AIMC Topic: DNA

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A sparse and wide neural network model for DNA sequences.

Neural networks : the official journal of the International Neural Network Society Dec 19, 2024
Accurate modeling of DNA sequences requires capturing distant semantic relationships between the nucleotide acid bases. Most existing deep neural network models face two challenges: (1) they are limited to short DNA fragments and cannot capture long-...
Neural Networks, Computer Humans Sequence Analysis, DNA DNA Deep Learning Base Sequence
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Ense-i6mA: Identification of DNA N-Methyladenine Sites Using XGB-RFE Feature Selection and Ensemble Machine Learning.

IEEE/ACM transactions on computational biology and bioinformatics Dec 10, 2024
DNA N-methyladenine (6mA) is an important epigenetic modification that plays a vital role in various cellular processes. Accurate identification of the 6mA sites is fundamental to elucidate the biological functions and mechanisms of modification. How...
Animals Computational Biology Machine Learning Algorithms DNA Drosophila melanogaster Adenine Sequence Analysis, DNA DNA Methylation Arabidopsis
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Self-distillation improves self-supervised learning for DNA sequence inference.

Neural networks : the official journal of the International Neural Network Society Dec 7, 2024
Self-supervised Learning (SSL) has been recognized as a method to enhance prediction accuracy in various downstream tasks. However, its efficacy for DNA sequences remains somewhat constrained. This limitation stems primarily from the fact that most e...
Humans DNA Neural Networks, Computer Supervised Machine Learning Deep Learning Sequence Analysis, DNA
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Representing DNA for machine learning algorithms: A primer on one-hot, binary, and integer encodings.

Biochemistry and molecular biology education : a bimonthly publication of the International Union of Biochemistry and Molecular Biology Dec 5, 2024
This short paper presents an educational approach to teaching three popular methods for encoding DNA sequences: one-hot encoding, binary encoding, and integer encoding. Aimed at bioinformatics and computational biology students, our learning interven...
Humans Students Computational Biology DNA Machine Learning Algorithms
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Translation as a Biosignature.

Astrobiology Nov 29, 2024
Life on Earth relies on mechanisms to store heritable information and translate this information into cellular machinery required for biological activity. In all known life, storage, regulation, and translation are provided by DNA, RNA, and ribosomes...
Ribosomes Nanopores RNA Protein Biosynthesis Machine Learning Exobiology DNA
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Developing a method for predicting DNA nucleosomal sequences using deep learning.

Technology and health care : official journal of the European Society for Engineering and Medicine Nov 20, 2024
BackgroundDeep learning excels at processing raw data because it automatically extracts and classifies high-level features. Despite biology's low popularity in data analysis, incorporating computer technology can improve biological research.Objective...
Sequence Analysis, DNA DNA Algorithms Nucleosomes Deep Learning Humans Neural Networks, Computer
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Deciphering Cas9 specificity: Role of domain dynamics and RNA:DNA hybrid interactions revealed through machine learning and accelerated molecular simulations.

International journal of biological macromolecules Nov 19, 2024
CRISPR/Cas9 technology is widely used for gene editing, but off-targeting still remains a major concern in therapeutic applications. Although Cas9 variants with better mismatch discrimination have been developed, they have significantly lower rates o...
CRISPR-Cas Systems Bacterial Proteins Molecular Dynamics Simulation RNA Protein Domains Francisella Machine Learning Substrate Specificity DNA CRISPR-Associated Protein 9
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Predicting cell type-specific epigenomic profiles accounting for distal genetic effects.

Nature communications Nov 16, 2024
Understanding how genetic variants affect the epigenome is key to interpreting GWAS, yet profiling these effects across the non-coding genome remains challenging due to experimental scalability. This necessitates accurate computational models. Existi...
Quantitative Trait Loci Genome-Wide Association Study Chromatin DNA Polymorphism, Single Nucleotide Epigenome Epigenomics Humans Epigenesis, Genetic Models, Genetic Deep Learning
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Visualization Methods for DNA Sequences: A Review and Prospects.

Biomolecules Nov 14, 2024
The efficient analysis and interpretation of biological sequence data remain major challenges in bioinformatics. Graphical representation, as an emerging and effective visualization technique, offers a more intuitive method for analyzing DNA sequence...
Sequence Analysis, DNA DNA Neural Networks, Computer Humans Machine Learning Computational Biology
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Deep learning enables the use of ultra-high-density array in DNBSEQ.

Scientific reports Nov 13, 2024
DNBSEQ employs a patterned array to facilitate massively parallel sequencing of DNA nanoballs (DNBs), leading to a considerable boost in throughput. By employing the ultra-high-density (UHD) array with an increased density of DNB binding sites, the t...
Deep Learning Image Processing, Computer-Assisted DNA High-Throughput Nucleotide Sequencing Sequence Analysis, DNA
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