AIMC Topic: Sequence Analysis, 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...
Humans Machine Learning Sequence Analysis, DNA Microbiota Metagenomics Bacteria RNA, Ribosomal, 16S Algorithms
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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 ...
High-Throughput Nucleotide Sequencing Cell-Free Nucleic Acids Whole Genome Sequencing Humans Software Sequence Analysis, DNA Machine Learning
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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...
Humans Neural Networks, Computer Nanopore Sequencing Deep Learning Sequence Analysis, DNA High-Throughput Nucleotide Sequencing Software 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 ...
Deep Learning Convolutional Neural Networks Computational Biology Enhancer Elements, Genetic Sequence Analysis, DNA DNA
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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...
Humans Deep Learning Liver Neoplasms Neural Networks, Computer 5-Methylcytosine DNA Methylation Carcinoma, Hepatocellular Cell-Free Nucleic Acids Sequence Analysis, DNA Adenine
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Geometric deep learning framework for de novo genome assembly.

Genome research Apr 14, 2025
The critical stage of every de novo genome assembler is identifying paths in assembly graphs that correspond to the reconstructed genomic sequences. The existing algorithmic methods struggle with this, primarily due to repetitive regions causing comp...
Sequence Analysis, DNA Genome Humans Software Deep Learning Algorithms Genomics
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CNRein: an evolution-aware deep reinforcement learning algorithm for single-cell DNA copy number calling.

Genome biology Apr 7, 2025
Low-pass single-cell DNA sequencing technologies and algorithmic advancements have enabled haplotype-specific copy number calling on thousands of cells within tumors. However, measurement uncertainty may result in spurious CNAs inconsistent with real...
DNA Copy Number Variations Humans Ovarian Neoplasms Single-Cell Analysis Algorithms Reinforcement Machine Learning Sequence Analysis, DNA Breast Neoplasms Deep Learning Female
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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...
Nanopores Quantum Theory Nucleotides Graphite Sequence Analysis, DNA DNA Machine Learning
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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...
Deep Learning Mice Computational Biology Humans Software Neural Networks, Computer Animals Escherichia coli Sequence Analysis, DNA Promoter Regions, Genetic DNA
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Optimized convolutional neural network using African vulture optimization algorithm for the detection of exons.

Scientific reports Jan 30, 2025
The detection of exons is an important area of research in genomic sequence analysis. Many signal-processing methods have been established successfully for detecting the exons based on their periodicity property. However, some improvement is still re...
Sequence Analysis, DNA Introns Algorithms Exons Humans Convolutional Neural Networks Computational Biology Neural Networks, Computer
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