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Whole Genome Sequencing

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OMeta: an ontology-based, data-driven metadata tracking system.

BMC bioinformatics
BACKGROUND: The development of high-throughput sequencing and analysis has accelerated multi-omics studies of thousands of microbial species, metagenomes, and infectious disease pathogens. Omics studies are enabling genotype-phenotype association stu...

Prognostic models in primary biliary cholangitis.

Journal of autoimmunity
Risk prediction modelling is important to better understand the determinants of the course and outcome of PBC and to inform the risk across the disease continuum in PBC enabling risk-stratified follow-up care and personalised therapy. Current prognos...

The first two mitochondrial genomes from Taeniopterygidae (Insecta: Plecoptera): Structural features and phylogenetic implications.

International journal of biological macromolecules
The complete mitochondrial genomes (mitogenomes) of Taeniopteryx ugola and Doddsia occidentalis (Plecoptera: Taeniopterygidae) were firstly sequenced from the family Taeniopterygidae. The 15,353-bp long mitogenome of T. ugola and the 16,020-bp long m...

Noninvasive fetal genotyping using deep neural networks.

Briefings in bioinformatics
Circulating cell-free DNA (cfDNA) is a powerful diagnostics tool that is widely studied in the context of liquid biopsy in oncology and other fields. In obstetrics, maternal plasma cfDNA have already proven its utility, enabling noninvasive prenatal ...

Prediction of Antibiotic Susceptibility in E. coli Isolates Using Machine Learning.

Studies in health technology and informatics
Antimicrobial resistance (AMR) poses a significant global health threat, resulting in 4.96 million deaths in 2019, with projections reaching 10 million by 2050. This resistance, primarily due to the overuse of antibiotics, complicates the treatment o...

Scalable de novo classification of antibiotic resistance of Mycobacterium tuberculosis.

Bioinformatics (Oxford, England)
MOTIVATION: World Health Organization estimates that there were over 10 million cases of tuberculosis (TB) worldwide in 2019, resulting in over 1.4 million deaths, with a worrisome increasing trend yearly. The disease is caused by Mycobacterium tuber...

A deep learning approach for filtering structural variants in short read sequencing data.

Briefings in bioinformatics
Short read whole genome sequencing has become widely used to detect structural variants in human genetic studies and clinical practices. However, accurate detection of structural variants is a challenging task. Especially existing structural variant ...

Pathogenic potential assessment of the Shiga toxin-producing by a source attribution-considered machine learning model.

Proceedings of the National Academy of Sciences of the United States of America
Instead of conventional serotyping and virulence gene combination methods, methods have been developed to evaluate the pathogenic potential of newly emerging pathogens. Among them, the machine learning (ML)-based method using whole-genome sequencing ...

[Application of the artificial intelligence-rapid whole-genome sequencing diagnostic system in the neonatal/pediatric intensive care unit].

Zhongguo dang dai er ke za zhi = Chinese journal of contemporary pediatrics
Pediatric patients in the neonatal intensive care unit (NICU) and the pediatric intensive care unit (PICU) have a high incidence rate of genetic diseases, and early rapid etiological diagnosis and targeted interventions can help to reduce mortality o...