AIMC Topic: Whole Genome Sequencing

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Machine learning based on pangenome-wide association studies reveals the impact of host source on the zoonotic potential of closely related bacterial pathogens.

Communications biology Aug 20, 2025
Variations in host species significantly impact bacterial growth traits and antibiotic resistance, making it essential to consider host origin when evaluating the zoonotic potential of pathogens. This study focuses on multiple Brucella species, which...
Humans Machine Learning Animals Swine Sheep Genome, Bacterial Zoonoses Brucella Genome-Wide Association Study Cattle Brucellosis Whole Genome Sequencing
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Non-coding genetic elements of lung cancer identified using whole genome sequencing in 13,722 Chinese.

Nature communications Aug 9, 2025
A substantial portion of lung cancer-associated genetic elements in East Asian populations remains unidentified, underscoring the need for large-scale genome-wide studies, particularly on non-coding regulation. We conducted a whole genome sequencing ...
China Genome-Wide Association Study Lung Neoplasms Genetic Predisposition to Disease Humans Female Male Whole Genome Sequencing Asian People Tumor Suppressor Proteins Gene Expression Regulation, Neoplastic NF-kappa B p50 Subunit Transcription Factors East Asian People
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Whole genome resequencing reveals genetic diversity, population structure, and selection signatures in local duck breeds.

BMC genomics Aug 8, 2025
BACKGROUND: Shandong's local duck breeds are renowned for their outstanding egg-laying performance and are regarded as valuable assets within China's waterfowl germplasm. Understanding the genetic characteristics of these populations, along with moni...
Breeding Selection, Genetic Animals Genetics, Population Phylogeny China Polymorphism, Single Nucleotide Whole Genome Sequencing Genetic Variation Ducks
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Chronological age estimation from human microbiomes with transformer-based Robust Principal Component Analysis.

Communications biology Aug 6, 2025
Deep learning for microbiome analysis has shown potential for understanding microbial communities and human phenotypes. Here, we propose an approach, Transformer-based Robust Principal Component Analysis(TRPCA), which leverages the strengths of trans...
RNA, Ribosomal, 16S Principal Component Analysis Skin Whole Genome Sequencing Middle Aged Deep Learning Gastrointestinal Microbiome Microbiota Humans Female Adult Male Aging
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Machine learning-based prediction of antimicrobial resistance and identification of AMR-related SNPs in Mycobacterium tuberculosis.

BMC genomic data Jul 12, 2025
BACKGROUND: Mycobacterium tuberculosis (MTB) is a human-specific pathogen that primarily infects humans, causing tuberculosis (TB). Antimicrobial resistance (AMR) in MTB presents a formidable challenge to global health. The employment of machine lear...
Isoniazid Rifampin Polymorphism, Single Nucleotide Antitubercular Agents Whole Genome Sequencing Algorithms Mycobacterium tuberculosis Drug Resistance, Bacterial Humans Microbial Sensitivity Tests Machine Learning
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Machine learning-selected minimal features drive high-accuracy rule-based antibiotic susceptibility predictions for via metagenomic sequencing.

Microbiology spectrum Jul 11, 2025
Antimicrobial resistance (AMR) represents a critical global health challenge, demanding rapid and accurate antimicrobial susceptibility testing (AST) to guide timely treatments. Traditional culture-based AST methods are slow, while existing whole-gen...
Genotype Staphylococcus aureus Whole Genome Sequencing Staphylococcal Infections Metagenomics Machine Learning Genome, Bacterial Anti-Bacterial Agents Humans Drug Resistance, Bacterial Microbial Sensitivity Tests
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Genome sequencing is critical for forecasting outcomes following congenital cardiac surgery.

Nature communications Jul 10, 2025
While exome and whole genome sequencing have transformed medicine by elucidating the genetic underpinnings of both rare and common complex disorders, its utility to predict clinical outcomes remains understudied. Here, we use artificial intelligence ...
Infant Child, Preschool Child Genotype Treatment Outcome Whole Genome Sequencing Heart Defects, Congenital Cardiac Surgical Procedures Exome Sequencing Prospective Studies Humans Female Forecasting Infant, Newborn Male
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Early detection of emerging SARS-CoV-2 Variants from wastewater through genome sequencing and machine learning.

Nature communications Jul 8, 2025
Genome sequencing from wastewater enables accurate and cost-effective identification of SARS-CoV-2 variants. However, existing computational pipelines have limitations in detecting emerging variants not yet characterized in humans. Here, we present a...
Genome, Viral Humans Machine Learning Wastewater COVID-19 SARS-CoV-2 Mutation Whole Genome Sequencing
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Multi-omics profiling of cross-resistance between ceftazidime-avibactam and meropenem identifies common and strain-specific mechanisms in clinical isolates.

mBio Jun 4, 2025
is a highly versatile and resilient pathogen that can infect different tissues and rapidly develop resistance to multiple drugs. Ceftazidime-avibactam (CZA) is an antibiotic often used to treat multidrug-resistant infections; however, the knowledge ...
Ceftazidime Microbial Sensitivity Tests Drug Resistance, Multiple, Bacterial Multiomics Proteomics Humans Drug Combinations Pseudomonas aeruginosa Anti-Bacterial Agents Bacterial Proteins Meropenem Whole Genome Sequencing Pseudomonas Infections Azabicyclo Compounds
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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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