AIMC Topic: High-Throughput Nucleotide Sequencing

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Molecular detection of hrHPV-induced high-grade squamous intraepithelial lesions of the cervix through a targeted RNA next generation sequencing assay.

Molecular medicine (Cambridge, Mass.) May 30, 2025
BACKGROUND: Cervical cancer screening programs are increasingly relying on sensitive molecular approaches as primary tests to detect high-risk human papillomaviruses (hrHPV), the causative agents of cervix cancer. Although hrHPV infection is a pre-re...
Uterine Cervical Neoplasms Middle Aged Papillomavirus Infections Humans Female Adult High-Throughput Nucleotide Sequencing Papillomaviridae Squamous Intraepithelial Lesions Squamous Intraepithelial Lesions of the Cervix Early Detection of Cancer Neoplasm Grading RNA, Viral
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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 ...
Humans Sequence Analysis, DNA Machine Learning Cell-Free Nucleic Acids Software Whole Genome Sequencing 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...
Neural Networks, Computer Software Algorithms Humans Nanopore Sequencing Deep Learning Sequence Analysis, DNA High-Throughput Nucleotide Sequencing
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Standardizing a microbiome pipeline for body fluid identification from complex crime scene stains.

Applied and environmental microbiology Apr 30, 2025
Recent advances in next-generation sequencing have opened up new possibilities for applying the human microbiome in various fields, including forensics. Researchers have capitalized on the site-specific microbial communities found in different parts ...
Humans Machine Learning Female Microbiota Male Body Fluids Bacteria High-Throughput Nucleotide Sequencing Saliva
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Performance and hypothetical clinical impact of an mNGS-based machine learning model for antimicrobial susceptibility prediction of five ESKAPEE bacteria.

Microbiology spectrum Apr 17, 2025
UNLABELLED: Antimicrobial resistance is an escalating global health crisis, underscoring the urgent need for timely and targeted therapies to ensure effective clinical treatment. We developed a machine learning model based on metagenomic next-generat...
High-Throughput Nucleotide Sequencing Metagenomics Acinetobacter baumannii Staphylococcus aureus Bacterial Infections Pseudomonas aeruginosa Adult Male Middle Aged Bacteria Escherichia coli Microbial Sensitivity Tests Klebsiella pneumoniae Anti-Bacterial Agents Female Aged Humans Machine Learning
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Circular RNA discovery with emerging sequencing and deep learning technologies.

Nature genetics Apr 17, 2025
Circular RNA (circRNA) represents a type of RNA molecule characterized by a closed-loop structure that is distinct from linear RNA counterparts. Recent studies have revealed the emerging role of these circular transcripts in gene regulation and disea...
High-Throughput Nucleotide Sequencing RNA, Circular Humans Artificial Intelligence Algorithms Single-Cell Analysis Sequence Analysis, RNA Animals Deep Learning
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Enhancing fever of unknown origin diagnosis: machine learning approaches to predict metagenomic next-generation sequencing positivity.

Frontiers in cellular and infection microbiology Apr 15, 2025
OBJECTIVE: Metagenomic next-generation sequencing (mNGS) can potentially detect various pathogenic microorganisms without bias to improve the diagnostic rate of fever of unknown origin (FUO), but there are no effective methods to predict mNGS-positiv...
Male Female Metagenomics Middle Aged Fever of Unknown Origin Humans Aged High-Throughput Nucleotide Sequencing Adult Machine Learning Algorithms
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Genome-wide methylome modeling via generative AI incorporating long- and short-range interactions.

Science advances Apr 11, 2025
Using millions of methylation segments, we developed DiffuCpG, a generative artificial intelligence (AI) diffusion model designed to solve the critical challenge of missing data in high-throughput methylation technologies. DiffuCpG goes beyond conven...
Algorithms Epigenesis, Genetic Epigenomics Epigenome CpG Islands DNA Methylation High-Throughput Nucleotide Sequencing Humans Genome, Human Artificial Intelligence
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T-cell receptor dynamics in digestive system cancers: a multi-layer machine learning approach for tumor diagnosis and staging.

Frontiers in immunology Apr 8, 2025
BACKGROUND: T-cell receptor (TCR) repertoires provide insights into tumor immunology, yet their variations across digestive system cancers are not well understood. Characterizing TCR differences between colorectal cancer (CRC) and gastric cancer (GC)...
Colorectal Neoplasms Complementarity Determining Regions Male Female Humans Digestive System Neoplasms Middle Aged Aged Machine Learning Receptors, Antigen, T-Cell Stomach Neoplasms Neoplasm Staging High-Throughput Nucleotide Sequencing
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GONNMDA: A Ordered Message Passing GNN Approach for miRNA-Disease Association Prediction.

Genes Apr 1, 2025
Small non-coding molecules known as microRNAs (miRNAs) play a critical role in disease diagnosis, treatment, and prognosis evaluation. Traditional wet-lab methods for validating miRNA-disease associations are often time-consuming and inefficient. Wit...
High-Throughput Nucleotide Sequencing Genetic Predisposition to Disease Computational Biology MicroRNAs Humans Neural Networks, Computer
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