AIMC Topic: Sequence Analysis, DNA

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Skin Microbiome alterations in heroin users revealed by full-length 16S rRNA sequencing.

BMC microbiology Jul 30, 2025
BACKGROUND: Identifying key characteristics of unknown suspects, such as age, height, and drug use, is essential for advancing forensic investigations.
Bacteria DNA, Bacterial RNA, Ribosomal, 16S Middle Aged Phylogeny Heroin Humans Heroin Dependence Female Skin Microbiome Skin Adult Microbiota Male Sequence Analysis, DNA Young Adult
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Advancements in DNA methylation technologies and their application in cancer diagnosis.

Epigenetics Jul 28, 2025
DNA methylation is a common epigenetic modification that maintains the integrity of the DNA sequence while profoundly influencing gene expression and phenotypic variation. Aberrant DNA methylation has been associated with the onset and progression of...
Humans Biomarkers, Tumor Sequence Analysis, DNA Neoplasms DNA Methylation Epigenesis, Genetic High-Throughput Nucleotide Sequencing
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Creating interpretable deep learning models to identify species using environmental DNA sequences.

Scientific reports Jul 28, 2025
Monitoring species' presence in an ecosystem is crucial for conservation and understanding habitat diversity, but can be expensive and time consuming. As a result, ecologists have begun using the DNA that animals naturally leave behind in water or so...
Neural Networks, Computer Animals Ecosystem DNA, Environmental Deep Learning Sequence Analysis, DNA
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DNA sequence classification for diabetes mellitus using NuSVC and XGBoost: A comparative.

PloS one Jul 18, 2025
Diabetes Mellitus is a global health concern, characterized by high blood sugar levels over a prolonged period, leading to severe complications if left unmanaged. The early identification of individuals at risk is critical for effective intervention ...
Sequence Analysis, DNA Boosting Machine Learning Algorithms Humans Diabetes Mellitus Support Vector Machine Machine Learning
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Random access and semantic search in DNA data storage enabled by Cas9 and machine-guided design.

Nature communications Jul 10, 2025
DNA is a promising medium for digital data storage due to its exceptional data density and longevity. Practical DNA-based storage systems require selective data retrieval to minimize decoding time and costs. In this work, we introduce CRISPR-Cas9 as ...
CRISPR-Associated Protein 9 CRISPR-Cas Systems Information Storage and Retrieval Semantics Machine Learning Sequence Analysis, DNA DNA
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TaxaCal: enhancing species-level profiling accuracy of 16S amplicon data.

BMC bioinformatics May 26, 2025
BACKGROUND: 16S rRNA amplicon sequencing is a widely used method for microbiome composition analysis due to its cost-effectiveness and lower data requirements compared to metagenomic whole-genome sequencing (WGS). However, inherent limitations in 16S...
RNA, Ribosomal, 16S Sequence Analysis, DNA Metagenomics Microbiota Algorithms Machine Learning Humans Bacteria
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A standardized framework for robust fragmentomic feature extraction from cell-free DNA sequencing data.

Genome biology May 23, 2025
Fragmentomics features of cell-free DNA represent promising non-invasive biomarkers for cancer diagnosis. A lack of systematic evaluation of biases in feature quantification hinders the adoption of such applications. We compare features derived from ...
Machine Learning Software Cell-Free Nucleic Acids Whole Genome Sequencing Sequence Analysis, DNA Humans High-Throughput Nucleotide Sequencing
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ConsensuSV-ONT - A modern method for accurate structural variant calling.

Scientific reports May 17, 2025
Improvements in sequencing technology make the development of new tools for detection of structural variance more and more common. However, since the tools available for the long-read Oxford Nanopore sequencing are limited, and the selection of the o...
High-Throughput Nucleotide Sequencing Nanopore Sequencing Deep Learning Sequence Analysis, DNA Neural Networks, Computer Software Humans Algorithms
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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 ...
Computational Biology Sequence Analysis, DNA DNA Deep Learning Convolutional Neural Networks Enhancer Elements, Genetic
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Transformer-based deep learning for accurate detection of multiple base modifications using single molecule real-time sequencing.

Communications biology Apr 14, 2025
We had previously reported a convolutional neural network (CNN) based approach, called the holistic kinetic model (HK model 1), for detecting 5-methylcytosine (5mC) by single molecule real-time sequencing (Pacific Biosciences). In this study, we cons...
Sequence Analysis, DNA Deep Learning Humans DNA Methylation Neural Networks, Computer Adenine Cell-Free Nucleic Acids Liver Neoplasms 5-Methylcytosine Carcinoma, Hepatocellular
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