian associative memory at the deoxyribonucleic acid (DNA) molecular level will promote the development of biological computing and broaden the a...
High-resolution dynamic imaging of chromatin DNA communication using Oligo-LiveFISH.
Cell
Apr 15, 2025
Three-dimensional (3D) genome dynamics are crucial for cellular functions and disease. However, real-time, live-cell DNA visualization remains challenging, as existing methods are often confined to repetitive regions, suffer from low resolution, or r...
A comprehensive review of computational methods for Protein-DNA binding site prediction.
Analytical biochemistry
Apr 8, 2025
Accurately identifying protein-DNA binding sites is essential for understanding the molecular mechanisms underlying biological processes, which in turn facilitates advancements in drug discovery and design. While biochemical experiments provide the m...
Design and Implementation of Pavlovian Associative Memory Based on DNA Neurons.
IEEE transactions on neural networks and learning systems
Apr 4, 2025
In the field of biocomputing and neural networks, deoxyribonucleic acid (DNA) strand displacement (DSD) technology performs well in computation, programming, and information processing. In this article, the multiplication gate, addition gate, and thr...
Critical Assessment of RNA and DNA Structure Predictions via Artificial Intelligence: The Imitation Game.
Journal of chemical information and modeling
Mar 30, 2025
Computational predictions of biomolecular structure via artificial intelligence (AI) based approaches, as exemplified by AlphaFold software, have the potential to model of all life's biomolecules. We performed oligonucleotide structure prediction and...
Machine Learning-Driven Quantum Sequencing of Natural and Chemically Modified DNA.
ACS applied materials & interfaces
Mar 29, 2025
Simultaneous identification of natural and chemically modified DNA nucleotides at molecular resolution remains a pivotal challenge in genomic science. Despite significant advances in current sequencing technologies, the ability to identify subtle cha...
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